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function addrsp combine two response matrices to make a composite RSP and return a structure in the same format as RD_OGIP_RMF() steps through each row of an RMF and tacks on the array from a 2nd RMF, updating the N_GRP, N_CHAN, F_CHAN elements as appropriate. syntax rsp=addrsp(rm1,rm2,ea1=ea1,ea2=ea2,eps=eps,verbose=verbose) parameters rm1 [INPUT; required] response matrix structure as read in by RD_OGIP_RMF rm2 [INPUT; required] response matrix structure to be added to RM1 * RM1 and RM2 are expected to have the following fields: NNRG,ELO,EHI,NCHAN,EMN,EMX,N_GRP,F_CHAN,N_CHAN,MATRIX,FIRSTCHAN keywords ea1 [INPUT] if set to a scalar or size matches RM1.ELO, then multiplies RM1 by EA1 prior to addition ea2 [INPUT] as EA1, but for RM2 * default for EA1 and EA2 is 1.0 eps [INPUT] a small number, below which to set everything to zero * default is 1e-6 morecol [INPUT] designed as a buffer so that a matrix won't overflow the bounds automatically set. by default, the new matrix is defined at an early stage to be max(RM1.N_CHAN)+max(RM2.N_CHAN)+100+MORECOL. * note that MORECOL can even be negative. * use wisely. verbose [INPUT] controls chatter ea3 [JUNK] here just to prevent user error ea4 [JUNK] here just to prevent user error ea5 [JUNK] here just to prevent user error ea6 [JUNK] here just to prevent user error * if EA3, EA4, EA5, or EA6 are set, the program will complain and quit. this is done to avoid the obvious user error of trying to specify EA3=EA3, etc. if adding a third RMF/ARF to a preexisting one. _extra [JUNK] here only to avoid crashing the program subroutines KILROY OGIPZIP history vinay kashyap (Nov2001) bug correction re max possible matrix elements when NGROUP>>1; added dummy keywords EA3, EA4, EA5, EA6 and extra checks against tricky inputs (VK; Aug02) bug correction: wasn't handling N_GRP=1 (VK; Aug04)
(See pro/util/addrsp.pro)
procedure adjustie adjust the parameters to account for any ties among them, and return the corrected set syntax adjustie,a,ties=ties,vname=vname parameters a [I/O; required] parameters to be updated keywords ties [INPUT] string array describing how a parameter is tied to other parameters. * must be a mathematical expression of the form "a0 = a1/10.", "a2=a3+a4", "a5 = a5 < 0", etc. vname [INPUT; default='a'] in case TIES contains variable names such as "p0=p2^2", etc, then set VNAME='p' NOTE: the following keywords are generated in situ the first time the function is called. on subsequent calls they are used instead of EXECUTEing TIES in order to improve speed. NOTE2: actually, they are not implemented yet. someday. ifit [I/O] integer array describing which parameters are frozen (0's) and which are not (1's). updated upon exit to include information given in TIES itie [I/O] integer array showing which parameters are tied. tieto [I/O] linked list showing which parameters each of the ITIE are tied to which parameter tieops [I/O] as TIETO, but containing information on which operator is used, e.g., "+", "-", "*", "/", "<", ">", etc. _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Oct98) converted to IDL5 (VK; OctMM)
(See pro/fitting/adjustie.pro)
function alaloess computes a loess/lowess type smoothed function for the given set of input points by fitting polynomials over the neighborhood of each point and using the local value of the polynomial fit as the smoothed curve another one in a hoary line of PINTofALE smoothing routines, joining SMOOTHIE, NOISMOOTH, VARSMOOTH, VOORSMOOTH, REGROUP, SPLAC, CONV_RMF, SCRMF, UNKINK, LINEREM, HAARLINE, etc. syntax yl=alaloess(yy,xx,hwidth=hwidth,ysig=ysig,ndeg=ndeg,$ yerr=yerr,verbose=vv) parameters yy [INPUT; required] the points that need to be smoothed xx [INPUT] the abscissae for which YY are defined * if size eq size of YY or +1, taken to be the midpoints or the grid * if insensible, taken to be array indices, LINDGEN(N(YY)) keywords hwidth [INPUT] half range over which local polynomial fits are to be performed * if XX are array indices, HWIDTH is forced to be >0 * if XX is a predefined grid, the default value is the minimum of delta(XX) ysig [INPUT] error on YY * if size matches that of YY, then maps 1-to-1 * if scalar, taken to be <0 : absolute error >0 and <1 : fractional error >1 : percentage error =0 : ignored in call to POLY_FIT() on YY * otherwise, assumed to be sqrt(abs(YY)+0.75)+1 ndeg [INPUT] degree of the polynomial to be fit * default is 3 yerr [OUTPUT] 1-sigma error at the smooth location from each fit. * WARNING: this is to be taken only as an illustrative number and not used for anything quantitative, because the errors in adjacent bins are not independent verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program example .run alaloess ;(requires PEASECOLR) these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (MarMMX) some bug fixes, and hardening to poly_fit failures -- where it fails now simply keep old value (VK; MayMMX) updated to be more robust to NaNs (VK; AprMMV)
(See pro/util/alaloess.pro)
procedure apedance remove or correct the abundance dependance of APED emissivities APED emissivities as stored on disk include both ion balance (Mazzotta et al.) and abundances (Anders & Grevesse). This can be inconvenient in some PINTofALE tasks since other line emissivity databases in PINTofALE do not include either factor. It is not possible to remove the effects of the included ion balance, but removing the abundance dependance is simply a matter of dividing the emissivity of each line by the abundance appropriate to the element producing that line. syntax apedance,line,Z,abund=abund,apabref=apabref,verbose=verbose parameters line [I/O] APED line emissivities * emissivity structure out of RD_LINE() * if 2D array, assumed to be an array of size (T,Wvl) Z [INPUT] atomic numbers * required if LINE is an array and not a structure * must match size of 2nd dimension in LINE keywords abund [INPUT] if given, updates LINE by multiplying by the ratio of ABUND/(Anders & Grevesse) * the default is to just divide by Anders & Grevesse abundances, effectively removing the abundance dependance from the emissivities apabref [INPUT] if set to a reference other than Anders & Grevesse, it is assumed that the input LINE emissivities need to be corrected according to the specified abundances. * WARNING: do not set this unless you know exactly what you are doing verbose [INPUT] controls chatter _extra [JUNK] here only to avoid crashing the program warning no checks are made to verify that the emissivities have have already had the abundances taken out, or that the abundances are corrected according to some other baseline. USE CAREFULLY! history vinay kashyap (Apr2004)
(See pro/apedance.pro)
function arithtogram return the result of an arithmetical operation on the frequency distributions of two lists syntax hx=arithtogram(x1,x2,xout,operator,/plus,/minus,/divide,$ w1=w1,w2=w2,nbin=nbin,xmin=xmin,xmax=xmax,/nonorm) parameters x1 [INPUT; required] list of numbers whose frequency distribution must be multiplied with that of X2 x2 [INPUT; required] list of numbers whose frequency distribution must be multiplied with that of X1 * it is assumed that X1 and X2 both have the same units because otherwise this kind of multiplication makes no sense xout [OUTPUT; required] the list of numbers at which the output is tabulated * by default, this is the sorted unique set of [X1,X2] * if NBIN is set, generates a logarithmic or linear grid of that size oper [INPUT] must be one of '+', '-', '/', '*': the arithmetical operation to carry out on the frequency distributions of X1 and X2, i.e., result = X1 OPER X2 * if not given, assumed to be '*', unless one of keywords PLUS, MINUS, or DIVIDE are set keywords plus [INPUT] if set, OPER is assumed to be '+' minus [INPUT] if set, OPER is assumed to be '-' divide [INPUT] if set, OPER is assumed to be '/' * DIVIDE takes precedence over MINUS takes precedence over PLUS w1 [INPUT] optional weight to be applied to histogram(X1) w2 [INPUT] optional weight to be applied to histogram(X2) * if not given, W1 and W2 are assumed to be 1 nbin [INPUT] number of bins in the output * if not set, will be the sorted unique set of [X1,X2] * if -ve, will produce logarithmic gridding xmin [INPUT] minimum value in the output grid * by default, uses min(X1)>min(X2) xmax [INPUT] maximum value in the output grid * by default, uses max(X1)<max(X2) nonorm [INPUT] if set, does not make a correction for the width of the bins in XOUT. _extra [JUNK] here only to prevent crashing the program description this program does not create histograms as intermediate products but rather produces an operation at the best available data resolution. this is of great use in Monte Carlo calculations or in creating probability distributions in MCMC. the algorithm is straightforward: build up a cdf for each list, and interpolate onto a common grid, and multiply, divide, add, or subtract the d(cdf)'s, suitably normalized for the bin widths and number of elements. example x1=randomn(seed,10000L) & x2=randomn(seed,10000L)+2. xmin=-2. & xmax=3. & nbin=101L hh=arithtogram(x1,x2,xout,'*',xmin=xmin,xmax=xmax,nbin=nbin,/nonorm) hp=arithtogram(x1,x2,xout,'+',xmin=xmin,xmax=xmax,nbin=nbin,/nonorm) hd=arithtogram(x1,x2,xout,'/',xmin=xmin,xmax=xmax,nbin=nbin,/nonorm) hm=arithtogram(x1,x2,xout,'-',xmin=xmin,xmax=xmax,nbin=nbin,/nonorm) h1=histogram(x1,min=xmin,max=xmax,binsize=median(xout[1:*]-xout)) h2=histogram(x2,min=xmin,max=xmax,binsize=median(xout[1:*]-xout)) plot,xout,hh,psym=10 & oplot,xout,h1,col=2 & oplot,xout,h2,col=3 oplot,xout,h1*h2,psym=10,col=4 plot,xout,hp,psym=10 & oplot,xout,h1,col=2 & oplot,xout,h2,col=3 oplot,xout,h1+h2,psym=10,col=4 plot,xout,hd,psym=10 & oplot,xout,h1,col=2 & oplot,xout,h2,col=3 oplot,xout,float(h1)/float(h2),psym=10,col=4 plot,xout,hm,psym=10 & oplot,xout,h1,col=2 & oplot,xout,h2,col=3 oplot,xout,h1-h2,psym=10,col=4 history vinay kashyap (Jun2005)
(See pro/util/arithtogram.pro)
function arrayeq checks whether two input arrays are equal, and returns 1: if they are identical 0: if at least one element differs past tolerance -1: if sizes differ, but one array is a simple subset of the other syntax AeqB=arrayeq(A,B,tol=tol) parameters A [INPUT; required] first array B [INPUT; required] second array * arrays must be of some >numerical< type keywords tol [INPUT; default: 1e-4] tolerance within which two numbers are said to be identical _extra [JUNK] here only to avoid crashing the program history vinay kashyap (Nov98) converted to IDL5 notation (VK; OctMM)
(See pro/util/arrayeq.pro)
function b11001001 returns the 0s and 1s of a byte variable syntax d=b11001001(b,/str,/otto) parameters b [INPUT; required] scalar or array of bytes keywords str [INPUT] if set, returns the 0s and 1s in a string * overrides OTTO otto [INPUT] if set, returns an 8xN(B) byte array as output history vinay kashyap (Jul97)
(See pro/util/b11001001.pro)
function bamabs return photoelectric absorption cross-sections in energy range 30 eV - 10 keV using the polynomial fit coefficients determined by Monika Balucinska-Church and Dan McCammon (Balucinska-Church, M.\ and McCammon, D.\ 1992, ApJ 400, 699). This is an update to Morrison & McCammon 1983. syntax sigabs=bamabs(w,abund=abund,/ikeV,/Fano,verbose=v) parameters w [INPUT; required] photon energy values at which to compute the absorption * default units are [Ang], unless IKEV is set, when they are assumed to be [keV] keywords abund [INPUT] abundances relative to H=1 * default is to use Anders & Grevesse 1982 ikeV [INPUT] if set, assumes that W are in units of keV Fano [INPUT] if set, the 4 strongest auto-ionizing resonances of He I are included; numbers come from Oza (1986, Phys Rev A, 33, 824), and Fernley et al. (1987, J.Phys B 20, 6457). noHeH [INPUT] if set to any number other than 1 or 2, excludes H and He from the cross-sections * if set to 1, only excludes H * if set to 2, only excludes He verbose [INPUT] controls chatter _extra [JUNK] here only to avoid crashing the program subroutines GETABUND INICON restrictions works only in energy range 30 eV - 10 keV be warned that the edges are idealized and thus unrealistic for high resolution spectra because they do not include any resonance structure history vinay kashyap (OctMM; based on TOTLXS.FOR and XSCTNS.FOR of Balucinska-Church & McCammon, obtained from ADC catalog VI/62A, ftp://adc.gsfc.nasa.gov/pub/adc/archives/catalogs/6/6062A/ ) bug corrections (Brian Kern, 5Dec2001): Ne cross-section was missing "^3"; Fano calc had EPSj[j] (VK; Dec2001) force calculations only in valid energy range; added keyword NOHEH (VK; Jun03) bug correction: "exclude=0" means "include" (VK; Jul03) bug correction: lambda selection for He (Andy Ptak; VK Jun05) edge lambda correction: O, N, C changed acc. to numbers in Atomic Data Booklet (2nd Edition), Thompson, A., et al., 2001, LBL/PUB-490 Rev. 2 (Jeremy Drake; VK Sep2006)
(See pro/bamabs.pro)
function BEHR_hug
IDL wrapper to Bayesian Estimate of Hardness Ratios (BEHR)
returns a structure containing the relevant outputs neatly
summarized into fields for IDL consumption
references:
"Bayesian Estimation of Hardness Ratios: Modeling and Computations",
Park, T., Kashyap, V.L., Siemiginowska, A., van Dyk, D., Zezas, A.,
Heinke, C., and Wargelin, B., 2006, ApJ, 652, 610
"BEHR: Bayesian Estimation of Hardness Ratios", Park, T., Kashyap, V.,
Zezas, A., Siemiginowska, A., van Dyk, D., Connors, A., and Heinke, C.,
2005, at Six Years of Science with Chandra Symposium, Nov 2-5, 2005, #5.6
"Computing Hardness Ratios with Poissonian Errors",
van Dyk, D.A., Park, T., Kashyap, V.L., \& Zezas, A.,
2004, AAS-HEAD #8, 16.27
http://www.aas.org/publications/baas/v36n3/head2004/137.htm
syntax
behr=behr_hug(softsrc,hardsrc,softbkg,hardbkg,softarea,hardarea,$
softeff=softeff,hardeff=hardeff,softidx=softidx,hardidx=hardidx,$
softscl=softscl,hardscl=hardscl,softtbl=softtbl,hardtbl=hardtbl,/post,$
level=level,algo=algo,details=details,nsim=nsim,nburnin=nburnin,$
/hpd,nbins=nbins,outputf=outputf,outputR=outputR,outputHR=outputHR,$
outputC=outputC,outputMC=outputMC,outputPr=outputPr,BEHRdir=BEHRdir,$
verbose=verbose)
parameters
softsrc [INPUT; required] counts in source region in soft (S) band
hardsrc [INPUT; required] counts in source region in hard (H) band
softbkg [INPUT; required] counts in background region in S band
hardbkg [INPUT; required] counts in background region in H band
softarea[INPUT; required] background scaling factor in S band
hardarea[INPUT; required] background scaling factor in H band
* (background region area)/(source region area)
* can also include differences in exposure time into
the ratio, in the same manner as geometric area
keywords
softeff [INPUT] effective area in soft (S) band
* if not set, then set equal to HARDEFF if given, or
1 otherwise
hardeff [INPUT] effective area in hard (H) band
* if not set, then set equal to SOFTEFF if given, or
1 otherwise
* can also be the effective area relative to some
special point on the detector (e.g., aimpoint)
or even some specific detector (e.g., ACIS-I v/s ACIS-S)
softidx [INPUT] index of prior on S (range = 0+)
* if not set, then set equal to HARDIDX if given, or
0.5 otherwise
hardidx [INPUT] index of prior on H (range = 0+)
* if not set, then set equal to SOFTIDX if given, or
0.5 otherwise
* similar to AGAMMA of PPD_SRC()
softscl [INPUT] scaling index of prior on S
* if not set, then set to HARDSCL if given, or
0 otherwise
hardscl [INPUT] scaling index of prior on H
* if not set, then set to SOFTSCL if given, or
0 otherwise
* similar to BGAMMA of PPD_SRC()
softtbl [INPUT] filename containing a tabulated prior for S
hardtbl [INPUT] filename containing a tabulated prior for H
* the table prior must be an ascii file with the following format:
line 1: number of entries, say NLIN
line 2: labels for the columns, ignored
lines 3..NLIN+2: two whitespace separated columns of numbers,
with each row containing the source intensity and the posterior
density, in that order
* the default filenames are "./tblprior_{soft|hard}.txt"
* the default filenames are used iff SOFTTBL and HARDTBL are set
but do not appear to exist
* WARNING: if regex is used in the filename specification, only the
first file from the list will be used. furthermore, if specified,
the table priors are applied to _all_ SOFTSRC and HARDSRC
post [INPUT] if set, suggests the values of (SOFTIDX,SOFTSCL)
and (HARDIDX,HARDSCL) going forward, i.e., what you should
set the priors to in your next calculation for the same
source
level [INPUT] percentage confidence level at which to report error
(default = 68)
details [INPUT] compute various ratios (true/false)?
(default = true)
algo [INPUT] calculation method, GIBBS (default) or QUAD
* if set to AUTO or AUTO=N, then uses GIBBS for any
case where {SOFT|HARD}SRC > N, and QUAD below that
unless one of {SOFT|HARD}SRC > 99, in which case
GIBBS is set automatically
- if N is not set, assumed to be 15
- N can be set to any integer less than 100
nsim [INPUT] number of draws if algo=gibbs (default=10000)
nburnin [INPUT] number of burn-in draws if algo=gibbs
(default=5000 or NSIM/2, whichever is smaller)
nbins [INPUT] number of bins in integration if algo=quad (default=500)
hpd [INPUT] if set, computes the highest posterior density interval,
which also is the smallest interval that includes the mode.
* this is set by default
* only has an effect if ALGO=QUAD
outputF [INPUT] root of filename in which to place output
(default = 'none')
* output will be placed in the file, OUTPUTF.txt
* unless OUTPUTF='none', in which case nothing is written out,
unless one of OUTPUT{R|C|HR|MC|PR} are set, in which case
the corresponding output is put in file BEHR_{R|C|HR|MC|PR}.txt
outputR [INPUT] if set, writes output for R in OUTPUTF_R.txt
outputC [INPUT] if set, writes output for C in OUTPUTF_C.txt
outputHR[INPUT] if set, writes output for HR in OUTPUTF_HR.txt
outputMC[INPUT] if set, writes Monte Carlo draws for lamS and lamH
to OUTPUTF_draws.txt when algo=gibbs
outputPr[INPUT] if set, writes the probability distributions for
R, HR, C, lamS, and lamH to OUTPUTF_prob.txt when algo=quad
BEHRdir [INPUT] full path to directory where BEHR executable resides
(default = '/fubar/kashyap/AstroStat/BEHR')
verbose [INPUT] controls chatter
requirements
BEHR executable must be installed in BEHRDIR
BEHR should be executable under the shell via SPAWN
BEHR output assumed to be compatible with 12-19-2005 version
side-effects
potentially creates numerous ascii files in $cwd
history
vinay kashyap (SepMMV)
bugfix: output file format was overflowing; force NBURNIN < NSIM;
outputF for 1st iteration; added more references (VK; NovMMV)
added keywords SOFTSCL,HARDSCL,POST,HPD; changed DETAILS default
to true, OUTPUTF default to none; added extra fields to output
structure; added ALGO option AUTO (VK; DecMMV)
altered behavior of ALGO=AUTO to use GIBBS if counts in one of the
bands exceeds 100 (VK; OctMMVI)
added keywords SOFTTBL and HARDTBL (VK; FebMMVIII)
updated default BEHRdir (VK; OctMMXV)
(See pro/stat/behr_hug.pro)
function binErsp
returns position indices of input energ(y/ies) appropriately
binned into the specified binning scheme
returns -1 where E is outside the bin range
syntax
iE=binersp(nrg,binmn,maxbin,bstr=bstr,nbin=nbin)
parameters
nrg [INPUT; required] photon energies for which to find
the binning numbers
binmn [INPUT] array of bin minimum values
* overrides all keywords
* if not given, see description below on how it is
derived from BSTR.ELO, and NBIN & NRG.
binmx [INPUT] maximum of the bin max values.
* if not a scalar, then the last element of array is used
* see description below for how it is determined if
not given.
keywords
bstr [INPUT] structure containing the following pieces of
information, as obtained from an OGIP-compliant response
matrix (see RDRESP.PRO/RDARF.PRO): {NNRG, ELO, EHI}
nbin [INPUT; default=101] number of equally spaced bins into
which to split the input array of photon energies
* if -ve, binning will be logarithmic!
_extra [JUNK] here only to prevent crashing the program
description
if BINMN is not given, then BINMN=BSTR.ELO
if BSTR is also not given (or is incorrect), then
BINMN=FINDGEN(ABS(NBIN))*DE+EMIN
where DE=(EMAX-EMIN)/(ABS(NBIN)-1), EMIN=MIN(EE,MAX=EMAX),
and EE=NRG if NBIN>0, EE=ALOG10(NRG) if NBIN<0
if BINMX < MAX(BINMN), BINMN is truncated
if BINMX < MIN(BINMN), BINMX is reset to MIN(BINMN)
if BINMX is not given, then BINMX=MAX(BINMN)+BINMX(LAST)-BINMX(LAST-1)
if BINMN is not given, BINMX=MAX(BSTR.EHI)
if BSTR is also not given (or is incorrect), then BINMX=EMAX
history
vinay kashyap (Jul97)
converted to IDL5 notation (VK; OctMM)
(See pro/util/binersp.pro)
function bland returns a "blending factor" for each line in the emissivity list, defined as the ratio of the flux in the line to that within the given range. (i.e., small values mean heavily blended lines) syntax b=bland(flstr,dwvl,flx=flx,wflx=wflx,arstr=arstr,$ dem=dem,abund=abund,effar=effar,wvlar=wvlar,$ /temp,/noph,/ikev,/regrid) parameters flstr [INPUT; required] structure containing emissivity and wavelength information. see RD_LINE for details. * ion-balance assumed to be included * if FLX and WFLX are set on input, FLSTR is ignored -- still required, but ignored. dwvl [INPUT; default=median(delta(FLSTR.WVL))] the spectral "resolution" -- any line nearer than this value at any given wavelength is considered to be blended in to this. * if array of size FLSTR.WVL (or twice that size), set to different values (with possible asymmetric ranges) at each wavelength. keywords arstr [INPUT] structure of structures containing effective area information (see ARIA or GRATFLX) * if given in the right format, overrides call to LINEFLX with call to GRATFLX flx [I/O] contains the calculated flux due to each line * may be given on input and if WFLX is also set, FLSTR and ARSTR are ignored wflx [INPUT] if size matches that of FLX, assumed to be the wavelengths of the lines. * if FLX and WFLX are set on input, FLSTR and ARSTR are ignored. _extra [INPUT] pass defined keywords to GRATFLX (DEM, ABUND, TEMP, NOPH, IKEV, REGRID) LINEFLX (DEM, ABUND, EFFAR, WVLAR, TEMP, NOPH, IKEV, REGRID) subroutines ARIA GRATFLX LINEFLX history vinay kashyap (Sep98) bug fix for when FLSTR is ignored (VK; Oct98) added keyword ARSTR, added call to GRATFLX (VK; Nov98) converted to IDL5 notation (VK; OctMM) bug fix: crashed if FLX and WFLX set, but DWVL not set (VK;JanMMI) bug fix: FLSTR can have more than 8 tags (JJD; MayMMVII)
(See pro/bland.pro)
function calc_ftest calculate the significance of a new model component using the F test. Returns the p-value that the observed change in the chisq values for the given degrees of freedom can be obtained as a fluctuation. syntax pval=calc_ftest(dof1,chi1,dof2,chi2,fstat=fstat,/wdchi, /double) parameters dof1 [INPUT; required] degrees of freedom of SIMPLE model chi1 [INPUT; required] min chisq of SIMPLE model dof2 [INPUT; required] degrees of freedom of COMPLEX model chi2 [INPUT; required] min chisq of COMPLEX model * if arrays, the sizes of all of them must match. the output will then be an array of the same size. * NOTE: complex model _must_ be a subset of simple model and the parameter values that define one of the models should not lie on the boundary of the other. keywords fstat [OUTPUT] the value of the F statistic * (CHI1/DOF1)/(CHI2/DOF2) * larger the FSTAT, the more plausible the complex model wdchi [INPUT] if set, uses a different F statistic, defined as (DELTA_CHI/DELTA_DOF)/(CHI2/DOF2) = ((CHI1-CHI2)/(DOF2-DOF1))/(CHI2/DOF2) * WARNING: if DOF1 is smaller than DOF2, that is, if it appears that the input is already in this format, additional subtractions are not done. _extra [INPUT ONLY] pass defined keywords to IBETA() description this is how CIAO/Sherpa's calc_ftest program works. I just implemented it as a quick way to get at the same results in IDL. Avoid using the F test unless you know that it is applicable for the problem you are working on. See Protassov et al., 2002, ApJ, 571, 545 http://adsabs.harvard.edu/abs/2002ApJ...571..545P history vinay kashyap (MMXII.VII)
(See pro/stat/calc_ftest.pro)
function cat_id
returns a concatenated structure of Line IDs
syntax
C=cat_id(A,B,pick=pick,ask=ask,/okev,comm=comm,flst=flst,dbdir=dbdir,$
fluxes=fluxes,fluxerr=fluxerr)
parameters
A [INPUT; required] output of LINEID
B [INPUT] output of LINEID to be merged with A
* if any wavelengths are common, the IDs in A take
precedence (but see keyword ASK)
* if not given, then the program *prints* a summary
of the IDs to the screen
keywords
pick [INPUT; default: all] position indices of elements in A
to be selected (or not).
* if scalar, returns all elements EXCEPT the specified one
* has no effect on B
* use these two to delete entries, for e.g.
ask [INPUT] if set, asks for confirmation before throwing
away an ID from B that also exists in A. allows overriding
the default action.
* ASK='n' will reverse the default by throwing away the
ID from A instead of the one from B
* ASK='r' *reverses* the default, in that if there is a
component in B that's also in A, the one in A is >replaced<
by the one in B (as opposed to if ASK='n', then the one in
A is deleted, and B is just appended at the end)
* ASK='k' overrides the default by keeping BOTH
okev [INPUT] if set, converts wavelengths [Ang] to energy [keV]
comm [INPUT] appends a comment to each line while printing
* takes the comments from A.LABL(1,i)+A.LABL(0,i)
* truncates the comment to a maximum of 30 characters
unless COMM is set to a higher number
* for this to work when FLST is set, make sure DBDIR is
also defined
flst [INPUT] if set, prints out the line list in the form that
RD_LIST likes
* if FLST is a string, writes to file FLST
mplet [OUTPUT] if set, will contain on output a 2 dimensional MPLET
string array as prescribed by MIXIE()
dbdir [INPUT] if set and FLST is set, appends DBDIR to IDs
* 1 => $SCAR , 2 => $SPEX , 3 => $CHIANTI
fluxes [INPUT] if set and matches either the number of components
or the number of matches, then renormalizes/overwrites the
line fluxes in the output.
* ONLY if IDs are being printed
fluxerr [INPUT] if set and matches either the number of components
or the number of matches, then appends an error to output
* ignored if FLST is not set
* if FLUXERR is given for each match, square-adds the errors
for the components
* if single element, but there are more than 1 component to
ID structure, this is assumed to be the fractional error
(if < 1) or S/N (if > 1) for each match
_extra [JUNK] here only to prevent crashing the program
restrictions
* works ONLY on the outputs of LINEID
* requires subroutines:
-- INICON
-- CREATE_STRUCT
-- LINEID
history
vinay kashyap (Feb97)
bug -- was breaking down in simplest case (VK; Mar97)
was breaking down if ID was unknown (VK; Jul97)
added keyword FLST (VK; Oct98)
added call to INITSTUFF; added Tmax to output; added keywords DBDIR,
FLUXES, FLUXERR; corrected bug re undefined output when FLST was set;
increased number of significant digits in FLST output; generalized
ASK to "Yes/No/Replace/Keep" (VK; Nov98)
updated FLUXERR behavior to account for new field (VK; Dec98)
modified to allow for field NOTES to be printed out (VK; Mar99)
changed call to INITSTUFF to INICON (VK; 99May)
added FLUXERR to output (VK; MarMM)
converted to IDL5 array notation (VK; OctMM)
changed keyword KEV to OKEV (VK; JanMMI)
now /COMM also works when FLST (and DBDIR) are defined (VK;Nov01)
added MPLET keyword (LL; Feb04)
adjusted print format a bit to avoid **** in FLUXERR (VK; Jul12)
(See pro/cat_id.pro)
function cat_ln returns a concatenated structure of Line emissivities syntax C=cat_ln(A,B,pick=pick,ask=ask,comm=comm,reord=reord,/okev,$ abund=abund,/noph,effar=effar,wvlar=wvlar,dem=dem,/temp,/ikev,/regrid) parameters A [INPUT; required] output of RD_LINE B [INPUT] output of RD_LINE to be merged with A * if any wavelengths are common, the IDs in A take precedence (but see keyword ASK) * if the temperature grids do not match, the emissivities in B are interpolated to the same grid as in A * if not given, then the program *prints* a summary of the lines to the screen keywords pick [INPUT; default: all] position indices of elements in A to be selected (or not). * if scalar, returns all elements EXCEPT the specified one * has no effect on B * use these two to delete entries, for e.g. ask [INPUT] specifies how to handle duplicate lines * if not set, doesn't care about duplicates and keeps all * if set (see exceptions below), will discard duplicates from B * ASK='n' will reverse the normal by throwing away the line from A instead of the one from B * ASK='r' will >replace< the emissivity, etc. in A with that of B * ASK='k' will act just as though ASK has not been set okeV [INPUT] if set, converts wavelengths [Ang] to energy [keV] in the screen listing comm [INPUT] appends a comment to each line while printing * takes the comments from A.DESIG[1,i]+A.DESIG[0,i] * truncates the comment to a maximum of 30 characters unless COMM is set to a higher number flst [INPUT] if set, prints out the line list in the form that RD_LIST likes * if FLST is a string, writes to file FLST reord [INPUT] if set, rearrange the order of the output * +ve: descending order of fluxes * -ve: ascending order of fluxes * if abs(REORD) .NE. 1, limit output to first REORD entries _extra [INPUT ONLY] use to pass defined keywords to LINEFLX: ABUND, NOPH, EFFAR, WVLAR, DEM, TEMP, REGRID restrictions * works ONLY on the outputs of RD_LINE * requires subroutines: -- LINEFLX [GETABUND, WHEE] -- RD_LINE -- CREATE_STRUCT -- INICON history vinay kashyap (Jun98, based on CAT_ID) changed keyword LNLST to FLST, added ABUND and REORD (VK; Jul98) delete keyword ABUND, and added call to LINEFLX (VK; Aug98) corrected bug that was skipping B because of roundoff error in first element; bug in handling ECONF (VK; Nov98) changed keyword KEV to OKEV to avoid conflict with LINEFLX keyword of same name (VK; 99Apr) added support for structure field JON (VK; 99May) allowed merging of mismatched LOGT grids (VK; 99Jul) converted to IDL5 array notation (VK; OctMM) added full RD_LIST compatible printout for FLST; changed output file wavelength format from f8.4 to f10.5 (VK; JanMMI) bug -- crashing on <empty> for FLST -- fixed (VK; Jul04) added extra columns (FLUX, logTMAX) to output of FLST (VK; Feb08)
(See pro/cat_ln.pro)
function chanarf compute the average effective area over each channel, as a weighted average of the effective area from all the energies that contribute to that channel. makes a difference mainly for low and medium spectral resolution data. for high-res grating data, not so much. syntax carf=chanarf(rmfstr,effar,spec=spec) parameters rmfstr [INPUT; required] response matrix structure, in the same format as returned from RD_OGIP_RMF() effar [INPUT] effective area as a function of energy [cm^2] * assumed to be on the same grid as the input energies of RMFSTR, i.e., RMFSTR.ELO and RMFSTR.EHI * ignored if size doesn't match RMFSTR keywords spec [INPUT] a spectrum to further weight the contribution of EFFAR * assumed to be on the same grid as RMFSTR.ELO and RMFSTR.EHI * ignored if size doesn't match EFFAR * ideally should be in units of [ph/keV/...] chnrg [OUTPUT] the average energy of a photon in this channel * it should be similar to 0.5*(RMFSTR.EMN+RMFSTR.EMX), and serves as a check on the gain calibration verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing history vinay kashyap (MMVI.IX)
(See pro/chanarf.pro)
function chandra_status_bit filters a Chandra event file or status bit array on each status bit and reports how many events are flagged, and returns the indices of the filtered events syntax idx=chandra_status_bit(inp,filter,bitstr=bitstr,verbose=verbose) parameters inp [INPUT; required] the input from which the ststus bits are to be filtered * if byte array, must be of size (4,NPH), and this is the IDL read-in of a 32-bit string of 0s and 1s. Note that the columns are ordered last to first. * if a structure, there must be a field in it named .STATUS and the byte array of above case is taken from that * if string, assumed to be the full path to a filename that contains an events list, and it is read in and the STATUS column is extracted from it filter [INPUT; optional] the filter to be used, in the same format as CIAO. e.g., HRC-I status-bit filtering uses 'xxxxxx00xxxx0xxx00000000x0000000', i.e., 0 or 1 matches exactly, and 'x' ignores it. keywords bitstr [OUTPUT] a structure that contains the bits that are turned on, the number of events that are flagged, and for each of those, the array of the flagged indices stabit [OUTPUT] ordered array of status bits, converted from IDL's 4xNPH to 32xNPH verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program requires B11001001 IDL-Astro library history vinay kashyap (2014jul, inspired by CIAO's summarize_status_bits)
(See pro/util/chandra_status_bit.pro)
chiompress.pro a script to compress the CHIANTI databases into a smaller dataset to make it easy to transport and easy to read. The max emissivity of each line is tested against the max emissivities of nearby lines and the line is retained iff it is above the locally defined threshold. usage chifulldir='/data/fubar/SCAR/emissivity/chi713' ;full database dir outdir='/data/fubar/SCAR/emissivity/chiompress713' ;compressed dir dynrng=1e2 ;dynamic range hwdth=1.0 ;half-width of window in AA .run chiompress side effects creates files in OUTDIR creates a postscript file in $CWD vinay kashyap (2010jul) bug fix: density sensitive lines were being ignored in the write (VK; 2010sep)
(See pro/scrypt/chiompress.pro)
PROJECT : CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME : CH_GET_FILE
PURPOSE : to select a file from either a selected directory or the working
directory, having an extension.
EXPLANATION : a file in either a selected directory or the working
directory, having an extension can be selected using a
widget. Note that both directory and extension have to be
supplied. If no file is found, an empty string is returned. ;
USE : IDL> name = ch_get_file( '~/', '.pro', tit=' Select a procedure ')
EXAMPLES : dir= concat_dir(!xuvtop),'dem')
dem_name=ch_get_file(path=dir,filter='*.dem',title='Select DEM File')
INPUTS : directory, extension
OPT. INPUTS :
OUTPUTS : the file name
OPT. OUTPUTS:
KEYWORDS : title
CALLS : findfile, break_file
COMMON : co
RESTRICTIONS: both directory and extension have to be
supplied.
SIDE EFFECTS:
CATEGORY :
PREV. HIST. : extracted from CDS/CHIANTI routines.
WRITTEN :
Giulio Del Zanna (GDZ),
DAMTP (University of Cambridge, UK)
MODIFIED : Version 1, GDZ 10-Oct-2000
V.2, GDZ, corrected a typo at the end of the file.
V.3, GDZ, generalized directory concatenation to work for
Unix, Windows and VMS.
V. 4, 19-July-2002, GDZ
Added the option to select files also with the standard IDL
dialaog_pickfile, and changed a few things...
V.5, 2-Aug-02, GDZ
reduced the size of the widget.
V.6, 12-Aug-02, GDZ
corrected for a bug in the directory output.
V.7, 3-Nov-03 GDZ
Fixed a bug when using Windows, the returned path was not
correct.
VERSION : 7, 3-Nov-03
(See pro/external/ch_get_file.pro)
function cltsmooth An adaptive smoothing technique that takes advantage of the central limit theorem. Applicable to background subtracted light curves or spectra that need to have the negative values removed without touching anything that is at large S/N. First picks out all the -ves, assumes these are normally distributed, and collects all +ves that are of the same magnitude. Then computes mean and stderr at all selected points, then at progressively smaller scales until at most 32 bins widths, and resets the local mean and stderr iff it is significantly different from that computed at larger scale. syntax sy=cltsmooth(y,syerr=syerr,swidth=swidth,verbose=verbose) parameters y [INPUT; required] the spectrum or light curve keywords syerr [OUTPUT] the errors computed at each bin * note that these will not be independent swidth [OUTPUT] the widths over which the SY and SYERR are computed verbose [INPUT] controls chatter _extra [JUNK] here only to avoid crashing the program these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales vinay kashyap (2015feb)
(See pro/util/cltsmooth.pro)
function colbehr
computes hardness ratios based on 3-band data by invoking
BEHR (Bayesian Estimate of Hardness Ratios) twice, and
returns the inputs as well as the following quantities
and their credible ranges in a structure:
{S, M, H, lS=log10(S), lM=log10(M), lH=log10(H),
SpM=S+M, MpH=M+H, SpH=S+H, T=S+M+H,
SmM=S-M, MmH=M-H, SmH=S-H,
R1=S/M, R2=M/H, R3=S/H,
C1=C_SM, C2=C_MH, C3=C_SH,
HR1=(S-M)/(S+M), HR2=(M-H)/(M+H), HR3=(S-H)/(S+H),
HRA=(S-M)/(S+M+H), HRB=(M-H)/(S+M+H), HRC=(S-H)/(S+M+H)}
Warning: Because of the necessity of combining two separate
runs of BEHR, only the MCMC option is used. Thus, if the
length of the chain is small, the computed values may be
subject to computational instability.
Warning: BEHR assumes that the passbands in question
do not overlap, and that the counts input to the program
are statistically independent. It is up to the users to
ensure the validity of this assumption. No checks are
made to verify it.
Reference:
"Bayesian Estimation of Hardness Ratios: Modeling and Computations",
Park, T., Kashyap, V.L., Siemiginowska, A., van Dyk, D., Zezas, A.,
Heinke, C., and Wargelin, B., 2006, ApJ, 652, 610
http://hea-www.harvard.edu/AstroStat/BEHR/
syntax
behr3=colbehr(Ssrc,Msrc,Hsrc,Sbkg=Sbkg,Mbkg=Mbkg,Hbkg=Hbkg,$
Sarea=Sarea,Marea=Marea,Harea=Harea,$
Seff=Seff,Meff=Meff,Heff=Heff,$
Sidx=Sidx,Midx=Midx,Hidx=Hidx,$
Sscl=Sscl,Mscl=Mscl,Hscl=Hscl,$
Stable=Stable,Mtable=Mtable,Htable=Htable,$
/post,level=level,nsim=nsim,nburnin=nburnin,hpd=hpd,$
outputf=outputf,BEHRdir=BEHRdir, verbose=verbose)
parameters
Ssrc [INPUT; required] counts in source region in the soft (S) band
Msrc [INPUT; required] counts in source region in the medium (M) band
Hsrc [INPUT; required] counts in source region in the hard (H) band
* can be arrays; if so, the array with the most elements
determines the size of the output and the shortfalls in the
others, if any, are made up by replicating the first elements
keywords
Sbkg [INPUT] counts in background region in the S band
Mbkg [INPUT] counts in background region in the M band
Hbkg [INPUT] counts in background region in the H band
* if not given, assumed to be 0
* if size smaller than Xsrc, first element gets replicated
Sarea [INPUT] background scaling factor in the S band
Marea [INPUT] background scaling factor in the M band
Harea [INPUT] background scaling factor in the H band
* (background region area)/(source region area)
* if not given, assumed to be 1
* can also include differences in exposure time into
the ratio, in the same manner as geometric area
* if size smaller than Xsrc, first element gets replicated
Seff [INPUT] effective area in S band
Meff [INPUT] effective area in M band
Heff [INPUT] effective area in H band
* if none are set, all are assumed to be 1,
else if one is set, all are assumed to be equal to that one,
else if two are set and unequal, third is assumed to be 1
* can also be the effective area relative to some
special point on the detector (e.g., aimpoint)
or even some specific detector (e.g., ACIS-I v/s ACIS-S)
* if size smaller than Xsrc, first element gets replicated
Sidx [INPUT] index of prior on S (range = 0+)
Midx [INPUT] index of prior on M (range = 0+)
Hidx [INPUT] index of prior on H (range = 0+)
* if none are set, all are assumed to be 0.5,
else if one is set, all are assumed to be equal to that one
else if two are set and are unequal, third is assumed to be 0.5
* if size smaller than Xsrc, first element gets replicated
* similar to AGAMMA of PPD_SRC()
Sscl [INPUT] scaling index of prior on Ssrc
Mscl [INPUT] scaling index of prior on Msrc
Hscl [INPUT] scaling index of prior on Hsrc
* if none are set, all are assumed to be 0
else if one is set, all are assumed to be equal to that one
else if two are set and are unequal, third is assumed to be 0
* if size smaller than Xsrc, first element gets replicated
* similar to BGAMMA of PPD_SRC()
Stable [INPUT] filename containing a tabulated prior for Ssrc
Mtable [INPUT] filename containing a tabulated prior for Msrc
Htable [INPUT] filename containing a tabulated prior for Hsrc
* the table prior must be an ascii file with the following format:
line 1: number of entries, say NLIN
line 2: labels for the columns, ignored
lines 3..NLIN+2: two whitespace separated columns of numbers,
with each row containing the source intensity and the posterior
density, in that order
* the default filenames are "./tblprior_{soft|med|hard}.txt"
* the default filenames are used iff Stable, Mtable, and Htable are set
but are not found
* WARNING: if regex is used in the filename specification, only the
first file from the list will be used. furthermore, if specified,
the table priors are applied to _all_ SSRC, MSRC, and HSRC
post [INPUT] if set, suggests the values of (Sidx,Sscl), (Midx,Mscl),
and (Hidx,Hscl) going forward, i.e., what you should set the
priors to in your next calculation for the same source -- the
suggested values are stored in the output structure
level [INPUT] percentage confidence level at which to report error
(default = 68)
details [INPUT] compute various ratios (true/false)?
(default = true)
nsim [INPUT] number of draws if algo=gibbs (default=10000)
nburnin [INPUT] number of burn-in draws if algo=gibbs
(default=5000 or NSIM/2, whichever is smaller)
outputF [INPUT] root of filename in which to place output
(default = 'none')
* output will be placed in the files OUTPUTF.txt and OUTPUTF_draws.txt
* NOTE: if OUTPUTF='none', then MC draws will be in BEHR_draws.txt
BEHRdir [INPUT] full path to directory where BEHR executable resides
(default = '/data/fubar/kashyap/AstroStat/BEHR')
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
requirements
uses subroutines HIPD_INTERVAL() and MODALPOINT()
BEHR executable must be installed in BEHRDIR
BEHR should be executable under the shell via SPAWN
BEHR output assumed to be compatible with 12-19-2005 version
side-effects
potentially creates numerous ascii files in $cwd or `basedir OUTPUTF`
history
vinay kashyap (Mar07; based on behr_hug.pro)
bug correction with NaNs not being caught in some cases
(VK; Mar07)
added keywords Stable,Mtable,Htable (VK; Feb08)
etymology
getting color-color diagrams using BEHR
(that's my story and I'm sticking to it)
(See pro/stat/colbehr.pro)
function colourcurve computes color (log(S)-log(H)) for given NH, for various temperatures, for a given ARF/RMF combo syntax colcurv=colourcurve(NH,arffil,rmffil,logT,Sband=Sband,Hband=Hband,$ n_e=n_e,logP=logP,abund=abund,$ ldbdir=ldbdir,ceroot=ceroot,cdbdir=cdbdir,ioneqf=ioneqf,$ lstr=lstr,cstr=cstr,verbose=verbose,$ chidir=chidir, cocofil=cocofil,chdwvl=chdwvl,/twoph,/noff,/nofb,$ nhne=nhne, fH2=fH2,He1=He1,HeII=HeII,/Fano,/wam,/bam,/mam,/vion,/noHeH,$ icrstr=icrstr,ionfrac=ionfrac, vfkydir=vfkydir,,nconsec=nconsec,$ EBV=EBV,R_V=R_V,LMC2=LMC2,AVGLMC=AVGLMC,ExtCurve=ExtCurve,$ fmgamma=fmgamma,fmx0=fmx0,fmc1=fmc1,fmc2=fmc2,fmc3=fmc3,fmc4=fmc4) parameters NH [INPUT; required] H I column density in [cm^-2] arffil [INPUT; required] name of ARF file * if blank, ignores RMFFIL and proceeds to compute flux ratios rather than counts ratios - hardcoded range of [15 kev, 200 Ang], edit the code, or keep SBAND and HBAND in this range rmffil [INPUT; required] name of RMF file * quits if ARFFIL and RMFFIL are set but files cannot be read logT [INPUT] temperatures at which to compute colors [log10([K])] * if not given, or if input is not understandable, assumed to be 5:8:0.1 keywords Sband [INPUT] 2-element float array of energies for the soft band [keV] * default is [0.5,2] * if 1-element, then alters the nearest bound. e.g., if Sband=0.3, changes to [0.3,2] Sband=1.24, changes to [1.24,2] Sband=1.26, changes to [0.5,1.26] Sband=4, changes to [0.5,4] * if integer, assumed to be channel number (cf. RMFFIL) Hband [INPUT] 2-element float array of energies for the hard band [keV] * default is [2.0,7.0] * if 1-element, then alters the nearest bound (cf. SBAND) * if integer, assumed to be channel number (cf. RMFFIL) n_e [INPUT] passed w/o comment to RD_LINE() and RD_CONT() logP [INPUT] passed w/o comment to RD_LINE() and RD_CONT() abund [INPUT] abundances * default is to use solar coronal ldbdir [INPUT] line emissivity database * default is '$APED' ceroot [INPUT] what type of continuum to use * default is 'apec' * options are 'cie' and 'chianti' (but latter has problems; still being investigated) cdbdir [INPUT] continuum emissivity database * default is '$CONT' ioneqf [INPUT] ion balance file * default is 'ioneq/chianti.ioneq' * not used for APED/ATOMDB lstr [I/O] structure that contains line emissivity database cstr [I/O] structure that contains continuum emissivity database * if LSTR and CSTR are given on input, then the emissivity databases are not read in verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines [RD_IONEQ] CHIDIR [RD_CONT] COCOFIL, CHDWVL, TWOPH, NOFF, NOFB [ISMTAU] FH2, HE1, HEII, FANO, VION, BAM, MAM, NOHEH, ICRSTR [IONABS] ICRSTR, IONFRAC, VFKYDIR, NCONSEC [FM_UNRED] EBV, R_V, LMC2, AVGLMC, EXTCURVE, FMGAMMA, FMX0, FMC1, FMC2, FMC3, FMC4 [LINEFLX] NHNE
(See pro/colourcurve.pro)
PROJECT: CHIANTI
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
convertname
PURPOSE:
Ion names as character strings are converted into
numerical values (note c_2 is C II or C^+1
in spectroscopic or atomic notation)
CATEGORY:
naming utility
CALLING SEQUENCE:
CONVERTNAME,Name,Iz,Ion
INPUTS:
Name: such as 'c_2'
OUTPUTS:
Iz: nuclear charge Z (6 for 'c_2', the equivalent of C II)
Ion: ionization stage: (2 for 'c_2')
OPTIONAL OUTPUTS
DIELECTRONIC Set to 1 if NAME has a 'd' appended to it
(indicating dielectronic recombination data) else
set to 0
EXAMPLE:
> convertname,'c_2',iz,ion
> print,iz,ion
> 6,2
> convertname,'o_6d',iz,ion
> print,iz,ion
> 8,6
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
October 1999: Version 3. by kpd
Ver.4, 11-Dec-01, Peter Young
Revised routine, removing ch_repstr call.
Added DIELECTRONIC optional output.
(See pro/external/convertname.pro)
NAME:
CONVERT_TO_TYPE
PURPOSE:
Converts its input argument to a specified data type.
AUTHOR:
FANNING SOFTWARE CONSULTING
David Fanning, Ph.D.
1645 Sheely Drive
Fort Collins, CO 80526 USA
Phone: 970-221-0438
E-mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com
CATEGORY:
Utilities
CALLING SEQUENCE:
result = Convert_To_Type(input, type)
INPUT_PARAMETERS:
input: The input data to be converted.
type: The data type. Accepts values as given by Size(var, /TNAME) or Size(var, /TYPE).
OUTPUT_PARAMETERS:
result: The input data is converted to specified data type.
KEYWORDS:
None.
RESTRICTIONS:
Data types STRUCT, POINTER, and OBJREF are not allowed.
MODIFICATION HISTORY:
Written by David W. Fanning, 19 February 2006.
(See pro/external/convert_to_type.pro)
procedure conv_rmf convolves input energy spectrum with the response matrix unlike the combination of RDRESP and FOLD_RESP, this one goes easy on memory at the expense of speed. syntax conv_rmf,nrg,flx,chan,spec,rmf,effar=effar,nrgar=nrgar,$ rmfstr=rmfstr,fchcol=fchcol,/shift1,verbose=verbose parameters nrg [INPUT; required] mid-bin values at which input FLX is defined. * usually [keV], depends on RMF file * if size = N(FLX)+1, assumed to be bin-boundaries flx [INPUT; required] fluxes in [ph/bin/(s/cm^2/sr/...)] chan [OUTPUT; required] bin boundary values at which output SPEC is defined * same units as NRG * WARNING: the values that populate this array are taken from the EMN and EMX values in the RMF. These are not exact values, and simply represent approximate bounds on the detector channels that the input spectrum gets redistributed into. They are to be used mainly for plotting purposes, and should not be used for scientific purposes unless the user recognizes their limitations. In other words, the array indices of SPEC are the detector channels, and the CHAN array is a mapping from channels to energy, as defined in the EBOUNDS extension of the RMF spec [OUTPUT; required] output, convolved spectrum rmf [INPUT; required] name of OGIP-compliant FITS file containing the response matrix * may also be a structure, such as the output of RD_OGIP_RMF() keywords effar [INPUT] effective areas [cm^2] nrgar [INPUT] energies at which EFFAR are defined * same units as NRG * sizes of EFFAR and NRGAR must match * range of NRGAR must overlap NRG * if EFFAR and NRGAR are legal, FLX is multiplied by EFFAR (over intersection of NRGAR and NRG; zeroed elsewhere) before convolving with response matrix * of course, this multiplication makes sense only if units on FLX are [ph/bin/cm^2/...] rmfstr [OUTPUT] structure containing info of response matrix, the output of RD_OGIP_RMF() verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines: RD_OGIP_RMF: FCHCOL, SHIFT1 REBINW : SLOWOK restrictions requires IDLAstro library requires RD_OGIP_RMF() requires REBINW() requires BINERSP() these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (Apr99) added keyword SHIFT1 (VK; JanMMI) bug: incorrect usage of WVLAR instead of NRGAR in effar block (Erica R; Aug01) deleted keyword SHIFT1, cleaned up and speeded up (VK; Nov2001) bug: when spectrum size < RMF size and RMF has multiple groups, was using only the first group (VK; Nov'02) bug: was crashing when NRG was outside the bounds of the RMF in cases where the RMF was at a higher resolution (LL/VK; Apr'03) added keyword VERBOSE (VK; MarMMV) bug: when input spectrum energy range was smaller than RMF range, was assuming RMF was at higher resolution even if it wasn't (VK; Aug'07) bug: wasn't checking for frequency beating between input spectrum grid and input RMF grid in above case; now if it does, and calls REBINW() and forces input spectrum to the right grid (VK; Aug'07) bug: EFFAR multiplication was being ignored when input spectrum had to be rebinned to match RMF grid (VK; Oct'07)
(See pro/util/conv_rmf.pro)
NAME:
CURVEFIT
PURPOSE:
Non-linear least squares fit to a function of an arbitrary
number of parameters. The function may be any non-linear
function. If available, partial derivatives can be calculated by
the user function, else this routine will estimate partial derivatives
with a forward difference approximation.
CATEGORY:
E2 - Curve and Surface Fitting.
CALLING SEQUENCE:
Result = CURVE_FIT(X, Y, Weights, A, SIGMA, FUNCTION_NAME = name, $
ITMAX=ITMAX, ITER=ITER, TOL=TOL, /NODERIVATIVE)
INPUTS:
X: A row vector of independent variables. This routine does
not manipulate or use values in X, it simply passes X
to the user-written function.
Y: A row vector containing the dependent variable.
Weights: A row vector of weights, the same length as Y.
For no weighting,
Weights(i) = 1.0.
For instrumental (Gaussian) weighting,
Weights(i)=1.0/sigma(i)^2
For statistical (Poisson) weighting,
Weights(i) = 1.0/y(i), etc.
A: A vector, with as many elements as the number of terms, that
contains the initial estimate for each parameter. IF A is double-
precision, calculations are performed in double precision,
otherwise they are performed in single precision. Fitted parameters
are returned in A.
KEYWORDS:
FUNCTION_NAME: The name of the function (actually, a procedure) to
fit. IF omitted, "FUNCT" is used. The procedure must be written as
described under RESTRICTIONS, below.
ITMAX: Maximum number of iterations. Default = 20.
ITER: The actual number of iterations which were performed
TOL: The convergence tolerance. The routine returns when the
relative decrease in chi-squared is less than TOL in an
interation. Default = 1.e-3.
CHI2: The value of chi-squared on exit (obselete)
CHISQ: The value of reduced chi-squared on exit
NODERIVATIVE: IF this keyword is set THEN the user procedure will not
be requested to provide partial derivatives. The partial
derivatives will be estimated in CURVEFIT using forward
differences. IF analytical derivatives are available they
should always be used.
OUTPUTS:
Returns a vector of calculated values.
A: A vector of parameters containing fit.
OPTIONAL OUTPUT PARAMETERS:
Sigma: A vector of standard deviations for the parameters in A.
COMMON BLOCKS:
NONE.
SIDE EFFECTS:
None.
RESTRICTIONS:
The function to be fit must be defined and called FUNCT,
unless the FUNCTION_NAME keyword is supplied. This function,
(actually written as a procedure) must accept values of
X (the independent variable), and A (the fitted function's
parameter values), and return F (the function's value at
X), and PDER (a 2D array of partial derivatives).
For an example, see FUNCT in the IDL User's Libaray.
A call to FUNCT is entered as:
FUNCT, X, A, F, PDER
where:
X = Variable passed into CURVEFIT. It is the job of the user-written
function to interpret this variable.
A = Vector of NTERMS function parameters, input.
F = Vector of NPOINT values of function, y(i) = funct(x), output.
PDER = Array, (NPOINT, NTERMS), of partial derivatives of funct.
PDER(I,J) = DErivative of function at ith point with
respect to jth parameter. Optional output parameter.
PDER should not be calculated IF the parameter is not
supplied in call. IF the /NODERIVATIVE keyword is set in the
call to CURVEFIT THEN the user routine will never need to
calculate PDER.
PROCEDURE:
Copied from "CURFIT", least squares fit to a non-linear
function, pages 237-239, Bevington, Data Reduction and Error
Analysis for the Physical Sciences. This is adapted from:
Marquardt, "An Algorithm for Least-Squares Estimation of Nonlinear
Parameters", J. Soc. Ind. Appl. Math., Vol 11, no. 2, pp. 431-441,
June, 1963.
"This method is the Gradient-expansion algorithm which
combines the best features of the gradient search with
the method of linearizing the fitting function."
Iterations are performed until the chi square changes by
only TOL or until ITMAX iterations have been performed.
The initial guess of the parameter values should be
as close to the actual values as possible or the solution
may not converge.
EXAMPLE: Fit a function of the form f(x) = a * exp(b*x) + c to
sample pairs contained in x and y.
In this example, a=a(0), b=a(1) and c=a(2).
The partials are easily computed symbolicaly:
df/da = exp(b*x), df/db = a * x * exp(b*x), and df/dc = 1.0
Here is the user-written procedure to return F(x) and
the partials, given x:
pro gfunct, x, a, f, pder ; Function + partials
bx = exp(a(1) * x)
f= a(0) * bx + a(2) ;Evaluate the function
IF N_PARAMS() ge 4 THEN $ ;Return partials?
pder= [[bx], [a(0) * x * bx], [replicate(1.0, N_ELEMENTS(f))]]
end
x=findgen(10) ;Define indep & dep variables.
y=[12.0, 11.0,10.2,9.4,8.7,8.1,7.5,6.9,6.5,6.1]
Weights=1.0/y ;Weights
a=[10.0,-0.1,2.0] ;Initial guess
yfit=curvefit(x,y,Weights,a,sigma,function_name='gfunct')
print, 'Function parameters: ', a
print, yfit
end
MODIFICATION HISTORY:
Written, DMS, RSI, September, 1982.
Does not iterate IF the first guess is good. DMS, Oct, 1990.
Added CALL_PROCEDURE to make the function's name a parameter.
(Nov 1990)
12/14/92 - modified to reflect the changes in the 1991
edition of Bevington (eq. II-27) (jiy-suggested by CreaSo)
Mark Rivers, U of Chicago, Feb. 12, 1995
- Added following keywords: ITMAX, ITER, TOL, CHI2, NODERIVATIVE
These make the routine much more generally useful.
- Removed Oct. 1990 modification so the routine does one iteration
even IF first guess is good. Required to get meaningful output
for errors.
- Added forward difference derivative calculations required for
NODERIVATIVE keyword.
- Fixed a bug: PDER was passed to user's procedure on first call,
but was not defined. Thus, user's procedure might not calculate
it, but the result was THEN used.
Steve Penton, RSI, June 1996.
- Changed SIGMAA to SIGMA to be consistant with other fitting
routines.
- Changed CHI2 to CHISQ to be consistant with other fitting
routines.
- Changed W to Weights to be consistant with other fitting
routines.
_ Updated docs regarding weighing.
Vinay Kashyap, CfA, Dec 1998
- Changed name to CURVE_FIT.
- Added keyword _EXTRA=E to calling sequence and to all
calls to CALL_PROCEDURE.
(See pro/external/curve_fit.pro)
function curvesect finds and returns the point(s) of intersection of two curves syntax xy=curvesect(y1,y2,xpt,verbose=verbose) parameters y1 [INPUT; required] points of curve Y1(X) y2 [INPUT; required] points of curve Y2(X) * Y1 and Y2 must be defined on the same grid xpt [INPUT] x-coordinates of Y1 and Y2 * if not supplied, uses the array index keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program restrictions only returns the intersections within the domain of XPT inputs must be sorted in X description a very simple algorithm that checks whether two curves have any crossings, and if they do, finds the point of intersection using the line segments that connect across the crossings. Don't push it. example .run curvesect history Vinay Kashyap (2012dec)
(See pro/util/curvesect.pro)
function cut_id add or delete IDs to an existing ID structure syntax newid=cut_id(idstr,idx,delet=delet,addon=addon,verbose=verbose,$ /incieq,dbdir=dbdir,sep=sep,pres=pres,logP=logP,n_e=n_e,$ chifil=chifil,chidir=chidir,eqfile=eqfile) warning will not keep track of relative fluxes or their errors properly, though the total flux will be conserved. parameters idstr [INPUT; required] an ID structure (see LINEID.PRO) containing line identifications of spectral features idx [INPUT; required] a zero-based index of the feature being (re)edited * must be a scalar * nothing happens if IDX is outside the legal range defined by IDSTR keywords delet [INPUT] set to a zero-based index to IDSTR.(IDX+1) * if float, assumed to refer to IDSTR.(IDX+1).WVL * if string, assumed to be in same format as understood by RD_LIST: "Z ION <sep> WAVE <sep> SOURCE <sep> DESCRIPTION" (RD_LIST will in fact be called in order to decipher it) * may be an array addon [INPUT] string describing the line to be added as an ID to IDSTR.(IDX+1) * must be in same format as that understood by RD_LIST: "Z ION <sep> WAVE <sep> SOURCE <sep> DESCRIPTION" * may be an array eps [INPUT] a small number * default is 1e-5 verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to RD_LIST: INCIEQ,DBDIR,SEP,PRES,LOGP,N_E,CHIFIL,CHIDIR,EQFILE LINEFLX: DEM,ABUND,NOPH,EFFAR,WVLAR restrictions requires subroutines: RD_LIST, RD_LINE, FOLD_IONEQ, READ_IONEQ, RD_IONEQ, LINEFLX, GETABUND, WHEE, SYMB2ZION, LAT2ARAB, CAT_LN requires IDL 5.3+ (because of use of STRSPLIT, STRJOIN, STRCMP) history vinay kashyap (JanMMI)
(See pro/cut_id.pro)
Purpose: checks input data for type, ndimension, etc
(uses IDL size function results)
Keyword Parameters:
type - if set, return idl data type from size function
type data type
0 ???
1 byte
2 integer
3 longword
4 floating point
5 double precision
6 ???
7 string
8 structure
ndimen - if set, return number dimensions (size(0))
nimages - if set, return #images (1->2D, NI->3D, else 0)
xsize - if set, return X size (size(data))(1)
nx - synonym for xsize
ysize - if set, return Y size (size(data))(2)
ny - synonym for ysize
string/struct/undefined - if set, return true if type matches
scalar, vector - if set, true if data of specified variety
Calling Examples:
if (data_chk(p1,/type) eq data_chk(p2,/type)) then...
case data_chk(data,/type) of...
if data_chk(data,/string,/scalar) then ...
if data_chk(data,/string,/struct,/undef,/orr)
case data_chk(maybe_cube,/nimages) of...
History:
27-Apr-1993 (SLF)
21-Mar-1994 (SLF) documentation header
10-oct-1996 (SLF) add SCALAR (synonym for the historical mispell SCALER)
2-oct-1997 (SLF) add NIMAGES
15-nov-1997 (SLF) add XSIZE and YSIZE keyword and function
20-oct-2002 (LWA) added list of data types to header
2-jan-2007 (SLF) removed vestigal references to ORR (not supported)
Restrictions:
some keywords are mutually exclusive - for self-documenting code
and reduction of code duplicataion
ORR not supported (place holder never realized - you'll have to
do your own 'ands' and 'ors' external (could write data_chks.pro
driver with keyword inherit via _extra to This routine...)
(See pro/external/data_chk.pro)
function date2decimal compute and return decimal representation of date as fraction of the year. syntax date=date2decimal(datestr,fod=fod,doy=doy,jday=jday) parameters datestr [INPUT; required] date string in format 'YYYY-MM-DDTHH:MM:SS' * can be an array * if given in an ununderstandable format, assumed to be today, now. keywords fod [OUTPUT] fraction of day doy [OUTPUT] day of year jday [OUTPUT] Julian day history vinay kashyap (2014nov) bug fix: Feb was resetting doy counter (VK; 2015jun)
(See pro/util/date2decimal.pro)
function date2timestamp given a decimal date (in units of [yr]), returns the calendar date as a timestamp in the format YYYY-MM-DDTHH:MM:SS.S syntax tstamp=date2timestamp(date,year=year) parameters date [INPUT; required] decimal date in years or fraction of year (see keyword YEAR) keywords year [INPUT] if given, adds this to DATE * useful for when only fraction of year is given _extra [JUNK] here only to prevent crashing the program example .run date2timestamp (calls date2decimal) history Vinay Kashyap (2015.4863)
(See pro/util/date2timestamp.pro)
function deg2hrs converts decimal degrees to sexagesimal system and returns a string array of properly formatted output parameters d [INPUT; required] degrees * may even be a string of comma separated numbers h [OUTPUT] hours m [OUTPUT] minutes s [OUTPUT] seconds keywords dec [INPUT] if set, does not divide by 15 (the RA v/s Dec thing) _extra [INPUT] allows passing defined keywords to STR_2_ARR: SEP, R8, SQUISH subroutines STR_2_ARR see also HRS2DEG history vinay kashyap (Nov98) changed call to str2arr to str_2_arr (VK; Sep14)
(See pro/util/deg2hrs.pro)
function demacs a DEM editor that allows interactively "tweaking" a specified DEM syntax dem=demacs(logt,dem0=dem0,logt0=logt0,norm=norm,slope=slope,$ group=group,igroup=igroup, PLOT_KEYWORDS) parameters logt [INPUT; required] log10(Temperature [K]) at which DEM is to be determined keywords dem0 [INPUT] initial DEM (just for guidance). * if size does not match LOGT0, gets stretched to suit. * overrides SLOPE, but not NORM * if max(DEM0)<100, assumed to be in log form -- i.e., plots are in "linear" form and +vity is not enforced. logt0 [INPUT] logT at which DEM0 are defined. if not given, assumed to be LOGT. norm [INPUT] if set, first element of initial DEM is set to NORM slope [INPUT; default=1] if given, generates initial DEM=NORM*T0^(SLOPE) * if DEM0 is specified, SLOPE is ignored group [OUTPUT] long-int array of same size as LOGT containing grouping information igroup [OUTPUT] array of same size as GROUP, containing index of "representative element" of each group _extra [INPUT] allows passing defined keywords (e.g., YRANGE) to PLOT. restrictions requires X-windows, display, and mouse capability. history vinay kashyap (Feb97) corrected log behavior, added _extra to PLOT (VK; Apr97) cleaned up log behavior, added keystrokes *,/,v,^,z (VK; Aug98) button press status now stored in !MOUSE, not !ERR (VK; Apr09)
(See pro/demacs.pro)
EXPLANATION
This routine descales all types of spline fits into upsilons or
rates, i.e., it does both electron upsilons and proton rates,
and both 5-point and 10-point splines. In addition it can
simultaneously descale several temperatures at once.
INPUTS
TEMP Temperature(s), K.
SPLSTR Structure output by read_splups.
INDEX Index of structure.
OUTPUTS
UPS Upsilon value(s) at temperature(s) TEMP.
EXAMPLES
read_splups,splupsfile,splstr
descale_all,[1.e6,2.e6],splstr,5,ups
print,ups
HISTORY
Ver.1, 15-Mar-01, Peter Young
adapted from Ken Dere's descale_ups.pro.
Ver.2, 12-Nov-01, Peter Young
added type 6 transitions (for protons)
Ver.3, 3-Jan-2012, Ken Dere
allowed for the number of spline points from 5 through 9
(See pro/external/descale_all.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
DESCALE_UPS_VK
(used to be) DESCALE_UPS
PURPOSE:
convert from Burgess-Tully scaling spline fits to Upsilons
CATEGORY:
science.
CALLING SEQUENCE:
DESCALE_UPS,Index,Jndex,xt,upsilion, T_TYPE,C_UPS,SPLUPS
INPUTS:
Index: index of lower energy level (lowest level is 1)
Jndex: index of upper energy level (lowest level is 1)
xt: scaled temperature
T_TYPE: 2 dimensional array contain values of the transition type
C_UPS: 2 dimensional array containing values of the Burgess and Tully
scaling parameter c
SPLUPS: spline fits to the scaled Upsilons
OPTIONAL INPUTS:
None:
KEYWORD PARAMETERS:
None:
OUTPUTS:
Upsilon: the Maxwellian averaged collision strength
COMMON BLOCKS:
NONE:
;common elvlc,l1a,term,conf,ss,ll,jj,ecm,eryd,ecmth,erydth,eref
;common wgfa, wvl,gf,a_value
;common upsilon,t_type,c_ups,splups
PROCEDURE:
see Burgess and Tully, 1992, Astron and Astrophys, 254, 436.
EXAMPLE:
;
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
December 1998: Include transition type 5 (kpd)
September 2000: Add parameters T_TYPE,C_UPS,SPLUPS and comment out
all common blocks (Vinay Kashyap)
THIS ROUTINE IS OBSOLETE FOR CHIANTIv4+ (VK; Jun02)
(See pro/external/descale_ups_vk.pro)
function detect_limit compute and return the counts upper limit for detection of a source at a given significance, given the background counts. description compute the cumulative significance of obtaining a specified number of counts given the background, and assume that a source would be considered detected if the counts were to exceed the NSIG threshold. see Pease, Drake, & Kashyap (2006, ApJ 636, 426) for full description. briefly, computes the probability that as many as D counts can be observed for a given background b, p(=<D|b), and thence the probability that a given number of counts can be obtained in an observation simply due to the background. The number of counts required for a detection at a specified probability is the upper limit. Note also that this goes only halfway towards a full upper limit (see Kashyap et al., 2008, AAS-HEAD, 2008.03.03) in that this produces an upper limit in counts space and not in intrinsic flux space. syntax ul=detect_limit(bkg,nsig,asrc=asrc,abkg=abkg,bgalt=bgalt,abgalt=abgalt,$ nsim=nsim,ulsig=ulsig,ulsim=ulsim,/gaussy,nxbin=nxbin,verbose=verbose) parameters bkg [INPUT; required] counts in the background nsig [INPUT] the Gaussian-equivalent sigma at which to compute upper limit to detection * if not given, assumed to be 3 keywords asrc [INPUT; default=1] area in which source counts are collected abkg [INPUT; default=1] area in which background counts are collected bgalt [INPUT; default=0] alternative set of background contamination, say from a different area of the instrument, or from a model, or from an extended source, etc. * may be an array * NOTE: the _same_ BGALT is appended to _all_ elements of BKG abgalt [INPUT; default=asrc] area in which BGALT is "collected" * size must match BGALT * if size < size(BGALT), first element is assumed to be the default nsim [INPUT; default=0] number of Monte Carlo simulations to run to account for error in background * setting this results in computing the upper limit for a number of realizations of BKG; the resulting 1-sigma range in the value of computed upper limits is reported in ULSIG, and a conservative upper limit based on combining all of the simulations is returned in ULSIM[*,0] ulsig [OUTPUT] the 1-sigma error on the upper limit, estimated by bootstrapping BKG ulsim [OUTPUT] a 2D array of size (NBKG,NSIM+1) which contains all the simulated limits * ULSIM[*,0] is identical to the primary output if NSIM=0 * for NSIM>0, ULSIM[*,0] is the conservative limit that is derived from the coadded probability distributions that take into account the variations in the background gaussy [INPUT] if set, computes the limit corresponding to the significance matching the location of the NSIG-sigma *intercept* of a Gaussian, rather than matching the total area under the curve. nxbin [INPUT] number of bins to use in the integration * the integration is carrid out over a range of 0..5*E(bg) or 20, whichever is greater. by default, the number of bins is set by the step size, which is set to 1 count, -- unless E(bg) < 1, in which case a bin width of 0.05 is used by default * changing NXBIN does not change the range, but only changes the bin size. * a hard lower limit of 20 is set -- cannot use a bin width larger than 1 count verbose [INPUT] controls chatter subroutines LNPOISSON() KILROY history vinay kashyap (Apr2004) added keyword ULSIG; changed name from PUPLIM to DETECT_LIMIT (VK; May2004) added keyword NXBIN (VK; Sep2004) added keywords BGALT and ABGALT (VK; Dec2004) modified output behavior of ULSIM[*,0]; now BGALT can be 0 (VK; Mar2005) fixed bug for when NXBIN is set; made the numerical precision problem at high NSIG explicit by making the code return -1 as the UL (VK; Mar2009)
(See pro/stat/detect_limit.pro)
procedure did2emis2em for a specified line, read in emissivities at various densities, compute fluxes, and invert to get emission measure estimates at each density. syntax did2emis2em,idstr,edens,fluxes=fluxes,/deblend,DEM=DEM,logT=logT,$ ldir=ldir,NH=NH,EMs=EMs,FXs=FXs,xtitle=xtit,ytitle=ytit,title=tit,$ verbose=v,dWVL=dWVL,eps=eps,/incieq,mapping=mapping,chifil=chifil,$ chidir=chidir,eqfile=eqfile,abund=abund,/noph,effar=effar,wvlar=wvlar,$ /kev,tol=tol,fH2=fH2,He1=He1,HeII=HeII,/Fano,/wam,/bam,/mam,/Zbeda,$ /Ibeda,Wbeda=Wbeda,/Lbeku,wform=wform,wstyle=wstyle,ziform=ziform,$ /nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol,stasiz=stasiz,$ stathk=stathk,charsize=charsize,align=align parameters idstr [INPUT; required] structure containing ID information (see LINEID for description) edens [I/O] array of electron densities [cm^-3] * default is [1e8,1e14] * if not specified, insufficiently specified, or otherwise meaningless, uses default and overwrites input keywords fluxes [I/O] observed fluxes * if size does not match the number of components or the number of IDs, will instead use IDSTR.(#).FLUX and overwrite the input * see UPDATID() for details deblend [INPUT] if _not_ set (which is the default), squishes multiple IDs of a single feature into one single flux and calculates only a "composite" ID. on the other hand, if set, leaves the multiple IDs alone. DEM [INPUT] differential emission measure to use in computing the fluxes * default is to use 1e12 [cm^-5] at each specified LOGT logT [INPUT] temperatures at which DEM is defined * if not specified, set to 6.5, unless DEM has more elements, in which case is interpolated into the 4..8 range ldir [INPUT] string array of database directories to use to search for the emissivities * default is '$CHIANTI' * if size does not match either number of IDSTR components or IDs, only the first element is used NH [INPUT] H column density [cm^-2] EMs [OUTPUT] array of emission measures EMS[EDEN,WVL] that are plotted. * at any given point, EMS = \int DEM[LOGT]*dLOGT, unless DEM has one or two elements only, in which case EMS = SUM(DEM) * what this implies is that the input DEM is scaled at each density to match the observed flux at each wavelength and this scaled DEM is represented in the plot by the summed measure. This ensures that all wavelengths considered are compared over the same temperature range, and the ambiguity regarding the temperature of peak emissivity, etc. has been removed. FXs [OUTPUT] the predicted fluxes FXS[EDEN,WVL] which are used to scale the EMs above. xtitle [INPUT] passed to PLOT ytitle [INPUT] passed to PLOT title [INPUT] passed to PLOT verbose [INPUT] controls chatter _extra [INPUT] pass defined keyword values to subroutines: ID2EMIS2ID: DWVL RD_LIST: EPS, INCIEQ, MAPPING FOLD_IONEQ: CHIFIL, EQFILE RD_IONEQ: CHIDIR SQUISHEM: ABUND LINEFLX: ABUND, NOPH, EFFAR, WVLAR, KEV ARRAYEQ: TOL ISMTAU: fH2, He1, HeII, FANO, WAM, BAM, MAM IDLABEL: ZBEDA, IBEDA, WBEDA, LBEKU, WFORM, WSTYLE, ZIFORM STAMPLE: NUTHIN,NODAY,NOTIME,NOUSER,NOPACK,STACOL,STASIZ,STATHK XYOUTS: CHARSIZE,ALIGN n_e [IGNORE] here only to trap boxing gloves restrictions requires IDL5.3+ because of use of STRMATCH, etc. requires subroutines BAMABS CAT_LN FOLD_IONEQ GETABUND ID2EMIS2ID IDLABEL INICON ISMTAU LAT2ARAB LINEFLX RDABUND RD_IONEQ RD_LINE RD_LIST READ_IONEQ SQUISHEM SYMB2ZION SYZE UPDATID WHEE ZION2SYMB side-effects generates a plot which erases any plot that exists beforehand history vinay kashyap (JanMMI; based on DID2EM) improved color-scale setting for 24-bit consoles (VK; FebMMI)
(See pro/did2emis2em.pro)
function discriminatemp an implementation of Mark Weber's scheme for determining the temperature discrimination ability of a given set of emissivity functions. the output is a square matrix of the same size as the temperature grid, showing the value of a statistic that can be used to infer whether two corresponding temperatures can be distinguished. the technique is simple -- compute fluxes at two temperatures for the same emission measure, and for an assumed uncertainty, ask whether the two sets of fluxes differ in a statistically significant manner. if they do, the two temperatures are distinguishable, and not if they do not. syntax dtemp=disriminatemp(emis,ferr,EM0=EM0,outflx=outflx,$ wvl=wvl,Z=Z,logT=logT,abund=abund,normark=normark,$ outeflx=outeflx,verbose=verbose,$ /noph,effar=effar,wvlar=wvlar,/ikev,metals=metals,fipbias=fipbias) parameters emis [INPUT; required] array of emissivities * EMIS is a 2D array with size (LOGT, WVL) * the units are assumed to be [1e-23 ergs cm^3/s] for anything else (e.g., for solar work), put the difference into EM0 and be sure to set the keyword NOPH=1, because it gets pushed into LINEFLX() ferr [INPUT] the assumed uncertainties on the lines * if not given, taken to be 0.1 of the computed fluxes for all lines * if scalar, then if >0 and <1, taken to be that fraction of the computed fluxes for all lines if >1 and <100, taken to be that percentage of the computed fluxes for all lines if >100, the reciprocal is taken to be the fraction of the computed fluxes for all lines if <0, the abs value is taken to be a constant absolute uncertainty for all lines * if vector, each individual value is used as given, with the same condition on each as for the scalar case * e.g., if there are 4 lines, and FERR=[-10,0.3,5,0], after the 4 fluxes are computed, the corresponding errors are set to [10.,0.3*F[1],0.05*F[2],0.1*F[3]] * the best way to set reasonable errors is to run this program once, extract the computed fluxes using keyword OUTFLX, figure out the appropriate errors, and then feed it back into another run keywords EM0 [INPUT] the emission measure to use * default is 1d14 cm^-5, fwiw outflx [OUTPUT] the fluxes calculated for each line for each temperature, is an array of size (LOGT,WVL), same as EMIS outeflx [OUTPUT] the flux errors calculated for each line for each temperature, is an array of size (LOGT,WVL), same as EMIS wvl [INPUT] line wavelengths for which EMIS is given * used only if keyword NOPH is _not_ set (i.e., in the conversion of [erg/...] to [ph/...]) and if size matches the 2nd dimension of EMIS Z [INPUT] atomic numbers of elements contributing to EMIS * used only if size matches 2nd dimension of EMIS, and is used to multiply EMIS with the appropriate abundance * if not given, assumed to be 1 (i.e., H), which is essentially a way to ignore ABUND logT [INPUT] log_10(Temperature [K]) at which EMIS are given * unused abund [I/O] element abundances * if size smaller than 30, calls GETABUND() and resets to use Anders & Grevesse normark [INPUT] a normalization factor, usually set to the maximum number of filters or lines that can be used, and whose squared reciprocal divided into the output -- Mark Weber uses this to "normalize" the results across different filter choices * hard minimum value is 1, also the default * if this is set, the diagonal elements of the output, which are identically zero, are reset to the mean of the nearest neighbors * if vector, only the first element is used and all the extra elements are ignored verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined variables to subroutines LINEFLX : /NOPH, /IKEV, EFFAR, WVLAR GETABUND : METALS, FIPBIAS description Weber et al., 2008, SPD? history vinay kashyap (2009mar) bigfix: wasn't dealing with vector FERR gracefully (VK; 2010aug)
(See pro/discriminatemp.pro)
function dorren
computes spot modulated stellar light curve using Dorren(1987)
syntax
curve = x, A, f, pder,ldstr=ldstr,ldspt=ldspt,rdns=rdns,$
photT=photT,spotT=spotT,wvl=wvl
parameters
x [INPUT;required] absissca points at which to compute spot
model. These are angular displacements with respect to the
initial spot longitude specified in A, in units of degrees.
A [INPUT;required] spot parameters for dorrens model in
radians where:
a(0) = stellar inclination to LOS
a(1) = spot latitude
a(2) = spot size
a(3) = initial spot longitude
pder[OUTPUT] partial derivative with respect to each
parameter in A
keywords
ldstr [INPUT] limb-darkening coefficient for star
default = 0.32 Van Hamme(1994)
ldspt [INPUT] limb-darkening coefficient for spot (umbra)
rdns [INPUT] set this parameter if spot parameters and absissca are input
in radians rather than degrees
photT [INPUT] photospheric temperature in degrees Kelvin
spotT [INPUT] spot temperature in degrees Kelvin
wvl [INPUT] wavelength in nanometers
subroutines
MOD
history
liwei lin (Sep 03) better documentation/functionality than
mod.pro. switch to modular
(Jul 06) removed loop over longitudes and add pder
(Aug 06) BUGFIX: note that T should be defined as:
Pi - ATAN((-SIN(h(tmp)))*(TAN(b1(tmp)))) when B1>=Pi/2
ATAN((SIN(h(tmp)))*(TAN(b1(tmp)))) when B1<Pi/2
to avoid dicontinuities. This differs from Dorren (1987)
formalism only in the '=' sign placement
(See pro/timing/dorren.pro)
function dove_ciclo this function acts as a wrapper to all the morphological operations that are used to extract pixels that define a loop from an image of the solar corona the general workflow is: - [CONVOL] - enhance contrast by subtracting background - [MORFO_ROTTANGOLI] open with rectangular structure element - [MORPH_CLOSE] close with small square kernel - [CONVOL] enhance contrast again by subtracting background - [MORFO_SOGLIA] threshold to selectively enhance structures - [MORPH_CLOSE] close the image again - [MORFO_SEGMENTO] group contiguous pixels into region blobs and throw out regions deemed too small - [ROI_SELEZIONI] interactively select some blobs for further study - [MORFO_SCHELETRO] create a skeleton for these blobs - [MORFO_POTARE] prune the skeleton to make a cleaner image - [] extract the pixels that form the pruned skeleton and convert them to heliographic coordinates keywords control whether any of the calls to the subroutines should be skipped or repeated. keywords also set up the input parameters to the subroutines. syntax oimg=dove_ciclo(inpimg,$ /xbgdat,icell=icell,$ /xrect,xsize=xsize,ysize=ysize,angle=angle,gray=gray,/readd,/reuse,$ /xrclose,$ /xbgsub,jcell=jcell,$ /xthresh,thrthr=thrthr,nsigma=nsigma,mimg=mimg,gamma=gamma,$ centrale=centrale,bitlev=bitlev,/zeromin,$ /xtclose,$ /xblob,blbthr=blbthr,areas=areas,$ subidx=subidx,/hardcut,deepimg=deepimg,$ /xroi,pixroi=pixroi,roithr=roithr,jitter=jitter,/hadrian,$ /xskel,skthr=skthr,rmin=rmin,$ /xprune,minpix=minpix,$ outx=outx,outy=outy,sunrad=sunrad,pixsiz=pixsiz,$ offsetx=offsetx,offsety=offsety,suncenx=suncenx,sunceny=sunceny,$ loopsav=loopsav, verbose=verbose) parameters inpimg [INPUT; required] image of the corona keywords For keywords with names beginning with "X", when set, the corresponding call to the subroutine is skipped. But if that keyword is set to a negative number -N, the subroutine is called N times in sequence (unless otherwise noted below). xbgdat [INPUT] if set, skips initial background subtraction icell [INPUT; default=1] defines the size of the cell to subtract background - the "source" is measured in a square of size 2*ICELL+1 and the "background" in a surrounding layer of 1pix xrect [INPUT] if set, skips morphological open with rectangular structure element xsize [INPUT; default=1] width of the structure element ysize [INPUT; default=10] height of the structure element angle [INPUT; default=findgen(36)*5] angle of tilt of the rectangle defined by (XSIZE,YSIZE) in [degrees] xrclose [INPUT] if set, skips morphological close apres open xbgsub [INPUT] if set, skips background subtraction of modified image jcell [INPUT; default=ICELL] defines size of cell to subtract background xthresh [INPUT] if set, skips image thresholding thrthr [OUTPUT] value used if histogram-threshold is applied nsigma [INPUT] if given, sets the threshold at mean+NSIGMA*stddev * default is 1 * if mean+NSIGMA*stddev < 0, this is not applied mimg [OUTPUT] the median threshold image, constructed if CENTRALE is set xtclose [INPUT] if set, skips morphological close apres thresholding xblob [INPUT] if set, skips grouping the image into distinct regions * if set to -ve number, gets automatically unset areas [OUTPUT] number of pixels in each labeled region arclev [INPUT; default=0.68] fraction of the area of the largest blob as the threshold below which to discard blobs deepimg [OUTPUT] an image that depicts the depth at which a particular pixel was added to a blob blbthr [INPUT; default=0] threshold value at which to convert grouped image to bitmap xroi [INPUT] if set, skips selecting a subset of regions * if set to -ve number, gets automatically unset pixroi [INPUT] if set, assumed to be a set of pixels around which to pick out the region of interest non-interactively roithr [INPUT; default=0] threshold value at which to ignore pixels xskel [INPUT] if set, skips making skeletons of regions * if set to -ve number, gets automatically unset rmin [INPUT; default=1] radius of circle that acts as structure element skthr [INPUT; default=0] threshold to filter region xprune [INPUT] if set, skips pruning skeletons * if set to -ve number, gets automatically unset minpix [INPUT; default=4] number of pixels above which a given branch must be kept while pruning outx [OUTPUT] the x-pixel indices of the pruned points outy [OUTPUT] the y-pixel indices of the pruned points * if SUNRAD is set, then floating point values defining the locations in heliospheric coordinates are returned sunrad [INPUT] radius of the Sun as seen from the spacecraft, in [arcsec] * if this is set, then OUTX and OUTY are transformed to heliospheric coordinate system * if set to 1, assumed to be (RSun/AU)*(180/!pi)*3600 pixsiz [INPUT; default=0.5] pixel size, in [arcsec] offsetx [INPUT; default=0] offset to be applied to OUTX to bring them in line with SUNCENX offsety [INPUT; default=0] offset to be applied to OUTY to bring them in line with SUNCENY suncenx [INPUT; default=0] the X coordinate distance of the center of INPIMG from Sun center in [arcsec] sunceny [INPUT; default=0] the Y coordinate distance of the center of INPIMG from Sun center in [arcsec] verbose [INPUT] controls chatter loopsav [INPUT] if set to a filename, saves all the intermediate arrays in the named IDL save file _extra [INPUT ONLY] pass defined keywords to subroutines MORFO_ROTTANGOLI: GRAY, READD, REUSE MORFO_SOGLIA: GAMMA, CENTRALE, BITLEV, ZEROMIN MORFO_SEGMENTO: SUBIDX, HARDCUT ROI_SELEZIONI: JITTER, HADRIAN subroutines MORFO_ROTTANGOLI MORFO_SOGLIA [GMASCL,ERROR_MESSAGE,PATH_SEP,SCALE_VECTOR,CONVERT_TO_TYPE,FPUFIX] MORFO_SEGMENTO ROI_SELEZIONI MORFO_SCHELETRO MORFO_POTARE INICON KILROY history vinay kashyap (May2007)
(See pro/ssw/dove_ciclo.pro)
procedure drakopy
set up the environment to make plots per individual preferences
syntax
drakopy,milieu,/HELP,/UNDO,MAGNIFY=MAGNIFY,VERBOSE=VERBOSE
parameters
milieu [INPUT] string specifying what sort of environment to set to.
accepted values are:
-- 'jeremy'
-- 'olivia'
-- 'jjd' (jeremy old preferences)
-- 'drake' (jeremy older preferences)
-- 'vinay' (different depending device at call time)
-- 'poster'
-- 'original'
keywords
help [INPUT] if set, prints out a somewhat verbose help
undo [INPUT] if set, restores original state
verbose [INPUT] controls chatter level
magnify [INPUT] scale all the variables by this factor
_extra [JUNK] here only to prevent crashing the program
commons
drakopy {old_P, old_X, old_Y, old_Z}
description
sets the !P, !X, !Y, and !Z variables to special and specific values.
stores the old values in a common block for later access.
example
set_plot,'ps' & device,file='/tmp/test_drakopy.ps'
plot,findgen(10),title='MILIEU=Original'
drakopy,'jeremy' & plot,findgen(10),title='MILIEU=Jeremy'
drakopy,'olivia' & plot,findgen(10),title='MILIEU=Olivia'
drakopy,'original' & plot,findgen(10),title='MILIEU=Original'
drakopy,/undo & plot,findgen(10),title='MILIEU=previous (Olivia)'
device,/close & set_plot,'x'
history
vinay kashyap (SepMM)
added option "drake" (VK; Aug01)
added option "jjd"; added keyword MAGNIFY (VK; Feb02)
added option "vinay" (VK; May03)
added option "poster" (VK; Jul03)
told the code that "poster" is a valid option (VK; Sep03)
now prints out help and exits if no input is given (VK; Jul13)
changed "jeremy" defaults (JD; Nov15)
(See pro/util/drakopy.pro)
function drat return the ratio of fluxes in one line relative to another line for a variety of densities syntax frat=drat(line1,line2,edens,DEM,logT,fx1=fx1,fx2=fx2,$ mapping=mapping,chifil=chifil,chidir=chidir,eqfile=eqfile,$ abund=abund,/noph,effar=effar,wvlar=wvlar,NH=NH,fH2=fH2,$ He1=He1,HeII=HeII,/Fano,dbdir=dbdir,sep=sep,prefix=prefix) parameters line1 [INPUT; required] string describing the line/wavelength-range that defines the numerator line2 [INPUT; required] string describing the line/wavelength-range that defines the denominator * LINE1 and LINE2 must be in the format used by RD_LIST, i.e., Z ION <sep> WAVE <sep> DBDIR <sep> DESCRIPTION and WAVE = "WVL"/"WVL +- dW"/"WMIN,WMAX"/"WMIN-WMAX" edens [INPUT; required] electron densities at which to compute the flux ratios DEM [INPUT; required] differential emission measure to use in computing the fluxes logT [INPUT; required] temperatures at which DEM is defined * size must match that of DEM keywords fx1 [OUTPUT] the fluxes due to line 1 at each EDENS fx2 [OUTPUT] the fluxes due to line 2 at each EDENS _extra [INPUT ONLY] pass defined keywords to subroutines RD_LIST: MAPPING,DBDIR,SEP,PREFIX FOLD_IONEQ: CHIFIL,EQFILE RD_IONEQ: CHIDIR LINEFLX: ABUND,NOPH,EFFAR,WVLAR ISMTAU: NH,fH2,He1,HeII,FANO,BAM BAMABS: ABUND subroutines RD_LIST RD_LINE FOLD_IONEQ LINEFLX ISMTAU BAMABS CAT_LN history vinay kashyap (MarMM)
(See pro/drat.pro)
function dummyid
Convert a RD_LINE() style emissivity structure into a dummy
ID structure such as that generated by LINEID()
syntax
idstr=dummyid(linstr,DEM=DEM,/temp,abund=abund,/noph,$
nhne=nhne,effar=effar,wvlar=wvlar,/ikeV,/noabund)
parameters
linstr [INPUT; required] RD_LINE() or RD_LIST() style line
emissivity structure
keywords
_extra [INPUT ONLY] use this to pass defined keywords to subroutines
LINEFLX: DEM,ABUND,EFFAR,WVLAR,NOABUND,NHNE,NOPH,TEMP,IKEV
subroutines
LINEFLX()
history
liwei lin (Feb06) lift parameter check from cat_ln()
cleaned up a bit (VK; Feb06)
(See pro/dummyid.pro)
function eqt_interval computes and returns the double-sided equal-tail interval [lower_bound,upper_bound] at a specified confidence level. interval includes the central mass of the probability distribution unless explicitly required otherwise. syntax hpd=eqt_interval(f,x,/fsample,clev=clev,pdfnorm=pdfnorm,$ xaround=xaround,verbose=verbose) parameters f [INPUT; required] the array for which the confidence interval must be computed * assumed to be a density function unless FSAMPLE is set x [INPUT; optional] abscissae values * if not given, and F is a density function, then taken to be the array indices * ignored if FSAMPLE is set * if N(X).GT.1 but N(X).NE.N(F), X is ignored and FSAMPLE is set automatically keywords fsample [INPUT] if set, assumes that F is a set of samples from a density function, as opposed to being the density function itself clev [INPUT] confidence level at which to compute the intervals * default is 0.68 * if < 0, abs(CLEV) is used * if > 1 and < 100, then assumed to be given as a percentage * if > 100, then 1-1/CLEV is used pdfnorm [INPUT] if set, forces F to integrate to abs(PDFNORM) * if explicitly set to 0, does not normalize F at all * if not set, normalizes to 1 * ignored if FSAMPLE is set * WARNING: do not use this keyword unless you know what you are doing xaround [INPUT] by default, the central part of the distribution is used, i.e., an equal area is left out on both ends. if this keyword is defined, a fraction CLEV/2 of the area is used on either side of XAROUND. * if F is a sample, XAROUND must be in the same units as F * you can return single-sided intervals by setting XAROUND to min(X) or max(X) (min/max of F if sample) * if not set, XAROUND is set to the median verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines example for i=1,20 do print,eqt_interval(randomn(seed,10000L)*i,/fsample) history vinay kashyap (Apr2006)
(See pro/stat/eqt_interval.pro)
procedure erors compute asymmetric error bars on fit parameters by projecting the chi-sq surface onto each parameter axis. what this means is that for each non-frozen parameter, step through a range of values of the parameter, finding the best-fit chi-square calculated by fitting the rest of the parameters, and report that range where the chi-square increases by a set amount from the minimum. this program tries to be a wee bit clever by starting from the best-fit value and then stumbling about on either side until the chi-sq goes above the mark; the length of the strides change according to the projected location of said mark. syntax erors,x,y,a,erru,errl,ysig=ysig,freeze=freeze,dchi=dchi,$ dchi=dchi,algo=algo,maxstep=maxstep,verbose=verbose,$ erra=erra,yfunc=yfunc,$ itmax=itmax,chithr=chithr,/dumb, jumpup=jumpup,jumpdn=jumpdn,$ svdthr=svdthr,funcs=funcs, function_name=function_name,$ type=type, missing=missing,/fwhm,/norm,betap=betap, /poisson parameters x [INPUT; required] data points y [INPUT; required] Y(X) * sizes of X and Y must match a [I/O; required] parameters for user-supplied function * on input, these are assumed to be initial guesses * on output, these contain the best-fit values erru [OUTPUT; required] upper limits of confidence range interval errl [OUTPUT] lower limits of confidence range interval * if ERRL is not specified on input, ERRU will contain the average value of the upper and lower >>deviations<<. keywords ysig [INPUT] standard deviations on Y * default=sqrt(abs(Y)+0.75)+1 * if single element, then sig(Y[*])=YSIG(0) * if -ve, taken to be the fractional error freeze [INPUT] freeze numbered parameters (index starts from 0!) dchi [INPUT] how big a change in chi-square to look for? * default is 2.7 (corresponding to 90% CL) algo [INPUT] fitting algorithm * only the following are implemented: -- LevMarq+SVD (default; calls FIT_LEVMAR) -- IDL-Curvefit (calls CURVE_FIT) maxstep [INPUT] maximum number of steps to take before giving up on actually finding the bounds * default is 100 verbose [INPUT] verbosity level erra [OUTPUT] formal "curvature" errors on the best-fit parameters yfunc [OUTPUT] best-fit Y(X;A) _extra [INPUT] pass defined variables to subroutines:- FIT_LEVMAR: ITMAX, CHITHR, DUMB ADJUSTIE: TIES, VNAME LEVMARQ: JUMPUP, JUMPDN, SVDTHR LMCOEFF: FUNCS, POISSON CURVE_FIT: FUNCTION_NAME note:- FUNCS and FUNCTION_NAME refer to name of user-defined function that takes as input X and A, and returns YMODEL(X;A), and the partial derivatives of the model function wrt A. Any function that was written to work with CURVEFIT or GHRS' WFIT will do. The default for FIT_LEVMAR is X3MODEL. MK_3MODEL: TYPE MK_GAUSS: MISSING, FWHM, NORM MK_LORENTZ: BETAP, MISSING, NORM history vinay kashyap (MM.I) (yes, I _do_ know how to spell "error") added call to ADJUSTIE to handle constraints on ERRU,ERRL (VK; FebMM) what if adjusted ERRA becomes 0? (VK; MarMM) allowed halting with either "q" or "x" (VK; SepMM) force extra iteration after "r"; increased wait time (VK; JanMMI) added confirmation check for too many thawed params (VK; FebMMI) interpol was crashing because it was getting only 1 element arrays; now correctly updates all parameters if better fit is found (VK; Aug01) made various bug fixes that was causing program to go bonkers for some special cases, such as small fluxes (VK; Apr02) added hooks into MPFIT (Liwei Lin/VK; Oct02) bug correction re VERBOSE (LL; Apr03) bug correction, first step was failing sometimes when input A were integers (VK; Mar08)
(See pro/fitting/erors.pro)
NAME:
ERROR_MESSAGE
PURPOSE:
The purpose of this function is to have a device-independent
error messaging function. The error message is reported
to the user by using DIALOG_MESSAGE if widgets are
supported and MESSAGE otherwise.
In general, the ERROR_MESSAGE function is not called directly.
Rather, it is used in a CATCH error handler. Errors are thrown
to ERROR_MESSAGE with the MESSAGE command. A typical CATCH error
handler is shown below.
Catch, theError
IF theError NE 0 THEN BEGIN
Catch, /Cancel
ok = Error_Message()
RETURN
ENDIF
Error messages would get into the ERROR_MESSAGE function by
throwing an error with the MESSAGE command, like this:
IF test NE 1 THEN Message, 'The test failed.'
AUTHOR:
FANNING SOFTWARE CONSULTING
David Fanning, Ph.D.
1645 Sheely Drive
Fort Collins, CO 80526 USA
Phone: 970-221-0438
E-mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
CATEGORY:
Utility.
CALLING SEQUENCE:
ok = Error_Message(the_Error_Message)
INPUTS:
the_Error_Message: This is a string argument containing the error
message you want reported. If undefined, this variable is set
to the string in the !Error_State.Msg system variable.
KEYWORDS:
ERROR: Set this keyword to cause Dialog_Message to use the ERROR
reporting dialog. Note that a bug in IDL causes the ERROR dialog
to be used whether this keyword is set to 0 or 1!
INFORMATIONAL: Set this keyword to cause Dialog_Message to use the
INFORMATION dialog instead of the WARNING dialog. Note that a bug
in IDL causes the ERROR dialog to be used if this keyword is set to 0!
TITLE: Set this keyword to the title of the DIALOG_MESSAGE window. By
default the keyword is set to 'System Error' unless !ERROR_STATE.NAME
equals "IDL_M_USER_ERR", in which case it is set to "Trapped Error'.
TRACEBACK: Setting this keyword results in an error traceback
being printed to standard output with the PRINT command. Set to
1 (ON) by default. Use TRACEBACK=0 to turn this functionality off.
OUTPUTS:
Currently the only output from the function is the string "OK".
RESTRICTIONS:
The WARNING Dialog_Message dialog is used by default.
EXAMPLE:
To handle an undefined variable error:
IF N_Elements(variable) EQ 0 THEN $
ok = Error_Message('Variable is undefined')
MODIFICATION HISTORY:
Written by: David W. Fanning, 27 April 1999.
Added the calling routine's name in the message and NoName keyword. 31 Jan 2000. DWF.
Added _Extra keyword. 10 February 2000. DWF.
Forgot to add _Extra everywhere. Fixed for MAIN errors. 8 AUG 2000. DWF.
Adding call routine's name to Traceback Report. 8 AUG 2000. DWF.
Added ERROR, INFORMATIONAL, and TITLE keywords. 19 SEP 2002. DWF.
Removed the requirement that you use the NONAME keyword with the MESSAGE
command when generating user-trapped errors. 19 SEP 2002. DWF.
Added distinctions between trapped errors (errors generated with the
MESSAGE command) and IDL system errors. Note that if you call ERROR_MESSAGE
directly, then the state of the !ERROR_STATE.NAME variable is set
to the *last* error generated. It is better to access ERROR_MESSAGE
indirectly in a Catch error handler from the MESSAGE command. 19 SEP 2002. DWF.
Change on 19 SEP 2002 to eliminate NONAME requirement did not apply to object methods.
Fixed program to also handle messages from object methods. 30 JULY 2003. DWF.
Removed obsolete STR_SEP and replaced with STRSPLIT. 27 Oct 2004. DWF.
Made a traceback the default case without setting TRACEBACK keyword. 19 Nov 2004. DWF.
(See pro/external/error_message.pro)
procedure exaped EX APED AD IDL extract line and/or continuum emissivity data from an APED file syntax exaped,filroot,emis,tlog,wvl,edens,Z,ion,desig,econf,jon,src,$ /llist,/coco,/tlist,/noerg,/okeV,atomdb=atomdb,verbose=verbose parameters filroot [INPUT; required] APED fits file root * if this includes a ".fits", the suffix is assumed to be already included and nothing extra is added. * the suffix '_linelist.fits' is automatically applied, so don't specify that part. (this is inflexible at this point because we only support reading in this file. sometime later on the other APED format will also be supported.) * looks for ".gz" automatically if the filename specified without it does not exist emis [OUTPUT; required] emissivity array, of the format (NTLOG,NWVL,NEDENS) * APED units are [ph cm^3/s], which will be converted into [1e-23 ergs cm^3/s] unless the NOERG keyword is set tlog [OUTPUT; required] log10(Temperature [K]) grid on which EMIS are placed wvl [OUTPUT; required] wavelength array * units are in [Ang] unless the OKEV keyword is set, in which case output in [keV] edens [OUTPUT; required] electron densities at which EMIS have been calculated Z [OUTPUT; required] atomic numbers of species producing the given line ion [OUTPUT; required] ionic state of species corresponding to the line desig [OUTPUT] (2,NWVL) string array of lower and upper level designation * currently, just the lower and upper levels econf [OUTPUT] (2,NWVL) string array of electron configuration of lower and upper levels of the transition in question * not implemented yet jon [OUTPUT] the ionic state that matters to the ion balance * not implemented yet src [OUTPUT] numeric code specifiying that this is an APED output, set to 3 keywords llist [INPUT] if set, reads from FILROOT_linelist.fits * currently this is the only option supported coco [INPUT] if set, reads from FILROOT_coco.fits * NOT YET IMPLEMENTED tlist [INPUT] if set, reads from FILROOT_line.fits * NOT YET IMPLEMENTED noerg [INPUT] if set, EMIS will be output in same units as in the APED files, i.e., [ph cm^3/s] okeV [INPUT] if set, WVL will be converted from [Ang] to [keV] atomdb [INPUT] directory containing input file * default is !ATOMDB * hardcoded default is /data/atomdb/ * prepended to FILROOT only if FILROOT does not begin with a '/' (UNIX), ':' (MacOS), '\' (Windows), or '[' (VMS?) logT [INPUT] if defined as an array, then interpolates/extrapolates EMIS(NTLOG,NWVL) to a new grid EMIS(NLOGT,NWVL) prior to output. TLOG will be overwritten by LOGT. verbose [INPUT] controls chatter _extra [JUNK] ignore -- here only to prevent crashing the program subroutines SETSYSVAL ARRAYEQ REBINX description The ATOMDB file format is described in http://cxc.harvard.edu/atomdb/features_formats.html In this case, the line list (grouped by line) file is read, and in particular, only the block EMISSIVITY is read. history vinay kashyap (Jul02) bug correction when multiple densities are included (VK; Mar03) for v2+, always go through the multiple densities code and ignore the short cut (VK; May11)
(See pro/mkemis/exaped.pro)
Project : SDAC
Name : EXIST
Purpose : To See if variable Exists
Explanation : So obvious, that explaining it will take more
lines than the code.
Use : A=EXIST(VAR)
Inputs : VAR = variable name
Opt. Inputs : None.
Outputs : 1/0 if variable exists or not
Opt. Outputs: None.
Keywords : None.
Calls : None.
Common : None.
Restrictions: None.
Side effects: None.
Category : Useful stuff
Prev. Hist. : None.
Written : Dominic Zarro (ARC)
Version : Version 1.0, 18 September 1993
(See pro/external/exist.pro)
procedure fidgit digitally (i.e., using Darwin-given fingers) fit a DEM to a given spectrum syntax fidgit,x,y,lstr,cstr,ysigma=ysigma,dem=dem,logt=logt,abund=abund,$ abfrac=abfrac,ldbdir=ldbdir,cdbdir=cdbdir,ceroot=ceroot,lsf=lsf,$ wdem=wdem,wspc=wspc,verbose=verbose,$ pres=pres,logP=logP,n_e=n_e,desig=desig,econf=econf,/allah,$ chidir=chidir,chifil=chifil,chidir=chidir,eqfile=eqfile,$ effar=effar,wvlar=wvlar parameters x [INPUT; required] wavelengths or channels of observed spectrum * if channels, must specify an RMF via the keyword LSF that matches the binning of the spectrum BEWARE: no checks are performed to verify that the supplied RMF is consistent with the input data y [INPUT; required] spectrum lstr [I/O; required] line emissivity structure of the sort read in by RD_LINE() * if not given on input, will call RD_LINE() and generate it cstr [I/O; required] continuum emissivity structure of the sort read in by RD_CONT() * if not given on input, will call RD_LINE() and generate it keywords ysigma [INPUT] errors on Y; default is 1+SQRT(0.75+ABS(Y)) dem [I/O] DEM to start out with, will contain the final result on output logt [I/O] log(T [K]) at which DEM are defined. ignored on input if it doesn't match the size of DEM abund [INPUT] abundances * if not set, assumed to be from Anders & Grevesse 1989 abfrac [I/O] multiplicative factor by which to modify ABUND * if scalar, assumed to be metallicity * if vector, must match size of ABUND, else gets reset to 1 * default is 1 ldbdir [INPUT] path to line emissivity database to read in if LSTR is not given * default is '$CHIANTI' * uses !LDBDIR if set cdbdir [INPUT] path to continuum emissivity database to read in if CSTR is not given * default is '$CONT' * uses !CDBDIR if set ceroot [INPUT] prefix for continuum emissivity files * default is 'cie' * uses !CEROOT if set lsf [INPUT] line spread function * if scalar, the width of the line in bins used as a halfwidth for boxcar smoothing * if vector, assumed to be the kernel with which to smooth * if RMF structure (of the type read in from RD_OGIP_RMF()) then convolves the theoretical spectrum with this RMF wdem [INPUT] window number to display DEM in wspc [INPUT] window number to display spectrum in verbose [INPUT] controls chatter * uses !VERBOSE if set _extra [INPUT] allows specifying defined keywords to subroutines called by this program * RD_LINE: PRES, LOGP, N_E, DESIG, ECONF, ALLAH * RD_CONT: PRES, LOGP, N_E * FOLD_IONEQ: CHIFIL, VERBOSE * RD_IONEQ: CHIDIR, EQFILE * LINEFLX: EFFAR, WVLAR restrictions * requires subroutines -- DEMACS -- WHEE -- RD_LINE [FOLD_IONEQ, RD_IONEQ, READ_IONEQ] -- RD_CONT -- LINEFLX -- CONV_RMF -- INICON history vinay kashyap (Feb97) modified ion balance calcs (VK; 99May) completely rewritten (VK; Aug04)
(See pro/fitting/fidgit.pro)
Name: file_exist
Purpose: returns true(1) if any files match pattern=file
false(0) if no files found
Input Parameters:
file - file, pathname or file filter to check
Optional Keyword Parameters
direct - set if want full check (slower) - use if might be an
empty directory you are looking for
History: written by slf, 11/30/91
4-Sep-92 (MDM) - Modified to handle an array of input files
23-sep-93 (slf) - make sure null file returns false
(findfile count=1! when null requested)
17-Mar-94 (SLF) - use file_stat(/exist) for non wild card cases
April Fools'94 (DMZ) -- added check for :: in file name
(file_stat doesn't work across DECNET)
31-May-94 (DMZ) -- added check for VMS directory name input
(file_stat doesn't seem to work on VMS
dir names like '[ys.atest.soft]')
16-Aug-94 (DMZ) -- added another VMS patch to handle
case when user enters a VMS subdirectory name
without a file name.
6-Aug-97 (Zarro/GSFC) -- added check for nonstring input
30-may-99 (rdb) -- stop use of file_stat with WINDOWS
cause access violation - for wildcard search
8-Jan-1999 - S.L.Freeland - put in IDL version check since 5.3/IRIX
(at least) not backwardly compatible (must use findfile)
10-Jan-1999 - S.L.Freeland - extended 8-jan mod to all UNIX 5.3
15-Feb-2000 - S.L.Freeland - removed 5.3 changes (moved fix to file_stat)
10-Feb-2005 - Kim Tolbert - changed '/' to get_delim()
(See pro/external/file_exist.pro)
Project : SOHO - SSW
Name : FILE_STAT()
Purpose : Vector version of FSTAT
Category : Utility, Operating_system
Explanation : Vector version of FSTAT
Syntax : Result = FILE_STAT( FILES )
Examples :
Inputs : FILES = List of files to check.
Opt. Inputs : None.
Outputs : None.
Opt. Outputs: None.
Keywords : EXIST = If set, then the returned values are whether the
files exist or not. This is the default behavior.
SIZE = If set, then the returned values are the sizes of the
files.
FSTAT_ALL = If set, return vector of 'fstat' structures. This
keyword is only compatible with files less than about
2 GB each in size.
Calls : DATA_CHK
Common : None.
Restrictions: None.
Side effects: None.
Prev. Hist. : 11-Mar-1994 (SLF) Wanted faster file_exist function
History : Version 1, 11-Mar-1994, S. Freeland
Version 1.1 05-Jun-1998, J. Newmark changed loop to long
Version 1.2 15-Feb-2000, S.L.Freeland - work around RSI
Version 5.3 non-backwardly compatible change....
Version 1.3 10-Mar-2000, S.L.Freeland - fix 5.3 /SIZE bug
Version 1.4 14-Jun-2002, S.L.Freeland - add FSTAT_ALL
Version 2, 1-Mar-2005, W.T. Thompson - Add support for files
greater than 2 GB
Contact : SFREELAND
Restrictions:
file size returned for directories under +5.3 is not valid
(See pro/external/file_stat.pro)
ROUTINE: findex
PURPOSE: Compute "floating point index" into a table using binary
search. The resulting output may be used with INTERPOLATE.
USEAGE: result = findex(u,v)
INPUT:
u a monitically increasing or decreasing 1-D grid
v a scalor, or array of values
OUTPUT:
result Floating point index. Integer part of RESULT(i) gives
the index into to U such that V(i) is between
U(RESULT(i)) and U(RESULT(i)+1). The fractional part
is the weighting factor
V(i)-U(RESULT(i))
---------------------
U(RESULT(i)+1)-U(RESULT(i))
DISCUSSION:
This routine is used to expedite one dimensional
interpolation on irregular 1-d grids. Using this routine
with INTERPOLATE is much faster then IDL's INTERPOL
procedure because it uses a binary instead of linear
search algorithm. The speedup is even more dramatic when
the same independent variable (V) and grid (U) are used
for several dependent variable interpolations.
EXAMPLE:
; In this example I found the FINDEX + INTERPOLATE combination
; to be about 60 times faster then INTERPOL.
u=randomu(iseed,200000) & u=u(sort(u))
v=randomu(iseed,10) & v=v(sort(v))
y=randomu(iseed,200000) & y=y(sort(y))
t=systime(1) & y1=interpolate(y,findex(u,v)) & print,systime(1)-t
t=systime(1) & y2=interpol(y,u,v) & print,systime(1)-t
print,f='(3(a,10f7.4/))','findex: ',y1,'interpol: ',y2,'diff: ',y1-y2
AUTHOR: Paul Ricchiazzi 21 Feb 97
Institute for Computational Earth System Science
University of California, Santa Barbara
paul@icess.ucsb.edu
REVISIONS:
(See pro/external/findex.pro)
function findscale returns the lengthscale in pixels at each point on the given curve syntax ls=findscale(curve,dim,/crunch,/half,pick=pick,choice=choice,eps=eps) parameters curve [INPUT; required] regularly gridded array of function values to be used to compute the length scales * if scalar, returns 0 * if 2D, -- use DIM to specify primary dimension -- compute lengthscales separately along each projection * if >2D, convert to 1D dim [INPUT; default=1] primary dimension in case of 2D array (e.g., if CURVE=CURVE(NX,NY), DIM=2 returns SCALE=SCALE(NY)) keywords crunch [INPUT] if set, and CURVE is 2D, collapses the array along the secondary dimension to generate 1D curve half [INPUT] if set, returns the half-scale pick [INPUT; default=0] if 2D, specifies how to combine the scales computed at the different cuts 0: pick the smallest scale 1: pick the largest scale 2: get the average choice [INPUT; default=0] what algorithm to use to find the scale? 0: MexicanHat wavelet 1: use inverse of 1st derivative 2: radius of curvature 3: stepped toggle eps [INPUT; default=1e-7] small number _extra [JUNK] ignore. here only to prevent crashing program. subroutines WVLT_SCALE [ROOFN] history vinay kashyap (Apr97) added CHOICE option 3 (VK; Feb03)
(See pro/findscale.pro)
function fitlines
widget-based procedure to fit Gaussians and Lorentzians (or
combinations, or other 3-parameter functions) to lines in a
spectrum and determine line fluxes. returns a structure of
the form
{POS,PERRP,PERRM,PERRC,$
FLX,FERRP,FERRM,FERRC,$
WDT,WERRP,WERRM,WERRC,$
THAW,TYPE,TIES,EPITHET,CONLEVX,CONLEV,CONSIGX,CONSIG,COMMENT}
All these are also available as output individually as keywords.
See keyword descriptions for what the variables mean.
syntax
fxstr=fitlines(x,y,ysig=ysig,funcs=funcs,/intens,dchi=dchi,$
pos=pos,perrp=perrp,perrm=perrm,perrc=perrc,$
flx=flx,ferrp=ferrp,ferrm=ferrm,ferrc=ferrc,$
wdt=wdt,werrp=werrp,werrm=werrm,werrc=werrc,$
thaw=thaw,type=type,epithet=epithet,ties=ties,$
conlev=conlev,consig=consig,comment=comment,$
histerix=histerix,$
/dumb,verbose=verbose,xsize=xsize,ysize=ysize,$
wid=wid,dynrng=dynrng,/posve,/negve,itmax=itmax,chithr=chithr,$
jumpup=jumpup,jumpdn=jumpdn,svdthr=svdthr,missing=missing,$
/noday,/notime,/nouser,/nopack,stacol=stacol,stacol=stacol,$
stathk=stathk,/nuthin)
parameters
x [INPUT; required] absissa, e.g., wavelength or energy
y [INPUT; required] count spectrum Y(X)
* size of Y must match that of X
keywords
ysig [INPUT] errors on Y
* default is sqrt(abs(Y)+0.75)+1.
funcs [INPUT] name of user defined function (actually a procedure)
that takes as input X and A (the model parameters), and returns
Y(X;A) and the partial derivatives dY/dA
* default is set to X3MODEL
* NOTE: if MPFIT is chosen as the optimization algorithm,
then "_f" is automatically appended to the name. This
is because MPFIT requires a _function_, not a procedure.
The program corresponding to X3MODEL is X3MODEL_F() and
that corresponding to LIBMODEL is LIBMODEL_F()
intens [INPUT] if set, Y(X) is assumed to be intensity, i.e.,
(counts|ergs|.../bin_unit/...)
* default is to take Y(X) to be (counts|ergs|.../bin/...)
* passed straight to FITLINES_EVENT
* WARNING: this has >not< been road-tested!
dchi [INPUT] delta-chisq threshold for projection errors
* default is 1.0
* may be changed within FITLINES_EVENT, but those changes
will not be propagated back.
pos [I/O] best-fit line positions
* length of vector shows number of components
perrp [I/O] 1-sided error on POS (POS+PERRP is upper bound)
perrm [I/O] 1-sided error on POS (POS-PERRM is lower bound)
perrc [I/O] DCHI threshold used in computing PERR?
flx [I/O] best-fit fluxes in the lines
ferrp [I/O] 1-sided error on FLX (FLX+FERRP is upper bound)
ferrm [I/O] 1-sided error on FLX (FLX-FERRM is lower bound)
ferrc [I/O] DCHI threshold used in computing FERR?
wdt [I/O] best-fit widths (sigma, core-radius, etc.) of the lines
werrp [I/O] 1-sided error on WDT (WDT+WERRP is upper bound)
werrm [I/O] 1-sided error on WDT (WDT-WERRM is lower bound)
werrc [I/O] DCHI threshold used in computing WERR?
* on input, FLX, WDT, and ?ERR? are forced to match the length
of POS: excess elements are thrown away, and insufficient
lengths are made up by padding with first elements, 1s, etc.
* on output ?ERRM are identical to ?ERRP >unless< the
projected errors have been calculated using ERORS, in
which case the values may be different
* on output, places where ?ERRC contain 0's are those where
the computed errors are 1-sigma formal curvature errors
thaw [I/O] integer array signaling frozen (0) or thawed parameter (1)
* refers to sequences of {POS,WDT,FLX} for each component in
a 3-parameter model (cf. X3MODEL) -- whatever goes for the
appropriate user-defined function.
* length must match 3*length(POS)
* default is to freeze defined input, thaw all new additions
type [I/O] type of model ('gauss', 'lorentz', etc.)
* default is 'gauss'
epithet [I/O] label for each component
* labels, obtained, for example, with IDLABEL
* Merriam-Webster> a characterizing word or phrase accompanying
or occurring in place of the name of a person or thing
ties [I/O] any ties between parameters?
conlev [I/O] the continuum that was taken out of the spectrum
* CONLEV must match the size of X and Y else ignored
consig [I/O] error on CONLEV
* default for CONSIG is sqrt(abs(CONLEV)+0.75)+1.
* NOTE: CONLEV and CONSIG are compressed using SPLAC in
the output that gets returned via the structure. That
structure therefore also has appropriate abscissae
CONLEVX and CONSIGX.
comment [OUTPUT] descriptive string
histerix [OUTPUT] a structure containing the state at each step
of the fitting process
* if explicitly set to 0, will not contain any output
* passed w/o comment to FITLINES_EVENT
oldstr [INPUT] old fitlines structure from which to start with
_extra [INPUT ONLY] use this to pass defined keywords to subroutines
PICKRANGE: XSIZE, YSIZE, WID, DYNRNG
LINEREM: POSve, NEGve
FIT_LEVMAR: ITMAX, CHITHR, DUMB
LEVMARQ: JUMPUP, JUMPDN, SVDTHR
MK_3MODEL: MISSING
MK_SLANT: ANGLE, BETAP
ERORS: VERBOSE
STAMPLE: NUTHIN, NODAY, NOTIME, NOUSER, NOPACK, STACOL,
STASIZ, STATHK
subroutines
FITLINES_EVENT
FMTSTUFF
PICKRANGE
FUNCS
(X3MODEL/LIBMODEL/MPFITFUN)
(MK_3MODEL, MK_GAUSS, MK_LORENTZ, MK_SLANT, MK_ROGAUSS, MK_POWLAM, MK_POLY1D)
LINEREM
SETCONT
ERORS
FIT_LEVMAR
ADJUSTIE
LEVMARQ
LMCOEFF
CURVE_FIT
SPLAC
WHICH
KILROY
WHEE
STAMPLE
PEASECOLR
IS_KEYWORD_SET
known bugs
cannot handle spectra with varying bin sizes
INTENS has not been tested
SPLAC keywords are not gracefully handled
help is available only in UNIX
history
vinay kashyap (Oct98)
added renormalization option (VK; Nov98)
added keywords INTENS,DCHI,PERRL,WERRL,FERRL,PERRC,WERRC,FERRC;
changed output structure format (VK; FebMM)
changed keywords PERR,WERR,FERR to PERRU,WERRU,FERRU; also the
corresponding output structure fields (VK; MarMM)
changed ?ERRU to ?ERRP and ?ERRL to ?ERRM to avoid confusion
with ERR[U,L] of ERORS (VK; MarMM)
moved QUIT to end of row, far from FIT; added ability to save
to disk; changed ?ERR[M,C] to be I/O; added TIES to output
structure (VK; JulMM)
added labeling capability via keyword EPITHET; reorganized
to combine 6th and 7th rows (VK; AugMM)
changed location of doc file to ardb ; allowed call to STAMPLE
(VK; DecMM)
changed default of ?ERRC to 0.0 (VK; JanMMI)
per Antonio Maggio's suggestion, removed keyword MULTIPLE from
call to WIDGET_LIST (VK; FebMMI)
changed suffix of help file from ".doc" to ".hlp" (VK; FebMMI)
added code to make it easier to switch between color tables
(VK; Oct02)
added monte-carlo errors as option (LL; Aug03)
added keyword HISTERIX (VK; Feb04)
added keyword OLDSTR (LL; Jul05)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
(See pro/fitting/fitlines.pro)
procedure fitlines_event widget event handler subroutine for FITLINES. see that routine for a description of variables, etc. only rudimentary consistency checks are carried out here. uses subroutine FMTSTUFF, which is included in this file. syntax fitlines_event,x,y,pos,wdt,flx,perr,werr,ferr,thaw,type,ties,epithet,$ conlev,consig,chisq,funcs,sigy,widg, perrm=perrm,werrm=werrm,$ ferrm=ferrm,perrc=perrc,werrc=werrc,ferrc=ferrc,/intens,rmfstr=rmfstr,$ histerix=histerix subroutines FMTSTUFF PICKRANGE FUNCS (X3MODEL/LIBMODEL) (MK_3MODEL, MK_GAUSS, MK_LORENTZ, MK_SLANT, MK_ROGAUSS, MK_POWLAM, MK_POLY1D) LINEREM SETCONT ERORS FIT_LEVMAR , CURVE_FIT , MPFITFUN ADJUSTIE LEVMARQ LMCOEFF STAMPLE KILROY WHEE PEASECOLR IS_KEYWORD_SET history vinay kashyap (Oct98) added renormalization option (VK; Nov98) various bug fixes and reorganizations (VK; Dec98) now allows fitting a single parameter (VK; Aug99) enhancements to include call to ERORS, setting YRANGEs, INTENSity units, etc. (VK; FebMM) avoid repeat calls to CW_BGROUP, saving tremendous headaches; bug correction CONTINUUM->AdjustNorm (VK; MarMM) bug correction -- undefined STYPE for new component; rudimentary changing parameter labels (VK; JunMM) moved QUIT to end of row, far away from FIT; added DUMP to disk (VK; JulMM) added error-bar plotting capability via VIEW->SetDefaults; pass x,y-range to setcont; added labeling capability via keyword EPITHET; merged 6th and 7th rows; bug correction with xcont in adjust norm (VK; AugMM) changed location of help file to ardb; added calls to STAMPLE (VK; DecMM) bug fixes: invisible error output, adding model deleted existing projected errors, streamlined saves (VK; JanMMI) per Antonio Maggio's suggestion, removed keyword MULTIPLE from call to WIDGET_LIST; improved color-scale setting for 24-bit consoles; replaced call to WHICH by call to ROUTINE_INFO (VK; FebMMI) various extra info messages (VK; AprMMI) changed y to z on lines 1012 and 1285, because.. y was inappropriate for some reason? (VK; Jun01) was crashing due to missing ZSIG in cont_acpt (VK; Aug01) bug was not passing predefined CONLEV to SETCONT (piecewise) (VK; Apr02) handle color tables in 24-bit displays (VK; Jun02) bug correction -- if all ties were deleted, then TIES was turning into and integer array (VK; Jul02) made changes to plotting so that hardcopy won't come out with annoying blank sheets (VK; Sep02) changed default colors to be compatible with PEASECOLOR (VK); added hooks into MPFIT (Liwei Lin/VK; Oct02) tied the left column of parameter values to changes in the main parameter list window on the right (VK; Apr03) added monte-carlo errors as option and added keyword RMFSTR (LL; Aug03) added keyword HISTERIX (VK; Jul03) bug correction: algo_type undefined unless fit is run first (LL; Aug04) updated for IDL5.6 keyword_set([0]) behavior change for vectors (VK; 20Mar2006) modified some widget instructions to be slightly clearer (VK; Aug06) ********************************************************************* subroutine fmtstuff takes in the model as described, and returns it properly formatted for display in the widget. parameters are named as before. only minimal consistency checks are carried out. usage fmtstuff,pos,wdt,flx,thaw,type,epithet,perr,werr,ferr,$ perrm=perrm,werrm=werrm,ferrm=ferrm,$ perrc=perrc,werrc=werrc,ferrc=ferrc,$ plist=plist,list=list,$ tiep=tiep,tiew=tiew,tief=tief,ties=ties,delcmp=delcmp keywords plist [OUTPUT] appropriately formatted model parameter list list [OUTPUT] denoting frozen/thawed components tiep [I/O] ties specially setting the range on positions tiew [I/O] ties specially setting the range on widths tief [I/O] ties specially setting the range on fluxes ties [I/O] rest of ties delcmp [ACTION] if set to component number, deletes component DELCOMP and all TIES that contain references to parameters in that component _extra [INPUT] pass defined keywords to STAMPLE (NODAY,NOTIME, NOUSER,NOPACK,STACOL)
(See pro/fitting/fitlines_event.pro)
script fitlines_undump restores the variables saved to disk from FITLINES_EVENT and calls FITLINES again. warning this will restore all saved variables from within FITLINES_EVENT. all of your existing variables with the same names will be overwritten. best to always start from a clean environment. save files written in IDL 5.4 are incompatible with earlier versions, but can be restored under certain circumstances using the CMSVLIB package of Craig Markwardt (http://cow.physics.wisc.edu/~craigm/idl/idl.html) This program has a "restore" command right at the start that may fail, but if the variables have already been loaded in, just type .SKIP and .CON, and bob's your uncle. usage fitsavfil='fitlines.save' .run fitlines_undump input FITSAVFIL name of IDL save file containing the variables dumped from within the FITLINES GUI output FITSTR structure containing the fit parameters history vinay kashyap (MMJul) cosmetic surgery (VK; DecMM) included keyword HISTERIX (VK; FebMMIV)
(See pro/scrypt/fitlines_undump.pro)
procedure fit_levmar uses the Levenberg-Marquardt method to find best-fit parameters syntax fit_levmar,x,y,a,yfunc,freeze=freeze,erra=erra,chisq=chisq,$ itmax=itmax,chithr=chithr,/dumb,ties=ties,vname=vname,$ jumpup=jumpup,jumpdn=jumpdn,svdthr=svdthr,funcs=funcs,sig=sig,$ /poisson parameters x [INPUT; required] data points y [INPUT; required] Y(X) * sizes of X and Y must match a [I/O; required] parameters for user-supplied function * on input, these are the initial guesses * on output, these contain the best-fit values yfunc [OUTPUT] best-fit Y(X;A) keywords freeze [INPUT] freeze numbered parameters (starting from 0!) erra [OUTPUT] formal errors on the best-fit parameters chisq [OUTPUT] the chi-sq statistic denoting degree of agreement between model and data itmax [INPUT; default=100] maximum number of iterations chithr [INPUT; default=0.1] stopping rule: ignore changes in CHISQ smaller than this amount dumb [INPUT] if set, skips the part where the user can readjust the parameter values in case the fit has gone bad. tiptoe [INPUT] if set, forces small steps on A verbose [INPUT] controls chatter _extra [INPUT] use this to pass defined variables to subroutines:- ADJUSTIE: TIES, VNAME LEVMARQ: JUMPUP, JUMPDN, SVDTHR LMCOEFF: FUNCS, SIG (note: FUNCS is actually the name of a _procedure_ -- CURVEFIT is to blame for the confusion) subroutines ADJUSTIE LEVMARQ LMCOEFF SVDC SVSOL history vinay kashyap (Oct98) added parameter YFUNC (VK; Dec98) bug fix: crashing if freeze not set (VK; 99Aug) now returns correct chisq if all params are frozen (VK; JanMM) also adjust ERRA for ties (VK; FebMM) what if adjusted ERRA becomes 0? (VK; MarMM) added keywords TIPTOE and VERBOSE, changed behavior if dead end to now tiptoe around point (VK; Nov04)
(See pro/fitting/fit_levmar.pro)
function flareclass compute the peak flux of a solar flare based on its GOES classification It is assumed that the classification is given as a letter followed by a number. The letter is used to define the intensity level, and the number is a multiple of it. The base levels are: A : 1e-8 - 1e-7 W/m^2 B : 1e-7 - 1e-6 W/m^2 C : 1e-6 - 1e-5 W/m^2 M : 1e-5 - 1e-4 W/m^2 X : >1e-4 W/m^2 see http://www.spaceweather.com/glossary/flareclasses.html syntax fx=flareclass(class,cgs=0,/atSun,verbose=verbose) parameters class [INPUT; required] string variable that contains the GOES class keywords cgs [INPUT] by default, the output is returned in cgs, as ergs/s/cm^2 at Earth * set this explicitly to 0 to return the output in SI units atSun [INPUT] if set, multiplies by 4*pi*AU^2 to return peak luminosity of flare at the Sun verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history Vinay Kashyap (MMXV.VI)
(See pro/ssw/flareclass.pro)
procedure fluxcurve compute a fluxed light curve from low-spectral-resolution events data syntax fluxcurve,time,chan,charf,chnrg,fluxlc,tgrid,flxerr,$ ctlc=ctlc,/adapbin,tmin=tmin,tmax=tmax,tbin=tbin,$ tstart=tstart,tstop=tstop,/shift1,verbose=verbose,$ /slowok,snrthr=snrthr parameters time [INPUT; required] photon arrival times chan [INPUT; required] the PI or PHA values of each photon charf [INPUT; required] the average effective area in each channel chnrg [INPUT; required] the average photon energy in each channel fluxlc [OUTPUT; required] the fluxed light curve, in [ergs/s/cm^2] tgrid [OUTPUT; required] the bin boundaries over which the light curve is computed flxerr [OUTPUT; optional] the standard errors on the fluxed light curve, computed as stddev(fluxes)/nphotons in each bin keywords ctlc [OUTPUT] the counts light curve, in [ct/s] adapbin [INPUT] if set, rebins adaptively to ensure a minimum number of counts in each bin, by pushing the counts histogram through SMOOTHIE * assumes errors to be sqrt(CTLC*TBIN) * for each group, the fluxes from the individual bins are averaged tmin [INPUT] the minimum time value to consider * default: min(TIME) < min(TSTART) tmax [INPUT] the maximum time value to consider * default: max(TIME) > max(TSTOP) tbin [INPUT] the bin size * default: TMAX-TMIN tstart [INPUT] array of start times of GTI's tstop [INPUT] array of stop times of GTI's shift1 [INPUT] if set, assumes that the channel numbers start from 1, not from 0 * see the FIRSTCHAN field in the response matrix structure read in via RD_OGIP_RMF() verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines SMOOTHIE : SNRTHR REBINW : SLOWOK subroutines TI_COVER REBINW FINDEX SMOOTHIE history vinay kashyap (MMVI.IX)
(See pro/timing/fluxcurve.pro)
function flux_to_em return emission measures (-1 where undeterminable) at various temperatures consistent with given line fluxes and line emissivities. for each temperature, assume a delta-function emission measure, compute line fluxes seen through some instrument, account for interstellar absorption, and scale to match the observed flux. syntax em=flux_to_em(emis,flux=flux,logT=logT,wvl=wvl,Z=Z,NH=NH,$ defEM=defEM,noph=noph,thresh=thresh, abund=abund,/temp,/ikev,$ effar=effar,wvlar=wvlar,fh2=fh2,he1=he1,heII=heII,/fano) parameters emis [INPUT; required] 2D array of line emissivities, EMIS(LOGT,WVL) * if 1-D, assumed to be EMIS(LOGT) keywords flux [INPUT] observed fluxes * if not given, assumed to be 1 [(ph|erg)/s/cm^2] * size is forced to match 2nd dimension of EMIS if <, filled with 1s if >, extra elements are ignored * NOTE: the author realizes that there may be multiple IDs for the single observed line, and directs the inquirer to the function ID_TO_EMIS, which returns the appropriately concatenated emissivity table. logT [INPUT] log_10(Temperature [K]) at which EMIS is defined * if not given, assumed to go from 4 to 8 in even steps * interpolated if size does not match 1st dimension of EMIS wvl [INPUT] wavelengths at which EMIS is defined * if not given or if size does not match 2nd dimension of EMIS, (a) interstellar absorption correction is not made (b) all fluxes >gotta be< [ergs/s/cm^2] Z [INPUT] atomic numbers * if not given, assumed to be 1s (i.e., H. i.e., no abundance corrections are made) * size is forced to match 2nd dimension of EMIS if <, filled with 1s if >, extra elements are ignored NH [INPUT] H column density [cm^-2] * ignored if WVL is incorrect defEM [INPUT; default=1e14] default EM to use prior to scaling [cm^-5] noph [INPUT] if set, FLUX is assumed to be in [ergs/s/cm^2], and no attempts are made to convert things to [ph/...] * forcibly set if WVL is incorrect thresh [INPUT; default=1e-2] dynamic range in output curves, relative to maximum in each curve _extra [INPUT ONLY] use this to pass defined keywords to subroutines LINEFLX [ABUND,TEMP,IKEV,EFFAR,WVLAR] ISMTAU [FH2,HE1,HEII,FANO] restrictions * EFFAR and WVLAR must be correctly defined, or else the output will be garbage * requires subroutines LINEFLX WHEE ISMTAU history vinay kashyap (Oct98) bug correction re 0 EMIS (VK; Nov98) bug correction re 0 NH (VK; AugMM)
(See pro/flux_to_em.pro)
function fold_ioneq folds in ionization equilibrium fractions of the various ions of a given element with line emissivities (which include only level population info; see RD_LINE()). returns emis(T;Z,ion)*ioneq(T;Z,ion) syntax lflx=fold_ioneq(emis,Z,ion,logt=logt,tmax=tmax,trng=trng,$ level=level,userarr=userarr,chifil=chifil,chidir=chidir,$ eqfile=eqfile,verbose=v) parameters emis [INPUT; required] 1- or 2-D array of line emissivities as a function of temperature * if 2D, assumed to be EMIS(Temperature,Wavelength) * if 1D, assumed to be EMIS(Temperature), unless the number of elements matches that of Z Z [INPUT; required] atomic number(s) corresponding to each wavelength * if size does not match the 2nd dimension of EMIS, then if >, ignore extra elements if <, but >0, use available ones, and use Z[0] for rest ion [INPUT; default: Z+1] ionic state(s) corresponding to each wavelength * if size does not match the 2nd dimension of EMIS, then if >, ignore extra elements if <, but >0, use available ones, and use ION[0] for rest * NOTE: this is the ionic state >>that matters<<, i.e., the ionic state of the species that populates the upper level. See keyword JON of RD_LINE, which is what is needed here. keywords logt [INPUT] 1D array of log10(temperature [K]) at which EMIS is given. (default: findgen(81)*0.05+4) * if size does not match that of EMIS, use default level [INPUT; default: 0.5] level at which to determine the temperature range on line flux (in other words, default will be to return the FWHM) * if <1, TRNG=LOGT(where(FLUX>LEVEL*MAX(FLUX)) * if >=1, TRNG=LOGT(where(FLUX>(LEVEL/100.)*MAX(FLUX)) * if <=0 or >=100, set to 0.5 tmax [OUTPUT] log10(temperature) at which contribution is maximum trng [OUTPUT] range in LOGT (LEVEL of MAX) -- TRNG(0,*) is lower bound, TRNG(1,*) is upper bound userarr [INPUT] an array of ionization fractions in the same format as is returned by RD_IONEQ(), and has the size [n(T),max(Z)+1,n(Z)] * if this is given and is legit (i.e., matches the supplied EMIS and LOGT), then EQFILE and CHIFIL are ignored eqfile [I/O] file from which to read in ion-balance data * default is to read in the CHIANTI file, !IONEQF * hard-coded default is ioneq/chianti.ioneq * if not given, but CHIFIL is given, uses that. chifil [I/O] if set, reads in from CHIANTI-type database; must be set to the name of the file containing the ionization equilibrium info (i.e., CHIDIR/CHIFIL) * may be overridden with EQFILE * default is ioneq/chianti.ioneq * currently, set automatically if not given. verbose [INPUT] higher the number, greater the chatter _extra [INPUT] use to transmit defined keywords to called functions * RD_IONEQ [CHIDIR] subroutines -- WHEE -- SETSYSVAL -- RD_IONEQ [READ_IONEQ (%)] (%) CHIANTI subroutine, used as is history vinay kashyap (Dec96) removed call to KILROY and added call to WHEE, hacked default use of READ_IONEQ until more options become available; corrected bug that was reading in ionstate-1 rather than ionstate; added code to handle Z=0 (VK; Feb97) bug: if Z is scalar take em all to be same element (VK; Apr97) added keyword VERBOSE (VK; MarMM) streamlined meanings of EQFILE, CHIFIL (VK; DecMM) changed default for EQFILE; now pass VERBOSE to RD_IONEQ; added call to SETSYSVAL (VK; Jul01) allowed EQFILE to be "none" (VK; Feb04) changed default behavior of Z and ION when sizes don't match EMIS; now uses first element of input if given (VK; Nov04) bug correction, ION is offset by 1 from array index (LL/VK; Dec04) added keyword USERARR, slightly modified behavior when EMIS was input as 1D (VK; Aug08) changed default of EQFILE and CHIFIL to ioneq/chianti.ioneq (VK; Aug13)
(See pro/fold_ioneq.pro)
NAME:
FPUFIX
PURPOSE:
This is a utility routine to examine a variable and fix problems
that will create floating point underflow errors.
AUTHOR:
FANNING SOFTWARE CONSULTING
David Fanning, Ph.D.
1645 Sheely Drive
Fort Collins, CO 80526 USA
Phone: 970-221-0438
E-mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com
CATEGORY:
Utilities
CALLING SEQUENCE:
fixedData = FPUFIX(data)
ARGUMENTS:
data : A numerical variable to be checked for values that will cause
floating point underflow errors. Suspect values are set to 0.
KEYWORDS:
None.
RETURN VALUE:
fixedData: The output is the same as the input, except that any values that
will cause subsequent floating point underflow errors are set to 0.
COMMON BLOCKS:
None.
EXAMPLES:
data = FPTFIX(data)
RESTRICTIONS:
None.
MODIFICATION HISTORY:
Written by David W. Fanning, from Mati Meron's example FPU_FIX. Mati's
program is more robust that this (ftp://cars3.uchicago.edu/midl/),
but this serves my needs and doesn't require other programs from
Mati's library. 24 February 2006.
(See pro/external/fpufix.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
FREEBOUND
PURPOSE:
Calculates the free-bound (radiative recombination) continuum.
A report giving detailed information on how the CHIANTI
free-bound is calculated is available at:
http://solar.bnsc.rl.ac.uk/~young/chianti/freebound.pdf
To calculate the continuum spectrum the user should specify
whether the plasma structure is specified through a differential
emission measure (DEM) curve or through emission measure (EM)
values. For the former, the DEM values are specified through the
DEM_INT keyword and for the latter the EM values are specified
through the EM_INT keyword. If neither are specified EM_INT
values of unity are assumed.
If DEM_INT values are specifed they must be specified on a
temperature scale that has constant intervals in log10(T). EM_INT
values do not have this restriction.
Note that EM_INT must be used for isothermal plasmas.
INPUTS
TEMP Temperature in K (can be an array). If the keyword
/DT is used, the
temperatures must be spaced at equal intervals of
log10(T). E.g., log T=6.0, 6.1, 6.2, 6.3, ...
WVL Wavelength in angstroms (can be an array). If /keV is
set, then WVL is assumed to contain energies in keV units.
OUTPUTS
INT Free-bound continuum intensity in units of
10^-40 erg cm^3/s/sr/Angstrom
( integral(N_H N_e dh) in cm^-5) if a DEM is not defined.
If DEM values are defined, it is assumed that they are given
as N_H N_e dh/dT. The units are 10^-40 erg/cm^2/s/srAngstrom
If T is given as a 1-D array, then the output will be a
2-D array, with one element for each temperature and
wavelength (but also see SUMT).
If the keyword /keV is set, then the units of INT will be
10^-40 erg cm^3/s/sr/keV.
OPTIONAL INPUTS
DEM_INT This should be the same size as TEMP and contain
differential emission measure values. Specifying
DEM_INT places a restriction on TEMP (see above). Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not.
EM_INT This should be the same size as TEMP and contain
emission measure values. Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not. If
neither EM_INT or DEM_INT are specified, then a EM_INT
vector of same size as TEMP with values of unity is
assumed.
IZ Only calculate continuum for the element with atomic
number IZ
ION (To be used in conjunction with IZ.) Calculated continuum
for a single ion (IZ, ION).
KEYWORDS
NO_SETUP If the procedure setup_elements has already been called
then the keyword /nosetup should be set to avoid
repeating this step
MIN_ABUND If set, calculates the continuum only from those
elements which have an abundance greater than
min_abund. Can speed up the calculations. For
example:
abundance (H) = 1.
abundance (He) = 0.085
abundance (C) = 3.3e-4
abundance (Si) = 3.3e-5
abundance (Fe) = 3.9e-5
PHOTONS The output spectrum is given in photon units rather
than ergs.
SUMT When a set of temperatures is given to FREEBOUND, the
default is to output INTENSITY as an array of size
(nwvl x nT). With this keyword set, a summation over
the temperatures is performed.
VERBOSE Output information from FREEBOUND.
KEV If set, then WVL is assumed to contain energies in keV units
rather than wavelengths in Angstroms.
COMMON BLOCKS
ELEMENTS
CALLS
FREEBOUND_ION, SETUP_ELEMENTS, READ_KLGFB, GET_IEQ
HISTORY
Ver.1, 24-Jul-2002, Peter Young
Ver.2, 26-Jul-2002, Peter Young
revised call to freebound_ion; corrected ion fraction problem
V 3, 25-May-2005, GDZ
corrected routine header.
Ver.4, 10-Mar-2006, Peter Young
added keV keyword
Ver.5, 8-Sep-2009, Peter Young
routine now checks to make sure temperatures are evenly
spaced when the DEM_INT keyword is used; if an error is
found due to incorrect temperature specificiations, then
the continuum intensity is returned as zero.
Ver.6, 6-Oct-2009, Peter Young
Introduced EM_INT keyword for specifying emission measure
values for isothermal plasmas.
VERSION : 6, 6-Oct-2009
Ver.PoA, 10-Aug-2010, Vinay Kashyap,
ala changes 18-Feb-2005, LiWei Lin
Commented common block out and
Added _extra keyword
Rename routine freebound_ch
(See pro/external/freebound_ch.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
FREEBOUND
EXPLANATION
Calculates the free-bound (radiative recombination) continuum
from a single ion. Note that the output does not contain the ion
fraction, element abundance or differential emission measure term.
INPUTS
TEMP Temperature in K (can be an array).
WVL Wavelength in angstroms (can be an array). If the keyword
/keV is set, then wvl should instead be given in units of
keV.
IZ Atomic number of ion (e.g., 26 = Fe)
ION Spectroscopic number of ion (e.g., 13 = XIII)
OUTPUTS
INT Free-bound continuum intensity. Needs to be multiplied by
element abundance, ion fraction and DEM to obtain the final
continuum intensity.
OPTIONAL INPUTS
IP The ionization potential of the ion.
VDATA An array containing the Verner & Yakovlev data array.
PE An array containing the PE data from READ_FBLVL
KLGFB An array containing the KLGFB data from READ_FBLVL
[Note: the above 3 inputs are used when calling freebound_ion from
freebound]
KEYWORDS
NOVERNER If set, then the Verner & Yakovlev cross-sections will
not be used.
KEV If set, then WVL is assumed to contain energies in keV units
rather than wavelengths in Angstroms.
COMMON BLOCKS
None.
CALLS
READ_FBLVL, ZION2FILENAME, VERNER_XS, KARZAS_XS, CONCAT_DIR,
READ_IP, READ_KLGFB, FILE_EXIST
PROGRAMMING NOTES
The way I treat the exponential function in the expression for the
emissivity may seem strange, but it saves a bit of time in the
calculation. Basically calculating exp(E-IP+E_i/T) for each level
was time consuming so I split it into exp(E-IP/T)*exp(E_i/T). The
first term comes out of the for loop, while the second term is the
exponential of a vector rather than an array. This made a ~30%
time-saving for freebound.
HISTORY
Ver.1, 24-Jul-2002, Peter Young
Ver.2, 26-Jul-2002, Peter Young
Added /noverner keyword.
Ver.3, 30-Jul-2002, Peter Young
Speeded up routine by modifying treatment of exponential.
Ver.4, 10-Mar-2006, Peter Young
Added /keV keyword
Ver. 5 8-Jun-2010, Ken Dere
added check for n_params()
(See pro/external/freebound_ion.pro)
PROJECT : CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
FREEFREE
PURPOSE:
This routine computes the free-free continuum (bremsstrahlung)
using the fitting formulae of Itoh et al. (ApJS 128, 125, 2000)
and Sutherland (MNRAS 300, 321, 1998).
The Itoh et al. data are valid for smaller ranges for temperature
and wavelength than Sutherland and so for points outside of their
ranges we use the data of Sutherland.
INPUTS
TEMP Temperature (in K). They do not have to be in monotonically
increasing order.
WVL Wavelengths in angstroms. Can be a scalar or vector. If /keV is
set, then WVL is assumed to contain energies in keV units.
OUTPUTS
INT Free-free continuum intensity in units of
10^-40 erg cm^3/s/sr/Angstrom
[ integral(N_H N_e dh) in cm^-5 ] if a DEM is not defined.
If DEM values are defined, it is assumed that they are given
as N_H N_e dh/dT. The units are 10^-40 erg/cm^2/s/sr/Angstrom.
If T is given as a 1-D array, then the output will be a 2-D array,
with one element for each temperature and wavelength
(but also see SUMT).
If the keyword /keV is set, then the units of INT will be
10^-40 erg cm^3/s/sr/keV
OPTIONAL INPUTS
DEM_INT This should be the same size as TEMP and contain
differential emission measure values. Specifying
DEM_INT places a restriction on TEMP (see above). Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not.
EM_INT This should be the same size as TEMP and contain
emission measure values. Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not. If
neither EM_INT or DEM_INT are specified, then a EM_INT
vector of same size as TEMP with values of unity is
assumed.
MIN_ABUND This keyword allows the specification of a minimum abundance,
such that any elements with an abundance (relative to
hydrogen) less than MIN_ABUND will not be included in the
calculation. E.g., MIN_ABUND=1e-5.
KEYWORDS
NO_SETUP By default the routine asks the user which ion balance
and abundance files to use via pop-up widgets. If
/no_setup is used then this data is taken from the common
block.
SUMT The default is to output the intensity array as an array
of size (nwvl x nT). Setting this keyword performs a sum
over the temperatures to yield a vector of same size as
the input wavelengths, thus producing the complete
free-free spectrum.
PHOTONS Gives output emissivity in photon units rather than ergs.
KEV If set, then WVL is assumed to contain energies in keV units
rather than wavelengths in Angstroms.
CALLS
SUTHERLAND_CH, ITOH_CH
COMMON BLOCKS
NONE (ELEMENTS commented out)
PROGRAMMING NOTES
The Itoh fitting formula is only valid for (6.0 LE logT LE 8.5).
For temperatures below this, we thus switch to the Sutherland
fitting formula. There is very little (<1%) between the two at
logT=6.
Itoh also has a constraint on the quantity u=hc/kTl (l=wavelength),
such that (-4 LE log u LE 1.0). The upper limit corresponds to the
continuum being cut-off prematurely at low wavelengths. E.g., for
T=10^6 the cutoff is at 14.39 angstroms. For these low wavelengths
we also use the Sutherland data to complete the continuum. Note that
the continuum at these wavelengths is very weak
MODIFICATION HISTORY
Ver.1, 5-Dec-2001, Peter Young
Completely revised to call the separate itoh.pro and
sutherland.pro routines.
V. 2, 21-May-2002, Giulio Del Zanna (GDZ),
Corrected the description of the units.
Added verbose keyword and a printout.
V. 3, 22-May-2002, Peter Young (PRY)
Added MIN_ABUND optional input.
Changed ioneq_t to ioneq_logt (GDZ).
V 4, 25-May-2005, GDZ
corrected routine header.
V. 5, 9-Mar-2006, Peter Young
Added /kev keyword
V. 6, 9-May-2008, Peter Young & Kevin Tritz
Modifed code so that temperatures can be specified in a unordered
list.
V. 7, 7-Oct-2009, Peter Young
Added EM_INT= keyword; simplified how the routine decides
which calculation to use (Itoh or Sutherland)
VERSION : 7, 7-Oct-2009
V.PoA, 10-Aug-2010, Vinay Kashyap
a la 18-Feb-2005, LiWei Lin
Commented common block out and
Added _extra keyword
Rename routine freefree_ch
Edit calls to sutherland and itoh to sutherland_ch and itoh_ch
(See pro/external/freefree_ch.pro)
procedure generatio a generalized mechanism to compute flux ratios and errors from given input fluxes and a well-defined definition of how the ratios are constructed all of the input fluxes are assumed to be independent of each other and uncorrelated syntax generatio,fx,rcode,rx,fxerr=fxerr,rxerr=rxerr,verbose=v,$ dfx_mul=dfx_mul,dfx_add=dfx_add parameters fx [INPUT; required] input fluxes rcode [INPUT] string array describing which of the input fluxes must be considered only as ratios * basic format is: "sP#[,sP#[,...]]" where -- "#" is an integer flag describing the ratio being constructed -- "P" is a positional descriptor and can take on values N (for numerator) or D (for denominator) -- "s" stands for the sign with which the flux goes into the ratio "+" or "-" * e.g., to construct a simple ratio FX[2]/FX[1], RCODE=['','+D1','+N1'] * e.g., to construct two hardness ratios FX[3]/FX[1] and (FX[3]-FX[1])/(FX[3]+FX[1]), RCODE=['','+D1,-N2,+D2','','+N1,+N2,+D2'] * if size is incompatible with FX, then no action is taken. rx [OUTPUT] array of ratios constructed using FX and RCODE keywords fxerr [INPUT] 1-sigma errors on FX * size must match that of FX. otherwise, -- if single-element, assumed to represent -- a fractional error if >0 and <1 -- a percentage error if >1 and <100 -- an abs(constant) error if >100 or <0 -- ignored otherwise rxerr [OUTPUT] 1-sigma errors on RX, computed only if FXERR is given and is legal verbose [INPUT] controls chatter dfx_mul [INPUT] multiplicative factor by which to jiggle FX while computing partial derivatives to propagate errors (default is 0.05) * if scalar, taken to be same factor for all FX * if vector, must be of same size as FX dfx_add [INPUT] additive factor by which to jiggle FX while computing partial derivatives to propagate errors (default is 0.05*FXERR) * if scalar, taken to be same offset for all FX * if vector, must be of same size as FX _extra [JUNK] here only to avoid crashing the program example ;this makes the ratios FX[0]/FX[1] and (FX[1]-FX[0])/(FX[1]+FX[0]) fx=[10.,5.] & fxerr=0.1 & rcode=['+N1,-N2,+D2','+D1,+N2,+D2'] generatio,fx,rcode,rx,fxerr=fxerr,rxerr=rxerr for i=0,n_elements(rx)-1 do print,rx[i],' +- ',rxerr[i] Warning: The numeral suffix in the ratio specification is only as a placeholder to determine uniqueness and does _not_ translate to the index in the output. For example, try: fx=[1.,2.,1.,3.,1.,4.,1.,5.,1.,6.] rcode=['+D1','+N1','+D2','+N2','+N3','+D3','+N4','+D4','+D5','+N5'] generatio,fx,rcode,rx,verbose=100 print,rcode & print,rx generatio,fx,reverse(rcode),rx_reverse,verbose=100 print,reverse(rcode) & print,rx_reverse subroutines IS_KEYWORD_SET history vinay kashyap (Nov'02) cosmetic changes (VK; Dec'02) won't spit out error messages if RCODE is 'X', though the FX corresponding to that is ignored (VK; Apr'03) added warning about ratio sequence -- it's a feature, not a bug; corrected bug in case of sequence number exceeding 9 (VK; Dec'03) now lets specifying just numerator or just denominator (VK,LL; Jun'04) updated for IDL5.6 keyword_set([0]) behavior change for vectors (VK; 20Mar2006) changed DFX_ADD and DFX_MUL to be arrays of same size as FX
(See pro/util/generatio.pro)
function getabund returns elemental abundances in an array syntax abund=getabund(hint,elem=elem,source=source,norm=norm,$ metals=metals,fipbias=fipbias,abunde=abunde) parameters hint [INPUT] some hint as to what output is required. examples: 'help' -- prints out usage 'angr', 'anders', 'anders & grevesse', '1989', etc. -- Anders & Grevesse (1989) 'meyer', '1985', etc. -- Meyer (1985) 'allen', 'cosmic', '1973' -- Allen (1973) 'ross', 'aller', 'ross & aller', '1976' etc. -- Ross & Aller (1976) 'grevesse', 'grevesse et al.', etc. -- Grevesse et al (1992) modifications to Anders & Grevesse (1989) 'feld', 'feldman', '1992', etc. -- Feldman et al (1992) 'waljeski', '1994', etc. -- Waljeski et al. (1994) 'murphy', 'chromospheric', etc. -- Murphy (1985) chromospheric 'grevesse & anders', '1991' -- Grevesse & Anders (1991) 'grsa', 'grevesse & sauval', '1998' -- Grevesse & Sauval (1998) "standard abundances" 'young', 'photo', '1997' -- photospheric abundances from Young et al. (1997) 'fludra', 'fludra & schmelz', 'hybrid', '1999' -- Fludra & Schmelz (1999) "hybrid coronal" 'asplund', '2005' -- Asplund, Grevesse, & Sauval (2005) 3D hydro (NOTE: even though it has a different reference, is identical to aspl) 'schmelz', 'schmelz et al', 'coronal', '2012' -- Schmelz et al (2012) "recommended coronal" 'aspl', 'asplund 2009', 'asp ... & scott', '2009', etc. -- Asplund, Grevesse, Sauval, & Scott (2009) model of solar atmosphere to constrain convection 'aneb', 'anders & ebihara', 'ebihara', '1982', etc. - Anders & Ebihara (1982) 'wilm', 'wilms, allen, mccray', '2000', etc. -- Wilms, Allen, & McCray (2000) 'lodd', 'lodders', '2003', etc. -- Lodders (2003) 'path/file', etc. -- if string contains a "/" in it, then read from disk file which contains one entry per line, with atomic symbol first, and abundance next keywords elem [INPUT] element -- if given, return abundances for only the specified element * if string, converts to atomic number using SYMB2ZION * if byte, integer, or float, assumed to be atomic number * may be an array source [INPUT] another way to say "hint" 1: Anders & Grevesse (1989) 2: Meyer (1985) 3: Allen (1973) 4: Ross & Aller (1976) 5: Grevesse et al. (1992) 6: Feldman et al. (1992) 7: Waljeski et al. (1994) 8: Murphy (1985) 9: Grevesse & Anders (1991) 10: Grevesse & Sauval (1998) 11: Young et al. (1997) 12: Fludra & Schmelz (1999) 13: Asplund, Grevesse, & Sauval (2005) 14: Schmelz et al. (2012) 15: Asplund, Grevesse, Sauval, & Scott (2009) 16: Anders & Ebihara (1982) 17: Wilms, Allen, & McCray (2000) 18: Lodders (2003) * overrides HINT iff HINT is not understood norm [INPUT] normalization * use this to set output format NORM=1: output will be n(Z)/n(H) (this is the default) NORM>1: output will be NORM(0)+log10(n(Z)/n(H)) (e.g., NORM=12 is the standard log form) 0<NORM<1: output will be NORM(0)*n(Z)/n(H) (this can be useful when ELEM is set) -1<=NORM<0: output will be n(Z)/DEFAULT_n(Z) (if you want to compare different abundance tables) NORM<-1: output will be log10(n(Z)/DEFAULT_n(Z)) (I have no idea why anyone would use this) metals [INPUT] metallicity. if set, modifies the abundances of all elements past He by the appropriate amount * if not set, makes no changes * assumed to be in log10 form if -- abs(NORM) > 1, or -- < 0 * assumed to be multiplicative factor otherwise * NOTE: for example, if norm=12 then metals=0 means Solar abundances, while if norm=1 then metals=0 means complete metal depletion! fipbias [INPUT] if set to a non-zero scalar, multiplies the abundances of low-FIP elements by this factor. be careful not to use it for abundance lists that already include the FIP effect. * if not set, or set to 0, does nothing. abunde [OUTPUT] errors on abundances _extra [INPUT] junk -- here only to prevent program from crashing subroutines RDABUND SYZE SYMB2ZION history vinay kashyap (Dec96) avoid analyzing HINT if SOURCE is set (VK; Jan97) added 'angr' and tightened 'Anders&Grevesse' v/s 'Grevesse' (VK; Jul97) added option of reading from disk file (VK; Jun98) added Murphy (1985) data, and allowed ELEM to be array (VK; Jul98) corrected bug associated with non-array ELEMs (VK; Sep98) added keyword METALS, deleted keywords ALTER, FORM, removed call to SETABUND, added call to RDABUND (VK; Dec98) added Grevesse & Anders (1991), Grevesse & Sauval (1998), Young et al (1998) (VK; Apr99) added keyword FIPBIAS (VK; Jul01) added Fludra & Schmelz (1999); now HINT overrides SOURCE and program warns if there is a conflict (VK; Jun02) corrected Meyer abundances for O and Na (VK; Apr04) corrected Fludra & Schmelz abundances (VK; Jun04) added Asplund, Grevesse, & Sauval abundances; added keyword ABUNDE (VK; Apr05) B was off by 2 orders of magnitude (thx Marc Audard; VK Jul06) streamlined input HINTs; added Schmelz et al. (2012); updated bracket notation to IDL5+ (VK Jul12) added 'aspl', 'aneb', 'wilm', and 'lodd' from the elemental abundance table used in XSPEC plasma code models, as given in ahelp get_xsabund; changed convection model from Asplund et al (2005) to aspl; streamlined selection keywords (VK Feb13) changed the behavior of default to accept !ABREF if defined (VK May28)
(See pro/util/getabund.pro)
function getlocmax returns the position indices where y(x) is a local maximum syntax ilm=getlocmax(x,y,width=width,sigma=sigma,nsigma=nsigma) parameters x [INPUT; required] abscissae where input function is defined y [INPUT] input function. if not given, X is taken to be Y and array position indices are taken to be X keywords width [INPUT; default: 1] window in which to search for local maxima -- window width = 2*abs(WIDTH)+1 or 3, whichever is greater. sigma [INPUT; default: 1+sqrt(abs(Y)+0.75)] error at each point * if scalar and NSIGMA is not defined, then SIGMA->NSIGMA nsigma [INPUT; default: 1] multiple of SIGMA to consider as a threshold filter * to use var(y) as a constant value of SIGMA, do ilm=getlocmax(x,y,sigma=sqrt((moment(y))(1)),/nsigma) _extra [INPUT] junk -- here only to keep routine from crashing history vinay kashyap (Dec96) corrected bug with 1-, 2-, or 3-element inputs (VK; Nov98)
(See pro/util/getlocmax.pro)
function getpoadef returns the default value for a common PINTofALE variable usually for filenames, which are often dependent on where the files are installed. The way this works is, if a system variable is already set, the default is taken from that. If not, after figuring out what the default is (usually by checking where this program is located), the appropriate system variable is set to it. syntax default=getpoadef(varname,/force,verbose=verbose) parameters var [INPUT] name of variable as a character string * may be an array of strings * special variable names are the only ones recognized * if 'help' or '?', lists all the variables for which defaults can be set * in some cases default might be a number, but if the input is an array, then the output will always be a string array keywords force [INPUT] if set, ignores whether any default (except TOPDIR) has already been set and resets it anyway * to reset TOPDIR, just do it on the command line, as !TOPDIR='/path/to/PINTofALE' verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history Vinay Kashyap (2015aug) now if input is scalar, returns scalar (VK; 2015sep)
(See pro/getpoadef.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
GET_IEQ()
EXPLANATION
For a specified ion (IZ, ION) and set of temperatures (TEMP) this
routine takes the ion fraction values tabulated in one of the CHIANTI
.IONEQ files, interpolates and extracts the values of the ion
fraction at the input temperatures.
INPUTS
TEMP The temperature(s) at which the ion fractions are required.
IZ The atomic number of the element (e.g., 26 = iron).
ION The spectroscopic number of the ion (e.g., 13 = XIII).
OPTIONAL INPUTS
IONEQ_LOGT The temperature output from the READ_IONEQ routine.
IONEQ_FRAC The ion fractions from the READ_IONEQ routine.
OUTPUT
A vector of same length as the input TEMP containing the ion
fractions at these temperatures.
CALLS
READ_IONEQ
HISTORY
Ver.1, 24-Jul-2002, Peter Young
v.2, 14-Sept-2005, GDZ
modified error message.
VERSION 2 14-Sept-2005
(See pro/external/get_ieq.pro)
function get_ionlist return a list of all the ions for a particular element that CHIANTI has data for syntax all_ions=get_ionlist(Z,dielec=dielec,chidir=chianti_topdir) parameters z [INPUT; required] atomic number * must be a scalar integer! keywords chidir [INPUT] path to CHIANTI top directory [default: /data/fubar/SCAR/CHIANTI/dbase] dielec [OUTPUT] integer array of same size as output, specifying whether given ion refers to dielectronic recombination lines (1) or not (0) _extra [JUNK] here only to prevent crashing program requires subroutines SYMB2ZION IS_KEYWORD_SET history vinay kashyap (Nov96; based on CHIANTI's SYNTHETIC.PRO) added keyword DIELEC, modified to include CHIANTIv3 dielectronic recombination directories (VK; OctMM) handle trailing whitespace in masterlist.ions (VK; Jun02) updated for IDL5.6 keyword_set([0]) behavior change for vectors (VK; 20Mar2006)
(See pro/mkemis/get_ionlist.pro)
function get_pimms_file returns a string containing the name of the file containing the effective areas for the given instrument. usage filnam=get_pimms_file(mission,instr,config,special=special,pdir=pdir) parameters mission [INPUT; required] e.g., 'ROSAT', 'AXAF', etc. instr [INPUT] instrument (e.g., 'PSPC', 'ACIS', etc.) config [INPUT] instrument configuration (e.g., 'OPEN', 'BI', etc.) keywords special [INPUT] any special requests * e.g., if MISSION='rosat', INSTR='pspc', and CONFIG='R4' and SPECIAL='R7', the output will be 'rosat_pspc_r4tor7.area' pdir [INPUT; default='/data/fubar/SCAR/ardb/pimms/data/'] directory containing the PIMMS data files history vinay kashyap (Mar98) changed PDIR default from /soft/prop_cli/config/pimms/data to /soft/pimms/data (VK; Feb03) changed PDIR default from /soft/pimms/data to /soft/ciao/config/pimms/data/ (VK; Mar06) changed PDIR default from /soft/ciao/config/pimms/data to !ARDB/pimms/data/ (VK; Mar13)
(See pro/util/get_pimms_file.pro)
NAME:
GMASCL
PURPOSE:
This is a utility routine to perform basic gray-level pixel
transformations of images. I think of it as BYTSCL on steroids.
It is similar to IMADJUST in _Digital Image Processing with MATLAB_
by Gonzales, Wood, and Eddins.
AUTHOR:
FANNING SOFTWARE CONSULTING
David Fanning, Ph.D.
1645 Sheely Drive
Fort Collins, CO 80526 USA
Phone: 970-221-0438
E-mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com
CATEGORY:
Utilities
CALLING SEQUENCE:
scaledImage = GMASCL(image)
ARGUMENTS:
image: The image to be scaled. Written for 2D images, but arrays
of any size are treated alike.
KEYWORDS:
GAMMA: The exponent in a power-law transformation (image^gamma). A gamma
value of 1 results in a linear distribution of values between
OMIN and OMAX. Gamma values less than 1 compress the
lower range of values and extend the upper range. Gamma values
greater than 1 compress the upper range of values and extend the
lower range. The gamma value is constrained to be greater than 1.0e-6.
MAX: Any value in the input image greater than this value is
set to this value before scaling.
MIN: Any value in the input image less than this value is
set to this value before scaling.
NEGATIVE: If set, the "negative" of the result is returned.
OMAX: The output image is scaled between OMIN and OMAX. The
default value is 255.
OMIN: The output image is scaled between OMIN and OMAX. The
default value is 0.
RETURN VALUE:
scaledImage: The output, scaled into the range OMIN to OMAX. A byte array.
COMMON BLOCKS:
None.
EXAMPLES:
LoadCT, 0 ; Gray-scale colors.
image = LoadData(11) ; Load image.
TV, GmaScl(image, Min=30, Max=100) ; Similar to BytScl.
TV, GmaScl(image, /Negative) ; Produce negative image.
power = Shift(ALog(Abs(FFT(image,-1))), 124, 124) ; Create power spectrum.
TV, GmaScl(power, Gamma=2.5) ; View power specturm with gamma correction.
TV, GmaScl(power, Gamma=2.5, /Negative) ; Reverse power spectrum.
RESTRICTIONS:
Requires SCALE_VECTOR from the Coyote Library:
http://www.dfanning.com/programs/scale_vector.pro
MODIFICATION HISTORY:
Written by: David W. Fanning, 17 February 2006.
(See pro/external/gmascl.pro)
function hastogram returns a frequency histogram over a specified grid, calculated in a fast and clever way. really. works in haste, without waste. works best when the grid is sparsely populated. if there are more items than bins, use IDL's built-in HISTOGRAM() function instead. syntax f=hastogram(list,x,wts=wts,verbose=verbose) parameters list [INPUT; required] list of numbers to bin x [I/O] the required binning scheme * if not set, assumes a linear grid of size 100 from min(LIST) to max(LIST) * if scalar or 1-element vector, assumes this to be the number of bins * if -ve, log grid, else linear * if vector with more than 1 element, assumes it to be the bin boundaries. * WARNING: if input as scalar, will overwrite with the adopted grip on output keywords wts [INPUT] if given, appropriately weights each element of LIST * default is unity * if size does not match size(LIST), will be appropriately interpolated verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description the problem is the following: if the number of bins is large, accumulating a frequency histogram by linear search takes too long, esp. in IDL if one uses for-loops. so, first create a monster array containing both the list elements and the grid values. then sort this array. this results in an array where the list elements are all nicely placed within the correct bins. now, if we've been keeping track of the positions of the list elements, it's an easy job to count up the number in each bin of the grid. to do the latter, we first create a new array made up of -1s in positions of list elements and position indices for grid values and reorder according to the above sort. then, replace each -1 by the nearest non-(-1) from the left. now each list element is assigned the correct bin number. voila! restrictions X must be sorted in increasing order. (no longer, as of Jun02) subroutines KILROY history vinay kashyap (Jan98) added kludge to speed up in case max(X) < max(LIST) (VK; Sep98) added quit in case X is not sorted in ascending order (VK; JanMMI) added keyword VERBOSE, and removed restriction on order of X (VK; Jun02) changed ints to longs (VK; Aug08) converted bracket notation to IDL5+ and fixed bug with inputs being array of size [1,N] (VK;Mar10)
(See pro/util/hastogram.pro)
function hinode_xrt_emis
compute and return the combined emissivities of Hinode/XRT
filters in an array of form [Ntemp,Nfilt] in units of
[1d-23 ergs cm^5/s] for each pixel
syntax
xrtemis=hinode_xrt_emis(filter,tgrid,ldbdir=ldbdir,$
cdbdir=cdbdir,ioneqf=ioneqf,abund=abund,cieroot=cieroot,$
n_e=n_e,NH=NH,xrteff=xrteff,lstr=lstr,cstr=cstr,$
/toel,/toph,/toDN,EM0=EM0,pixsize=pixsize,verbose=verbose,$
chidir=chidir,fH2=fH2,He1=He1,HeII=HeII)
parameters
filter [INPUT; required] scalar or array of filter names
* for Hinode/XRT, acceptable filter names are
Al-mesh, Al-poly, C-poly, Ti-poly, Be-thin,
Be-med, Al-med, Al-thick, Be-thick,
Al-poly/Al-mesh, Al-poly/Ti-poly, Al-poly/Al-thick,
Al-poly/Be-thick, C-poly/Ti-poly
* set to 'all' to get everything
tgrid [I/O] the log(T[K]) grid over which the output
is to be defined
* if not specified on input, will be set to be
the same as that in the emissivity tables,
the PoA default, findgen(81)*0.05+4
keywords
ldbdir [INPUT; '$CHIANTI'] line emissivity database directory
cdbdir [INPUT; '$CONT'] continuum emissivity database directory
ioneqf [INPUT; 'ioneq/mazzotta_etal.ioneq'] location of the
ion fraction tables
abund [INPUT; getabund('Grevesse et al')] abundances
cieroot [INPUT; 'cie'] root name for the files in $CONT
n_e [INPUT; 1e9] electron number density in the plasma
NH [INPUT; 0] H column density to apply
xrteff [I/O] the XRT effective areas; input can be any of the
following:-
- a structure that contains the following fields --
{TYPE, CHANNEL_NAME, WAVE, EFF_AREA, LENGTH}
which can be generated using the SSW routine
xrteff = MAKE_XRT_WAVE_RESP(contam_time=contam_time)
- the name of a save file that contains the previously
generated structure, named either XRTEFF or EFF
- a flag that indicates that this must be calculated
in situ by calling MAKE_XRT_WAVE_RESP() (requires SSW)
- this can be accomplished by setting /XRTEFF, but
that will prevent it from being returned up. instead,
it is better to do something like
xrteff=1 & xrtemis=hinode_xrt_emis(...,xrteff=xrteff,...)
* on output, will always contain the structure that
was read in or calculated
lstr [OUTPUT] line emissivities structure, as read in
from RD_LINE()
cstr [OUTPUT] continuum emissivities structure, as read in
from RD_CONT()
toel [INPUT; default=0] if set, returns the output in units
of [el cm^5/s]
toph [INPUT; default=0] if set, returns the output in units
of [ph cm^5/s]
toDN [INPUT; default=0] if set, returns the output in units
of [DN cm^5/pix]
* NOTE: TODN overrides TOPH overrides TOEL
EM0 [INPUT; default=1] if set, multiples the output by
this value to derive [ph/s] or [ph/cm^2/s] depending
on whether the input has units [cm^-3] or [cm^-5]
pixsize [INPUT; default=1.0024 arcsec] the size of a pixel on
the detector
xrtl [OUTPUT] the response due solely to lines
xrtc [OUTPUT] the response due solely to continuum
* both XRTL and XRTC are identical in size and units
to the primary output, XRTEMIS
verbose [INPUT; default=0] controls chatter
_extra [INPUT ONLY] pass defined keywords to subroutines
FOLD_IONEQ : CHIDIR
ISMTAU : FH2, HE1, HEII
MAKE_XRT_WAVE_RESP : INDEX, CONTAM_THICK, CONTAM_TIME
history
vinay kashyap (Jun2007)
added keywords TOEL, PIXSIZE, XRTL, XRTC (VK; Mar2008)
changed call from CALC_XRT_EFFAREA() to MAKE_XRT_WAVE_RESP() (VK; Apr2009)
bugfix: FILTER was failing to match to XRTEFF.NAME when specified
(VK; Nov2009)
(See pro/ssw/hinode_xrt_emis.pro)
function hipd_interval computes and returns the interval [lower_bound,upper_bound] at a specified confidence level that includes the highest probability densities. by definition, this is the shortest possible interval. syntax hpd=hipd_interval(f,x,/fsample,clev=clev,pdfnorm=pdfnorm,$ fmode=fmode,verbose=verbose) parameters f [INPUT; required] the array for which the confidence interval must be computed * assumed to be a density function unless FSAMPLE is set x [INPUT; optional] abscissae values * if not given, and F is a density function, then taken to be the array indices * ignored if FSAMPLE is set * if N(X).GT.1 but N(X).NE.N(F), X is ignored and FSAMPLE is set automatically keywords fsample [INPUT] if set, assumes that F is a set of samples from a density function, as opposed to being the density function itself clev [INPUT] confidence level at which to compute the intervals * default is 0.68 * if < 0, abs(CLEV) is used * if > 1 and < 100, then assumed to be given as a percentage * if > 100, then 1-1/CLEV is used pdfnorm [INPUT] if set, forces F to integrate to abs(PDFNORM) * if explicitly set to 0, does not normalize F at all * if not set, normalizes to 1 * ignored if FSAMPLE is set * WARNING: do not use this keyword unless you know what you are doing fmode [OUTPUT] the mode of the distribution verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines MODALPOINT: EPS subroutines MODALPOINT description * if density function, find the cumulative integral around the mode and interpolate at CLEV to derive the HPD interval * if array of sample values, find all intervals corresponding to CLEV that contain the mode and pick the smallest of the lot. this is a method devised by Vinay K and Taeyoung Park during the course of developing BEHR. * works well only for unimodal distributions (and for multimodal distributions where all the modes are within the interval), but that's better than nothing. * note that this interval is not invariant under transformations. for that, one must use equal-tail intervals, see eqt_interval() example for i=1,20 do print,hipd_interval(randomn(seed,10000L)*i,/fsample) history vinay kashyap (Mar2006) bug correction with FSAMPLE cdf (VK; Apr2006) added keyword FMODE (VK; Nov2006) bug correction with F(X) case (VK; Apr2007) now handles NaNs in input (VK; Apr2014)
(See pro/stat/hipd_interval.pro)
function hrs2deg converts sexagesimal angles to decimal degrees and returns a numerical array of decimal angles parameters hms [INPUT; required] string array of sexagesimal angles * may even be a string of FSEP separated sexagesimals keywords fsep [INPUT] field separator in HMS * if FSEP=":", only the first 3 are used dec [INPUT] if set, does not multiply by 15 (the RA v/s Dec thing) * if the H part is -ve, automatically set _extra [INPUT] allows passing defined keywords to STR2ARR: SEP, SQUISH subroutines STR_2_ARR see also DEG2HRS history vinay kashyap (Nov98) now calls STR_2_ARR instead of STR2ARR (VK; Mar08)
(See pro/util/hrs2deg.pro)
function hullsort reorder a 2D list from outside in and return the indices of the reorderd list. At each stage, compute the convex hull and remove the "farthest" point from the hull centroid. syntax iout=hullsort(xin,yin,xout=xout,yout=yout,xcen=xcen,ycen=ycen,$ areap=areap,/bycen,twait=twait,verbose=verbose) parameters xin [INPUT; required] 1D array of x-coordinate points yin [INPUT; required] 1D array of y-coordinate points * sizes must match * only useful if there are more than 4 points keywords xout [OUTPUT] reorderd XIN yout [OUTPUT] reorderd YIN xcen [OUTPUT] centroid x-coordinate computed at each step ycen [OUTPUT] centroid y-coordinate computed at each step areap [OUTPUT] area covered by the convex hull at each stage bycen [INPUT] if set, eliminates points from convex hull based on distance to center * default is to eliminate those farthest from all other points on the convex hull twait [INPUT] waiting time for replotting on screen [seconds] * only applies if VERBOSE>10 * default is 0.001 verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program example .run hullsort subroutines QHULL (IDL built-in) KILROY AREAPOLY history vinay kashyap (MMXII.VII) added call to AREAPOLY() (VK; MMXII.X)
(See pro/util/hullsort.pro)
function id2emis2id takes an ID structure, strips it into component parts, reads in new emissivities, and puts them back in. syntax newidstr=id2emis2id(idstr,ldbdir,dWVL=dWVL,verbose=verbose,$ eps=eps,/incieq,mapping=mapping,pres=pres,logP=logP,n_e=n_e,$ chifil=chifil,chidir=chidir,eqfile=eqfile) warning new emissivities will not necessarily reflect the fluxes as distributed among the components. also, if the database is changed, there is no reason to believe a priori that the correct lines are really read back in. we strongly recommend using a high (say 10) verbosity level. parameters idstr [INPUT; required] ID structure, see LINEID for description ldbdir [INPUT] directory in which to look for line database * default is "$CHIANTI" * if array size matches the number of features, is distributed among components appropriately; if size matches that of total number of lines, maps one-to-one onto line list; if size is incompatible with IDSTR, then uses only what is in the first element. keywords dWVL [INPUT] slack in wavelength search in which to find the matching line (this comes in handy when databases are being changed around) * default is 0.005 verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to RD_LIST: EPS,INCIEQ,MAPPING,PRES,LOGP,N_E,CHIFIL,CHIDIR,EQFILE restrictions requires subroutines: RD_LIST, RD_LINE, FOLD_IONEQ, RD_IONEQ, READ_IONEQ, SYMB2ZION, ZION2SYMB, LAT2ARAB, CAT_LN, LINEFLX, INICON, WHEE, GETABUND, RDABUND, SYZE requires IDL 5.3+ history vinay kashyap (AugMM) catch if correct emissivities not found; added keywords VERBOSE, DWVL; allowed LDBDIR to be array (VK; JanMMI)
(See pro/id2emis2id.pro)
function idlabel return a string array containg a nicely formatted set of labels, appropriate for each of the IDs in an ID structure. syntax label=idlabel(idstr,idx,/Zbeda,/Ibeda,/Wbeda,/Lbeku,$ wform=wform,wstyle=wstyle,sep=sep,intex=intex, ziform=ziform) parameters idstr [INPUT; required] the ID structure containing the features with attached IDs. (see LINEID for description) idx [OUTPUT] an integer array pointing out which label belongs to which feature. this is of use in case of multiple IDs. * begins from 0, not 1 keywords Zbeda [INPUT] if set, does not include the atomic symbol in label Ibeda [INPUT] if set, does not include the ionic state in label Wbeda [INPUT] if set, does not include the line wavelength in label Lbeku [INPUT] if set, includes a description of the transition, in the form of the level-designation and electronic configuration (if available) in label wform [INPUT] wavelength format, relevant if Wbeda=0 * default: 'f7.2' if WSTYLE = 1, unadorned WFORM if WSTYLE = 2, automatically prepends $\lambda$: '"!4k!3 ",'+WFORM if WSTYLE = 4, automatically appends \AA: WFORM+',"'+string(byte(197))+'"' if WSTYLE = 8, automatically appends keV: WFORM+'," keV"' wstyle [INPUT] bit-style flag shortcut to various WFORMs * see above for effect on WFORM * if -ve, uses the wavelength of the ID'd feature, not the wavelength of the ID itself sep [INPUT] separator between "Z Ion", wvl, and description * default is "<tab>", unless INTEX is set, in which case the default is " & " intex [INPUT] if set, encloses the description (see LBEKU) within "$...$" _extra [INPUT] pass defined keywords to subroutines ZION2SYMB: ZIFORM restrictions requires input to be in format generated by LINEID, CAT_ID, etc. requires subroutines ZION2SYMB [INICON] examples l=idlabel(idstr,idx,wform='f5.1') l=idlabel(idstr,/Wbeda) l=idlabel(idstr,wstyle=4) l=idlabel(idstr,wstyle=6) history vinay kashyap (AugMM) added keywords SEP,INTEX; implemented LBEKU (VK; JanMMI) back-compatibility: STRMID must have 3 args (VK; FebMMI/A.Maggio) bug fix: IDNAM[2] is ID1, not ID2 (VK; MayMMVI/L.Lin)
(See pro/idlabel.pro)
Project : SOHO - CDS
Name : IDL_RELEASE
Purpose : check if IDL release version within specified range
Category : system
Explanation :
Syntax : IDL> a=idl_release(lower=lower,upper=upper)
Examples :
Inputs : None
Opt. Inputs :
Outputs : 1/0 if IDL version is within specified range
Opt. Outputs: None
Keywords : LOWER = lower version to check
UPPER = upper version to check
INCLUSIVE = make check inclusive
VERS = IDL version
Common : None
Restrictions: None
Side effects: None.
History : Version 1, 27-Feb-1997, D M Zarro. Written
Contact : DZARRO@SOLAR.STANFORD.EDU
(See pro/external/idl_release.pro)
procedure id_to_fitpar
given the ID structure resulting from LINEID, figures out
initial fitting parameters for use in, e.g., FITLINES, FIT_LEVMAR,
etc.
syntax
id_to_fitpar,idstr,pars,ties,thaw,pos=pos,wdt=wdt,flx=flx,$
lsfwdt=lsfwdt,shackle=shackle,leeway=leeway,perr=perr,werr=werr,$
ferr=ferr
parameters
idstr [INPUT; required] ID structure containing the observed
wavelengths and appropriate matches
pars [OUTPUT] initial values of all the parameters set up in
a single array for consumption by, e.g., FIT_LEVMAR or
X3MODEL.
ties [OUTPUT] constraints on the parameters
thaw [OUTPUT] integer array of same size as PARS, signaling
frozen (0) or thawed (1) parameter
* all parameters that are SHACKLEd are frozen
keywords
pos [OUTPUT] initial-guess positions of all lines
wdt [OUTPUT] initial-guess widths of all lines
flx [OUTPUT] initial-guess fluxes of all lines
epithet [OUTPUT] species label (e.g. 'OVII' or 'FeXIX') string array
lsfwdt [INPUT] width of the instrument's line spread function, and
the minimum value of WDT
* if not defined, assumed to be same as PERR
(on the theory that your position determination is uncertain
on the same order as the LSF width)
shackle [INPUT] specify how to handle multiple ID components:-
"position" => line centers are fixed relative to location
of line of maximum strength
"width" => freeze all WDT at maximum determined value OR
value of WERR if given
"flux" => relative strengths of fluxes are held fixed
* if array, only the first element is considered
* if integer (as in /shackle), all 3 of above are set
* any two (or all 3) may be specified simply as "flux & pos",
"width and flux", "position,width,flux", etc.
* all affected parameters are frozen
leeway [INPUT] specify how to handle multiple ID components:-
"position" => relative locations of line centers are held
to within a narrow range of position of line of maximum
strength, defined by PERR
"width" => all WDT are constrained to be > minimum determined
width, and < maximum determined width, and this range may
be further expanded by WERR
"flux" => relative strengths of fluxes are held to within
a narrow range defined by FERR
* obviously, SHACKLE takes precedence if both are set
* if array, only the first element is used
* if integer (e.g., /leeway), all of above are set
* unlike SHACKLE, all affected parameters are kept THAWed.
perr [INPUT; default=1.0] slippage allowed in POS
* setting this is crucial in case the IDs include lines
from higher orders or unknown IDs, because this will
tell the program that deviations larger than PERR from
the location of the observed line are suspect.
* if LSFWDT is not set, PERR constitutes a >lower limit< to WDT
werr [INPUT] allowed excess variation in range of WDT
* default is 0.5*PERR[0]
* subtracted from min and added to max if LEEWAY requires it
ferr [INPUT; default=0.1] allowed fractional error in FLX
* has an effect only if LEEWAY is set
* NOTE: for PERR,WERR,FERR, if size does not match that of
POS,WDT,FLX respectively OR the number of components in
IDSTR, only the first element is used
numer [INPUT; default = 0] if set, ties specified via leeway, perr,
werr, and ferr will be specified numerically rather than
symbolically
nozero [INPUT; default = 0] if set, then fluxes are constained to
be positive. if set negative, then fluxes are constrained
to be negative
_extra [JUNK] here only to prevent crashing the program
history
vinay kashyap (Nov98)
added keyword LSFWDT (VK; Mar99)
changed call to INITSTUFF to INICON (VK; 99May)
added EPITHET keyword (LL; Feb04)
added NUMER keyword (LL; Jul05)
BUGFIX: for multiplet component leeway width specification (LL; Jul 05)
had used lower bound for position instead of width
added NOZERO keyword (LL; Jul05)
BUGFIX: for multiplet component leeway position specification
was written with the wrong sign (VK; May06)
(See pro/fitting/id_to_fitpar.pro)
procedure inicon return atomic symbols, names, ionization potentials, fundamental and other fun constants, atomic weights, roman numerals syntax inicon,atom=atom,aname=aname,amu=amu,fip=fip,fundae=fundae,$ roman=roman,/help parameters NONE keywords atom [OUTPUT] atomic symbols aname [OUTPUT] names of elements amu [OUTPUT] structure containing atomic weights in AMU (1H=1) * AMU.(Z) is an array, with first element the atomic weight for terrestrial composition, then the AMUs of the isotopes in order of abundance (i.e., most abundant is 2nd element, second most abundant is 3rd element, etc. -- but not completely implemented) fip [OUTPUT] first ionization potentials [eV] * set to -1 if not known fundae [OUTPUT] structure containing some useful physical and astronomical constants * just do help,fundae,/str -- should be obvious roman [OUTPUT] roman numerals, upto max(ATOM)+1 * beware that CHIANTI has a function named ROMAN() which returns numerals that are offset by 1 compared to this variable. NOTE: in IDL versions prior to 5, the keywords must be pre-defined if output is desired requires CREATE_STRUCT history modified from INITSTUFF (VK; 99May) bug correction -- ROMAN wasn't working (VK; 99Jul) added Jupiter (VK; MIM.XI) added keV-to-Ang (VK; MMII.I) added planetary data (VK; MMII.IX) changed AMU tag names from symbol to full names (VK; MMII.X) corrected AMU value (JD; IMVIM.I) added JouleV, ergeV, and arcsr (VK; IMVIM.V) corrected Bode's Law and extended to 12 "planets" (VK; MMV.VII) changed Planets field to "Classical Planets", moved Pluto to separate Plutoid field (VK; MMVIII.VII) added Thompson cross section (per JJD req), Compton wvl (VK; MMXI.XI) new IAU definition for A.U. (VK; MMXII.IX) added new Pluto and Charon measurements from New Horizons (VK; MMXV.VII)
(See pro/util/inicon.pro)
script initale extremely flexible initialization script for the Package for Interactive Analysis of Line Emission (PINTofALE); defines some useful variables as system variables. Examples and scripts in the standard distribution use these variables. NOTE: Strictly speaking, none of these system variables are _necessary_ in order to use basic PINTofALE functionality. However, they set up the default values for some commonly used keywords and usually must be explicitly included in calls to PINTofALE routines. Most scripts and documentation examples do use these directly, and some routines set their default values at run-time if the system variables are defined. An additional use of this script is that it sets up the !PATH to include PINTofALE, CHIANTI, and IDL-Astro if they are not already included. syntax .run initale (or) .run /full/path/initale system variables and hardcoded default values !PoA current version number !TOPDIR the top-level PINTofALE directory * first checks for environment variables PINTofALE, PoA, SCARDIR, and SCAR in that order. if none of them exist, then uses value deduced from the location of _this_ script. !LDBDIR [!TOPDIR+'emissivity/chianti'] directory of line emissivities !CDBDIR [!TOPDIR+'emissivity/cont'] directory of continuum emissivities !CHIDIR [!TOPDIR+'CHIANTI'] path to CHIANTI installation NOTE: !TOPDIR is added to initial values of above 3 ONLY IF: -- !TOPDIR is not already contained in them -- the first character is not a "$" -- the first character is not a "/" -- for CHIANTIv4+, path name must include the "dbase" part !ATOMDB [!TOPDIR+'atomdb/'] directory of local installation of ATOMDB !APECDIR where the IDL tools of APED are * first checks for environment variable APEC_DIR, and if that is missing, looks in succession in -- !ATOMDB+'apec_v11_idl/' -- !TOPDIR+'apec_v11_idl/' -- !TOPDIR+'atomdb/apec_v11_idl/' !ARDB [!TOPDIR+'ardb/'] the Analysis Reference DataBase directory, contains sundry useful documents !CEROOT ['cie'] root prefix for continuum emissivity files !IONEQF ['ioneq/bryans_etal_09.ioneq'] path name relative to !CHIDIR of the ion-balance file to be used !ABREF ['grevesse et al.'] abundance reference !CALDB ['/data/caldb/'] directory containing instrument calibration data products !METALS [0.0] [Fe/H] relative to !ABREF !ABUND abundances of elements H..Zn corresponding to !ABREF and !METALS !GASPR [1e15 cm^-3 K] gas pressure !LOGPR [15] log10(gas pressure) -- if set, overrides !GASPR !EDENS [1e10 cm^-3] electron density -- if set, overrides use of !GASPR and !LOGPR !LOGT [findgen(81)*0.05+4] the default temperature grid !DEM [dblarr(81)+1d12] a sample DEM(!LOGT) !NH [1e18 cm^-2] H column density !FH2 [0.26] fraction of molecular H2 relative to HI !HE1 [1e17 cm^-2] He I column !HEII [1e16 cm^-2] He II column !WMIN [1.239854 Ang] minimum wavelength !WMAX [3000.0 Ang] maximum wavelength !VERBOSE [5] verbosity -- controls chatter !ATOM atomic symbols !AMU atomic weights !FUNDAE a whole bunch of fundamental constants !FIP firt ionization potentials [eV] !ROMAN roman numerals, upto max(!ATOM)+1 !AA ['!3'+string(byte(197))+'!X'] the symbol for Angstrom !ANGSTROM An array of Angstrom symbols, should work for every conceivable font choice. control variables factory determines whether to reset all the system variables to the "factory default" or not. set this variable to 0 or 1 prior to running the script. * if explicitly set to 0, then only initializes those variables which have not been defined yet * if PARFIL is defined, automatically gets unset * if set, or is not defined, then overwrites all variables with hardcoded defaults -- one may want to use FACTORY=0 when some of the variables have been set (e.g, !TOPDIR) during the session without an initial call to this script, or when a limited number of the variables are being reset via a parameter file. -- upon execution, if FACTORY is not set, it will be set to 0 parfil if set to a named parameter file that contains new definitions of the defined system variables. They must be placed one on each line, and must be fully legal IDL statements. * if not set, will automatically look in !ARDB+'initale.par' * DO NOT try to define the following in PARFIL: !ABUND, !ATOM, !AMU, !FUNDAE, !FIP, !ROMAN, !PoA yCHIANTI if set then checks to see whether the CHIANTI distribution is available for use and includes it if it is not. yATOMDB if set then checks to see whether the ATOMDB IDL routines are accesible and adds them if they are calls subroutines GETABUND INICON PEASECOLR restrictions subroutine WHICH works only in UNIX, but it is used only if none of the environment variables PINTofALE, PoA, SCARDIR, or SCAR are set. Unlike normal IDL variables, system variables, once defined, cannot change their size, though their values may be changed. Thus, care must be taken to match the expected sizes of the following variables to the hardcoded defaults if they are to be redefined within PARFIL: !ABUND, !LOGT, !DEM, !ATOM, !AMU, !FUNDAE, !FIP, !ROMAN history Vinay Kashyap(OctMM) set FACTORY to 0 if undefined; changed !ABREF default; added !ARDB; !TOPDIR now automagic (VK; DecMM) added !PoA, !CALDB, !LOGT, !DEM, and !AA (VK; JanMMI) fixed bug with !TOPDIR becoming an array if none of the env vars were defined; change prompt for large !VERBOSE (VK FebMMI/Dan Dewey) changed call to WHICH to WHEREIS (VK; Dec2001) commented out call to WHEREIS by using the output of HELP, and now adds !TOPDIR/pro to !PATH if it doesn't exist; also check for other packages such as IDL-ASTRO and CHIANTI; more robust to OS filename dependencies for v5.3+ due to extensive use of FILEPATH function; added !ATOMDB, !APECDIR, and yATOMDB (VK; Jun2002) added call to PEASECOLR (VK; Jul02) some people have IDL-ASTRO installed under 'astrolib' (VK; Aug02) added !ANGSTROM; made !AA robust to font choices (VK; Dec'02) suppose environment variable is defined, but incorrectly? i.e., what if $PINTofALE, $SCARDIR, etc. do not exist? (VK; May'03) if IDL_DIR is not defined, assumes that IDL library is in anything that has '...idl/lib' (VK; Jul'03) corrected case where if env variable defining TOPDIR had a trailing "/", would miss matching it in !PATH and not reset the order of directories (VK; MarMMIV) made a few of the system variables read-only (VK; May04) made windows compatible, by and large (VK; Apr05) forced IDL-Astro to move ahead of Chianti's astron directory in !PATH (VK; FebMMVII) removed early call to strsplit() and forced restoration of correctly compiled versions of STRSPLIT, UNIQ, and STR_2_ARR (VK; JunMMVII) bugfix: wasn't setting TOPDIR correctly when it had to be determined from the location of this file (VK; OctMMIX) changed default for !IONEQF from Mazzotta et al. to Bryans et al. (2009) (VK; MayMMXIII)
(See pro/scrypt/initale.pro)
procedure intersect procedure to obtain common elements of two numeric arrays sorted in ascending order and with no duplicates syntax intersect,lis1,lis2,y1y2,y1n2,n1y2,/val,$ ny1y2=ny1y2,ny1n2=ny1n2,nn1y2=nn1y2,verbose=verbose parameters lis1 [INPUT; required] input list #1, array lis2 [INPUT; required] input list #2, array y1y2 [OUTPUT; required] elements in LIS1 also in LIS2 y1n2 [OUTPUT] elements in LIS1 that are not in LIS2 n1y2 [OUTPUT] elements not in LIS1 that are in LIS2 keywords val [INPUT] if set, returns the actual values in x1x2 rather than the array position numbers ny1y2 [OUTPUT] number of elements in Y1Y2 ny1n2 [OUTPUT] number of elements in Y1N2 nn1y2 [OUTPUT] number of elements in N1Y2 verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description Y1Y2 contains indices of elements of LIS1 that are common to both LIS1 and LIS2. Y1N2 contains indices of elements of LIS1 that are not in LIS2. N1Y2 contains indices of elements of LIS2 that are not in LIS1. if Y1Y2/Y1N2/N1Y2 is empty, it is set equal to -1L if keyword VAL is set, actual array elements are returned instead of indices, and if Y1Y2/Y1N2/N1Y2 is empty, it is set equal to !values.F_NAN history algorithm by mala viswanath idl version (but not optimized for it) by vinay kashyap (8/27/1992) added keyword VAL (3/26/93) added keyword VERBOSE (4/14/02) added keywords NY1Y2,NY1N2,NN1Y2, cleaned up edge case outputs, check for sorted arrays (VK; 7/18/15)
(See pro/util/intersect.pro)
function ionabs
returns the photoelectric absorption cross-sections for a given
photon energy for specified chemical composition, and ion fractions.
Uses ground state photoionisation cross-sections computed using the
fortran code of Verner, D.A., Ferland, G.J., Korista, K.T., & Yakovlev,
D.G., 1996, ApJ, 465, 487 and is supplemented with high resolution
cross-sections in the vicinity of 1s-2p resonances for
O (from Garcia et al., 2005, ApJS, 158, 68),
Ne (from Juett et al., 2006, ApJ, 648, 1066), and
C (from Hasogle et al, 2010, ApJ, 724, 1296).
syntax
sigabs=ionabs(w,abund=abund,ionfrac=ionfrac,vfkydir=vfkydir,/ikeV,$
nconsec=nconsec,DEM=DEM,logt=logt,verbose=verbose,noHeH=noHeH,$
icrstr=icrstr,chidir=chidir,eqfile=eqfile)
parameters
w [INPUT; required] photon energy values at which to compute
the absorption cross-section
* default units are [Ang], unless IKEV is set, when they are
assumed to be [keV]
keywords
abund [INPUT] abundances relative to H=1
* default is to use Grevesse & Sauval
ionfrac [I/O] the ion fraction for all elements
* must be a 2D array of size (NZ,NION), where
NION=NZ+1 and usually NZ=30
* note that in normal cases, total(IONFRAC,2)
is an array of 1s.
* if not given, assumed to be all neutral, IONFRAC[*,0]=1
- unless DEM is given, see below
* if non-zero scalar, assumed to be all neutral
- DEM is ignored
* if given as an array of size NZ, each element
is assumed to have a total of that fraction,
and all the ions have the same fraction
- this is clearly an artificial case, to be used mainly
for debugging and the like
- DEM is studiously ignored
* if given as a 1D array of size not matching NZ,
is ignored with a warning and the default is used
- unless DEM is given, see below
* if given as a 2D array of size not matching (NZ,NZ+1),
program quits with an error
- unless DEM is given, see below
* if DEM (see below) is given, is read in as a 3D array
of size (NT,NZ+1,NZ1) from the database (using the PINTofALE
function RD_IONEQ(), which calls the CHIANTI procedure
READ_IONEQ), weights the fractions according to the DEM
and is converted into a 2D array of size (NZ,NZ+1)
vfkydir [INPUT] where to find the save files that contain the
cross-sections calculated for each ionization state
* default is '$ARDB'
* NOTE: the cross-sections are not read in if the keyword
ICRSTR is properly defined
ikeV [INPUT] if set, assumes that W are in units of keV
nconsec [INPUT] number of grid points that define the cross-sections
that must fall within one bin of the user defined grid before
the switch from averaging to interpolating occurs
* default=1
DEM [INPUT] the Differential Emission Measure that will be
used to weight the different temperatures to compute the
ionization fraction
* looked at only if IONFRAC is not supplied as input
* size must match LOGT, otherwise ignored
logT [INPUT] the temperature grid over which DEM is defined
* size must match DEM, otherwise DEM is ignored
noHeH [INPUT] if set to any number other than 1 or 2, excludes
H and He from the cross-sections
* if set to 1, only excludes H
* if set to 2, only excludes He
icrstr [I/O] the cross-sections calculated for each ionization
state, stored in a structure of structures of the form
ICRSTR.(Z) = {EVSPLAC, CROSSI}
* if given on input, will use these numbers
* if the structure does not contain enough tags, or if
any one of the substructures does not contain enough
tags, will be read in using the data in VFKYDIR
verbose [INPUT] controls chatter
_extra [INPUT ONLY] pass defined variables to subroutines
-- RD_IONEQ : CHIDIR, EQFILE
subroutines
GETABUND()
RD_IONEQ()
READ_IONEQ
INICON
GETPOADEF()
history
written as IONTAU by Jeremy Drake (Apr07)
further shoehorned into PoA format by Vinay Kashyap (Apr07)
bug fixes and corrections and changed behavior of IONFRAC
(VK; May09)
updated references (JJD; Aug11)
BUG: DEM was not being normalized when weighting IONFRAC (JJD; Nov11)
added call to GETPOADEF (VK; Aug15)
(See pro/ionabs.pro)
function ismtau
returns the optical depth for a given photon energy at specified
column density. i.e., the $\tau$ of $e^{-\tau}$.
ingredients:
* in the UV/Opt/IR regime, calls IDLastro's FM_UNRED.PRO
* in the EUV regime, cannibalizes ISMEUV.PRO for
-- HI photoionization (Spitzer 19??, "Physical Processes in the
Interstellar Medium", p105), between 0.03 keV (413.3A) and 911.75A
-- HeII photoionization (ibid), between 0.03 keV (413.3A) and 911.75A
-- HeI with auto-ionization resonances (Marr & West 1976;
Oza 1986, Phys.Rev.A 33 824; Fernley et al. 1987, J.Phys.B 20,
6457; Rumph, Bowyer, & Vennes 1994, AJ 107, 2108) below 503.97A
-- NOTE: these are extended down to 43.657 AA when the X-ray
calculations are not being done.
* in the X-ray regime (0.03 - 10 keV), either
-- Morrison & McCammon (1983, ApJ 270, 119) polynomial fit between
0.03 keV and 10 keV, or
-- Balucinska-Church & McCammon (1992, ApJ 400, 699) cross-sections,
which allows abundance variations, or
-- Wilms, Allen, & McCray (2000, ApJ, in press) calculations
that use cross-sections from Verner & Yakovlev (1995, A&AS,
109, 125), which also allows abundance variations
-- Verner, Ferland, Korista, & Yakovlev (1996, ApJ, 465, 487)
ground state photoionisation cross-sections that allows for
abundance variations (down to 911.75 Ang)
* in the hard X-ray regime and beyond (>10 keV),
-- Tanaka & Bleeker (1977, ???) power-law extended past 10 keV
* Molecular H (Cruddace et al. 1977, ApJ 187, 497; Kashyap et
al. 1992, ApJ 391, 684) between 12.3985A (1 keV) to 911.75A
to extract only the cross-sections, set NH=1
to obtain transmission factors, use exp(-ismtau(...))
syntax
tau=ismtau(w,NH=NH,fH2=fH2,He1=He1,HeII=HeII,Fano=Fano,/ikev,$
/vion,/wam,/bam,/mam, abund=abund,noHeH=noHeH,verbose=verbose,$
tauH1=tauH1,tauH2=tauH2,tauHeII=tauHeII,tauHe2=tauHe2,tauHe1=tauHe1,$
tauX=tauX,tauTB=tauTB,$
R_V=R_V,LMC2=LMC2,AVGLMC=AVGLMC,ExtCurve=ExtCurve,$
fmgamma=fmgamma,fmx0=fmx0,fmc1=fmc1,fmc2=fmc2,fmc3=fmc3,fmc4=fmc4,$
icrstr=icrstr,ionfrac=ionfrac,vfkydir=vfkydir,nconsec=nconsec,$
DEM=DEM,logT=logT,chidir=chidir,eqfile=eqfile)
parameters
w [INPUT; required] photon energy values at which to compute
the optical depth.
* default units are [Ang], unless IKEV is set, when they are
assumed to be [keV]
keywords
NH [INPUT; default=1] atomic H I column density [cm^-2]
* when keyword VION is set, IONABS() is called to deal
with partially ionized media. In this case, NH is
assumed to be total H column, i.e., H I + protons
* note that when NH=1, the function essentially returns
the absorption cross-section in units of [cm^2]
* to set the "column" for UV/optical/IR, use the keyword
EBV, which defines the E(B-V) and gets passed down to
the routine FM_UNRED
- this means that the "feature" of getting the cross-section
out for NH=1 that is available for high-energy photons is
not available at wavelengths > 911.75 Ang
fH2 [INPUT; default=0.] N(H2)/N(HI)
* originally was set to a default of 0.26, the Galactic
average -- comes from the asymptotic value of
N(H2)/N(HI) computed with the 3 component model (cold
HI, warm HI, H2) of Bloemen, J.B.G.M. (1987, ApJ 322, 694)
-- but has now been changed to 0. explicitly set it to a
float number to include H2 cross-sections
* if NoHeH is set to exclude H, fH2 is assumed to be 0
He1 [INPUT; default=0.1*NH] neutral He column density [cm^-2]
HeII [INPUT; default=0.1*He1] ionized He column density [cm^-2]
* if NoHeH is set to exclude He, both HeI and HeII cross-sections
will be excluded regardless of what the keywords He1 and
HeII are set to
Fano [INPUT] if set, the 4 strongest auto-ionizing resonances
of He I are included; the shape of these resonances are
given by a Fano profile (cf. Rumph, Bowyer, & Vennes 1994,
AJ 107, 2108).
* input wavelength grid between 190 A and 210 A should be
~0.01 A for this to be useful
ikev [INPUT] if set, assumes that W are in units of keV
vion [INPUT] if set, uses Verner et al. (1996) cross-sections
* calls IONABS()
wam [INPUT] if set, uses Wilms, Allen, & McCray cross-sections
* NOT IMPLEMENTED YET -- if set, defaults to Balucinska-Church
& McCammon.
bam [INPUT] if set, uses Balucinska-Church and McCammon updates
to Morrison & McCammon cross-sections in 30 eV - 10 keV range
* calls BAMABS()
mam [INPUT] if set, uses Morrison and McCammon photoionization
cross-sections in the 30 eV - 10 keV range
* This is the default
* VION takes precedence over
WAM takes precedence over
BAM takes precedence over MAM.
* if MAM is explicitly set to 0 and none of VION, BAM, or WAM are
set, then the original ISMEUV code is used from 43 AA longwards
noHeH [INPUT] passed on unchanged to BAMABS() and IONABS()
if set to any number other than 1 or 2, excludes H and He
cross-sections in BAMABS (and ensures that even if fH2 and
He1 are not zero, they are properly excluded within ISMTAU)
* if set to 1, excludes only H
* if set to 2, excludes only He
* NOTE: if set, will supersede fH2, He1 and HeII keyword
values in that H, H2, He1, He2 are all appropriately
excluded
tauH1 [OUTPUT] optical depth due to H
tauH2 [OUTPUT] optical depth due to molecular H2
tauHe2 [OUTPUT] optical depth due to HeII
tauHeII [OUTPUT] same as TAUHE2
* both present here for backwards compatibility
tauHe1 [OUTPUT] optical depth due to HeI
* NOTE: if VION is set, it computes H, HeI, and HeII
cross-sections, so the parts of tauH1, tauHe1, tauHe2
that overlap the relevant range get set to zero
tauX [OUTPUT] optical depth in EUV and X-ray regime (0.03-10 keV)
tauTB [OUTPUT] optical depth in hard X-ray regime (>10 keV)
icrstr [I/O] passed without comment to IONABS()
EBV [INPUT] color excess, E(B-V), passed on to FM_UNRED
* default is 0
* note that -ve values are not forbidden in FM_UNRED,
but are ignored here because we don't want any
confusion with the other optical depths
R_V [INPUT] passed without comment to FM_UNRED
LMC2 [INPUT] passed without comment to FM_UNRED
AVGLMC [INPUT] passed without comment to FM_UNRED
ExtCurve[INPUT] passed without comment to FM_UNRED
fmgamma [INPUT] passed without comment to FM_UNRED
fmx0 [INPUT] passed without comment to FM_UNRED
fmc1 [INPUT] passed without comment to FM_UNRED
fmc2 [INPUT] passed without comment to FM_UNRED
fmc3 [INPUT] passed without comment to FM_UNRED
fmc4 [INPUT] passed without comment to FM_UNRED
* note: all of these keywords are explicitly included
because FM_UNRED doesn't have an _EXTRA keyword
_extra [INPUT ONLY] pass defined variables to subroutines
BAMABS: ABUND,VERBOSE
IONABS: ABUND,IONFRAC,VFKYDIR,NCONSEC,DEM,LOGT,CHIDIR,EQFILE
restrictions
requires BAMABS and IONABS (part of PINTofALE) and
FM_UNRED and associated subroutines (from IDLastro)
history
written by Vinay Kashyap (Feb97), based on
ISMEUV.PRO (W.Landsman [Oct94], via ISM.C@cea-ftp.cea.berkeley.edu
(Pat Jelinsky, Todd Rumph, et al.)) and ISMABS.PRO (VK; Dec91)
changed default on HeII from 0 to 0.1*He1 (VK; Jan MM)
changed default on NH from 1e20 to 1.0 (VK; MarMM)
changed keyword KEV to IKEV; also for some reason H and He
photoionization from ISMEUV had been cut off at the C edge,
now corrected; added keywords WAM, BAM, and MAM, and call to BAMABS
(VK; OctMM)
bug correction: BAM was not filtering on energy; allowed setting
MAM=0 to recover original ISMEUV calc (VK; Jun03)
follow-up bug correction (VK; Jul03)
added keyword NOHEH to streamline behavior of handling H and He
cross-sections with BAMABS (thanks Christian Schneider; VK Feb07)
added keywords TAUH1,TAUH2,TAUHE2,TAUHE1,TAUX,TAUTB, VION,ICRSTR,;
changed all array index notation from old "()" to new "[]";
**WARNING** changed behavior of FH2 -- new default is 0, not 0.26;
added call to IONABS();
(VK; May09)
added call to FM_UNRED for wvl > 911.75 Ang (VK; Aug11)
bug fixes (Jon Slavin; Sep13):
/vion was double counting tauH,tauHe1,tauHe2
(WARNING: changes behavior of tauH, tauHe1,tauHe2 on output)
added keyword TAUHE2 (VK; Sep13)
(See pro/ismtau.pro)
Project : HINODE/EIS
Name : IS_DIR
Purpose : Test if input is a valid directory
Inputs : DIR = directory name to test
Outputs : None
Keywords : See IS_DIR2
Version : Written 12-Nov-2006, Zarro (ADNET/GSFC)
- uses better FILE_TEST
Modified 5-Jan-2009, Zarro (ADNET/GSFC)
- return boolean instead of long
Contact : dzarro@solar.stanford.edu
(See pro/external/is_dir.pro)
function is_keyword_set a wrapper to KEYWORD_SET(), in order to produce the same behavior with vector [0] as with IDL 5.6 and prior parameters key [INPUT] the keyword to test for keywords none isn't this ironic? description prior to IDL 5.6, keyword_set(0) returned false and keyword_set([0]) returned true. this behavior changed in IDL 5.6 to match the documentation of keyword_set, so that both 0 and [0] now return false. it is far too difficult to change the code logic of all the programs written with old IDLs, so better to have a wrapper that duplicates the same behavior instead. history Vinay Kashyap (Mar2006)
(See pro/util/is_keyword_set.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
ITOH_CH
EXPLANATION
Calculates the relativistic free-free continuum using the fitting
formula of Itoh et al. (ApJS 128, 125, 2000).
To calculate the continuum spectrum the user should specify
whether the plasma structure is specified through a differential
emission measure (DEM) curve or through emission measure (EM)
values. For the former, the DEM values are specified through the
DEM_INT keyword and for the latter the EM values are specified
through the EM_INT keyword. If neither are specified EM_INT
values of unity are assumed.
If DEM_INT values are specifed they must be specified on a
temperature scale that has constant intervals in log10(T). EM_INT
values do not have this restriction.
Note that EM_INT must be used for isothermal plasmas.
INPUTS
TEMP Temperature (in K). If the keyword DEM_INT= is set, then the
temperatures must be specified with a fixed spacing in
logT. E.g., TEMP=10.^[4.0,4.1,4.2].
WVL Wavelengths in angstroms. Can be a scalar or vector. If /keV is
set, then WVL is assumed to contain energies in keV units.
OUTPUTS
INT Free-free continuum emissivity in units of
10^-40 erg cm^3 / s / sr / Angstrom per unit emission
measure [ integral(N_e N_H dh) in cm^-5 ]. If T is given as
a 1-D array, then RAD will be output as a 2-D array,
with one element for each temperature and wavelength
(but also see SUMT).
If the keyword /keV is set, then the units of INT will be
10^-40 erg cm^3/s/sr/keV
OPTIONAL INPUTS
DEM_INT This should be the same size as TEMP and contain
differential emission measure values. Specifying
DEM_INT places a restriction on TEMP (see above). Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not.
EM_INT This should be the same size as TEMP and contain
emission measure values. Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not. If
neither EM_INT or DEM_INT are specified, then a EM_INT
vector of same size as TEMP with values of unity is
assumed.
MIN_ABUND This keyword allows the specification of a minimum abundance,
such that any elements with an abundance (relative to
hydrogen) less than MIN_ABUND will not be included in the
calculation. E.g., MIN_ABUND=1e-5.
KEYWORDS
NO_SETUP By default the routine asks the user which ion balance
and abundance files to use via pop-up widgets. If
/no_setup is used then this data is taken from the common
block.
SUMT The default is to output the intensity array as an array
of size (nwvl x nT). Setting this keyword performs a sum
over the temperatures to yield a vector of same size as
the input wavelengths, thus producing the complete
free-free spectrum.
PHOTONS Gives output emissivity in photon units rather than ergs.
KEV If set, then WVL is assumed to contain energies in keV units
rather than wavelengths in Angstroms.
CALLS
SETUP_ELEMENTS
PROGRAMMING NOTES
In the Itoh et al. paper they state that their fitting formula is
valid for ion charges (Z_j) of 1-28. The data-file they provide
actually goes up to Z_j=30, and so you will see that the loop over
z (see below) goes up to 30.
There is no restriction on the elements for which the fitting
formula is valid, and so all elements are allowed to be included
(subject to their abundances being non-zero).
HISTORY
Ver.1, 3-Dec-2001, Peter Young
Ver.2, 22-May-2002, Peter Young
Added MIN_ABUND optional input.
Ver.3, 28-May-2002, Peter Young
Corrected way in which DEM is handled.
Ver.4, 9-Mar-2006, Peter Young
Added /keV keyword.
Ver.5, 10-Sep-2009, Peter Young
Routine now checks that temperatures are evenly spaced
when DEM_INT is specified. Also 0.1 dex spacing is no
longer assumed.
Ver.6, 6-Oct-2009, Peter Young
Introduced EM_INT keyword for specifying emission measure
values for isothermal plasmas.
ver.PoA 10-Aug-2010, Vinay Kashyap
a la 18-Feb-2005, LiWei Lin
Commented out common block
Added abund, ioneq, ioneq_logt keywords
Replaced variable ioneq_t with ieq_logt, _extra
Renamed routine itoh_ch
(See pro/external/itoh_ch.pro)
procedure kaboom produces BOOMs and BANGs (to be used only to indicate catastrophic failure, OK? don't overdo it) syntax kaboom,boom,bang=bang,/beep,/flash,/help parameters boom [INPUT; default='KABOOM!!'] could be 'BIFF'. or 'POW'. could even be an array keywords bang [INPUT; default=42] number of "KABOOM"s to produce beep [INPUT] if set, also produces beeps flash [INPUT] if set, flashes the window help [INPUT] prints usage and quits _extra [JUNK] here only to prevent crashing the program usage examples kaboom,boom,bang=bang,/beep,/flash,/help kaboom,'?',bang=100,/beep,/flash side-effects makes an almighty mess of the plot window; may also make noises history vinay kashyap (rewritten from memory of 1993 program) added keywords FLASH, HELP, and _EXTRA (VK; Nov98) improved color-scale setting for 24-bit consoles (VK; FebMMI) added a brief pause (VK; Apr04)
(See pro/util/kaboom.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
KARZAS_XS()
EXPLANATION
Outputs the photoionization cross-section at the wavelengths WVL for
ionization of an N,L electron with ionization energy IONIZ_EN,
calculated using the Karzas & Latter (ApJS 6, 167, 1961) formulation.
The bound-free gaunt factor is derived from the tables of Karzas &
Latter.
INPUTS
WVL Wavelengths (in angstroms) for which cross-sections are
required (1-D array).
N Principal quantum number of the electron being removed in the
ionization.
L The orbital angular momentum of the electron being removed in the
ionization.
IONIZ_EN The ionization energy (in cm^-1) of the electron being
removed.
OPTIONAL INPUTS
PE Allows the PE array from READ_KLGFB to be directly input to
KARZAS_XS thus avoiding the need to read the K&L data
repeatedly for many ions. Requires KLGFB to also be input.
KLGFB Allows the KLGFB array from READ_KLGFB to be directly input to
KARZAS_XS thus avoiding the need to read the K&L data
repeatedly for many ions. Requires PE to also be input.
OUTPUT
The photoionization cross-section for the ionization of the outer
electron in units of mega-barns (Mb = 10^-18 cm^2) at the input
wavelengths. E.g., for Fe XIII (ground configuration
1s2.2s2.2p6.3s2.3p2) it is the cross-section for the removal of the
3p electron.
CALLS
READ_KLGFB
HISTORY
Ver.1, 24-Jul-2002, Peter Young
(See pro/external/karzas_xs.pro)
procedure kilroy "kilroy was here" writes a little something to the screen every time it is called syntax kilroy,here,ndot=ndot,dot=dot,say=say parameters here [I/O; optional] if given, is included in the output and is increased by 1 upon output. * cannot be a string keywords ndot [INPUT] number of dots to write out (default is 1) dot [INPUT] symbol to use (default is ".") say [INPUT] an extra word or whatever to print out _extra [JUNK] here only to avoid crashing the program history vinay kashyap (Aug 1996)
(See pro/util/kilroy.pro)
function lat2arab return arabic (decimal) equivalent of a latin numeral syntax arabic=lat2arab(latin) parameters latin [INPUT; required] the latin numeral keywords NONE restrictions * spaces, "."s, and anything that is not part of the roman numeral system (I V X L C D M) is ignored. * there is no reverse function, to go from arabic to latin, because that is not a unique transformation. e.g., 1995 could be either MDCCCCLXXXXV (the BBC way), or MVM, or all steps in between. * guaranteed to work only in simple cases. DON'T push the envelope! * CAVEATVSVATOR history vinay kashyap (Nov95)
(See pro/util/lat2arab.pro)
function legalvar returns 1 or 0 depending on whether VAR is a legal IDL variable or not. simply calls EXECUTE. need to put this inside a subroutine to protect possible existing variables of same name in main routine. syntax l=legalvar(vars,verbose=verbose) parameters var [INPUT; required] string of candidate variable names * if array, output will also be an array of 1s and 0s keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (MM.I) bug fix if input is scalar (VK; MM.X) added keyword verbose (VK; IMVIM.VIII)
(See pro/util/legalvar.pro)
procedure levmarq
Levenberg-Marquardt method, attempting to reduce the value chi^2 of a
fit between a set of data points Y(X) with individual std.dev.s SIG,
and a nonlinear function dependent of A parameters. The input array
IFIT indicates by non-zero entries those components of A that should
be fitted for, and by 0 entries those components that should be held
fixed at their input values. The program returns current best-fit
values for the parameters A and the value of CHISQ. The arrays
COVAR and ALPHA are used as working space during most iterations.
Supply a routine FUNCS(x,a,yfit,dYdA) that evaluates the fitting
function YFIT, and its derivatives dY/dA wrt fitting parameters A@X.
On the first call, provide an initial guess for parameters A, and
set ALAMDA < 0 for initialization. If a step succeeds, CHISQ becomes
smaller and ALAMDA decreases by a factor 10. If a step fails, ALAMDA
grows by a factor 3. Call this routine repeatedly until convergence
is achieved. Then, make one final call with ALAMDA=0, so that COVAR
returns the covariance matrix, and ALPHA the curvature matrix. Those
parameters held fixed will return zero covariances.
syntax
levmarq,x,y,a,chisq,funcs=funcs,sig=sig,ifit=ifit,alamda=alamda,$
jumpup=jumpup,jumpdn=jumpdn,ochisq=ochisq,alpha=alpha,covar=covar,$
bvec=bvec,svdthr=svdthr,trial=trial,yfunc=yfunc,/tiptoe,$
funcs=funcs,sig=sig,ties=ties, FUNCS_KEYWORDS
parameters
x [INPUT; required]
y [INPUT; required] size must match that of X
a [INPUT; required]
chisq [OUTPUT; required] the chi-sq statistic denoting degree of
agreement between model and data
keywords
ifit [INPUT] integer array of same size as A, with 0's indicating
frozen parameters and 1's indicating thawed parameters
* if IFIT does not match A for any reason, all parameters
are assumed to be thawed
jumpup [INPUT; default=3] factor by which to increase ALAMDA if
current trial fails
jumpdn [INPUT; default=0.1] factor by which to decrease ALAMDA if
current trial succeeds
alamda [I/O] if not defined on input or is -ve, initializes the
procedure.
ochisq [OUTPUT] the old value of the chi^2
alpha [OUTPUT] if ALAMDA=0, the curvature matrix
covar [OUTPUT] if ALAMDA=0, the covariance matrix
bvec [OUTPUT] the BETA fitting-vector
svdthr [INPUT; default=1e-6] threshold for singular values of
diagonal SVD matrix
trial [OUTPUT] current trial values of the parameters
yfunc [OUTPUT] best-fit Y(X;A)
tiptoe [INPUT] if set, forces small steps on A
verbose [INPUT] controls chatter
_extra [INPUT] pass defined keywords to subroutines
LMCOEFF: FUNCS, SIG
ADJUSTIE: TIES
FUNCS: whatever is needed
subroutines
LMCOEFF
SVDC
SVSOL
ADJUSTIE
history
(C) Copr. 1986-92 Numerical Recipes Software =$j!]Y'1,).
translated from MRQMIN.F to IDL by Vinay Kashyap (Oct98)
changes: (i) matrix solution method from Gauss-Jordan elimination
to Singular-Value Decomposition; (ii) if trial fails, ALAMDA
increased by x{JUMPUP=3} instead of x10 and if trial succeeds,
decreased by x{JUMPDN=0.1} to avoid obvious oscillations;
(iii) call to COVSRT avoided; (iv) call to ADJUSTIE included;
(v) no resetting chisq within procedure (VK; Oct98)
added keyword YFUNC (VK; Dec98)
allowed "inversion" of 1-element "matrices" bypassing
SVDC and SVSOL (VK; Aug99)
now returns correct chisq if all params are frozen (VK; JanMM)
added keyword VERBOSE (VK; Nov04)
(See pro/fitting/levmarq.pro)
procedure libmodel computes F(X;A) and dF/dA for a library of model functions. procedure written to be compatible with FIT_LEVMAR, and also with IDL's CURVEFIT, GHRS-IDL's WFIT, etc. syntax libmodel,x,a,f,pder,anew,type=type,verbose=verbose,$ missing=missing,/norm,/fwhm,betap=betap,angle=angle,vrot=vrot,$ Xo=Xo,pbreak=pbreak,NH=NH,wvlar=wvlar,effar=effar,exptime=exptime,$ dellam=dellam,X0=X0,angrise=angrise,angfall=angfall,ybase=ybase,$ yoff=yoff parameters x [INPUT; required] points at which to generate models a [INPUT; required] array of parameter values * should match the number expected from TYPE. * no checks are made to verify that the user is not shooting hirself in the foot. f [OUTPUT; required] output f=f(x;a) pder [OUTPUT; optional] partial derivatives for each parameter anew [OUTPUT; optional] return a new set of A in which the normalization parameters have all been adjusted to account for the supplied RENORM keywords type [INPUT; required] string array denoting the model functions to be called. * this should rightly be a parameter, because it is a very necessary part of the program. however, most fitting functions do not allow that degree of flexibility and so we are forced to use this hack. * some models may be multiplicative (e.g., 'absorb'), and their location in the TYPE array matters. a multiplicative model multiplies the model that is defined after it. so to apply the same absorption model to a powerlaw and a gaussian, set TYPE=['absorb','power','absorb','gauss'] and then use TIES=['a6=a1'],FREEZE=[6] to make sure the same absorption is applied to both components betap [I/O] keyword passed w/o checking to MK_LORENTZ and MK_SLANT angle [I/O] keyword passed w/o checking to MK_SLANT vrot [I/O] keyword passed w/o checking to MK_ROGAUSS x0 [I/O] keyword passed w/o checking to MK_POWLAM,MK_BKNPOWER pbreak [I/O] keyword passed w/o checking to MK_POWLAM,MK_BKNPOWER phase [I/O] keyword passed w/o checking to MK_SINUSOID angrise [I/O] keyword passed w/o checking to MK_LCECLIPSE angfall [I/O] keyword passed w/o checking to MK_LCECLIPSE ybase [I/O] keyword passed w/o checking to MK_LCECLIPSE yoff [I/O] keyword passed w/o checking to MK_LCECLIPSE verbose [INPUT; default=0] controls chatter renorm [INPUT; default=1] renormalize the output by multiplying by this factor * the adjusted normalizations for each component that correspond to this renormalization are returned in ANEW _extra [INPUT] pass defined keywords to subroutines MK_GAUSS: MISSING, FWHM, NORM MK_LORENTZ: BETAP, MISSING, NORM MK_SLANT: ANGLE, BETAP, MISSING, NORM MK_ROGAUSS: VROT, FWHM, NORM, MISSING MK_POWLAM: XO,PBREAK,NH,WVLAR,EFFAR,EXPTIME,DELLAM MK_BKNPOWER: XO,NOBREAK,VERBOSE MK_POLY1D: X0 MK_SINUSOID: PHASE, MISSING MK_SINE: MISSING MK_LCECLIPSE: ANGRISE, ANGFALL, YBASE, YOFF MK_ABSORB: FH2,HE1,HEII,FANO,IKEV,WAM,BAM,MAM,NOHEH,ABUND MK_EFOLD: VERBOSE MK_BBANG: VERBOSE MK_BBKEV: VERBOSE MK_RECIPROCALPOW: VERBOSE MK_SPLINE1D: XLOC,USEINIT,TENSION,VERBOSe subroutines MK_GAUSS MK_LORENTZ MK_SLANT MK_ROGAUSS MK_POWLAM MK_BKNPOWER MK_POLY1D MK_LCECLIPSE MK_ABSORB MK_EFOLD MK_BBANG MK_BBKEV MK_RECIPROCALPOW MK_SINUSOID MK_SINE history vinay kashyap (Aug01; based on X3MODEL and MK_3MODEL) added call to MK_SINUSOID (VK; Sep04) added call to MK_LCECLIPSE, allowed return of extra parameters via keywords (VK; May07) added call to MK_BKNPOWER via "pow" and "pe"; added MK_ABSORB via "absorb"; allowed for multiplicative as well as additive models (VK; Jul08) added call to MK_EFOLD via "ef", "efold", and "exp" and to MK_BBANG and MK_BBKEV via "bbang" and "bbkev" (VK; Aug08) added call to MK_RECIPROCALPOW via "reci/pow" and MK_SPLINE1D via "spline=KNOTS"; added parameter ANEW and keyword RENORM (VK; Sep08) added call to MK_SINE (VK; Jan13)
(See pro/fitting/libmodel.pro)
procedure licospec
compute the contributions of line and continuum
emissivities over a specified wavelength grid.
syntax
licospec,wgrid,lspec,cspec,at_logT,lrf=lrf,lstr=lstr,cstr=cstr,$
lemis=lemis,cemis=cemis,abund=abund,lcthr=lcthr,constr=constr,$
ldbdir=ldbdir,cdbdir=cdbdir,ceroot=ceroot,verbose=verbose,$
pres=pres,logP=logP,n_e=n_e,chifil=chifil,chidir=chidir,$
eqfile=eqfile,logT=logT,DEM=DEM,effar=effar,wvlar=wvlar,$
type=type,/norm,/fwhm,betap=betap,angle=angle,vrot=vrot
parameters
wgrid [INPUT; required] wavelength bin boundaries over
which to compute line and continuum contributions
* must be in same units as the wavelengths stored
in LDBDIR, i.e., Angstroms
lspec [OUTPUT; required] line emission at each wavelength bin
cspec [OUTPUT; required] continuum emission at each wavelength bin
* note that these are essentially spectra, and include
the effects of specified abundance, DEM, and any input
RMFs, LRFs, or effective areas.
at_logT [INPUT] if set to a scalar, assumes a delta-function
emission measure to compute the appropriate fluxes;
the default is to assume a DEM that covers the range
4..8 in logT (but note that any arbitrary DEM can be
defined using keywords LOGT and DEM).
* NOT TESTED
keywords
lrf [INPUT] if scalar, the width of the line response function
NOTE: the function used to define the LRF can be set
using the keyword TYPE (e.g., TYPE='gauss', TYPE='beta=2.5')
* if float, the width in the same units as WGRID
* if integer, the width in number of bins
* if RMF structure (e.g., output of RD_OGIP_RMF()), use
it to convolve the output and place in channels defined
by WGRID indices (i.e., if LRF is defined as an RMF,
it _must_ match the wavelength grid)
lstr [I/O] line emissivity structure out of RD_LINE()*FOLD_IONEQ()
* if defined on input, RD_LINE() and FOLD_IONEQ() will not
be called unless bounds of WGRID spill out, in which case
the user will be asked what to do
* unlike LEMIS below, abundances are _not_ included
(unless in case of APED)
cstr [I/O] continuum emissivity structure out of RD_CONT() --
* if defined on input, RD_CONT() will not be called unless
bounds of WGRID spill out, in which case the user will be
asked what to do
ldbdir [INPUT; '$CHIANTI'] line emissivity database directory
cdbdir [INPUT; '$CONT'] continuum emissivity database directory
ceroot [INPUT; 'cie'] prefix of files containing the continuum
emissivities
abund [INPUT] element abundances to use while computing the
continuum emissivities, the line and continuum fluxes,
combining line emissivities into wavelenth bins, etc.
* if not defined, calls GETABUND(!ABREF)
* if !ABREF is not defined, adopts Grevesse et al.
lemis [OUTPUT] line emissivities recast to be on the input
wavelength grid, i.e., an array of size N(LOGT)xN(WGRID)
and with units [1e-23 ergs cm^3/s]
* the output line emissivities _include_ the specified
ion balances and abundances
cemis [OUTPUT] continuum emissivities recast to be on the input
wavelength grid, i.e., an array of size N(LOGT)xN(WGRID)
and with units [1e-23 ergs cm^3/s]
* NOTE: the /Ang usually present in continuum emissivities
is missing here
lcthr [INPUT] if set, combines the continuum emissivity from all
the bins with LSPEC/CSPEC less than LCTHR and returns it
in CONSTR
* if negative, then combines all bins with CSPEC < LCTHR
constr [OUTPUT] continuum emissivity structure with the emissivities
marginalized over wavelength
allah [INPUT] if set, no bounds of WGRID are not checked against
LSTR and the structure is used as is
verbose [INPUT] controls chatter
_extra [INPUT ONLY] pass defined keywords to subroutines
RD_LINE: PRES, LOGP, N_E
FOLD_IONEQ: CHIFIL, CHIDIR, EQFILE
RD_CONT: PRES, LOGP, N_E, ABUND
LINEFLX: LOGT, DEM, ABUND, EFFAR, WVLAR
LIBMODEL: TYPE, NORM, FWHM, BETAP, ANGLE, VROT
example
; make a wavelength grid
wgrid=findgen(2001)*0.001+18. & lrf=0.02 & type='beta=2.5'
; call LICOSPEC
licospec,wgrid,lspec,cspec,verbose=10,lstr=lstr,cstr=cstr,$
lcthr=0.1,constr=constr,lemis=lemis,cemis=cemis,n_e=1e10,$
lrf=lrf,type=type
; plot line to continuum flux ratio
plot,wgrid,lspec/cspec,/ylog,$
xtitle='wavelength [Ang]',ytitle='line-to-continuum'
; plot line and continuum integrated emissivities
tmpl=dblarr(81) & for i=0,80 do tmpl[i]=total(lemis[i,*])
tmpc=dblarr(81) & for i=0,80 do tmpc[i]=total(cemis[i,*])
plot,lstr.LOGT,tmpl,/yl & oplot,cstr.LOGT,tmpc,thick=3,line=2
; integrated emissivities over a sub range
oo=where(lspec/cspec lt 0.1)
tmpl=dblarr(81) & for i=0,80 do tmpl[i]=total(lemis[i,oo])
tmpc=dblarr(81) & for i=0,80 do tmpc[i]=total(cemis[i,oo])
plot,lstr.LOGT,tmpl,/yl & oplot,cstr.LOGT,tmpc,thick=3,line=2
subroutines
CONV_RMF [RD_OGIP_RMF]
FOLD_IONEQ [RD_IONEQ [READ_IONEQ], WHEE]
GETABUND
HASTOGRAM [KILROY]
LIBMODEL [MK_GAUSS, MK_LORENTZ, MK_ROGAUSS [MK_GAUSS], MK_SLANT]
LINEFLX [GETABUND, WHEE]
MID2BOUND
RD_CONT [SETSYSVAL [LEGALVAR], SYMB2ZION [LAT2ARAB]]
RD_LINE [INICON, SETSYSVAL [LEGALVAR], SYMB2ZION [LAT2ARAB]]
REBINW [FINDEX]
SETSYSVAL [LEGALVAR]
IS_KEYWORD_SET
history
vinay kashyap (Dec2003)
added keywords LEMIS,CEMIS,LCTHR,CONSTR,ABUND,LDBDIR,CDBDIR,CEROOT;
corrected bug with CSTR.CONT_INT being degraded in repeated calls;
now -asks- if input wavelength range has changed and LSTR/CSTR do
not span this range (VK; Jan2004)
cleaned up behavior of CSTR.CONT_INT for compatibility with RD_CONT();
now output LEMIS and CEMIS add up in photon space (VK; Apr2004)
added ALLAH keyword to facilitate use of ZRESP keyword in
SOLAR_TRESP() (LL; Sep2005)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
(See pro/licospec.pro)
function likeli returns p(D|M), the likelihood of observing the data for the given model. the default action is to return exp(-chi^2/2) syntax prob=likeli(data,model,derror,dsigma=dsigma,ulim=ulim,$ /binom,/chi2,/rchi,/cash,/castor,softlim=softlim) parameters data [INPUT; required] observed data model [INPUT; required] predicted model or model parameters derror [INPUT] errors on DATA * if specified, overrides keyword DSIGMA keywords dsigma [INPUT] errors on DATA * if not specified, taken to be 1+sqrt(abs(DATA)+0.75) * used only if DERROR is not present ulim [INPUT] long-integer array specifying which elements of DATA are upper limits (1: UL, 0: not) * applies only to CHI2 and RCHI cash [INPUT] if set, returns the Cash (19??, ApJ 228, 939) statistic castor [INPUT] if set, returns the Castor correction to Cash binom [INPUT] if set, likelihood is computed as MODEL(0)^(d1)*(1.-MODEL(0))^(d0) where d1=total(DATA(where(DATA ge BINOM))) and d0=total(DATA(where(DATA lt BINOM))) chi2 [INPUT; default] if set, returns -alog(p(D|M)) rchi [INPUT] if set, returns alog(p(D|M))/n_elements(D) * priority: CASH supercedes CASTOR supercedes BINOM supercedes CHI2 supercedes RCHI softlim [INPUT] if set, then likelihood is unaffected when model values are below data values, and drops as a Gaussian centered on SOFTLIM*DSIGMA with error DSIGMA otherwise * if not set, upper limits are taken to be hard limits, i.e., likelihood drops to 0 if model values exceed data values _extra [INPUT] junk -- here only to avoid crashing the program history vinay kashyap (Mar 97) added keywords CASH and CASTOR (VK; Jul98) changed keyword name SIGMA to DSIGMA (VK; MMaug) had forgotten to actually include CASH and CASTOR in call (VK; May02) added parameter DERROR as a dupe for DSIGMA (VK; Jun05) BUGFIX to not crash if all DATA are upper limits (VK; Sep05) added keyword SOFTLIM (VK; May06) bug correction re SOFTLIM model estimate (VK; Jul07) corrected output to be same as all the others when /BINOM,/CHI2 is set or when /RCHI is set but not /CHI2 (VK; Apr08) fixed a lower bound of 1e-30 for model intensities for CASH per discussion with Jan-Uwe (VK; Aug08)
(See pro/stat/likeli.pro)
function lineflx computes observeable counts [ct/s] or flux [ergs/s] from spectral line for specified DEM by simple trapezoidal integration over temperatures. if effective area is not specified, output will be [ph/s/cm^2] or [ergs/s/cm^2] input line emissivities are in [1e-23 ergs cm^3/s]. these include ionization balance, but not (necessarily) abundances. the line emissivities are multiplied by the differential emission measure and element abundance to get fluxes, then divided by the line energy to get photon fluxes, and multiplied by the supplied effective areas to get count rates. no effort is made to determine line profiles or to include spectral responses (beyond the effective areas). syntax fx=lineflx(line,logT,wvl,Z,DEM=DEM,/temp,abund=abund,/noph,$ nhne=nhne,effar=effar,wvlar=wvlar,/ikev,/noabund) parameters line [INPUT; required] array of line cooling emissivities in units of 1e-23 erg cm^3/s * if 2D array, LINE==LINE(logT,WVL) * WARNING: will return garbage if given 1D array LINE(WVL) (or even 2D array LINE(1,WVL)) use a for-loop to handle such a case * WARNING: will get converted to 1-element vector if input as scalar logT [INPUT; required] array of log10(Temperature [K]) at which emissivities are given. * array size MUST match that of LINE * if not regularly gridded, remember to set REGRID! wvl [INPUT; required] wavelength(s) [Angstrom] of lines at which LINE is given * array size MUST match LINE Z [INPUT] atomic number of element that generates each WVL * if Z has less elements than WVL, Z is ignored * if Z is to be ignored, all lines are assumed to be from same element, and abundance values are ignored keywords DEM [INPUT] Differential Emission Measure at each T [cm^-5/logK] * default is a constant=1e14!! * if array size does not match that of LOGT, then DEM is assumed to cover the same range and is linear interpolated * if defined at only 1 temperature, assumed to be EM [cm^-5] temp [INPUT] if set, assumes that logT is actually in T [K], and that DEM is given in units of [cm^-5/K] * ignored if logT is defined at only one bin abund [INPUT] abundances relative to H (abund(0)=1) * abund(Z-1) contains the abundance for element Z * if array size is smaller than the largest present Z, the last element is replicated to fill the gap * default: Anders & Grevesse (1989) noph [INPUT] if set, does not do the conversion to [ph] from [ergs] nhne [INPUT] the ratio of N(H)/n_e needed to complete the intensity calculation * if not set, assumes 0.83, which is the limiting value for high-temperature plasma with approximately cosmic abundances * if array and size does not match LOGT, then uses only the first element * if Z is not defined, or is 1, then it is **IGNORED** * see discussion in the documentation of POPSOL() effar [INPUT] effective area [cm^2] * if not set, assumed to be 1 cm^2 wvlar [INPUT] wavelengths at which effective area is defined. * if not set, assumed to be WVL * array size MUST match that of EFFAR ikev [INPUT] if set, assumes that WVL and WVLAR are in [keV], NOT [Angstrom] noabund [INPUT] if set, ABUND values are ignored in the calculations, same as though they (or Z) had been set to 1 * but NHNE gets applied regrid [INPUT] if set, assumes that LOGT is irregularly sampled and regrids it (and LINE) to a regular grid * NOT IMPLEMENTED YET _extra [INPUT] junk -- here only to prevent crashing the program subroutines GETABUND WHEE usage examples * f=lineflx(rd_line(logP=20,wvl=w,logT=T,/allah),T,w,dem=10.D^(5*t)) * fl=rd_line(wr=16.776,wvl=w,logT=T,/allah) & t=10.^(t) f=lineflx(fl,T,w,dem=10.D^(5*alog10(t)),/temp) history vinay kashyap (Nov96) added keywords EFFAR and WVLAR (VK; Jan96) added call to WHEE, removed call to KILROY, ensured DEM stretches to fit logT, added case of EM masquerading as DEM, removed the [/sr] from the output (VK; Feb97) changed integration style; restructured to ignore effective area if not supplied; added keyword REGRID (VK; Apr97) corrected ln v/s log10 bug (VK; Jun97) added keyword NOPH; bug correction -- dlogT should in in base 10 (VK; Jan98) changed keyword KEV to IKEV (VK; DecMM) EFFAR and WVLAR ignored if set to 0 (VK; JanMMI) added keyword NHNE (VK; Jun02) added keyword NOABUND (VK; Apr03) changed bad input check from LINE(0)=-1 to total(LINE)=-N(LINE) (VK; Feb06) changed back integration style to simple from trapezoidal (VK; Mar06) changed check for whether WVL are given (VK; Jun07) bug fix: was including 0.83 factor even when continuua and broad-band emissivities were being used [thx P.Testa]; now anything with Z=1 will exclude the NHNE correction -- for H lines, fold the NHNE factors into the emissivities manually (VK; Dec10)
(See pro/lineflx.pro)
function lineid
allows identification of spectral features and returns ID
information in a structure (see structure variable IDHLP
for complete description of fields)
syntax
id=lineid(lamda,spec,elem,wrng=wrng,wshift=wshift,locmax=locmax,$
best=best,topX=topX,batch=batch,stor=stor,oldid=oldid,omatch=omatch,$
markw=markw,feature=feature,verbose=verbose,$
n_e=n_e,logP=logP,pres=pres,dbdir=dbdir,/allah,chifil=chifil,$
eqfile=eqfile,chidir=chidir,dem=dem,abund=abund,effar=effar,$
wvlar=wvlar,sigmay=sigmay,xsize=xsize,ysize=ysize,wid=wid,$
dynrng=dynrng,markp=markp,marks=marks,marko=marko,$
/nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol,stasiz=stasiz,$
stathk=stathk)
parameters
lamda [INPUT; required] wavelength(s) at which spectrum is defined
* interactive if LAMDA is a multi-element array, batch mode
otherwise (also see keyword BATCH)
spec [INPUT; optional] the spectrum
* default is 10+random
* if SPEC is a character string or array, taken to be ELEM
* if LAMDA and SPEC do not match in size, taken to be atomic
numbers
elem [INPUT; optional] confine matches to this particular element
* overrides anything inferred "via" SPEC
keywords
wrng [INPUT] interval in which to search for matches
* default is WRNG=0.01
* if scalar and between 0 and 1, look for matches in the range
[W-W*WRNG,W+W*WRNG]
* if scalar and > 1, or scalar and < 0, abs(WRNG) is assumed
to be the actual step size and is used as is, i.e.,
W+abs(WRNG)*[-1,1]
* if 1-element vector, then range is W+abs(WRNG(0))*[-1,1]
* if multi-element vector, then [W-WRNG[0],W+WRNG[1]]
* NOTE: in interactive mode the range may be altered, but
the >behavior< of the range is set by the initial values.
* also note that WRNG is not changed on output.
wshift [INPUT] amount by which to shift the wavelength scale
* WRNG will be reset to WRNG+WSHIFT
locmax [INPUT] if set, finds matches at all local maxima
* search window width (2*abs(LOCMAX)+1)>3
best [INPUT] if set, returns "best" match -- the strongest
possible nearest line
* obviously, there is weighting involved
* BEST.GE.0: pick largest of Flx[w]/(w-w0)^BEST
* otherwise: return the nearest match(es)
topX [I/O; default: 20] returns at most TOPX matches
* MUST be scalar
* in interactive mode, presents only TOPX for matching choice
* if 0 < TOPX < 1, uses this as a >threshold<, selecting only
those lines whose theoretical predicted fluxes are this
fraction or higher than the maximum flux in the set.
* if TOPX < 0, the integer value is used as the upper limit
to number of matches, and the fractional value is used as
the threshold.
* may get altered within LINEID_MENU
* examples:
TOPX = 0 brings up 20 matches
TOPX = 10 brings up 10 matches
TOPX = 0.6 brings up all lines with fluxes > 0.6 of max
TOPX = -40.01 brings up 40 lines with fluxes > 1% of max
batch [INPUT] if set, operates in batch mode (i.e., no widget-based
selections)
* batch mode is also forced if:-
o N_ELEMENTS(LAMDA)=1
o LOCMAX is set
o TOPX is set to 1
o !D.NAME is not 'X'
stor [I/O] if present in call, will store the output of RD_LINE and
FOLD_IONEQ as a structure. if a structure, then MUST be of
the form {LINE_INT,LOGT,WVL,Z,ION,DESIG,CONFIG}, because
then RD_LINE and FOLD_IONEQ will be bypassed!
* use with caution!!
oldid [INPUT] if set and is in the same format as the output of
LINEID, starts off from this point. i.e., things can be
added or modified from here on.
omatch [INPUT] if OLDID is given *and* OMATCH is set, forces each
wavelength selection to match the nearest matched wavelength
in OMATCH.
* if OMATCH < 0, won't verify, but will force a match if
new location is within abs(OMATCH), and will force a new
match otherwise
* if OMATCH > 0, will ask
markw [INPUT] if set, places marks on the plot at these wavelengths
feature [INPUT] labels for MARKW
* passed with minimal modification to PICKRANGE
verbose [INPUT] controls chatter
wrange [IGNORED] keyword for RD_LINE, will be trapped and ignored.
temp [IGNORED] keyword for LINEFLX, will be trapped and ignored.
_extra [INPUT ONLY] pass predefined input keywords to subroutines:
pres (RD_LINE) pressure [cm^-3 K]
logP (RD_LINE) log10(pressure [cm^-3 K])
n_e (RD_LINE) electron density [cm^-3]
dbdir (RD_LINE) line emissivity database
allah (RD_LINE) which elements to choose
chifil (FOLD_IONEQ) set to read CHIANTI ion balance files
eqfile (FOLD_IONEQ) name of ion balance file
chidir (RD_IONEQ) location of CHIANTI installation
DEM (LINEFLX) Differential Emission Measure distribution
abund (LINEFLX) abundances
effar (LINEFLX) effective area [cm^2]
wvlar (LINEFLX) wavelength grid for EFFAR
sigmaY (PICKRANGE) error-bars on SPEC
xsize (PICKRANGE) window size
ysize (PICKRANGE) window size
wid (PICKRANGE) window ID
dynrng (PICKRANGE) dynamic range in log scale
markp (PICKRANGE) PSYM for (FEATURE,MARKW)
marks (PICKRANGE) SYMSIZE for (FEATURE,MARKW)
marko (PICKRANGE) ORIENTATION for (FEATURE,MARKW)
oxr (PICKRANGE) final output XRANGE
oyr (PICKRANGE) final output YRANGE
nuthin (STAMPLE) don't stamp the plots
noday (STAMPLE) don't stamp the plots with day
notime (STAMPLE) don't stamp the plots with time
nouser (STAMPLE) don't stamp the plots with username
nopack (STAMPLE) don't stamp the plots with package name
stacol (STAMPLE) stamp color
stasiz (STAMPLE) stamp size
stathk (STAMPLE) stamp thickness
description
read in database of line cooling intensities and for each observed
wavelength which requires a match, find the set of matches. if
interactive, allow selection of multiple matches. once done,
reorganize into structure of
{WVL: observed wavelength;
{corresponding
WVL: matched wavelengths,
Z: atomic numbers,
ION: ionic states,
LABL: e-configurations or whatever is available,
FLUX: theoretical fluxes for all new or modified matches
(fluxes in OLDID are not touched unless ID is changed),
FLUXERR: errors on FLUX (set to zero),
LOGT: temperatures at which emissivities are defined
EMIS: line emissivities for all IDs (ion-balance included)
NOTES: scribbles about this ID, for human eyes only
}
}
restrictions
requires IDL v5 or greater
interactive selections require X-windows
requires subroutines
RD_LINE [KILROY, SYMB2ZION [LAT2ARAB]]
FOLD_IONEQ [WHEE, GETLOCMAX, RD_IONEQ [READ_IONEQ]]
LINEFLX [WHEE]
GETLOCMAX
PICKRANGE
LINEID_MENU [CAT_ID]
CREATE_STRUCT
KABOOM
INICON
STR_2_ARR
usage examples
* lid=lineid(12.3985/7.83,['Fe','Ni'],wr=0.1*[1,1],topX=50)
* stor=1 & lid=lineid(x,y,wr=[1],/allah,logP=20,stor=stor)
lid=lineid(x,y,wr=[1],/allah,logP=20,stor=stor)
* lid=lineid(x,y,'Fe',logP=20,econf=0)
history
vinay kashyap (Dec96)
bug corrections: ion balance in STOR, format sizes in menu input;
added ID history info to PICKRANGE and menu; added keyword OLDID
(VK; Feb97)
added keyword OMATCH; allowed expeditious return when no matches
found (VK; Jun98)
modified behavior of STOR to eliminate excess variables (VK; Oct98)
added LOGT and EMIS (EMIS includes ion balance) to the output; bug
correction re STOR not being specified; corrected bug with
BEST actually returning the worst; added keywords BATCH, MARKW,
FEATURE; added calls to KABOOM, INITSTUFF, STR2ARR; TOPX now acts
as threshold too; added support for multiple grating orders
(VK; Nov98)
changed behavior of WRANGE; added renormalization of fluxes; bug fix
older matches not echoing in menu window; added field FLUXERR to
ID structure (VK; Dec98)
added field NOTES to ID structure (VK; Mar99)
modified ion balance calcs (VK; 99May)
changed call to INITSTUFF to INICON (VK; 99May)
changed to full IDL5+ compatibility ("()"->"[]"); stor does not
have to be defined on input, just be present in the call; added
dummy keywords WRANGE and TEMP (VK; AugMM)
added keyword VERBOSE, and now doesn't default to random if NX eq NY+1
(i.e., bin boundaries are given rather than mid-bin values: VK; Nov01)
changed call to STR_2_ARR from STR2ARR (VK; AprMMV)
(See pro/lineid.pro)
function lineid_menu function to select matches to wavelengths and return position indices of selected matches. syntax oo=lineid_menu(menu,w0,w,f,wshift,topX,wrange,cord,code,scratch,$ wvls=wvls,idwvls=idwvls,gwvl=gwvl,renorm=renorm) parameters menu [INPUT] list of items to choose from; string array w0 [INPUT] wavelength that needs match w [INPUT] wvls of matched lines (must be of same size as MENU) f [INPUT] fluxes of all matched lines (same size as MENU) wshift [I/O] wavelength shift topX [I/O] maximum number of matches wrange [I/O] interval in which to search for matches cord [I/O] comma-separated list of grating orders code [OUTPUT] 0: NEXT WAVELENGTH 1: QUIT LINEID 2: REPEAT FOR NEW PARAMETERS scratch [OUTPUT] human readable notation keywords wvls [INPUT] wavelengths which are previously identified idwvls [INPUT] structure describing IDs gwvl [INPUT] grating-order corrected wavelengths renorm [INPUT] renormalization factor restrictions * widget based * dedicated subroutine to LINEID (written simply to avoid making LINEID too large to comprehend) * no error checking is done. it is assumed that this function is called from LINEID, and naught else. * requires subroutines -- CAT_ID -- CREATE_STRUCT warning * here be hippogrif * don't even <<think>> about understanding this program history author of this hack prefers anonymity, thank you very much (Dec96) some cosmetic surgery, added button STATUS and call to CAT_ID (Feb97) corrected bug with reordering (Jul98) added CORD, GWVL, changed TOP field from /LONG to /FLOAT (Nov98) changed behavior of UNDO LAST; renamed NEXT as HELP; renamed DONE as NEXT; added keyword RENORM and entry field PARS_NORM; changed MBAR_NEXT to MBAR_HELP (Dec98) added output SCRATCH (Mar99) bug correction re SCRATCH (FebMM)
(See pro/lineid_menu.pro)
function linerem remove lines from input spectrum and return the "cleaned" spectrum syntax cleanspec=linerem(lamda,spec,sig=sig,cell=cell,nsigma=nsigma,$ bkgval=bkgval,bkgerr=bkgerr,/quiet,/posve,/negve) parameters lamda [INPUT; required] wavelengths at which spectrum is defined. spec [INPUT; optional] the spectrum. NOTE: if not given, LAMDA is taken to be SPEC and the array indices are taken to be LAMDA keywords sig [INPUT] error at each point; if not given, the errors are taken to be 1+sqrt(abs(SPEC)+0.75). nsigma [INPUT; default: 4] multiple of SIG to consider as a threshold for detection of features cell [INPUT] 1D filter to use in computing the background * default is [1,1,0,0,0,1,1] * if scalar, then [IC+1,ICC,IC+1], where IC=intarr(2*CELL), ICC=intarr(2*CELL+1) bkgval [OUTPUT] final background values at each bin NOTE: This is essentially a smoothed version of the cleaned spectrum! bkgerr [OUTPUT] error estimates on BKGVAL quiet [INPUT] if set, doesn't show, doesn't tell posve [INPUT] if set, removes only +ve deviations negve [INPUT] if set, removes only -ve deviations _extra [JUNK] here only to prevent crashes description 1. make sure that the spectrum is defined on a regular grid. (if not, rebin [NOT IMPLEMENTED!]) 2. convolve the spectrum with background cell to determine local background. 3. also propagate errors (assume gaussian; if poisson, use gaussian approximation) 4. compare local value with local background 5. flag those bins which are significantly different from local background (use +-NSIGMA*SIG as a threshold value) 6. reset the flagged bin values to local background values 7. repeat 2-6 until no new bins are flagged these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (Oct96) changed keyword SIGMA to SIG (VK; Jun98) CELL was being altered if input as scalar -- corrected; altered behavior of output when no deviations are found (VK; Oct98) now if QUIET>1, won't ask to quit if many bins are found (VK; 99Aug) changed POS and NEG to POSVE and NEGVE (VK; MMJul)
(See pro/linerem.pro)
function linespec returns a spectrum of atomic lines. output will be in units of [erg,ph]/s/cm^2/[keV,Ang] if IKEV is set, WMIN,WMAX,WW must be input in [keV] and the output will have units .../keV if NOPH is set, output will have units of erg/... if EFFAR and WVLAR are not set, output will have units of .../cm^2 syntax spec=linespec(atom,wmin=wmin,wmax=wmax,nbin=nbin,/wlog,ww=ww,/ikev,$ fstr=fstr,pres=pres,logP=logP,n_e=n_e,desig=desig,econf=econf,$ /allah,dbdir=dbdir,dem=dem,abund=abund,effar=effar,wvlar=wvlar,$ /noph,chifil=chifil,chidir=chidir,eqfile=eqfile,verbose=verbose) parameters atom [INPUT; default: all] element(s) whose line intensities are to be read. * can specify ionic state (e.g., 'FeXX') * may be an array (e.g., ['He', 'c 5', 'N V', 's_8']) keywords wmin [I/O] minimum value of wavelength range * default is 1.23985A (10 keV) * overwritten if WW is set wmax [I/O] maximum value of wavelength range * default is 900A * overwritten if WW is set nbin [I/O] number of bins in spectrum * default is 100 * overwritten if WW is set wlog [I/O] if set, binning will be logarithmic ww [I/O] if set as an array on input, assumed to be the bin boundaries -- * NBIN will be reset to n_elements(WW)-1 on output * WMIN will be reset to min([WW(0),WW(nbin)]) on output * WMAX will be reset to max([WW(0),WW(nbin)]) on output ikev [INPUT] if set, WMIN,WMAX,WW are all assumed to be in keV * it is also caught at this stage and is not passed down to LINEFLX fstr [I/O] if defined on input, will return all the spectral lines info LINE_INT,LOGT,WVL,Z,ION,DESIG,ECONF in that order in a structure. * ion balance is included in LINE_INT, but abundances are not. * if defined as a structure on input, RD_LINE and FOLD_IONEQ will not be called, so use with caution! _extra [INPUT] allows specifying defined keywords to subroutines called by this program * RD_LINE: PRES,LOGP,N_E,DESIG,ECONF,ALLAH,DBDIR,VERBOSE * FOLD_IONEQ: CHIFIL,VERBOSE * RD_IONEQ: CHIDIR,EQFILE * LINEFLX: DEM,ABUND,EFFAR,WVLAR,NOPH subroutines RD_LINE [KILROY, SYMB2ZION [LAT2ARAB]] FOLD_IONEQ [WHEE, GETLOCMAX, RD_IONEQ [READ_IONEQ (CHIANTI)]] LINEFLX [WHEE] HASTOGRAM [KILROY] history vinay kashyap (Jan97) included ion balance into FSTR (VK;Feb97) bug -- crashes when FSTR not specified (VK;Mar97) speeded up spectrum accumulation by adding call to HASTOGRAM (VK;Jan98) modified ion balance calcs (VK; 99May) changed keyword KEV to IKEV; DESIG and ECONF must be explicitly set to 0 to avoid reading them in in RD_LINE; streamlined IKEV behavior (VK; JanMMI)
(See pro/linespec.pro)
function linespec_em returns a spectrum of atomic lines for a 1-T EM. output will be in units of [erg,ph]/s/cm^2/[keV,Ang] if IKEV is set, WMIN,WMAX,WW must be input in [keV] and the output will have units .../keV if NOPH is set, output will have units of erg/... if EFFAR and WVLAR are not set, output will have units of .../cm^2 syntax spec=linespec_em(atom,wmin=wmin,wmax=wmax,nbin=nbin,/wlog,ww=ww,/ikev,$ tlog=tlog,EM=EM,fstr=fstr,pres=pres,logP=logP,n_e=n_e,desig=desig,$ econf=econf,/allah,dbdir=dbdir,abund=abund,effar=effar,wvlar=wvlar, /noph,chifil=chifil,chidir=chidir,eqfile=eqfile,verbose=verbose) parameters atom [INPUT; default: all] element(s) whose line intensities are to be read. * can specify ionic state (e.g., 'FeXX') * may be an array (e.g., ['He', 'c 5', 'N V', 's_8']) keywords wmin [I/O] minimum value of wavelength range * default on input is 1.23985A (10 keV) wmax [I/O] maximum value of wavelength range * default on input is 900A nbin [I/O] number of bins in spectrum * default on input is 100 wlog [I/O] if set, binning will be logarithmic ww [I/O] if set as an array on input, assumed to be the bin boundaries -- * NBIN will be set to n_elements(WW)-1 on output * WMIN will be set to min([WW(0),WW(nbin)]) on output * WMAX will be set to max([WW(0),WW(nbin)]) on output ikev [INPUT] if set, WMIN,WMAX,WW are all assumed to be in keV * it is also caught at this stage and is not passed down to LINEFLX fstr [I/O] if defined on input, will return all the spectral lines info LINE_INT,LOGT,WVL,Z,ION,DESIG,ECONF in that order in a structure. * ion balance is included in LINE_INT, but abundances are not. * if defined as a structure on input, RD_LINE and FOLD_IONEQ will not be called, so use with caution! tlog [INPUT] log10(T [K]) at which EM is defined EM [INPUT] Emission Measure [cm^-5; if not, output units must be suitably mangled] _extra [INPUT] allows specifying defined keywords to subroutines called by this program * RD_LINE: PRES, LOGP, N_E, DESIG, ECONF, ALLAH, DBDIR * FOLD_IONEQ: CHIFIL * RD_IONEQ: CHIDIR, EQFILE * LINEFLX: DEM, ABUND, EFFAR, WVLAR, NOPH subroutines RD_LINE [KILROY, SYMB2ZION [LAT2ARAB]] FOLD_IONEQ [WHEE, GETLOCMAX, RD_IONEQ [READ_IONEQ (CHIANTI)]] LINEFLX [WHEE] HASTOGRAM [KILROY] history vinay kashyap (Apr97; modified from LINESPEC.PRO) speeded up spectrum accumulation by adding call to HASTOGRAM; speeded up cycling thru lines by modifying DEM (VK;Jan98) modified ion balance calcs (VK; 99May) changed keyword KEV to IKEV; DESIG and ECONF must be explicitly set to 0 to avoid reading them in in RD_LINE; streamlined IKEV behavior (VK; JanMMI)
(See pro/linespec_em.pro)
FUNCTION line_chianti returns a 2D array containing line cooling emissivities at a set of temperatures for all available spectral lines (in a CHIANTI style database [http://wwwsolar.nrl.navy.mil/chianti.html]) for the specified element at the specified pressure or density [1e-23 erg cm^3 s^-1] (NTEMP,NANG) NOTE: Ion Balance is NOT included!!! SYNTAX fx=line_chianti(elem,pres,logT,ang,trans,kev=kev,ikey=ikey,jkey=jkey,$ econf=econf,wmn=wmn,wmx=wmx,n_e=n_e,istate=istate,/tex,chidir=chidir) PARAMETERS elem [INPUT; required] name of element e.g., "He", "C", etc. * may specify ionic state (e.g., 'Fe XXII') * if an array, only the first element is looked at pres [INPUT; default: 1e15 cm^-3 K] pressure at which to compute level populations temp [INPUT/OUTPUT] log(Temperature[K]) at which to compute the line fluxes. if not given, then TEMP=4.0+FINDGEN(81)*0.05 * best results if evenly spaced in log(T) ang [OUTPUT] all the wavelengths [Angstrom] trans [OUTPUT] 2D array of transitions -- trans[0,*] lower levels; trans[1,*] upper levels KEYWORDS kev [OUTPUT] all the line energies (same as ANG, but in [keV]) ikey [OUTPUT] ionic state of element producing the line at ANG jkey [OUTPUT] ionic state that matters to ion balance econf [OUTPUT] 2D string array of e-configurations -- econf[0,*] lower levels; econf[1,*] upper levels wmn [INPUT; default: 0 Angstrom] minimum value of wavelength to include in output wmx [INPUT; default: 900 Angstrom] maximum value of wavelength to include in output n_e [INPUT] electron density [/cm^3] * OVERRIDES values determined using PRES and TEMP istate [INPUT; default: ALL; overridden by ELEM] limit calculations to specified ionic states (1=neutral, 2=singly ionized, etc.; can be an array) _extra [INPUT ONLY] used to specify * /TEX -- TRANS in TeX format (1) or not (0) * CHIDIR -- path name to the CHIANTI installation RESTRICTIONS * uses the CHIANTI database * requires subroutines: -- GET_IONLIST -- SYMB2ZION [LAT2ARAB] -- RD_CHIANTI [READ_WGFA2(%), READ_ELVLC(%), READ_SPLUPS(%), READ_IP(%)] -- POPSOL [DESCALE_UPS(%), NENH] -- TRANSLABEL -- KILROY -- IS_KEYWORD_SET (%): CHIANTI subroutine, used as is HISTORY vinay kashyap (Nov96) removed ion balance, changed input keyword CONF to output ECONF, changed mult. factor from 1e30 to 1e23 (VK; Dec96) added level excitation check (VK; Jun97) corrected bug with TEMP specification; forced ELEM to be scalar (VK; Nov98) changed call from POPLEV to POPSOL (VK; SepMM) added keyword JKEY; corrected calls to modifications of GET_IONLIST, RD_CHIANTI, and POPSOL to account for dielectronic recombination lines; converted syntax to IDL5 (VK; OctMM) bug correction: CHIDIR was not being passed on; caught and filtered -ve population levels (VK; DecMM) bug correction: transition labels were being filtered on wavelength twice, once within TRANSLABEL and once here. now forced the range in TRANSLABEL to be ignored (VK; Jun01) bug correction: was failing if ELEM contained ION info (VK; May02) modified call to POPSOL, per CHIANTI 4.2 changes (VK; Apr04) updated for IDL5.6 keyword_set([0]) behavior change for vectors (VK; 20Mar2006) made loops go over long integers (VK; 11Jun2010)
(See pro/mkemis/line_chianti.pro)
procedure lmcoeff used by LEVMARQ (formerly MRQMIN.F) to evaluate the linearized fitting matrix ALPHA and vector BVEC (BETA in Numerical Recipes) and calculate chi^2 syntax lmcoeff,x,y,a,funcs=funcs,sig=sig,ifit=ifit,alpha=alpha,bvec=bvec,$ chisq=chisq,yfunc=yfunc,poisson=poisson parameters x [INPUT; required] data points y [INPUT; required] Y(X) * sizes of X and Y must match a [INPUT; required] parameters for user-supplied procedure keywords funcs [INPUT] name of user-defined procedure that takes as input X and A, and returns YMODEL(X;A), and the partial derivatives of the model function wrt A. Any procedure that was written to work with CURVEFIT or GHRS' WFIT will do. * default is set to X3MODEL * why is it a procedure and not a function? well, ask the person who wrote CURVEFIT. sig [INPUT; default=sqrt(abs(Y)+0.75)+1] standard deviations on Y ifit [INPUT] integer array of same size as A, with 0's indicating frozen parameters and 1's indicating thawed parameters * if IFIT does not match A for any reason, all parameters are assumed to be thawed alpha [OUTPUT] fitting matrix bvec [OUTPUT] fitting vector chisq [OUTPUT] chi^2, or ln(p(D|M)) if POISSON is set yfunc [OUTPUT] Y(X;A) -- function values poisson [INPUT] if set, returns the log of the poisson likelihood, p(D|M) instead of the chi-sq * do _not_ use this keyword for background-subtracted data!! _extra [JUNK] here only to prevent crashing the program subroutines LNPOISSON history (C) Copr. 1986-92 Numerical Recipes Software =$j!]Y'1,). translated from MRQCOF.F to IDL by Vinay Kashyap (Oct98) now returns correct chisq if all params are frozen (VK; JanMM) added keyword POISSON and call to LNPOISSON (VK; Aug01)
(See pro/fitting/lmcoeff.pro)
function lnpoisson
returns the natural log of the poisson likelihood of observing
the specified counts given the model source intensity,
p(D|M) = M^D * exp(-M) / D!
syntax
lnp=lnpoisson(d,m,/chilike,verbose=verbose)
parameters
d [INPUT; required] data counts
m [INPUT; required] model intensity
* output will be array of size [N(D),N(M)]
unless CHILIKE is set, in which case output will be N(M)
(beware that IDL automatically compresses trailing
dimensions if any of them are equal to 1)
keywords
chilike [INPUT] if set, returns -2*SUM_{D}(ln(p(D|M)))
verbose [INPUT] controls chatter
_extra [JUNK] here only to avoid crashing the program
history
vinay kashyap (Aug01)
bug correction: m^d was not translated correctly (VK; Mar02)
(See pro/stat/lnpoisson.pro)
function locmax returns the local maxima of a 1D array syntax fmax=locmax(f,sigma=sigma,thresh=thresh,width=width,prob=prob,$ /poisson,nubin=nubin,fmin=fmin,fmax=fmax) parameters f [INPUT; required] input array keywords sigma [INPUT] errors on F (ignored if POISSON is set) * ignored if POISSON is set AND F(*).GE.0 * default is sqrt(abs(F)+0.75)+1 thresh [INPUT; default: 0.5] threshold probability below which to ignore a calculation width [INPUT; default: 1] compare value in bin to values on either side averaged over WIDTH bins * NOTE: WIDTH is the *half*width poisson [INPUT] if set, assumes a poisson error distribution * automatically UNSET if min(F) < 0 prob [OUTPUT] returns the computed probabilities the following are not to be changed unless the user understands what's going on! nubin [INPUT; default: 100] size of uniform grid to superpose on F fmin [INPUT] minimum value for integration. default is 0.2*min(F) or if min(F)<0 then 5*min(F) fmax [INPUT] maximum value for integration. default is 5*max(F) or if max(F)<0 then 0.2*max(F) description at each point, compute the probability that given value is a local maximum. p = \int dF p(f|f[i],s[i])*p(f[i-1]<f|s[i-1])*p(f[i+1]<f|s[i+1]) find all the peaks in the distribution of probabilities that lie above a given threshold. the positions of these peaks are identified with positions of local maxima. requires LOCMAX_CDF (included in file) IGAMMA (not in old IDLs) ERRORF (not in old IDLs?) history vinay kashyap (Oct96)
(See pro/util/locmax.pro)
procedure locus_ellipse make a curve describing the locus of an ellipse syntax locus_ellipse,xout,yout,xcen=xcen,ycen=ycen,amajor=amajor,$ aminor=aminor,theta=theta,npt=npt,verbose=verbose parameters xout [OUTPUT; required] x-coordinates of the locus yout [OUTPUT; required] y-coordinates of the locus keywords xcen [INPUT; default=0] x-coordinate of the center ycen [INPUT; default=0] y-coordinate of the center amajor [INPUT; default=1] length of the semi-major axis aminor [INPUT; default=1] length of the semi-minor axis * if AMINOR is not defined, it is set to AMAJOR to make a circle * if AMINOR>AMAJOR, no harm done, program will run regardless of mathematical purity theta [INPUT; default=0 degrees] anticlockwise angle made by AMAJOR with x-axis npt [INPUT; default=101] number of points along the locus, spaced equally along THETA * note that the first and the last points are identical unless NPT < 0, in which case abs(NPT) points are returned without the overlap verbose [INPUT; default=0] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Mar2008)
(See pro/util/locus_ellipse.pro)
function logit compute and return the logit function. LOGIT() maps a variable in the [0,1] range to the real number line [-\infty,+\infty] by applying the transformation ln(x/(1-x)). conversely, UNLOGIT() maps the real number line to [0,1] by applying the transformation e^y/(1+e^y). syntax lx=logit(x,sigx,sigl=sigl) parameters x [INPUT; required] a variable in the range [0,1] * can be an array * value is set to NaN in output if input falls outside valid range sigx [INPUT] standard error on X * if <0 and >-1, then ABS(SIGX) is taken to be the fractional error * if <-1 and >-100, then ABS(SIGX) is taken to be the percentage error * if <-100, then 1/ABS(SIGX) is taken to be the fractional error keywords sigl [OUTPUT] standard error on LOGIT(X) * note that SIGL = SIGX/(X*(1-X)) _extra [JUNK] here only to prevent crashing the program history vinay kashyap (3may04; based on conversation with Xiao-li Meng)
(See pro/stat/logit.pro)
function loopem convert a set of integrated emission measures to a differential emission measure distribution assuming a hydrostatic-loop type distribution and return computed DEM DEM(T) is generally n^2*dX/dlnT, and EM(T) == \int_0^T dlnT' DEM(T') = \int_0^T dT' DEM(T')/T' In particular, DEM is parameterized as DEM(T)=a*T^b So for a given EM(T), we obtain EM(T)=(a/b)*(Tmax^(b)-Tmin^(b)), Tmin=0, b>0 with Tmin=0 for b>0 syntax dem=loopem(logTmax,EM,logT=logT,sloop=sloop,verbose=verbose) parameters logTmax [INPUT; required] loop top temperature(s) in log10(deg K) EM [INPUT] if given, normalize the output DEM to give a total Emission Measure equal to this. * size must match that of logTmax -- if fewer, fills out with 1st element; if more, ignored keywords logT [INPUT] temperature grid over which output DEM is returned * default is 4..8 in steps of 0.05 sloop [INPUT] slope of DEM in log(DEM)-log(T) space * default is 1.5 verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Nov01) changed NORM calc to allow for large values of SLOOP (VK; Feb05)
(See pro/loopem.pro)
function lsd
returns list of density sensitive lines in given wavelength range
syntax
ld=lsd(wrange,fluxes,wvls,elem=elem,edens=edens,DEM=DEM,tlog=tlog,$
dbdir=dbdir,ceiling=ceiling,flor=flor,ratmax=ratmax,flxmax=flxmax,$
outZ=outZ,outIon=outIon,outIDX=outIDX, tol=tol,chifil=chifil,$
chidir=chidir,eqfile=eqfile,/temp,abund=abund,/noph,effar=effar,$
wvlar=wvlar,/ikev)
parameters
wrange [INPUT; required] wavelength range in which to search for
density sensitive lines
* if only one element is given, set the range to be 10% of
it on either side
* if the single element is a string, apply RD_LIST rules
to decipher it ("WVL +- dW", "WMIN,WMAX", "WMIN-WMAX"
are all allowed)
fluxes [OUTPUT] 2D array of predicted fluxes for lines that are
found to be density sensitive, FLUXES(EDENS,WVLS)
wvls [OUTPUT] array of wavelengths of lines that are found to
be density sensitive
keywords
elem [INPUT] if set, confine attention to just those elements and
ionic species specified.
* default is to look at all available lines
edens [I/O] array of electron densities [cm^-3] at which to
check for density sensitivity.
* default is [1e8,1e14]
* if not specified, insufficiently specified, or otherwise
meaningless, uses default
DEM [INPUT] input array of differential emission measures [cm^-5]
* default is to use 1e12 [cm^-5] at specified TLOG
tlog [INPUT] log(temperatures) at which DEM is defined
* if not specified, set to 6.0, unless DEM has more steps,
in which case interpolated to the 4..8 range
dbdir [INPUT] line database directory to use to search for the
density sensitive lines
* default is $CHIANTI
ceiling [INPUT] maximum relative variation the fluxes of a given
line must have before it is accepted as density sensitive
* default is 2
* if 0 < CEILING < 1, it is assumed that the *reciprocal*
of CEILING is given (e.g., CEILING=0.5 is translated to 2)
* if CEILING < 0, assumed to be percentages (e.g., CEILING=-1
is translated to 1/0.01 == x100)
flor [INPUT] if set, ignores any line which has a peak flux
a factor FLOR below the flux of the strongest of the
lines filtered through CEILING.
* default is 0
* if FLOR > 1, assumed that the reciprocal of FLOR is given,
i.e., FLOR=100 translates to 0.01
* if FLOR < 0, taken to be the absolute flux threshold, in
whatever units it is being calculated in
* NOTE on difference between CEILING and FLOR:-
CEILING works on ratios, and FLOR works on the intensities
ratmax [OUTPUT] the maximum deviations found for each of the
density-sensitive lines found
flxmax [OUTPUT] the peak fluxes for each of the density sensitive
line found
outZ [OUTPUT] atomic numbers
outIon [OUTPUT] atomic numbers
outIDX [OUTPUT] indices which passed the test
* be careful in how you use this. a common mistake is to
assume that it matches with whatever line emissivity
database that has been read in. that might very well be
true, but is definitely not guaranteed.
_extra [INPUT] use this to pass defined keywords to subroutines:-
FOLD_IONEQ: CHIFIL
RD_IONEQ: CHIDIR, EQFILE
LINEFLX: TEMP, ABUND, NOPH, EFFAR, WVLAR, IKEV
ARRAYEQ: TOL
example usage
ls=lsd('10-120',dbdir='$CHIANTI',edens=[1e9,1e12],ceiling=2,ratmax=rmx)
for i=0,n_elements(ls)-1 do print,ls(i),1./rmx(i),i
;
eden=10.^(findgen(6)+8)
ls=lsd('113.35?0.1',flx,elem='Fe20',dbdir='$CHIANTI',edens=eden)
plot,eden,flx
subroutines
MK_DEM
RD_LINE
FOLD_IONEQ
RD_IONEQ
READ_IONEQ (CHIANTI subroutine)
LINEFLX
ARRAYEQ
KABOOM
INICON
IS_KEYWORD_SET
history
vinay kashyap (Nov98)
changed default EDENS to [1e8,1e14]; added keywords DEM,TLOG,OUTZ,
OUTION; added call to MK_DEM; changed keyword FLOOR to FLOR; changed
behavior of FLOR<0 (VK; Dec98)
modified ion balance calcs (VK; 99May)
changed call to INITSTUFF to INICON (VK; 99May)
added keyword outIDX (VK; JanMMI)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
(See pro/lsd.pro)
script make_spectrum compute a spectrum using line and continuum emissivities warning all program variables have names that begin as "v_" or "jnk_" if you have any preexisiting variables with these names, they will be overwritten. inputs ATOMIC: line emissivities and wavelengths continuum emissivities and wavelength grid (subsumed in database directory names) ion fractions STELLAR: coronal electron density coronal abundances Differential Emission Measure distance Galactic coordinates (or absorption column density) OBSERVATIONAL: instrument effective area synthetic spectrum wavelength grid photon redistribution matrix exposure time outputs v_linint line intensities @ source (@ wavelengths v_lwvl; from species v_Z,v_ion) v_conint continuum intensities @ source (@ wavelength grid v_cww) v_linflx theoretical line fluxes @ earth (using ISM transmission factors v_ltrans) v_conflx theoretical continuum fluxes @ earth (using ISM transmission factors v_ctrans) v_linspc theoretical line spectrum @ earth v_conspc theoretical continuum spectrum @ earth v_flxspc predicted spectrum through telescope v_wvls mid-bin values of predicted spectrum wavelength grid v_ctspc predicted count spectrum for detector v_chan energy channels for count spectrum how to use 1. initialize the PINTofALE environment using INITALE 2. the parameters that will be set with INITALE are: -- ATOMIC: !LDBDIR, !IONEQF, !CDBDIR, !CEROOT, !CHIDIR -- STELLAR: !EDENS, !ABUND, !NH, !FH2, !HE1, !HEII verify that they are initialized to the right values 3. define DEM as a function of LOGT (use DEMACS() or MK_DEM()) -- place in variables v_LOGT [K] and v_DEM [cm^-3] 4. define distance in [pc] -- place in variable v_DIST 5. read in the instrument effective area -- place in variables v_EFFAR [cm^2] and v_WVLAR [Ang] 6. read in (or define) the synthetic spectrum wavelength grid -- place in variable v_WGRID [Ang] (must be _bin boundaries_) 7. define the exposure time [ks] -- place in variable v_EXPTIME 8. define the name of the OGIP-style RMF -- place in variable v_RMF (set to 'NONE' if, e.g., grating spectrum is being analyzed) 9. run this script history vinay kashyap (OctMM)
(See pro/scrypt/make_spectrum.pro)
function marfrmf returns the instrument response matrix computed as the product of the redistribution matrix with the ancillary response. syntax rsp=marfrmf(arffil,rmffil,ostr,effar=effar,/noext,/nofull,$ fchcol=fchcol,/shift1) parameters arffil [INPUT; required] OGIP-compliant Ancillary Response File * appends a ".arf" if missing (overridden by NOEXT) rmffil [INPUT; required] OGIP-compliant Redistribution Matrix File * appends a ".rmf" if missing (overridden by NOEXT) ostr [OUTPUT] structure containing the axes information for the response matrix -- see RD_OGIP_RMF() keywords effar [OUTPUT] returns the effective area as a function of ELO noext [INPUT] normally, if an extension is missing from ARFFIL or RMFFIL, the program will append the appropriate extension. if this keyword is set, no such action will occur. nofull [INPUT] if set, bypasses RDRESP() and the accompanying computation of the full response matrix (i.e., with the OGIP compression removed). this is useful for those cases where the uncompressed matrix is too large for memory. * if this is set, the output will be simply the same as OSTR.MATRIX, which is the compressed version of the effective area weighted redistribution matrix _extra [INPUT] pass defined keywords to subroutines RD_OGIP_RMF: FCHCOL, SHIFT1 restrictions * requires subroutines RD_OGIP_RMF, RDRESP and RDARF * requires IDLASTRO library of routines history vinay kashyap (Jul97) allowed for keyword SHIFT1 (VK; JanMMI) added keyword NOFULL; now multiplication also works on OSTR.MATRIX (VK; Nov2001) changed output in case of /NOFULL from 1.0 to OSTR.MATRIX (VK; Oct2008)
(See pro/util/marfrmf.pro)
procedure mcerror
procedure that estimates confidence bounds for model fits by
fitting to different monte-carlo realizations of the data and
estimating the bounds from the distribution of the resulting
parameter values.
generates NN number of synthetic data sets by randomly varying
each data point within its estimated error. fits these NN
synthetic data sets to generate parameter sets a(1),a(2),..a(NN),
so that we can estimate distribution of a(x)-a(best). Uses this
as a basis for confidence bound estimation. Finds smallest possible
bounds giving required confidence (as opposed to 'counting' up
and down from best fit by required fraction)
syntax
mcerror,x,y,a,erru,errl,ysig=ysig,freeze=freeze,mcfuncs=mpfuncs,$
algo=algo,verbose=verbose, erra=erra,yfunc=yfunc,mciter=mciter,$
itmax,chitr=chitr,mcconf=mcconf,/dumb, jumpup=jumpup,jumpdn=jumpdn,$
=svdthr,funcs=funcs, function_name=function_name,$
ype, missing=missing,/fwhm,/norm,betap=betap, /poisson
parameters
x [INPUT; required] data points
y [INPUT; required] Y(X)
* sizes of X and Y must match
a [I/O; required] parameters for user-supplied function
* on input, these are assumed to be initial guesses
* on output, these contain the best-fit values
erru [OUTPUT; required] upper limits of confidence range interval
errl [OUTPUT] lower limits of confidence range interval
* if ERRL is not specified on input, ERRU will contain the
average value of the upper and lower >>deviations<<.
keywords
ysig [INPUT] standard deviations on Y
* default=sqrt(abs(Y)+0.75)+1
* if single element, then sig(Y[*])=YSIG(0)
* if -ve, taken to be the fractional error
mciter [INPUT] number of additional iterations for each parameter:
total iterations = (mciter x number of parameters) > 2xmciter+1
default: mciter=30
mcconf [INPUT] (two-sided) confidence for bound estimation,
default: mpfunc =0.68
mcsims [OUTPUT] 2 dimensional array MCSIMS==MCSIMS(free,sims)
where free are the number of thawed paramters and sims
is the number of simulations. contains all simulations
on output
mpfunc [INPUT] contains name of input function to fit
REQUIRED WHEN USING MPFIT
freeze [INPUT] freeze numbered parameters (index starts from 0!)
algo [INPUT] fitting algorithm
* only the following are implemented:
-- LevMarq+SVD
-- IDL-Curvefit
-- Mardkwardt's MPFIT
verbose [INPUT] verbosity level
erra [OUTPUT] formal "curvature" errors on the best-fit parameters
yfunc [OUTPUT] best-fit Y(X;A)
_extra [INPUT] pass defined variables to subroutines:-
FIT_LEVMAR: ITMAX, CHITHR, DUMB
ADJUSTIE: TIES, VNAME
LEVMARQ: JUMPUP, JUMPDN, SVDTHR
LMCOEFF: FUNCS, POISSON
CURVE_FIT: FUNCTION_NAME
note:- FUNCS, FUNCTION_NAME, and MPFUNC refer to name
of user-defined function that takes as input X
and A, and returns YMODEL(X;A), and the partial
derivatives of the model function wrt A. Any
function that was written to work with CURVEFIT
or GHRS' WFIT will do.
The default for FIT_LEVMAR is X3MODEL.
MK_3MODEL: TYPE
MK_GAUSS: MISSING, FWHM, NORM
MK_LORENTZ: BETAP, MISSING, NORM
history
Liwei Lin (Apr03) idenentical to ERORS.pro in input/output/parameter checks
added keyword MPFUNC for compatability with MPFIT
added keyword MCCONF so user can toggle confidence required
BUG FIX, mcerror not mcerors LL/SC JUL03
BUG FIX, yfunc was being recursivly overwritten in
synthetic loop LL/SC JUL03
added forward_function (VK; Jul03)
some cosmetic changes (VK; Feb04)
added MCSIMS (LL; Mar04)
BUG FIX algo keyword incorrectly processed (LL ; Sep05)
(See pro/fitting/mcerror.pro)
function mcmc_abund
An abundance-independent DEM-reconstruction can be achieved
by running a Monte Carlo Markov-Chain DEM reconstruction
mcmc_dem() on a set of He-like to H-like flux ratios.
A DEM realized in this fashion together with the observed
line fluxes give implied abundances. This function returns
fractional abundnaces relative to solar 'grevesse & sauval'
(not logarithmic values) given a set of MCMC realized DEMS
(mcmc_dem ouput), fluxes, and line details.
parameters
simdem [INPUT;required] an array of size
(NT,NSIM+1), with last column containing the best-fit
logt [INPUT] log_10(Temperature [K]) at which DEMS are given
wvl [INPUT; required] wavelengths [Ang]
flx [INPUT; required] flux [ph/s] at each WVL ([ph/s/cm^2]
fsigma [INPUT; required] errors for flx
emis [INPUT; required] line emissivities [1e-23 ergs cm^3/s]
* EMIS==EMIS(LOGT,WVL)
z [INPUT; required] atomic numbers of the elements
generating the lines at WVL.
asig [OUTPUT] error in the weighted mean abundance
zout [OUTPUT] atomic numbers corresponding to output abundances
keywords
abund [INPUT] set of abundances. see GETABUND(). Output
will be relative to this set. Default is Grevesse &
Sauval (1998)
abweight [INPUT] if a different weighting is required to compute
abundances then specify abweight as an array of weights of
the same size as flx (e.g. one can use fsigma)
elogt [INPUT] log_10(Temperature[K]) at which EMIS are
defined if different from logt
nosol [INPUT] if set, then output abundances will not be
relative to solar
olog [INPUT] if set, outputs abundances and asig will be
logarithmic values.
crctn_factor [INPUT] if set, correctin factor is applied to
theoretical fluxes before calculation of abundnaces
_extra [INPUT ONLY] use this to pass defined keywords to subroutines
subroutines
MC_EROR (/home/llin/mc_eror.pro) not PoA standard yet
LINEFLX
history
Liwei Lin 5/03
ADDED keyword log for logarithmic output (LL 7/03)
BUG FIX elogt is actually taken into account when set (LL/WB 8/03)
LL/CA 9/03 BUGFIX Costanza points out error calculation bug
which gives overestimation in errors
BUG FIX elogt handler (call to rebinx) should have logt
not dlogt as input (LL/WB 9/03)
LL 01/04
ADDED keyword crctn_factor for use with mixie
LL 01/04
H abundance cannot be updated
LL/SC 2/04
BUGFIX HISTOGRAM will give a one element array if given
just one atomic number to bin up.
LL ADDED _extra keyword to lineflx
LL 5/05 Change the asig determination to only include the errors
as determined from the DEMs.THIS SHOULD HAVE BEEN FIXED 9/03 AS
stated above. (do not include the error in the
fluxes a second time).
ADDED keyword abweight
LL 6/05 ADDED keyword abund
BUGFIX previous error calculation would fail for highly
assymetric cases
LL/DG 6/05 BUGFIX crash when MC_EROR returns two-element
arrays
(See pro/fitting/mcmc_abund.pro)
function mcmc_dem
performs Markov-Chain Monte-Carlo using a Metropolis algorithm
on a set of supplied line fluxes and returns an estimate of the
DEM that generates observed fluxes.
syntax
dem=mcmc_dem(wavelengths,fluxes,emissivities,Z=Z,logt=logt,$
diffem=initial_DEM,abund=abundances,fsigma=flux_errors,$
onlyrat=onlyrat,sysdev=sysdev,sysgrp=sysgrp,$
sampenv=sampenv,storpar=storpar,storidx=storidx,$
stordem=stordem,bestpar=bestpar,$
simprb=simprb,simdem=simdem,simabn=simabn,simflx=simflx,simprd=simprd,$
ulim=upper_limit_flag,softlim=softlim,demrng=DEMrange,abrng=abrng,$
smoot=smooth,loopy=loopy,/spliny,verbose=verbose, xdem=DEM_bins,xab=ABUND_bins,$
nsim=nsim,nbatch=nbatch,/steps,weight=weight,/gauss,type=type,/boxcar,$
nburn=nburn,/nosrch,savfil=savfil,bound=bound,demerr=demerr,$
aberr=aberr,/temp,/noph,effar=effar,wvlar=wvlar,/ikev,/regrid,$
mproxy=mproxy,mplet=mplet)
parameters
wvl [INPUT; required] wavelengths [Ang] at which fluxes are
observed
* NOTE: these are used only if the keyword NOPH is _not_ set,
i.e., when the input is to be converted from [erg/...] to
[ph/...]. In cases when the EMIS is precomputed with the
effective area and abundances (e.g., for filter data from
solar observatories), this is a dummy variable.
flx [INPUT; required] flux [ph/s] at each WVL ([ph/s/cm^2]
if EFFAR and WVLAR are not passed to LINEFLX)
emis [INPUT; required] line emissivities [1e-23 ergs cm^3/s]
* EMIS==EMIS(LOGT,WVL)
* DEM is computed at all temperatures that EMIS are defined.
* NOTE: the units are assumed to be [1e-23 ergs cm^3/s],
but of course the code doesn't care what they are exactly.
So it is perfectly possible to have them in units of, e.g.,
[DN cm^5 s^-1 pix^-1] if one so chooses (see SOLAR_TRESP.PRO)
keywords
Z [INPUT] atomic numbers of the elements generating the
lines at WVL.
* if not given, assumed to be Fe
* if EMIS are precalculated including abundances, then
set this to *1* (to mimic H)
logt [INPUT] log_10(Temperature [K]) at which EMIS are given
* if not supplied, assumed to go from 4 to 8
* if there is a size mismatch, logT will get stretched/shrunk
to cover EMIS
diffem [INPUT] initial guess for DEM(LOGT); default is 1e14 [cm^-5]
abund [I/O] abundances. default is to use Anders & Grevesse (see
GETABUND)
* if ABRNG is non-trivial, will be allowed to vary and on
exit will contain the MAP estimates of the abundances.
* minimum is hardcoded at 1e-20
fsigma [INPUT] error on FLX; if not given, taken to be
1+sqrt(abs(FLX)+0.75)
ulim [INPUT] long-integer array specifying which of the fluxes
are upper limits (1: UL, 0: not)
onlyrat [INPUT] string array describing which of the input fluxes
must be considered only as ratios
* each element of ONLYRAT corresponds to the fate of the
corresponding element of FLX
* basic format is: "sP#[,sP#[,...]]" where
-- "#" is an integer flag describing the ratio being
constructed
-- "P" is a positional descriptor and can take on
values N (for numerator) or D (for denominator)
-- "s" stands for the sign with which the flux
goes into the ratio "+" or "-"
* e.g., to construct a simple ratio FLUXES[2]/FLUXES[1],
ONLYRAT=['','+D1','+N1']
* e.g., to construct two hardness ratios
FLUXES[3]/FLUXES[1] and
(FLUXES[3]-FLUXES[1])/(FLUXES[3]+FLUXES[1]),
ONLYRAT=['','+D1,-N2,+D2','','+N1,+N2,+D2']
sysdev [INPUT] systematic deviations in the underlying atomic
physics data, multiplies the emissivity for a given line
by a random number in each iteration to mimic systematic
uncertainty in EMIS
* it is assumed that these modifications are small -- if
you do use this option, please check the output traces
to make sure that the chain is stable
* should be an array of the same size as FLX, and each
number defines the range over which EMIS[*,WVL] varies,
10.^(randomn(seed)*SYSDEV[i])*EMIS[*,i]
* if size is smaller than FLX, the missing elements are
set to 0, i.e., no modifications are made
sysgrp [INPUT] group different rows in EMIS to vary the same way
in each iteration, is simply an array of 1-based grouping
indices
* e.g., if N(WVL)=6, and SYSGR=[0,1,2,1,0,2], then rows
1 and 3 are modified in conjunction (i.e., if #1 is
changed by a factor 10^(r*SYSDEV[1]), then #3 is changed
by a factor 10^(r*SYSDEV[3]), where r is the same for both),
2 and 5 are modified in conjunction, but 0 and 4 are
_not_ tied together and are independently varied
* if SYSDEV is not defined, SYSGRP is ignored
* size must match that of FLX, but if smaller, the missing
elements are set to -1, i.e., are all tied together
- so if SYSGRP is not defined at all, all the rows are
tied together, and only SYSDEV[0] is used
demrng [INPUT] array containing the allowed range of variation
in DEM: DEMRNG(i,0) < DEM(i) < DEMRNG(i,1)
* if not supplied, DEMRNG(*,0)=DEM/1e5 & DEMRNG(*,1)=DEM*1e5
* if DEMRNG(k,0)=DEMRNG(k,1), this component is frozen
abrng [INPUT] as DEMRNG, for ABUND.
* if not supplied, ABRNG(*,0)=ABUND(*)=ABRNG(*,1)
xdem [INPUT] bin boundaries for accumulating the realized DEMs
* if scalar or 1-element vector, taken to be bin-width in log10
* if not specified, runs from min(DEMRNG) to max(DEMRNG)
in steps of 0.1 in log10
xab [INPUT] bin boundaries for accumulating the realized ABUNDs
* if scalar or 1-element vector, taken to be bin-width
* if not specified, runs from min(ABRNG) to max(ABRNG) in
steps of 0.1 in log10
xnsig [INPUT; default=3] force a minimum search range of
XNSIG*sigma_determined_internally
nsim [INPUT; default: 100; min=10] # of batches
nbatch [INPUT; default: 10; min=5] # simulations per batch
nburn [INPUT; default=NSIM/10] max # of simulations to run
before assuming that solution has stabilized
* note that this is a maximum -- if burn-in is achieved
earlier, the algorithm will move on to standard MCMC
nosrch [INPUT] if set, does *not* carry out a (crude) grid search
for a best guess initial starting point.
* if set to a IDL savefile name, restores the best guess
from said file
savfil [INPUT] if set, saves all variables to an IDL save file
prior to exit
* if not a string, or is an array, saves to 'mcmc.sav'
bound [INPUT; default=0.9] confidence interval of interest
* minimum=0.1
hwhm [INPUT] if set, returns the upper and lower Half-Widths
at Half-Maxmimum in DEMERR and ABERR.
demerr [OUTPUT] confidence bounds on MAP estimates of DEM
* DEMERR(*,0) are lower bounds, DEMERR(*,1) are upper bounds
aberr [OUTPUT] confidence bounds on MAP estimates of ABUND
* ABERR(*,0) are lower bounds, ABERR(*,1) are upper bounds
smoot [INPUT] if set, multiplies the local length scale determined
using FINDSCALE by SMOOT.
smooscl [INPUT] if set, bypasses FINDSCALE and uses the scales input
via this keyword as the local length scales
* _must_ be in units of [bins], not delta_T, dlogT, or whatever
* if vector and size matches LOGT, then uses the input values
as the [bins] over which to smooth
* otherwise assumes constant smoothing scale corresponding to
first element
loopy [INPUT] if set, "smooths" by converting to T^3/2, loop-like DEM
* use keyword SLOOP to change the index
* set to a number >1 to limit the maximum number of
temperature components
spliny [INPUT] if set, "smooths" by making a spline interpolation
sampenv [INPUT] envelope from which to sample the temperature bins.
this is a way to avoid T bins which may have no data and thus
work more efficiently to explore just that part of the parameter
space that is interesting.
* if not given, or is not understandable, assumed to be the
simple envelope of all the emissivities in EMIS
* if set to:
'ONLYRAT' - then the envelope is computed taking
into account the ratios
'INCABUND' - then use emissivities weighted by the abundance
'FLAT' - then make no distinction between different T bins
'INCALLT' - then force a look at all T bins at a 1% level
'STEPPED' - then zero everywhere EMIS does not cover the
T range, and at least 25% of maximum where it does
'COVER' - then zero everywhere EMIS does not cover the
T range, and constant where it does
* NOTE: multiple SAMPENV settings may be specified, and
they will be applied in the above sequence -- whether the
sequence makes sense or not is up to the user to determine
* if set to a numerical array the same size as LOGT, then
simply use that array as the envelope
* NOTE: recommend using 'COVER' or 'STEPPED' for EMIS
derived from broad-band filters such as for solar data
storpar [OUTPUT] parameters from the MCMC chain
storidx [OUTPUT] index of the parameters stored in STORPAR
stordem [OUTPUT] DEMs calculated from the parameters for given STORIDX
bestpar [OUTPUT] best values of the parameters as found in the chain
simprb [OUTPUT] the metric at the end of each batch, an array of size
(NSIM+1), with last element containing the value for the best-fit
simdem [OUTPUT] the DEM at the end of each batch, an array of size
(NT,NSIM+1), with last column containing the best-fit
simabn [OUTPUT] same as SIMDEM, but for abundances
simflx [OUTPUT] same as SIMDEM, but for the fluxes with each [DEM,ABUND]
simprd [OUTPUT] same as SIMFLX, but for the ratios, only if ONLYRAT is used
mixsstr [I/O] Set to turn on line deblending via MIXIE().
Line (and/or conitnuum) structure of
RD_LIST() format containing info (wvl,emis,z) on
lines (and/or continuum) for which possible contaminants will be identified
and for which correction factors will be
calculated. Assumes that ion equilibria are
included. (see RD_LIST() keyword INCIEQ).
mixlstr [I/O] Line (and/or conitnuum) structure of
RD_LIST() format containing info (wvl,emis,z) on
lines (and/or continuum) for which possible contaminants will be identified
and for which correction factors will be
calculated. Assumes that ion equilibria are
included. (see RD_LIST() keyword INCIEQ)
set to turn on line deblending via MIXIE().
verbose [INPUT] explicitly set to 0 to avoid making plots
* THINK TWICE before doing this!!
_extra [INPUT] pass defined keywords to subroutines
ties [ADJUSTIE] tie abundance parameters
temp [LINEFLX] assume input LOGT are actually T [K]
noph [LINEFLX] compute fluxes in [ergs/s/...] not [ph/s/...]
effar [LINEFLX] effective area in [cm^2]
wvlar [LINEFLX] wavelengths at which EFFAR are defined [Ang]
nhne [LINEFLX] ratio of N(H)/n_e, assumed to be 0.83
softlim [LIKELI] allow for upper limits to be softly defined
steps [VARSMOOTH] assume stepped averaging from smoothing scale
weight [VARSMOOTH] allow weighting of adjacent points in boxcar smooth
type [VARSMOOTH] functional form to smooth with, see X3MODEL/LIBMODEL
boxcar [VARSMOOTH] controls smoothing behavior at endpoints
betap [MK_LORENTZ/MK_SLANT] index of beta-profile
angle [MK_SLANT] angle of tilt
fwhm [MK_GAUSS/MK_LORENTZ/MK_ROGAUSS] return FWHM rather than
sigma or core width
sloop [LOOPEM] slope of loop DEM
dfx_mul [GENERATIO] multiplicative delta_Fx to compute partials
dfx_add [GENERATIO] additive delta_Fx to compute partials
choice [FINDSCALE] flag to choose algo to find the scales
pick [FINDSCALE] flag on hoe to collapse scales from 2D to 1D
crunch [FINDSCALE] collapse 2D to 1D prior to finding scales
half [FINDSCALE] return half-scale
eps [FINDSCALE] a small number
mproxy [MIXIE] see MIXIE()
mplet [MIXIE] see MIXIE()
restrictions
requires subroutines
-- KILROY
-- GETABUND
-- MCMC_DEM_ONLY [LINEFLX, LIKELI, MK_DEM, VARSMOOTH, LOOPEM]
-- LINEFLX [GETABUND, WHEE]
-- LIKELI [SOFTLIM]
-- FINDSCALE [WVLT_SCALE [ROOFN]]
-- MK_DEM
-- LOOPEM
-- VARSMOOTH
-- GENERATIO
-- ADJUSTIE
history
vinay kashyap (Apr 97)
added keyword SMOOT (VK; May97)
added keyword LOOPY and replaced call to VARSMOOTH by call to
MK_DEM (VK; Nov01)
added keyword ONLYRAT and call to GENERATIO (VK; Nov'02)
numerous bug fixes (VK/LL; Dec'02)
ratio stuff was not being passed on to MCMC_DEM_ONLY; now stores
simulated DEMs, ABUNDs, fluxes, and ratios (VK/LL; Jan'03)
added keywords SAMPENV,STORPAR,STORIDX,SIMPRB,SIMDEM,SIMABN,
SIMFLX,SIMPRD,NBURN (VK; Feb'03)
added keyword SMOOSCL (VK; May'03)
added keyword SPLINY (VK; Jun'03)
added _extra to call to PRED_FLX (VK; Jul'03)
bugfix sampenv ONLYRAT keyword handler included (VK/LL:Dec'03)
bugfix sampenv was ignored if input as array (LL: Dec'03)
bugfix nemt is undefined in logt keyword handler(LL:Dec'03)
added BRNSTR in call to MCMC_DEM_ONLY() to enable deblending
via MIXIE() (LL:Jan'04)
bugfix abndupdt, a MIXIE keyword now set by default and
turned off if abrng keyword is set (LL:Mar'04)
added keyword XNSIG (VK; Jun'04)
bug fix: compute DEMs for /LOOPY and /SPLINY on correct T grid
(VK; Jan05)
allow limiting number of T components for LOOPY (VK; Mar05)
added call to adjustie and MIXLSTR keyword (LL; Jun05)
added LCOMP to call to MK_DEM, check to make sure FSIGMA
are all +ve definite, and a warning if ABUND[0] is not 1,
force single T deviate per iteration for LOOPY (VK; Jun05)
bug correction: if no update found in a batch, was still
storing DEM from that batch; now corrected (VK; Jul05)
added options COVER and STEPPED for SAMPENV (VK; Jan06)
include extra kick at NPAR+1 to unfreeze parameters in case
of LOOPY getting stuck; also bug correction for NPAR+1
selections in regular case if some T bins are frozen
(VK; Apr06)
added keyword VERBOSE (VK; Jun07)
added keyword BESTPAR (VK; Nov08)
added keywords SYSDEV and SYSGRP (VK; Apr09)
changed how stddev of proposal distr. is calculated, from using
histograms to using unbinned distr.; added keyword STORDEM and
now STORPAR outputs unsmoothed parameters (VK; Apr12)
(See pro/fitting/mcmc_dem.pro)
procedure mcmc_dem_only
dedicated subroutine to MCMC_DEM, written only to make MCMC_DEM
more readable. this part decodes the parameters, calls LINEFLX
to get predicted fluxes and LIKELI to get the likelihood.
syntax
mcmc_dem_only,pars,fobs,fsigma,ulim,line,logT,wvl,Z,scale,ff,prb,$
dem,abnd,loopy=loopy,/spliny,nrats=nrats,onlyrat=onlyrat,obsdat=obsdat,$
obssig=obssig,idxflx=idxflx,prddat=prddat, _extra=e
parameters
pars [I/O] parameters {DEM(T),ABUND}, ABUND can be updated
via MIXIE()
fobs [INPUT] observed fluxes
fsigma [INPUT] errors on FOBS
ulim [INPUT] integer array specifying upper limits (1: UL, 0: not)
line [INPUT] emissivities of lines identified with FOBS
logT [INPUT] temperatures at which LINE is defined
wvl [INPUT] wavelengths at which fluxes are observed
Z [INPUT] atomic numbers of each id'd line
scale [INPUT] smoothing scale
ff [OUTPUT] predicted fluxes
prb [OUTPUT] likeihood (could be chi^2)
dem [OUTPUT] DEM
abnd [OUTPUT] abundances
keywords
loopy [INPUT] if set, "smoothing" by converting to T^3/2 DEM
spliny [INPUT] if set, "smooth" by using spline interpolation
onlyrat [INPUT]
obsdat [INPUT]
obssig [INPUT]
idxflx [INPUT]
nrats [INPUT]
verbose [INPUT]
_extra [INPUT] pass defined keywords to LINEFLX (TEMP, EFFAR,
WVLAR, KEV, REGRID), LIKELI (SOFTLIM, CHI2, RCHI, BINOM),
VARSMOOTH (STEPS, WEIGHT, TYPE), LOOPEM (SLOOP), or
ADJUSTIE (TIES)
restrictions
no error checking is done because it is assumed that this is
called from and only from MCMC_DEM
history
vinay kashyap (May97)
changed SIGMA to FSIGMA; added DEM and ABND to parameter list
(VK; AugMM)
added keyword LOOPY, and switched out VARSMOOTH for MK_DEM
(VK; Nov01)
added keywords ONLYRAT,OBSDAT,OBSSIG,IDXFLX,NRATS and call to
GENERATIO (VK; Dec'02)
numerous bug fixes (liwei lin/VK; Dec'02)
added keyword PRDDAT (VK; Jan'03)
added keyword SPLINY (VK; Jun'03)
added keywords BRNSTR,MIXLSTR,MIXSSTR,BRNSTR,XFRAC, as well as
abundance updating via parameter PARS. PARS now
contains updated abundances from MIXIE() on
output if MIXIE() keyword ABNDUPDT is set (LL; Jan'04)
bug fix: compute DEMs for /LOOPY and /SPLINY on correct T grid (VK; Jan05)
allow limiting number of T components for LOOPY (VK; Mar05)
added call to ADJUSTIE to tie ABUND values (LL; Jun05)
added keyword VERBOSE (VK; Jun07)
(See pro/fitting/mcmc_dem_only.pro)
function mcmc_dem_post
returns the best-fit values and the error ranges for the
various parameters in a structure of the form:
{LOGT, NUEFF, MINCHISQ, BOUND,$
DEM_BEST,DEM_MODE,DEM_HPD,DEM_EQT,DEM_MEDIAN,DEM_RNG,DEM_ENV,DEM_FRAC,$
AB_BEST,AB_MODE,AB_HPD,AB_EQT,AB_MEDIAN,AB_RNG,AB_ENV}
syntax
mcmcstr=mcmc_dem_post(savfil,clev=clev,verbose=verbose)
parameters
savfil [INPUT; required] full pathnmae to the save file
that is written out by MCMC_DEM()
keywords
clev [INPUT] set this to override the confidence level at
which to determine the bounds on the parameters
* default is to use EBOUND in SAVFIL
* if < 0, abs value is used
* if > 1 and < 100, then assumed to be given as a percentage
* if > 100, then 1-1/CLEV is used as the true value
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
output description
LOGT: the temperature grid
NUEFF: the effective degrees of freedom for adopted smoothing
MINCHISQ: the minimum chisq achieved
BOUND: the confidence level at which to compute errors
*_BEST: best-fit parameter value
*_MODE: mode of parameter
*_MEDIAN: median of parameter
*_HPD: highest probability-density range at confidence BOUND
*_EQT: equal-tail range at confidence BOUND
*_RNG: half-tail range at confidence BOUND measured from best-fit
*_ENV: envelope range of best BOUND fraction (by chisq)
DEM_FRAC: number of hits at each temperature bin
HELP: a description of the output
subroutines
MODALPOINT
HIPD_INTERVAL
EQT_INTERVAL
history
vinay kashyap (Apr2006)
bug fix: simprb was being compared to chisqcvf rather than half that
(LL; May2006)
(See pro/fitting/mcmc_dem_post.pro)
procedure mcmc_dem_whiskerplot make a nice whisker plot of the DEM solutions from MCMC_DEM. The central box covers 50% of the solutions at each temperature, and the whiskers cover the full range. Individual points are also overplotted, along with the mode at each temperature, and the full DEM(T) that corresponds to the mode at each T, as well as the overall best-fit solution. syntax mcmc_dem_whiskerplot,savedem,epsroot=epsroot,thrfrac=thrfrac,thrnum=thrnum,/dvdt,$ logT=logT,simdem=simdem,storidx=storidx,$ cbox=cbox,cwhisk=cwhisk,cdots=cdots,cbest=cbest,cmode=cmode,cgrey=cgrey,cnum=cnum,$ labul=labul,labur=labur,labll=labll,lablr=lablr,yul=yul,yur=yur,yll=yll,ylr=ylr,$ xrange=xrange,yrange=yrange,xtitle=xtitle,ytitle=ytitle,title=title,cthick=cthick,csize=csize,$ verbose=verbose,$ other PLOT keywords parameters savedem [INPUT; required] this is the name of the file where MCMC_DEM saves its state * if set to 'NONE' or 'none', looks for keywords LOGT,SIMDEM,STORIDX for input keywords epsroot [INPUT] root name for encapsulated postscript file * if set, puts the plot in EPSROOT.eps thrfrac [INPUT] the fraction of the maximum of the histogram of selected temperatures in MCMC iteration to use * this looks at how many times a given temperature index is present in the MCMC trace * default is 0.05 * if 0, assumes default * if >1, the reciprocal is used * if <0, abs value fraction is taken of the _total_ number of of iterations, not of the max amongst different T * NOTE: the greater of THRFRAC and THRNUM is used thrnum [INPUT] the minimum _number_ of points of a given T that should be present * default is 100 * if 0, assumes default * if <0, abs value is used * there is a hardcoded minimum of 5 * NOTE: the greater of THRFRAC and THRNUM is used dvdt [INPUT] if set, converts the units of DEM to [.../degK] before plotting * MCMC_DEM computes DEMs as dV/dlogT == dV/dlnT/ln(10) == (T/ln(10))*dV/dT so if this is set, divides SIMDEM by T/ln(10) logT [INPUT] logT grid, used iff SAVEDEM='NONE' simdem [INPUT] simulated DEMs, used iff SAVEDEM='NONE' storidx [INPUT] logT index selections during MCMC iterations, used iff SAVEDEM='NONE' cbox [INPUT; default=none] color index for box * a color is applied only if set cwhisk [INPUT; default=3] color index for whiskers cdots [INPUT; default=4] color index for dots on whiskers * recommend setting this to 0 for postscript output cbest [INPUT; default=8] color index for best-fit curve cmode [INPUT; default=1] color index for mode marker cgrey [INPUT; default=95] color index for example curves * set CWHISK,CDOTS,CBEST,CMODE,CGREY explicitly to 0 to prevent plotting cnum [INPUT; default=9] color index for marking the number of samples labul [INPUT] LABel to put on Upper Left of plot labur [INPUT] LABel to put on Upper Right of plot labll [INPUT] LABel to put on Lower Left of plot lablr [INPUT] LABel to put on Lower Right of plot yposul [INPUT] y-location of LABUL yposur [INPUT] y-location of LABUR yposll [INPUT] y-location of LABLL yposlr [INPUT] y-location of LABLR * there are no equivalent XPOS because they can always be adjusted with judicious use of spaces within the label strings xrange [INPUT] passed on to PLOT without comment yrange [INPUT] passed on to PLOT without comment xtitle [INPUT] passed on to PLOT without comment ytitle [INPUT] passed on to PLOT without comment title [INPUT] passed on to PLOT without comment cthick [INPUT] line thickness * default is 2, unless EPSROOT is set, when it is 5 csize [INPUT] character and symbol sizes * default is 2, unless EPSROOT is set, when it is 1.2 verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines requires subroutines PEASECOLR MODALPOINT history Vinay Kashyap (2015sep) bug fix with lower bound of whisker box not including mode; ensure clean quit when NSIM is small (VK; 2015nov)
(See pro/fitting/mcmc_dem_whiskerplot.pro)
procedure mcmc_plot
This procedure plots Monte Carlo Markov-Chain DEM
reconstruction results. One sigma uncertanties are
shown as a grey scale (or otherwise specified) with a gradient
determined by how the N simulated DEMs (which ordain the one sigma
confidence intervals) are distributed about the best-fit DEM.
Alternatively, the gradient may be determined by the p(D|M) of
each DEM.
NOTE: ALL REQUIRED INPUTS ARE STANDARD MCMC_DEM() OUTPUTS
parameters
logt [INPUT; required] array which determines the mid-bin values
of the temperature grid on which DEM is defined
simdem [INPUT; required] two dimensional array [NT, NSIM+1]
simulated arrays, the last of which is the best fit.
demerr [INPUT; required] confidence bounds on MAP estimates of DEM
* DEMERR(*,0) are lower bounds, DEMERR(*,1) are upper bounds
simprb [INPUT; required] the p(D|M) of each DEM
schme [INPUT; optional] string designating plotting strategy. Can be:
'ERRBAR' - Just plot error bars using DEMERR (default)
'DIFFERENCE' - Colors are determined by
difference of each DEM simulation
bin value from the best fit DEM
values. Colors are polyfilled
between simulated values within
each logT bin.
'INDEX' - Colors are determined by the order in which
they appear (starting from the best
DEM outwards). Colors are polyfilled
between simulated values within each
logT bin.
'SPLINE INDEX'- Colors are determined by the order in which
they appear (starting from the best
DEM outwards). Colors are polyfilled
between simulated values within each
logT bin. Spline interpolated
curves are plotted in lieu of
histogram style bins
'PROB' - Colors are determined by the p(D|M)
of each DEM. Values are oploted
with thick bars between simulated
values within each logT bin.
'SPLINE' - Simulated DEMS are spline
interpolated and colors determined
by the p(D|M) associated with
each. Each spline is oploted onto
a best-fit dem plot.
'NICE' - For each temperature bin, a median simulation
value is calculated. The median values will be
plotted (dotted line) together with the DEM
simulation (solid line) that best fits them.
Uncertainty will be displayed by plotting the MIN and
MAX simulation values for each
bin. (dashed lines) Use the SLECT and CLEV
keywords to limit which simulations to include.
'NICE DIFFERENCE' - A combination of DIFFERENCE and NICE
Colors are determined by
difference of each DEM simulation
bin value from the best fit DEM
simulation to the median value as
described in the 'NICE'
definition. Colors are polyfilled
between simulated values within
each logT bin.
'NICE INDEX' - A combination of DIFFERENCE and NICE
Colors are determined by the order in
which they appear (starting from the
best fit simulation to the median value
as described in the 'NICE' definition.
Colors are plyfilled between simulated
values within each logT value.
'SUPPORT' - Just plot upper and lower bounds of the
support in each bin given the set of
selected DEMs (see SLECT keyword)
storidx [INPUT ; optional] from MCMC_DEM(), contains the indices of
of all the sampled parameters stored in
STORPAR. If a temperature bin has not been
adequately sampled ( default threshold is
nsim*0.10 ), then the bin is not
plotted. Only bins at the ends of the Log
T range are thrown out. (see SAMPCT keyword)
keywords
slect [INPUT] choose which DEMS to include default=[2]
1:ALL -Include all simulations
2:CHI^2 -Limit simulations to best 50% p(D|M) DEMS
(default = 50, use CLEV keyword to toggle)
3:Errors -Limit simulations to values in each bin that
lie within the specified confidence bounds (demerr)
clev [INPUT] To be used in conjunction with slect=2,
determines what percentage by which to limit
sims in p(D|M)
col_rng [INPUT] index range in the color table to cover.
gradient will taper
off from 0 (darkest) to
col_rng (brightest). (maximum is 255)
col_tabl [INPUT] color table on which to base the gradient
col_shft [INPUT] number of color indices by which to shift
brighter(or darker if black background), col_rng will
be adjusted accordingly
ps_fil [I/O] name of ps file to output. If not specified
plot will be sent to current device
demslope [I/O] if set, linear fits are made to the simulated DEMs
in a temperature range specefied by keyword SLOPEDT
and DEMSLOPE will return the mean slope. The
distribution of slopes will be plotted
slopesig [OUTPUT] if set, returns standard deviation slopes of
linear fits
slopedt [INPUT] temperature range specified in Log(T[K]) within which
to make linear fits to DEM
* if 2-element array, then SLOPEDT =
[min(SLOPEDT),max(SLOPEDT)]
* if 1-element array, then SLOPEDT =
[SLOPEDT, logt(max(bestdem)))] or
[SLOPEDT, logt(min(bestdem))]
if logt(max(bestdem)) eq SLOPEDT
* if not set, then SLOPEDT = [min(logt),
logt(max(bestdem))] or [SLOPEDT,
logt(min(bestdem))] if logt(max(bestdem)) eq SLOPEDT
sampct [INPUT] when STORIDX is input, set this to threshold for T
bin to be included. Expressed as percent of nsim. (default = 10)
goodt [OUPUT] if STORIDX is input, GOODT will containt the log T
range used to plot
tbuff [INPUT] if STORIDX is set, TBUFF can be set to the number of
bins to add on either side of the temperature range
determined with STORIDX
monochrom[INPUT] set this to a value between 0 and 255 to make
all the plots in this color.
restrictions
The SPLINE and SPLINE INDEX plotting schemes may not be used with slect = 3
NOT tested yet with positional parameters e.g. !P.POSITION
subroutines
mid2bound
peasecolr
stample
history
(LL 6/03)
ADDED 'Nice' and 'Nice Difference' option for schme parameter (LL 2/04)
ADDED call to STAMPLE (LL 2/04)
ADDED call to PEASECOLR to restore settings after loadct (LL 2/04)
ADDED recognition of weather plot background is black or white
and and adjustment to col_shft accordingly (LL 2/04)
FIXED SPLINE INDEX schme so that it actually polyfills and doesn't just
oplot i.e. no more 'speckled' look. Also added a NOERASE
plot statement to prevent polyfills from hiding tickmarks (LL 2/04)
FIXED color schemes so that the background color recognition
scheme would work with both psuedo color and true color (LL 2/04)
REMOVED PEASECOLR because IDL dynamically updates the x windows
display whith the current color table (LL 2/04)
BUGFIX variables CUPBND and CLOBND should be of size nT not nkpt (LL 3/04)
if this affected you the routine would have crashed.
ADDED 'NICE INDEX' scheme. (LL 10/04)
CHANGED 'PROB' color schme so best-fit is plotted brightest for
'x' and darkest for 'ps', order in which bars plotted matters! (LL 9/05)
BUGFIX now compatible with multiple plots per page via !p.multi (LL 10/05)
ADDED 'SUPPORT' scheme and keywords MONOCHROM and OUTMED (LL 11/05)
CHANGED col_tabl behavior, only loads col_tabl when set, so default is
now whatever is currently loaded and not B/W Linear (LL 11/05)
ADDED keywords DEMSLOPE, SLOPSIG, SLOPEDT and parameter STORIDX (LL 1/06)
CHANGED behavior of output to be not in color if COL_TABL is 0 (VK 8/07)
(See pro/fitting/mcmc_plot.pro)
procedure mc_eror
simple procedure that calculates confidence bounds
about a given parameter value g given a certain number
of monte carlo simulations contained in array sims.
assumes the simulations are distributed normally about
the 'candidate' parameters.
by default,set to find smallest possible bounds. can also
be set to find confidence bounds by counting upward
and downwards by required fraction.
syntax
mc_eror, g, sims, erru, errl, confidence=confidence
parameters
g [input, required] parameter about which to estimate bounds
sims [input, required] array of monte carlo simulated g's
minimum 10 simulations [though this
seems a ridiculous number]
bndu [output] upper confidence bound
bndl [output] lower confidence bound
keywords
confidence [default = 0.68269] confidence limit at which bounds
are desired.
alas find confidence bounds by counting upward
and downwards by required
fraction. may also be set
to find smallest possible bounds.
history
LL Jan03
(See pro/stat/mc_eror.pro)
procedure mc_eror
simple procedure that calculates confidence bounds
about a given parameter value g given a certain number
of monte carlo simulations contained in array sims.
assumes the simulations are distributed normally about
the 'candidate' parameters.
by default,set to find smallest possible bounds. can also
be set to find confidence bounds by counting upward
and downwards by required fraction.
syntax
mc_eror, g, sims, erru, errl, confidence=confidence
parameters
g [input, required] parameter about which to estimate bounds
sims [input, required] array of monte carlo simulated g's
minimum 10 simulations [though this
seems a ridiculous number]
bndu [output] upper confidence bound
bndl [output] lower confidence bound
keywords
confidence [default = 0.68269] confidence limit at which bounds
are desired.
alas find confidence bounds by counting upward
and downwards by required
fraction. may also be set
to find smallest possible bounds.
history
LL Jan03
(See pro/util/mc_eror.pro)
function mdlpoly compute and return the minimum description length statistic obtained by fitting polynomials of different orders syntax mdl=mdlpoly(ydat,xdat,yfit=yfit,kord=kord,pfit=pfit,$ kmin=kmin,kmax=kmax,verbose=verbose) parameters ydat [INPUT; required] data to be fit xdat [INPUT] abscissae for YDAT * if not given, assumeed to be lindgen(n_elements(YDAT)) keywords yfit [OUTPUT] best-fit function corresponding to KORD and PFIT kord [OUTPUT] polynomial order at which minimum MDL is achieved pfit [OUTPUT] parameters for the best-fit function kmin [INPUT] minimum polynomial order to consider * default is 0, corresponding to a constant kmax [INPUT] maximum polynomial order to consider * default is the smaller of 10 or half the number of data points verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (2014sep)
(See pro/stat/mdlpoly.pro)
function mid2bound given mid-bin values, make an intelligent determination of the bin boundaries and return said boundaries. given input array of N elements, returns array of N+1 elements. (actually, it's not all that intelligent. uses spline interpolation) syntax dm=mid2bound(m,/halfit,eps=eps,verbose=verbose) parameters m [INPUT; required] the mid-bin values from which to expand out keywords halfit [INPUT] if set, does the simpleminded thing, i.e., puts the bin half-way between 2 points, and extrapolates by repeating previous bins eps [INPUT] a small number, default is 1e-6 verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (OctMM) added keyword HALFIT (VK; Jul01) default EPS had not been defined (VK; Jan05)
(See pro/util/mid2bound.pro)
function mixie
MIXIE() computes correction factors for line blends given a set of
intersting lines (LSTR) and a set of contaminants (SSTR).
LSTR and SSTR should both be RD_LIST() style structures, which
contain necessary line information (emissivity, wvl, z, etc.)
MIXIE() will identify which lines in SSTR are possible contaminants
for each line in LSTR. SSTR lines must meet two criteria to be
included in the correction fraction computation of each LSTR line:
1) The SSTR line lies within 2*NSIG*LWDT on either side of the LSTR line
2) The total contribution of the line is greather than a
user-defined threshold: LTHR * INTENSITY OF LINE (LTHR is
keyword input while intensity of the interesting line is
computed internally.)
Correction factors are estimated by computing complimentary
error functions with an IDL native routine ERRORF() for each
contaminant (i.e. gaussian profiles are assumed). If an
OGIP-compliant rmf is fed via the RMFSTR keyword, the rmf
will be used to estimate correction factors rather than
ERRORF() <<RMFSTR NOT IMPLEMENTED YET>>.
The correction factor is defined as follows:
CORRECTION FACTOR = INT / (INT + total contributions from blends)
where INT = intensity of interesting line
If set, the MIXSTR keyword can return a structure containing the
identification, emissivities, and wavelengths of each contaminant
line, together with LSTR and SSTR indices which match contaminated line
to contaminant (VICTIM and CULPRIT respectively). Also to be contained in
the structure are the fractional contributions CONTAMFRAC and intensity of
of the contaminant CONTAMINT (i.e. the total contribution of the contaminant is
CONTAMINT*CONTAMFRAC). The fields in the output structure will be the
the following (see KEYWORDS for individual descriptions):
{CONTAMFRAC,CONTAMINT,VICTIM,CULPRIT,WVL,IDTAG}
syntax
x=mixie(lstr,sstr,lwdt=lwdt,nsig=nsig,lthr=lthr,rmfstr=rmfstr,mixstr=mixstr,$
contamfrac=contamfrac,victim=victim,culprit=culprit,contamint=contamint,$
idtag=idtag,vint=vint,mproxy=mproxy,mplet=mplet,_extra=e)
parameters
lstr [INPUT;required] Line (and/or conitnuum) structure of
RD_LIST() format containing info (wvl,emis,z) on
lines (and/or continuum) for which possible contaminants will be identified
and for which correction factors will be
calculated. Assumes that ion equilibria are
included. (see RD_LIST() keyword INCIEQ)
sstr [I/O] Line structure of RD_LIST() format
containing user specified line contaminant suspect
info (wvl, emis, z). Assumes that ion equilibria are
included. (see RD_LIST() keyword INCIEQ). If SSTR is
ommitted or undefined on input, the emissivity database will
read with RD_LIST() in the neccessary wavelength range
and including all species to create a list of suspects.
If undefined on input, will contain RD_LIST() structure
on output.
keywords
lwdt [INPUT] Std. deviation to be used as an estimate for
line broadening. Only contamination candidate profiles (sstr)
within 2*lwdt*nsig of the line in question will
be considered. May be single value or an array
with values for each element in LSTR. (must
match number of lines+continuum specified in LSTR)
default = 0.2 pixels
nsig [INPUT] number of standard deviations from line of interest that
defines wavelength range within which to consider contamination.
If not set, the default is determined by LTHR.
May be single value or an array of values for
each element in lstr. If array, must match the
number of lines+continuum specified in LSTR.
So the range within which to consider
contamination for each line is defined as:
WRANGE = [LSTR.WVL(x)-LWDT*NSIG,LSTR.WVL(x)+LWDT*NSIG]
or if LWDT and NSIG are arrays:
WRANGE = [LSTR.WVL(x)-LWDT(x)*NSIG(x),LSTR.WVL(x)+LWDT(x)*NSIG(x)]
NOTE: To handle continuum measurements,
choose an NSIG which adequatly covers your
continuum measurement wavelength range.
lthr [INPUT] fraction of intensity of the line of interest to
use as cut-off intensity value for contaminant
candidate fractional flux contributions. default = 1e-4
i.e. cutoff = (intnsity of line of interest)/100
rmfstr [INPUT] <<NOT IMPLEMENTED YET>> structure containing OGIP compliant RMF. see
RD_OGIP_RMF(). If set, contamination will be
estimated by analyzing RMF instead of using ERRORF()
mixstr [OUTPUT] Structure containing detailed information for
each pair of blends. The structure fields are
the following:
{CONTAMFRAC,CONTAMINT,VINT,VICTIM,CULPRIT,WVL,IDTAG}
Each field can also be returned individually:
contamfrac [OUTPUT] array containting contribution fractions for
each culpable line
contamint [OUTPUT] the contaminant line intensities
vint [OUTPUT] the victim line intensities
victim [OUTPUT] lstr index of intersting line being contaminated
culprit[OUTPUT] sstr index of indices of contaminant lines
idtag [OUTPUT] string containing derscription of each culprit.
the description is as follows:
SPECIES, WVL, DATABASE, DESCRIPTION
SPECIES gives atomic symbol and ionic
state. WVL gives Wavelength. DATABASE gives
the name of the DATABASE used. And DESCRIPTION
gives the level designations and electron
configurations of the transition. e.g.
MgXII 8.41920 $CHIANTI (1s) 2S_1/2 (2p) 2P_3/2
OVIII 18.9726 $CHIANTI (1s) 2S_1/2 (2p) 2P_1/2
vidtag [OUPUT] string containing description of each victim
and of same format as idtag
mproxy [INPUT] If a correction factor is needed for a
multiplet measured using a single profile,
then MPROXY will specify the
multiplet components on input, and contain
the multiplet correction factor on output.
One component of the multiplet is to stand
proxy for the group, and must be specified in
LSTR.
MPROXY is defined as follows:
mproxy = strarr(2,N) or
mproxy = intarr(2,N)
N is the number of component-proxy
relationships. Each component-proxy
relationship is expressed as a two
element string array. The first element should
contain the LSTR index of the proxy. The
second element should contain either the LSTR index of the
component if it is included in LSTR, or a
string description of the component in IDTAG format.
One may optionally leave out:
o the DESCRIPTION field (e.g. just use SPECIES, WVL,DATABASE).
o the DATABASE and WVL fields (e.g. just use
SPECIES, DATABASE)
On output, one correction factor will be given
for each multiplet. The index of this
correction factor in the output correction
factor array is determined by the position of
the proxy in LSTR. (See examples below)
mplet [INPUT] If blending between one or
more multiplet components is already accounted
for (e.g. a multiplet is modelled with
serveral profiles) then MPLET can
specify which multiplet component to leave
out of the correction factor calculation of
another component.
MPLET is defined as follows:
mplet = strarr(2,N)
mplet = intarr(2,N)
N is the number of component-component
relationships. Each component-component
relationship is expressed as a two element
string array. The first element should
contain the LSTR index of the component
whose correction factor is needed.
The second element should contain either the
LSTR index of the component to leave out, or
a string description of the component to
leave out in IDTAG format.
One may optionally leave out:
o the DESCRIPTION field (e.g. just use SPECIES, WVL,DATABASE).
o the DATABASE or WVL fields (e.g. just use
SPECIES, DATABASE)
Correction factors will not be calculated for
lines specified to be left out of another
lines' correction factor calculation. See
examples below.
brnstr [I/O] if mixie is to be run multiple times
(e.g. using MCMC_DEM() ) the brnstr keyword can
be set so that MIXIE() creates a sturcture
containing internally calculated and recycle-able information, to be fed
to subsequent MIXIE() calls. The structure is
of the form:
{FRACS,NDX,INTNDX,NSS,NNSS,PRXBSE,MULTSTR}
where:
FRACS = float array contribution fractions of all non-exempt lines
NDX = long array sstr index of each of thes lines
INTNDX = float array ndx and fracs index intervals corresponding to each victim
NSS = float array lstr index of each victim
NNSS = long array number of actual victims i.e. n_elements(nss)
PRXBSE = long array lstr index of the proxy in each proxy relation.
MULTSTR = STRUCT rd_line structure of proxee in each relation
When fed as input, BRNSTR allows MIXIE to avoid
explicit contribution factor calculations for
each suspect and cumbersome MPROXY and
MPLET sting parsing.
DEM [INPUT] differential emission measure at each T [cm^-5/logK]
* default is a constant=1e14!!
* if defined, DLOGT must also be specified
* if LSTR and SSTR emissivity temperature grids do not
match DLOGT then they are rebinned and
resampled so that they do
DLOGT [INPUT logarithmic temperature grid at which DEM is defined
* default is 4.0 to 8.0 in steps of 0.05
ABUND [I/O] abudnanaces relative to H abund(0) = 1
* abund(Z-1) contains the abundance for element Z
* default: Grevesse & Sauval(1998)
ABNDUPDT [INPUT] If set, then abundnaces will be updated on
output. Abundances are calculated after taking
into account the correction factors
OBSFLX [INPUT] Obseved fluxes used to calculate abundnaces,
must match the number of correction factors
calculated
OFSIG [INPUT] errors for OBSFLX
MULTIPLET [INPUT] temporary, same as MPLET
MULTPLET [INPUT] temporary, same as MPLET
MULTPROXY [INPUT] temporary, same as MPROXY
MULTIPROXY[INPUT] temporary, same as MPROXY
verbose[INPUT] set verbosity
_extra [INPUT] pass defined keywords to
LINEFLX (DEM, ABUND, EFFAR, WVLAR, TEMP, NOPH, IKEV, REGRID)
RD_LIST (DBDIR,LOGP,PRES,N_E,EQFILE)
subroutines
LINEFLX
RD_LIST
INICON
CAT_LN
REBINX
MCMC_ABUND
MCMC_EROR
IS_KEYWORD_SET
restrictoins
Is is suggested that LSTR and SSTR be read from a common
database to avoid accidentally identifying a line as 'self blending'
MIXIE() will NOT compute correct correction factors for DR lines.
usage examples
* !LDBDIR = '$CHIANTI'
Ne9 = rd_list('Ne9|[13.44,13.45]',/incieq,sep='|')
cand = rd_list('ALL|[12.44,15.45]',/incieq,sep='|')
factor = mixie(Ne9,Cand,lwdt=0.008,nsig=5,lthr=0.02,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag, mixst=mixstr)
for j = 0,n_elements(culprit)-1 do print,mixstr.idtag(j), mixstr.contamint(j)* mixstr.contamfrac(j)
* !LDBDIR = '$CHIANTI'
Ne9 = rd_list('Ne9|[13.44,13.45]',/incieq,sep='|')
factor = mixie(Ne9,lwdt=0.008,nsig=5,lthr=0.02,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag, mixst=mixstr)
for j = 0,n_elements(culprit)-1 do print,mixstr.idtag(j), mixstr.contamint(j)* mixstr.contamfrac(j)
* !LDBDIR = '$CHIANTI'
T_components = [6.6,6.9,7.4] ; log(T[K]) components in the EM
EM_components = [3.05,3.05,3.55]*1d11 ; Emission Measure [cm^-3]
!DEM=mk_dem('delta', logT = !LOGT, pardem=T_components, indem=EM_components)
Ne9 = rd_list('Ne9|[13.44,13.45]',/incieq,sep='|')
factor = mixie(Ne9,lwdt=0.008,nsig=5,lthr=0.02,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag, mixst=mixstr,DEM=!DEM, DLOGT=!LOGT)
for j = 0,n_elements(culprit)-1 do print,mixstr.idtag(j),mixstr.contamint(j)* mixstr.contamfrac(j)
* !LDBDIR = '$CHIANTI'
N7 = rd_list('N7|[24.77,24.79]',/incieq,sep='|'); this list specifies a triplet
mproxy = [ [2,1], [2,0] ] ; We use one triplet component as proxy
factor = mixie(N7,lwdt=0.008,nsig=5,lthr=0.008,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag,mproxy=mproxy,$
mixstr=mixstr)
* !LDBDIR = '$CHIANTI'
N7 = rd_list('N7|[24.7846,24.7847]',/incieq,sep='|'); this list contains one N7 triplet component
; use MPROXY to specify N7 triplet components the one component are to stand proxy for
mproxy = [['0','NVII 24.7793 $CHIANTI (1s) 2S_1/2 (2p) 2P_3/2'], $
['0','NVII 24.7844 $CHIANTI (1s) 2S_1/2 (2s) 2S_1/2']]
factor = mixie(N7,njk,lwdt=0.008,nsig=5,lthr=0.008,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag,$
mixst=mixstr,mproxy=mproxy )
* !LDBDIR = '$CHIANTI'
N7 = rd_list('NVII|24.7847|$CHIANTI|(1s) 2S_1/2 (2p) 2P_1/2',sep='|',/incieq)
; use MPROXY to specify multiplet components the N7 at 24.7847 is to stand proxy for
mproxy = [['0','NVII 24.7793 $CHIANTI (1s) 2S_1/2 (2p) 2P_3/2'], $
['0','NVII 24.7844 $CHIANTI (1s) 2S_1/2 (2s) 2S_1/2']]
factor = mixie(N7,j,lwdt=0.008,nsig=5,lthr=0.008,contamfrac=contamfrac,victim=victim,$
culprit=culprit,contamint=contamint,idtag=idtag,$
mixst=mixstr,mproxy=mproxy)
history
INTENDED as an improvement on bland() (LL:Jul'03)
NEW documentation new default nsig
output now correction factor and not mixstr (LL:Aug'03)
BUG FIX: 1/SQRT(2) factor needed for arguement of ERRORF so
lwdt is actually standard deviation
now prints message when no blends are found
now robust to theoretical lines (designated by
negative wavelengths)
BUG FIX correction factor calculations for multiple
victim list was incorrect (LL/DG:Sep'03)
ADDED keyword COMPOSITE to handle doublets (LL:Sep'03)
REPLACED keyword COMPOSITE with MUTLPROXY which now handles
multiplets. ADDED related keyword MULTIPLET. (LL:Oct'03)
ADDED correction for 'over correction' i.e. a CULPRIT now
cannot 'overdistribute' its flux when contaminating
several VICTIMS at once. (LL:Oct'03)
CHANGED LTHR and NSIG so that they can handle arrays
so correction factors for continuum measurements
are possible (LL:Oct'03)
CHANGED default RD_LIST() call so that makes
intelligent efficient wrange decision (LL:Oct'03)
ADDED BRNSTR keyword so that doesn't bog down
MCMC_DEM(). ALSO included explicit intensity
calculations so to avoid being slowed by LINEFLX(). (LL:Oct'03)
ADD ABNDUPDT keyword to toggle ABUND updating on
output (LL:Jan'04)
CHANGED location of ABUNDANCE calculation so that it
abundances get updated after contamination
correction. ADDED keyword OFSIG (LL:Jan'04)
CHANGED MULTIPLET KEYWORD to MPLET and MULTPROXY to
MPROXY (LL/DG:Jan'04)
changed default of LTHR to 1e-4 (VK;Jan'04)
ADDED new MPLET and MPROXY format (LL:Feb'04)
BUG FIX over correction mechanism (i.e. considering
situations of one culprit and two victims) was not
working properly, leading to correction factors >
1. (LL/DG:Feb'04)
BUG FIX total(contamfrac) gt 1 changed to
n_elements(culprit) gt 1 (LL:Feb'04)
BUG FIX keywords idtag and mixstr were failing
because need to handle with keyword_set() not
arg_present() (LL:Mar'04)
VARIOUS BUG FIXES
sstr enteed as dummy argument = crash
mixstr and idtag fix (LL:Mar'05)
replaced direct reference to !LOGT with calls to
defsysv and setsysval (VK; Apr'05)
BUG FIX if sstr is one component only it was
ignored. (LL:Apr'05)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
(See pro/mixie.pro)
function mk_3model generate and return a compound model using the supplied parameters of components made up of 3-parameter functions syntax model=mk_3model(x,p,w,h,pder,group=group,delp=delp,type=type,/asis,$ /allcomp,/fwhm,/normflx,missing=missing,betap=betap,vrot=vrot) parameters x [INPUT; required] points where model is computed p [INPUT; required] positions of components w [INPUT; required] widths of components h [INPUT; required] heights of components pder [OUTPUT] contains 2D array (NX,3*NPAR) of partial derivatives of each component wrt parameters keywords group [INPUT] grouping index of gaussians delp [INPUT] offsets from first position value in group NOTE: GROUP and DELP are ignored if ASIS is set NOTE: if GROUP and DELP are not given, ASIS is set type [INPUT; default='G*aussian'] what type of curve to generate for the model. other possibilities are L*orentzian B*eta-profile (set "Beta=<value>") SL*ant (set "slant=<angle>,<beta>") R*otation-convolved Gaussian (set "rot=<velocity>") P*ower-law (set "pw=<break>" or "pe=<break>") I*dentity U*ser_defined (not yet implemented), etc. SI*nusoid (set "sin=<phase>") * if not defined, uses "Gauss" * if insufficiently defined, uses last defined as default for the rest asis [INPUT] the default action is to verify that the p are consistent with GROUP and DELP and to correct as necessary. if ASIS is set, this is not done. allcomp [INPUT] if set, returns the sum of components and also each component in a separate column of a 2D array of size (N_ELEMENTS(P)+1,N_ELEMENTS(X)) _extra [INPUT] pass defined variables to subroutine:- MK_GAUSS: MISSING, FWHM, NORMFLX MK_LORENTZ: BETAP, MISSING, NORMFLX MK_SLANT: ANGLE, BETAP, MISSING, NORMFLX MK_ROGAUSS: VROT, MISSING, FWHM, NORMFLX MK_IDENT: GIGO MK_SINUSOID: PHASE, MISSING usage summary * call as a function * returns composite model by adding up components * input component parameters as sequence of arrays of positions, widths, and heights * input grouping info by 2 additional arrays * specify type of model with keyword TYPE * partial derivatives are computed only if ALL 5 parameters are supplied in call * example TYPEs: 'Gauss', 'gaussian', 'gau', 'g' 'Lorentz', 'lorentz', 'lorentzian', 'lor', 'l' 'beta=1.8', 'BETA=2.4', 'B=2', 'b 1.8', 'b:1.8', 'b 1.8' 'slant=45,1.8','SLANT=89,2.4', 's=10','s=,2', 's:3,2' 'rotational velocity=1e-4', 'rot=30', 'r:30e5', 'R 1e-4' 'pe=1', 'pw=12.3985', 'pw@12.4' 'sin', 'sin=90' subroutines MK_GAUSS MK_LORENTZ MK_SLANT MK_ROGAUSS MK_POWLAM MK_SINUSOID KILROY history vinay kashyap (Oct96) added parameter to return partial derivatives (VK; Nov96) added _EXTRA, added call to MK_LORENTZ (VK; Oct98) allowed setting BETAP for MK_LORENTZ via TYPE definition (VK; Dec98) added MK_SLANT calls (VK; MarMM) added MK_ROGAUSS, MK_POWLAM calls (VK; JunMM) changed name from MK_MODEL to MK_3MODEL (VK; Aug01) converted array notation to IDL 5; added MK_IDENT (VK; Apr02) changed keyword NORM to NORMFLX (VK; Oct02) added call to MK_SINUSOID (VK; Sep04)
(See pro/fitting/mk_3model.pro)
function mk_absorb returns a multiplicative transmission factor for ISM absorption syntax ismcorr=mk_absorb(x,NH,pder, fH2=fH2,He1=He1,HeII=HeII,/Fano,/ikev,$ /wam,/bam,/mam,/noHeH,abund=abund,verbose=verbose) parameters x [INPUT array; required] where the function must be computed NH [INPUT; default: 1e18] H column pder [OUTPUT; optional] partial derivatives of model wrt parameter at each X; calculated only if 3 parameters are supplied in call. keywords _extra [INPUT ONLY] pass defined keywords to subroutines ISMTAU: FH2, HE1, HEII, FANO, IKEV, WAM, BAM, MAM, NOHEH, ABUND description wrapper to ISMTAU subroutines ISMTAU history vinay kashyap (Jul08)
(See pro/fitting/mk_absorb.pro)
function mk_bbang returns the Planck function B(lam) [ph/s/cm^2/Ang] as a function of lam [Ang] at a given temperature T. In general, B(nu)d(nu) = (R/d)^2*(2*pi/c^2) * d(nu)*nu^2/(exp(h*nu/kT)-1) for lam=c/nu, B(lam)d(lam) = (R/d)^2 * (2*pi*c) * d(lam) * (1/lam^4)/(exp(hc/lam/k/T)-1) == A * (lam^-4/(exp(hc/lam/k/T)-1)) * d(lam) syntax b=mk_bbang(x,norm,temperature,pder,verbose=verbose) parameters x [INPUT array; required] where B(X) must be computed norm [INPUT; required] normalization for B(X) temp [INPUT; required] temperature in [K] pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 4 parameters are supplied in call. keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing usage summary * call as a function subroutines NONE history vinay kashyap (Aug08; based loosely on 1993 blackbody.pro)
(See pro/fitting/mk_bbang.pro)
function mk_bbkev returns the Planck function B(E) [ph/s/cm^2/keV] as a function of E [keV] at a given temperature T. In general, B(nu)d(nu) = (R/d)^2*(2*pi/c^2) * d(nu)*nu^2/(exp(h*nu/kT)-1) for E=h*nu, B(E)dE = (R/d)^2 * (2*pi/c^2/h^3) * dE*E^2/(exp(E/kT)-1) == A * (E^2/(exp(E/kT)-1)) * dE syntax b=mk_bbkev(x,norm,temp,pder,verbose=verbose) parameters x [INPUT array; required] where B(X) must be computed norm [INPUT; required] normalization for B(X) temp [INPUT; required] temperature in [K] pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 4 parameters are supplied in call. keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing usage summary * call as a function subroutines NONE history vinay kashyap (Aug08; based loosely on 1993 blackbody.pro)
(See pro/fitting/mk_bbkev.pro)
function mk_bknpower
returns a broken Power-law function,
p(X) = NORM*(X/Xo)^gamma1 {X.le.PBREAK}
= NORM*(PBREAK/Xo)^(gamma1-gamma2)*(X/Xo)^gamma2 {X.ge.PBREAK}
syntax
p=mk_bknpower(x,norm,gamma1,gamma2,pbreak,pder,Xo=Xo,/nobreak,verbose=verbose)
parameters
X [INPUT; required] where p(X) must be computed
norm [INPUT; required] normalization
gamma1 [INPUT; required] power-law index 1 (valid for 0<X<PBREAK)
gamma2 [INPUT; necessary] power-law index 2 (valid for X>PBREAK)
pbreak [INPUT; necessary] break point
* GAMMA2 and PBREAK are ignored if NOBREAK is set
pder [OUTPUT; optional] partial derivatives of model wrt parameters
at each X; calculated only if 6 parameters are supplied in call.
* array of size [N(X),4], with columns containing the partial
derivatives wrt NORM, GAMMA1, GAMMA2, and PBREAK respectively
* to have it return PDER as [N(X),2] for a non-broken power-law
distribution, set NOBREAK (must have GAMMA2 and PBREAK in the
call, but they will be ignored)
keywords
Xo [INPUT] X-value at which which normalization is defined
* default is 1.0
nobreak [INPUT] if set, ignores GAMMA2 and PBREAK, essentially assuming
that PBREAK=$\infty$
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
example
x=(findgen(100)+1)/10. & p=mk_bknpower(x,1.,-1,-3,1.5) & plot,x,p,/xl,/yl
p2=mk_bknpower(x,1.,-1,-3,1.5,/nobreak) & oplot,x,p2,line=2,thick=2
history
Vinay Kashyap (Apr2008)
(See pro/fitting/mk_bknpower.pro)
function mk_dem returns DEM(T) [cm^-5] syntax DEM=mk_dem(type,logT=logT,indem=indem,pardem=pardem,$ sloop=sloop,xcur=xcur,ycur=ycur,loopy=loopy,lcomp=lcomp,$ weight=weight,/gauss,verbose=verbose) description this provides a way to generate DEMs quickly by various means. TYPE, a string variable, decides what sort of method to use to generate the DEM. TYPE can be 'help' 'constant' PARDEM = value 'chebyshev' PARDEM = coefficients 'cursor' PARDEM = max range in DEM 'interpolate' PARDEM = original logT 'loop' PARDEM = original logT 'rebin' PARDEM = rebinning scales 'spline' PARDEM = logT location of points 'varsmooth' PARDEM = smoothing scales 'delta' PARDEM = logT locations of EM components if a particular method requires an input DEM (e.g., 'interpolate'), feed that in via the keyword parameter INDEM. any parameters that the method requires go in via PARDEM (e.g., for 'interpolate', PARDEM would be the temperature grid at which INDEM is defined). parameters type [INPUT; required] specifies what type of DEM. * if 'help', prints out available options keywords logT [INPUT; default=findgen(81)*0.05+4] log10(T [K]) at which to return DEM(T) pardem [INPUT] parameters to be used to figure out the DEM. strictly case dependent. indem [INPUT] for those cases that require an input/initial DEM xcur [I/O] cursor X locations for the "cursor" option ycur [I/O] cursor Y locations for the "cursor" option loopy [INPUT] set to the maximum number of loop components that should be used for LOOP type DEMs * the top LOOPY EM values are kept as is, and the rest are discarded * LCOMP lists the components that _must_ be kept lcomp [INPUT] scalar or vector which contains the indices of the parameters that must be used to compute loops -- if LCOMP exceeds LOOPY, only the largest of the specified components that are within quota are kept -- if LCOMP is less than LOOPY, the remaining slots are filled in by the largest of the remaining components _extra [INPUT ONLY] allows setting defined keywords to subroutines -- VARSMOOTH (WEIGHT, GAUSS, STEPS) -- LOOPEM (SLOOP, VERBOSE) subroutines CHEBYSHEV, VARSMOOTH, LOOPEM history vlk (Jun98) added option to interpolate (VK; Dec98) added option for variable scale rebin (VK; 1999) added option to interactively specify DEM (VK; MMJul) rebin option now works (VK; AugMM) added keywords XCUR and YCUR (VK; JanMMI) converted array notation to IDL 5 (VK; Apr02) added 'delta' option (VK; Mar03) now correctly converts EM to DEM for 'delta' (VK; Jun03) added keyword LOOPY; allows limiting the number of T components for LOOP (VK; Mar05) added keyword LCOMP (VK; Jun05) button press status now stored in !MOUSE, not !ERR (VK; Apr09)
(See pro/mk_dem.pro)
function mk_efold returns an exponential, NORM*exp(-x*SCALE)+YOFF syntax f=mk_efold(x,norm,scale,yoff,pder,verbose=verbose) parameters x [INPUT array; required] where F(X) must be computed norm [INPUT; required] normalization for exponential scale [INPUT; required] reciprocal of e-folding decay scale yoff [INPUT; required] offset from Y=0 * NORM,SCALE,YOFF must be scalars or single-element vectors -- extra elements, if present, are silently ignored pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if supplied in the calling sequence. keywords verbose [INPUT; default=0] controls chatter _extra [JUNK] here only to prevent crashing example x=findgen(100) & plot,x,mk_efold(x,100.,0.05,20.) subroutines NONE history vinay kashyap (Aug08)
(See pro/mk_efold.pro)
function mk_gauss
returns a gaussian G(X)
syntax
g=mk_gauss(x,mean,sig,peak,pder,/fwhm,/normflx,missing=missing,/widebin)
parameters
x [INPUT array; required] where G(X) must be computed
mean [INPUT; default: mid_point(X)] position of peak
sig [INPUT; default: 0.1*range(X)] std. deviation
peak [INPUT; default: 1] max(G)
pder [OUTPUT; optional] partial derivatives of model wrt parameters
at each X; calculated only if 5 parameters are supplied in call.
keywords
fwhm [INPUT] if set, the std.deviation is SIG/2.355
normflx [INPUT] if set, the *normalization* is set to PEAK
missing [INPUT] 3 element array to populate missing values of
MEAN, SIG, and PEAK
widebin [INPUT] if set, assumes that the bins are wide compared
to the width of the Gaussian and returns the integral
over the bins rather than just the value at each X
* this part requires a call to MID2BOUND()
_extra [JUNK] here only to prevent program from crashing
description
if NORMFLX == 0 && FWHM == 0:
G(X)=PEAK*exp((X-MEAN)^2/2/SIGMA^2)
if NORMFLX != 0 && FWHM == 0:
G(X)=(PEAK/SIGMA/sqrt(2*!PI))*exp((X-MEAN)^2/2/SIGMA^2)
if NORMFLX == 0 && FWHM != 0:
G(X)=PEAK*exp(2.355^2*(X-MEAN)^2/2/SIGMA^2)
if NORMFLX != 0 && FWHM != 0:
G(X)=(2.355*PEAK/SIGMA/sqrt(2*!PI))*exp(2.355^2*(X-MEAN)^2/2/SIGMA^2)
usage summary
* call as a function
* generates gaussian model only at specified points X
* needs MEAN, SIG, PEAK for complete specification
subroutines
MID2BOUND
history
vinay kashyap (Oct96)
added PDER (VK; Nov96)
added _EXTRA, changed SIGMA to SIG (VK; Oct98)
big correction, if MEAN,SIG,PEAK are undefined on input (VK; JunMM)
now works even if X are integers (VK; Jul01)
converted array notation to IDL 5 (VK; Apr02)
check to see if X is defined (VK; Sep02)
changed keyword NORM to NORMFLX (VK; Oct02)
added keyword WIDEBIN and call to MID2BOUND (VK; Apr11)
(See pro/fitting/mk_gauss.pro)
function mk_ident returns the input as the output (hence the name) it is useful as an "identity translator" to make a model out of whatever input array. syntax gy=mk_ident(x,y0,x0,m0,pder,gigo=gigo,verbose=verbose) parameters x [INPUT array; required] the points at which the output is computed. y0 [INPUT] the normalization of the output function * if not given, assumed to be 1.0 x0 [INPUT] the zero-point of the output, i.e., how much to shift the input * if not given, assumed to be 0.0 m0 [INPUT] a stretching factor * if not given, assumed to be 1.0 * if Y0, X0, or M0 are arrays, only the first element is used * NOTE: for X0.NE.0 and M0.NE.1, the new functions are simply interpolated from GIGO pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 5 parameters are supplied in call. keywords gigo [INPUT] the array which goes into the output * if not given, assumed to be 0.*X+1. * if size does not match X, truncated or filled out with 1st element verbose [INPUT; default=0] controls chatter _extra [JUNK] here only to prevent crashing usage summary * call as a function subroutines NONE history vinay kashyap (Apr02)
(See pro/fitting/mk_ident.pro)
function mk_lceclipse returns the light curve of a hard eclipse of an almost point source syntax lc=mk_lceclipse(x,midpt,hwidth,depth,pder,angfall=angfall,angrise=angrise,$ ybase=ybase,yoff=yoff,/steep) parameters x [INPUT array; required] where LC(X) must be computed midpt [INPUT; default: mid_point(X)] position of central point of eclipse hwidth [INPUT; default: 0.1*range(X)] half-width of eclipse depth [INPUT; default: 1] depth of eclipse pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 5 parameters are supplied in call. * array of size [N(X),7], with columns containing the partial derivatives wrt MIDPT,WIDTH,DEPTH,ANGFALL,ANGRISE,YBASE,YOFF keywords angfall [INPUT; default=3*!pi/2] angle of lightcurve descent in radians angrise [INPUT; default=!pi/2] angle of lightcurve ascent in radians * NOTE: if STEEP is set, ANGFALL and ANGRISE are assumed to be slopes and the default values are set to -1000 and +1000 respectively steep [INPUT] if set, assumes that ANGFALL and ANGRISE are given as slopes ybase [INPUT; default=0] baseline emission yoff [INPUT; default=0] offset on the other side of eclipse eps [INPUT; default=1e-6] a small number _extra [JUNK] here only to prevent crashing description The eclipse curve is: slp1=tan(ANGFALL) & slp2=tan(ANGRISE) LC(X) = YBASE+DEPTH for X < MIDPT-HWIDTH+DEPTH/slp1 = slp1*X+(YBASE-slp1*MIDPT+slp1*HWIDTH) for MIDPT-HWIDTH-DEPTH/slp1 .LE. X .LE. MIDPT-HWIDTH = YBASE for MIDPT-HWIDTH < X < MIDPT+HWIDTH = slp2*X+(YBASE-slp2*MIDPT-slp2*HWIDTH) for MIDPT+HWIDTH .LE. X .LE. MIDPT+HWIDTH+(DEPTH+YOFF)/slp2 = YBASE+DEPTH+YOFF for X > MIDPT+HWIDTH+(DEPTH+YOFF)/slp2 usage summary * call as a function * generates hard eclipse light curve at specified points subroutines NONE example x=findgen(100) y=mk_lceclipse(x,60,20,0.77,pder,ybase=0.4,yoff=0.11,$ angfall=178*!pi/180.,angrise=10.*!pi/180.) & plot,x,y history vinay kashyap (MayMMVII; based on MK_LORENTZ) added keyword STEEP, also corrected bug of pderiv wrt ANG (VK; AugMMVII)
(See pro/fitting/mk_lceclipse.pro)
script MK_LCOOL_APED.PRO IDL program to set up the call to EXAPED and write out the emissivities from the linelist.fits file usage wmn=0. & wmx=3000. atomdb='/data/fubar/SCAR/atomdb/atomdb_v2.0.2/' ;path to ATOMDB apeddir='/data/fubar/SCAR/emissivity/apedD' ;output directory .run mk_lcool_aped vinay kashyap (Jul02)
(See pro/scrypt/mk_lcool_aped.pro)
script MK_LCOOL_CHIANTI IDL program to call WRT_LN_CHIANTI repeatedly for various pressures and densities to generate a database of line intensities for all available CHIANTI ions usage set the variables WMN and WMX to fix wavelength range in [Ang] set the variables NE_MIN, NE_MAX, D_NE [log10[cm^-3]] to set range of densities, and P_MIN, P_MAX, D_P [log10[cm^3 K]] to set range of pressures at which to compute the emissivities set CHIDIR as the path to the CHIANTI installation set OUTDIR as the path to where the outputs should be stored if initale has been run, CHIDIR is set to !CHIDIR, and OUTDIR is set to !TOPDIR/emissivity/chianti invoke as .run mk_lcool_chianti vinay kashyap (Dec96) updated to make it more robust to other people's setups (VK; Jul13)
(See pro/scrypt/mk_lcool_chianti.pro)
function mk_linstr create a standard emissivity structure by putting together the various inputs. this emissivity structure can then be used in PINTofALE exactly as though it had been read in via RD_LINE(). syntax linstr=mk_linstr(emis,logT=logT,wvl=wvl,Z=Z,ion=ion,jon=jon,$ desig=desig,econf=econf,src=src,verbose=verbose) parameters emis [INPUT; required] emissivities * if 2D, assumed to be an array of size (NLOGT,NWVL) * if 1D, makes a semi-intelligent guess as to whether it is an array corresponding to LOGT or WVL -- first checks with LOGT and if size matches, that's it -- else checks with WVL and -- if that doesn't match then quits with an error keywords logT [INPUT] log10(Temperatures [K]) * default is a regular grid going from 4..8 * if any of the values are > 100, then it is assumed that the input is in [K] and the log10 is taken * if size does not match first dimension of 2D EMIS, then ignored and default is used wvl [INPUT] wavelengths [Angstroms] * if size does not match 2nd dimension of EMIS, then quits with an error Z [INPUT] atomic numbers of elements generating given WVL * missing values will be set to 1 ion [INPUT] ionic state of element generating given WVL * missing values are set to 1 jon [INPUT] the ionic state that matters as far as ion-balance is concerned * missing values are set to ION src [INPUT] reference to source of line info * e.g., 1=SPEX, 2=CHIANTI, 3=APED * if not set, assumed to be -99 * if given but in insufficient numbers, the value of the first element is extrapolated out desig [INPUT] level designations for lower & upper level econf [INPUT] e-configurations for lower & upper level * DESIG and ECONF are expected to be array of size (2,NWVL) and are filled out with blank strings if parts are missing verbose [INPUT] controls chatter _extra [JUNK] ignore -- here only to prevent crashing the program history vinay kashyap (Jun02)
(See pro/mkemis/mk_linstr.pro)
function mk_lorentz
returns a modified Lorentzian, Lb(X)
syntax
l=mk_lorentz(x,mean,core,peak,pder,/betap,/normflx,missing=m,/fwhm)
parameters
x [INPUT array; required] where G(X) must be computed
mean [INPUT; default: mid_point(X)] position of peak
core [INPUT; default: 0.1*range(X)] core width
peak [INPUT; default: 1] value of Lb(X=MEAN)
pder [OUTPUT; optional] partial derivatives of model wrt
parameters at each X; calculated only if 5 parameters
are supplied in call.
* array of size [N(X),4], with columns containing the partial
derivatives wrt MEAN, CORE, PEAK, and BETAP respectively
keywords
betap [INPUT; default=1] the index of the beta-profile. default
is regular Lorentzian.
* if NORMFLX is set and BETAP.le.0.5, the default is used
normflx [INPUT] if set, {\int_{-\infty}^{\infty} dX Lb(X) = PEAK}
missing [INPUT] 3 element array to populate missing values of
MEAN, CORE, and PEAK
fwhm [INPUT] if set, assumes that the input CORE is actually
given as full-width at half-max, and converts to the true
core width prior to calculation, and then converts back to
full-width at half-max post-calc.
_extra [JUNK] here only to prevent crashing
description
The Lorentzian is
L(X) = PEAK / ( 1 + ((X-MEAN)/CORE)^2 )
The modified Lorentzian is
Lb(X) = PEAK / ( 1 + ((X-MEAN)/CORE)^2 ) ^ BETAP
When integrated over the real axis (Gradshteyn & Ryzhik, 3.251,2),
\int dX Lb = PEAK*CORE*B(1/2, BETAP-1/2),
where B(x,y) is the Beta-function, with BETAP > 1/2
hence, if NORMFLX is set,
Lb(X) = (PEAK/CORE/B(1/2,beta-1/2))/(1+((X-MEAN)/CORE)^2)^BETAP
The hwhm is defined as that value of X=W such that
Lb(W)=0.5*Lb(X=MEAN)
i.e., Lb(W)=(stuff)/(1+((W-MEAN)/CORE)^2)^(BETAP)=0.5*(stuff)
hence, hwhm = W-MEAN = CORE*sqrt(2^(1/BETAP)-1)
or, fwhm = CORE*2*sqrt(2^(1/BETAP)-1)
usage summary
* call as a function
* generates modified Lorentzian model only at specified points X
* needs MEAN, CORE, PEAK for complete specification
examples
x=findgen(1000)*0.01 & peasecolr & b=2.5
L1=mk_lorentz(x,5,1,1) & L2=mk_lorentz(x,5,1,1,/fwhm)
Lb1=mk_lorentz(x,5,1,1,betap=b) & Lb2=mk_lorentz(x,5,1,1,betap=b,/fwhm)
Lf1=mk_lorentz(x,5,1,1,/normflx) & Lf2=mk_lorentz(x,5,1,1,betap=b,/norm)
plot,x,L1 & oplot,x,L2,col=2
oplot,x,Lb1,thick=2 & oplot,x,Lb2,thick=2,col=2
oplot,x,Lf1,thick=2,line=1 & oplot,x,Lf2,thick=2,col=3,line=1
subroutines
NONE
history
vinay kashyap (Oct98)
changed keyword BETA to BETAP; corrected normalization (VK; Dec98)
recomputed partial derivatives (VK; MarMM)
now works even if X are integers (VK; Jul01)
what if PEAK=0? (VK; Apr02)
converted array notation to IDL 5 (VK; Apr02)
added partial derivative wrt BETAP to PDER output array (VK; Jun02)
changed keyword NORM to NORMFLX (VK; Oct02)
added keyword FWHM (VK; Apr03)
(See pro/fitting/mk_lorentz.pro)
function mk_model generate and return a compound model using the supplied parameters of components made up of 3-parameter functions syntax model=mk_model(x,p,w,h,pder,group=group,delp=delp,type=type,/asis,$ /allcomp,/fwhm,/norm,missing=missing,betap=betap,vrot=vrot) parameters x [INPUT; required] points where model is computed p [INPUT; required] positions of components w [INPUT; required] widths of components h [INPUT; required] heights of components pder [OUTPUT] contains 2D array (NX,3*NPAR) of partial derivatives of each component wrt parameters keywords group [INPUT] grouping index of gaussians delp [INPUT] offsets from first position value in group NOTE: GROUP and DELP are ignored if ASIS is set NOTE: if GROUP and DELP are not given, ASIS is set type [INPUT; default='G*aussian'] what type of curve to generate for the model. other possibilities are L*orentzian B*eta-profile (set "Beta=<value>") S*lant (set "slant=<angle>,<beta>") R*otation-convolved Gaussian (set "rot=<velocity>") P*ower-law (set "pw=<break>" or "pe=<break>") U*ser_defined (not yet implemented), etc. * if not defined, uses "Gauss" * if insufficiently defined, uses last defined as default for the rest asis [INPUT] the default action is to verify that the p are consistent with GROUP and DELP and to correct as necessary. if ASIS is set, this is not done. allcomp [INPUT] if set, returns the sum of components and also each component in a separate column of a 2D array of size (N_ELEMENTS(P)+1,N_ELEMENTS(X)) _extra [INPUT] pass defined variables to subroutine:- MK_GAUSS: MISSING, FWHM, NORM MK_LORENTZ: BETAP, MISSING, NORM MK_SLANT: ANGLE, BETAP, MISSING, NORM MK_ROGAUSS: VROT, MISSING, FWHM, NORM usage summary * call as a function * returns composite model by adding up components * input component parameters as sequence of arrays of positions, widths, and heights * input grouping info by 2 additional arrays * specify type of model with keyword TYPE * partial derivatives are computed only if ALL 5 parameters are supplied in call * example TYPEs: 'Gauss', 'gaussian', 'gau', 'g' 'Lorentz', 'lorentz', 'lorentzian', 'lor', 'l' 'beta=1.8', 'BETA=2.4', 'B=2', 'b 1.8', 'b:1.8', 'b 1.8' 'slant=45,1.8','SLANT=89,2.4', 's=10','s=,2', 's:3,2' 'rotational velocity=1e-4', 'rot=30', 'r:30e5', 'R 1e-4' 'pe=1', 'pw=12.3985', 'pw@12.4' subroutines MK_GAUSS MK_LORENTZ MK_SLANT MK_ROGAUSS MK_POWLAM KILROY history vinay kashyap (Oct96) added parameter to return partial derivatives (VK; Nov96) added _EXTRA, added call to MK_LORENTZ (VK; Oct98) allowed setting BETAP for MK_LORENTZ via TYPE definition (VK; Dec98) added MK_SLANT calls (VK; MarMM) added MK_ROGAUSS, MK_POWLAM calls (VK; JunMM)
(See pro/fitting/mk_model.pro)
function mk_poly1d
returns a polynomial, \Sum_{i=0}^{N} a_i (x-x0)^i
syntax
py=mk_poly1d(x,aa,pder,x0=x0,verbose=verbose)
parameters
x [INPUT array; required] where G(X) must be computed
aa [INPUT; required] array of coefficients for the polynomial
* the degree of the polynomial that is returned is N(AA)-1
pder [OUTPUT; optional] partial derivatives of model wrt parameters
at each X; calculated only if 4 parameters are supplied in call.
keywords
x0 [INPUT; default=0] zero-point of function
verbose [INPUT; default=0] controls chatter
_extra [JUNK] here only to prevent crashing
usage summary
* call as a function
subroutines
NONE
history
vinay kashyap (Aug01)
converted array notation to IDL 5; summation of powers now kosher;
corrected sign of partial wrt X0 (VK; Apr02)
(See pro/fitting/mk_poly1d.pro)
function mk_powlam returns a power-law in WAVELENGTH G(X) syntax g=mk_powlam(x,gamma1,gamma2,normE,pder,Xo=Xo,pbreak=pbreak,$ NH=NH,wvlar=wvlar,effar=effar,exptime=exptime,dellam=dellam) parameters X [INPUT array; required] where G(X) must be computed gamma1 [INPUT; required] power-law index 1 gamma2 [INPUT; required] broken power-law index 2 normE [INPUT; required] power-law normalization * as appropriate for an _energy [keV]_ scale pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 5 parameters are supplied in call. * array of size [N(X),4], with columns containing the partial derivatives wrt GAMMA1, GAMMA2, NORME, and PBREAK respectively keywords Xo [INPUT] Wavelength for which normalization is defined 1.0; default is 1.0 Angstroms pbreak [INPUT] Wavelength at which power-law "breaks" NH [INPUT] Hydrogen column density for computing ISM absorption wvlar [INPUT array] wavelength grid of Chandra/HRC-S/LETG effective area effar [INPUT array] Chandra/HRC-S/LETG effective area exptime [INPUT] exposure time dellam [INPUT] wavelength binsize for computing COUNTS spectrum _extra [JUNK] description for X <= pbreak, G(X)=exp(-tau)*norm*(X/Xo)^(gamma1-2)*effar*exptime*dellam for X > pbreak, G(X)=exp(-tau)*norm*(pbreak/Xo)^(gamma1-gamma2)*(X/Xo)^(gamma2-2) *effar*exptime*dellam usage summary * call as a function * generates model only at specified points X * needs for complete specification subroutines ISMTAU history Deron Pease (June 2000) call ISMTAU only if NH is defined (VK; MMJul) bug correction: if NH not defined, etau must be set to 1 (VK; Jun01) converted array notation to IDL 5 (VK; Apr02) added partial derivatives wrt PBREAK (VK; Jun02) pushed partial derivatives wrt PBREAK inside if..then (VK; Nov02)
(See pro/fitting/mk_powlam.pro)
function mk_reciprocalpow returns a reciprocal double Power-law function, p(X) = 1/(A1*X^GAMMA1 + A2*X^GAMMA2), with A1*J^GAMMA1 = A2*J^GAMMA2, so A2 == A1*J^(GAMMA1-GAMMA2) and A1 == NORM for X>0 syntax p=mk_reciprocalpow(x,norm,gamma1,gamma2,pjoin,pder,verbose=verbose) parameters X [INPUT; required] where p(X) must be computed norm [INPUT; required] normalization gamma1 [INPUT; required] power-law index 1 gamma2 [INPUT; required] power-law index 2 pjoin [INPUT; required] the joining point where the two power-law components are equal pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 6 parameters are supplied in call. * array of size [N(X),4], with columns containing the partial derivatives wrt NORM, GAMMA1, GAMMA2, and PJOIN respectively keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program example x=(findgen(100)+1)/10. & p=mk_reciprocalpow(x,1.,1.5,0.2,2) & plot,x,p,/xl,/yl contrast with: oplot,x,mk_bknpower(x,0.3,-1/1.5,-5,2),line=2 history Vinay Kashyap (Sep2008)
(See pro/fitting/mk_reciprocalpow.pro)
function mk_rogauss convolves a gaussian line profile with a rotational broadening function and returns the broadened profile. syntax rg=mk_rogauss(x,mean,sig,peak,pder,vrot=vrot,/fwhm,/normflx,$ missing=missing) parameters x [INPUT array; required] where rG(X) must be computed * generally in a wavelength grid mean [INPUT] passed w/o comment to MK_GAUSS sig [INPUT] passed w/o comment to MK_GAUSS peak [INPUT] passed w/o comment to MK_GAUSS pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X * calculated only if 5 parameters are supplied in call. * numerically computed because of intractable convolution * array of size [N(X),4], with columns containing the partial derivatives wrt MEAN, SIG, PEAK, and VROT respectively keywords vrot [INPUT; default=0] the rotational velocity, as a fraction of light speed * if > 1 and < 3e5, assumed to be in [km/s] * if > 3e5 and < 3e10, assumed to be in [cm/s] * if -ve, then convolves with a fixed rotation profile whose width is defined with reference to MEAN _extra [JUNK] pass defined keywords to MK_GAUSS FWHM, NORMFLX, MISSING description NORMFLX=0 && FWHM=0: G(X)=PEAK*exp((X-MEAN)^2/SIGMA^2) NORMFLX=1 && FWHM=0: G(X)=(PEAK/SIGMA/sqrt(2*!PI))*exp((X-MEAN)^2/2/SIGMA^2) NORMFLX=0 && FWHM=1: G(X)=PEAK*exp(2.355^2*(X-MEAN)^2/2/SIGMA^2) NORMFLX=1 && FWHM=1: G(X)=(2.355*PEAK/SIGMA/sqrt(2*!PI))*exp(2.355^2*(X-MEAN)^2/2/SIGMA^2) G(X) is then convolved with V(X';X)=(2/!PI/HW)*sqrt(1.-((X'-X)/HW)^2), where HW=VROT*X (note that V(X';X) *changes* across the range of X) usage summary * call as a function * needs MEAN, SIG, PEAK for complete specification subroutines MK_GAUSS also makes recursive call to itself if PDER is required history vinay kashyap (JunMM, based on MK_SLANT) converted array notation to IDL 5 (VK; Apr02) added partial wrt VROT to PDER (VK; Jun02) changed keyword NORM to NORMFLX (VK; Oct02)
(See pro/fitting/mk_rogauss.pro)
function mk_sinusoid returns a sinusoid, A*sin(f*X+p)+c syntax s=mk_sinusoid(x,ampl,freq,offset,pder,phase=phase,/normflx,$ missing=missing) parameters x [INPUT array; required] where G(X) must be computed ampl [INPUT; default: 1] amplitude of the sinusoid freq [INPUT; default: 2*!pi/range(X)] frequency of sinusoid offset [INPUT; default: 1] constant offset for sinusoid pder [OUTPUT; optional] partial derivatives of model wrt parameters at each X; calculated only if 5 parameters are supplied in call. * array of size [N(X),4], with columns containing the partial derivatives wrt AMPL, FREQ, OFFSET, and PHASE respectively keywords phase [INPUT; default=0] the phase of the sinusoid in [deg] normflx [INPUT] not used yet missing [INPUT] 3 element array to populate missing values of AMPL, FREQ, and OFFSET _extra [JUNK] here only to prevent crashing description The sinusoid is S(X) = AMPL * sin(FREQ*X+PHASE) + OFFSET usage summary * call as a function * generates sinusoid values only at specified points X * needs AMPL, FREQ, OFFSET, and PHASE for complete specification examples subroutines NONE history vinay kashyap (Sep04)
(See pro/fitting/mk_sinusoid.pro)
function mk_slant
returns the product of a slanted line with a modified
Lorentzian, Lb(X)
the idea is to model the asymmetrical line profiles seen in
CXO grating data.
syntax
Lbs=mk_slant(x,mean,core,peak,pder,angle=angle,betap=betap,$
/normflx,missing=missing)
parameters
x [INPUT array; required] where G(X) must be computed
mean [INPUT; default: mid_point(X)] position of peak
core [INPUT; default: 0.1*range(X)] core width
peak [INPUT; default: 1] value of Lb(X=MEAN)
pder [OUTPUT; optional] partial derivatives of model wrt parameters
at each X; calculated only if 5 parameters are supplied in call.
* array of size [N(X),5], with columns containing the partial
derivatives wrt MEAN, CORE, PEAK, BETAP, and ANGLE respectively
keywords
angle [INPUT; default=0] the atan(slope) of the straight line
that makes the Lorentzian asymmetric
betap [INPUT; default=1] the index of the beta-profile. default
is regular Lorentzian.
* if NORMFLX is set and BETAP.le.0.5, the default is used
normflx [INPUT] if set, {\int_{-\infty}^{\infty} dX Lbs(X) = PEAK}
missing [INPUT] 3 element array to populate missing values of
MEAN, CORE, and PEAK
_extra [JUNK] here only to prevent crashing
description
The Lorentzian is
L(X) = PEAK / ( 1 + ((X-MEAN)/CORE)^2 )
The modified Lorentzian is
Lb(X) = PEAK / ( 1 + ((X-MEAN)/CORE)^2 ) ^ BETAP
The asymmetric modified Lorentzian is
Lbs(X) = (PEAK + PEAK*SLOPE*(X-MEAN)) / $
( 1 + ((X-MEAN)/CORE)^2 ) ^ BETAP
When integrated over the real axis (Gradshteyn & Ryzhik, 3.251,2),
the second terms drops out and the integral is identical to that
of the modified Lorentzian itself, i.e.,
\int dX Lbs = CORE*PEAK*B(1/2,BETAP-1/2)
where B(x,y) is the Beta-function, with BETAP > 1/2
if NORMFLX is set,
Lbs(X) = ((PEAK+PEAK*SLOPE*(X-MEAN))/CORE/B(1/2,beta-1/2)) / $
(1+((X-MEAN)/CORE)^2)^BETAP
usage summary
* call as a function
* generates modified Lorentzian model only at specified points X
* needs MEAN, CORE, PEAK for complete specification
subroutines
NONE
history
vinay kashyap (MarMM, based on MK_LORENTZ)
now works even if X are integers (VK; Jul01)
converted array notation to IDL 5 (VK; Apr02)
accounted for case PEAK=0, added partial derivatives of BETAP and
ANGLE to PDER (VK; Jun02)
changed keyword NORM to NORMFLX (VK; Oct02)
(See pro/fitting/mk_slant.pro)
function modalpoint returns the mode of distribution defined by set of unbinned array values syntax arraymode=modalpoint(array,eps=eps,verbose=verbose) parameters array [INPUT; required] array of values for which mode must be found keywords eps [INPUT; default=1e-6] a small number verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description sort the array, divide into two sets around midpoint of range, choose the set that contains more elements, and repeat until the range is sufficiently small, and declare the midpoint of the range to be the mode warning may fail for multimodal distributions example for i=0,20 do print,i,modalpoint(randomn(seed,10000L)+i) history translated to IDL by Vinay Kashyap from C code written for BEHR by Taeyoung Park c.2003 (MarMMVI) now correctly handles case when input is quantized (VK; SepMMVI)
(See pro/stat/modalpoint.pro)
function morfo_circolare
returns an image that is morphologically manipulated with a
rotated, annular arclike structure element
if MOPEN is set then an opening operation is applied
if MCLOSE is set then a closing operation is applied
syntax
result=morfo_circolare(image,arc,rzero,rstep,nstep,gray=gray,$
/mopen,/mclose,verbose=verbose)
parameters
image [INPUT; required] the image you want to smooth
* must be a 2-D array
arc [INPUT; required] the angular size of the arc to be used
as a structuring element [degree]
* the full circle is completed by moving the arc by ARC/2
and combining the results
rzero [INPUT; required] radius of the innermost annulus to consider
rstep [INPUT; required] the annular width of structure elements [pix]
nstep [INPUT] number of annuli to use
* if not given, carries on until the outer radius equals
the larger of the image width or height
keywords
gray [INPUT] explicitly set to 0 to carry out the morphological
operations in binary rather than grayscale; default is to
use grayscale
mopen [INPUT] if set, runs the IDL function morph_open()
mclose [INPUT] if set, runs the IDL function morph_close()
* NOTE: if more than one of MOPEN,MCLOSE
are set, the operations will be daisy-chained in that
particular order
readd [INPUT] if set, adds up the output from the morphological
operations at one annular arc to the output from another
* the default is to record, at any pixel, the largest
response obtained from all the bits
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
history
vinay kashyap (july 06; based on morfo_rottangoli)
added keyword _EXTRA (VK; may 07)
(See pro/util/morfo_circolare.pro)
function morfo_potare prunes the little tributaries from a morphological skeleton of an image and returns a cleaner image of the skeleton. this pruning works as follows: first, branch points in the skeleton are identified, and they and their neighboring points are extracted and set aside; next, the remaining points are segmented into distinct and separate lines and then all segments which are smaller than some threshold are discarded; and finally the branch points and their neighborhoods are added back on. this is not the standard algorithm for pruning, as far as I know. syntax pruned_skeleton=morfo_potare(skel,minpix,verbose=verbose) parameters skel [INPUT; required] the input 2D bitmap image that contains a morphological skeleton * NOTE: input _must_ be a skeleton, otherwise the program will fail miserably minpix [INPUT] minimum number of pixels that must exist in a given branch for it to be kept on * default is 4 keywords verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines MORFO_SEGMENTO history vinay kashyap (Jul2006) added _EXTRA keyword; changed call from MORFO_FILTRI to MORFO_SEGMENTO (VK; May2007)
(See pro/util/morfo_potare.pro)
function morfo_rottangoli
an image that is morphologically manipulated with a
rotated, rectangular structure element
if MGRAD is set then a gradien operation is applied
if MTOP is set then a tophat operation is applied
if MOPEN is set then an opening operation is applied
if MCLOSE is set then a closing operation is applied
if MTHIN is set then a thinning operation is applied
syntax
result=morfo_rottangoli(image,xsize,ysize,angle,gray=gray,$
/mgrad,/mtop,/mopen,/mclose,/mthin,/readd,/reuse,$
verbose=verbose)
parameters
image [INPUT; required] the image you want to smooth
* must be a 2-D array
xsize [INPUT; required] the width of the structure element in pixels
ysize [INPUT; required] the height of the structure element in pixels
angle [INPUT; default=0] the angle in degrees by which to rotate the
rectangular structure element defined by (XSIZE,YSIZE)
* if a vector, the output will be the summed images
from the application of the rectangular structure
element at each of the angles
keywords
gray [INPUT] explicitly set to 0 to carry out the morphological
operations in binary rather than grayscale; default is to
use grayscale
mgrad [INPUT] if set, runs the IDL function morph_grad()
mtop [INPUT] if set, runs the IDL function morph_tophat()
mopen [INPUT] if set, runs the IDL function morph_open()
mclose [INPUT] if set, runs the IDL function morph_close()
mthin [INPUT] if set, runs the IDL function morph_thin()
* NOTE: if more than one of MGRAD,MTOP,MOPEN,MCLOSE,MTHIN
are set, the operations will be daisy-chained in that
particular order
readd [INPUT] if set, adds up the output from the morphological
operations at one ANGLE to the output from another ANGLE
* the default is to record, at any pixel, the largest
response obtained from all the ANGLEs
reuse [INPUT] if set, uses the output from the morphological
operations at one ANGLE as the input for the next ANGLE
* overrides both default and READD
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
history
julia sandell (july 06)
tightened up and made bulletproof and changed name from morph_rot
to morfo_rottangoli; morphological analysis with rotating rectangles;
added keywords GRAY, READD, REUSE, VERBOSE (Vinay Kashyap; july 06)
added _EXTRA keyword (VK; may 07)
(See pro/util/morfo_rottangoli.pro)
function morfo_scheletro compute and return the skeleton representation of an image A using a circular structuring element B. a skeleton is defined as the union of the sets Erosion(A,k*B) - Opening(Erosion(A,k*B),B) for k=0,..K where K is the largest value of k before the sets become empty. syntax skel=morfo_scheletro(image,rmin,thresh=thresh,verbose=verbose) parameters image [INPUT; required] image whose skeleton must be obtained. * must be a 2-D array rmin [INPUT] radius of the circle that acts as a structuring element * if not given, the default is to use a 3x3 array * if given, uses DIST() to define the array -- minimum possible radius is hardcoded as 1pix keywords thresh [INPUT; default=0] filter IMAGE such that only values greater than THRESH are considered. * if size matches that of IMAGE, a pixel-by-pixel filtering is carried out verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Jul2006)
(See pro/util/morfo_scheletro.pro)
function morfo_segmento percolates along adjacent connected pixels in a bitmap until all the pixels that are connected to each other get grouped into contiguous regions and are so labeled; an image containing the region numbers for each pixel is returned syntax oimg=morfo_segmento(img,areas,thresh=thresh,arclev=arclev,$ subidx=subidx,/hardcut,deepimg=deepimg,verbose=verbose) parameters image [INPUT; required] 2D image in which to separate out the connected blobs * the blobs are defined as any pixel with intensity>0 unless keyword THRESH is set areas [OUTPUT] number of pixels in each labeled region * remember the IDL index shift! AREAS[0] is the number of pixels in the background, and AREAS[SOURCE] gives the number of pixels that constitute the blob SOURCE keywords thresh [INPUT] the threshold value at which to convert the input image into a bitmap * if not set, assumed to be 0 arclev [INPUT] fraction of the maximum area size to keep in the output -- all regions of size smaller than this are zeroed out * default is 0, i.e., no filtering is done * if .le. -1, taken to be an absolute value cut if .gt. -1 && .lt. 0, absolute value is choosen if .ge. 1 && .lt. 100, assumed to be percentage if .ge. 100, assumed to be 1-1/ARCLEV subidx [INPUT] index array defining a subset of IMAGE to which one must confine attention * if not set, assumed to be LINDGEN(N_ELEMENTS(IMAGE)) hardcut [INPUT] if set, places a hard cut at the boundaries defined by SUBIDX -- the default is to track the region out of SUBIDX if any part of it overlaps deepimg [OUTPUT] an image that depicts the depth at which a particular pixel was added to a blob verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description this is an updated version of morfo_filtri(), and is much faster because it uses a few algorithmic and IDL tricks to speed things up. for example, rather than do a linear search going through every pixel once, it does array operations. each pixel is initially assigned a unique number, and at each iteration, the numbers of each adjacent pixels are compared and the smallest of the numbers is assigned to all of them. thus, all the pixels that belong to each blob end up having the same number. these numbers are then recast into a gap-free sequence thereafter. note: there will be no significant improvements in speed in some special cases, such as if there is a very large connected region; this is never *slower* than morfo_filtri() however. subroutines KILROY history vinay kashyap (Sep2006; based on morfo_filtri.pro) added keywords ARCLEV and _EXTRA (VK; May2007) was failing when there was only one blob (VK; Jun2007)
(See pro/util/morfo_segmento.pro)
function morfo_soglia threshold the image based on some cut derived from applying some kind of filter, and return the image, ideally with the interesting features enhanced syntax fimg=morfo_soglia(img,gamma=gamma,nsigma=nsigma,centrale=centrale,$ bitlev=bitlev,/zeromin,mimg=mimg,thresh=thresh,verbose=verbose) parametes img [INPUT; required] input image to be filtered * must be 2D keywords snr [INPUT] if given, computes a threshold based on a S/N criterion * if set, IMG is _not_ converted to a byte scale gamma [INPUT] if given and is +ve, calls GMASCL() to transform the image first according to the power-law scaling transformation nsigma [INPUT] if given, sets the threshold at mean+NSIGMA*stddev * default is 1 * if mean+NSIGMA*stddev < 0, this is not applied centrale [INPUT] if set, carries out a local median filtering with a box of size 2*fix(CENTRALE>1)+1 * NSIGMA thresholding is ignored unless NSIGMA is explicitly set * the filtered pixels are zero'd out unless the keyword ZEROMIN is explicitly set to 0 bitlev [INPUT] if set, carries out a bit-level filtering down to level BITLEV, with 1=most significant and 7 or more=least significant * both CENTRALE and NSIGMA are ignored zeromin [INPUT] if set, sets all pixels that do not pass the threshold to 0; otherwise will be set to the threshold value mimg [OUTPUT] the median image, constructed if CENTRALE is set thresh [OUTPUT] the threshold value used, if histogram-threshold is applied verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program restrictions requires David Fanning's GMASCL() function history vinay kashyap (Jul2006) added _EXTRA keyword; bugfix when NSIGMA was very small (VK; May2007)
(See pro/util/morfo_soglia.pro)
procedure munge_list
chomps through ascii file containing observed wavelengths/fluxes
and possible matches to them, then generates the appropriate
line database and ID structures (see RD_LINE and LINEID)
syntax
munge_list,list,idstr,lnstr,wvl,flux,fluxerr,dbdir=dbdir,$
sep=sep,prefix=prefix,comment=comment, mapping=mapping,pres=pres,$
logp=logp,n_e=n_e,desig=desig,econf=econf,chifil=chifil,chidir=chidir,$
eqfile=eqfile,DEM=DEM,abund=abund,/noph,effar=effar,wvlar=wvlar
parameters
list [INPUT; required] file containing wavelengths, fluxes, and
matches.
* see format below
idstr [OUTPUT] LINEID type structure
lnstr [OUTPUT] RD_LINE type structure
wvl [OUTPUT] all the observed wavelengths
flux [OUTPUT] all the measured wavelengths
fluxerr [OUTPUT] errors on FLUX
keywords
dbdir [I/O] directory in which to look for files
* will be used ONLY if not given in LNLIST
* if not specified, *default* will be set at run-time to
whatever was used last
* on output, will contain complete list of line database
directories used
sep [INPUT; default=<tab>] separator used to delineate fields
in LNLIST
prefix [INPUT; default='*'] any line beginning with this letter
is considered a comment
* this is in addition to "%", "#", ";", "/"
comment [OUTPUT] any commented lines are returned in this variable
as a string array
_extra [INPUT ONLY] use this to pass defined keywords to
-- RD_LIST (MAPPING)
-- RD_LINE (PRES,LOGP,N_E,DESIG,ECONF,VERBOSE)
-- FOLD_IONEQ (CHIFIL,CHIDIR,EQFILE,VERBOSE)
-- LINEFLX (DEM,ABUND,NOPH,EFFAR,WVLAR)
input file format
* one entry per line
* each observed wavelength and related IDs must be in a block
of the form
/{ <sep> WVL <sep> FLUX <sep> FLUXERR
ELEM1 ION1 <sep> WAVE1 <sep> SOURCE1 <sep> DESCRIPTION1
ELEM2 ION2 <sep> WAVE2 <sep> SOURCE2 <sep> DESCRIPTION2
...
ELEMn IONn <sep> WAVEn <sep> SOURCEn <sep> DESCRIPTIONn
// human readable comments
/}
* the beginning and ending "/{" and "/}" are REQUIRED
* WVL, FLUX, and FLUXERR are optional, and will be guessed at from
the IDs:
WVL is set to 0 or the WAVE of the strongest line;
FLUX is the total of the peak emissivities of the IDs;
FLUXERR is 1% of FLUX (if non-zero), or 1 otherwise.
* obviously, WVL is required if FLUX is given, and WVL and FLUX
are required if FLUXERR is given.
* of the IDs, ELEM is required, ION is useful, WAVE and SOURCE are
optional (obviously, WAVE is required if SOURCE is given, and
WAVE and SOURCE are required if DESCRIPTION is given.)
* due to a shortcoming in ZION2SYMB, it is best if "ELEM ION" is
given as "ELEMENT ION", e.g., "Fe XII" or "FeXII" or "Fe 12"
and not "26 12" or "26_12"
* <SEP> is a separator, usually a <tab>, but had better not be any
of "," "+-" "-" and "?"
* WAVE may be (any combination of):-
exact match -- "WVL"
inexact match -- "WVL +- dW" or "WVL ? dW"
range -- "WMIN,WMAX" or "WMIN-WMAX"
enclosed in brackets -- "()" "[]" "{}"
* lines prefixed by PREFIX, "%", "#", ";" and "/" are ignored
(except for "/{", "/}", and "//" -- the last is treated as
scribbles to go into the NOTES field of the ID)
* if no IDs are found, WVL is flagged as "UNKNOWN"
* emissivities of IDs not attached to any WVL are returned in LNSTR
subroutines
RD_LIST
RD_LINE
SYMB2ZION
LAT2ARAB
FOLD_IONEQ
RD_IONEQ
READ_IONEQ
CAT_LN
LINEFLX
GETABUND
WHEE
IS_KEYWORD_SET
history
vinay kashyap (Nov98)
updated to include FLUXERR in IDSTR (VK; Dec98?)
updated to include NOTES in IDSTR (VK; Mar99)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
corrected bug where LNSTR was being concatenated if defined
on input; now input is ignored (VK; Jul2008)
corrected bug where LNSTR was not being output (VK; Jan2015)
(See pro/munge_list.pro)
procedure nary2dec converts num from n-ary base to decimal syntax nary2dec,num,dec,/binary,/octal,/hex parameters num [INPUT] n-ary number or string dec [OUTPUT] corresponding decimal number keywords binary [INPUT] if set, NUM taken to be in binary notation octal [INPUT] if set, NUM taken to be in octal notation hex [INPUT] if set, NUM taken to be in hexadecimal notation _extra [JUNK] here only to prevent crashing the program history vinay kashyap (1996?)
(See pro/util/nary2dec.pro)
function nenH calculate the ratio N(e)/N(H) (or N(e)/N(p) -- see keyword NPROTON below) in a plasma of specified temperature syntax r=nenh(logT,abund=abund,eqfile=eqfile,chidir=chidir,elem=elem,$ xelem=xelem,/nproton) parameters logT [INPUT; required] temperature(s) (log_10(T [K])) at which to compute ratio. keywords abund [I/O] abundances of elements. default is Allen abundances. eqfile [INPUT] pathname, relative to CHIDIR, of file containing ionization equilibrium values, passed w/o comment to RD_IONEQ chidir [INPUT] path name to the CHIANTI installation, passed w/o comment to RD_IONEQ elem [INPUT] return data for only these elements (default: all) xelem [INPUT] exclude these elements (overrides ELEM) * default: none (note that older CHIANTI ion balance files do not have Cu, Zn, so originally XELEM was set by default to [29,30]) nproton [INPUT] if set, returns the ratio N(e)/N(p) _extra [JUNK] ignore -- here only to prevent crashing program subroutines GETABUND [RDABUND] RD_IONEQ [READ_IONEQ (a CHIANTI routine)] SYMB2ZION [LAT2ARAB] KILROY history vinay kashyap (Sep97) modified to have just one call to RD_IONEQ instead of one for each Z, changed default of XELEM to none (VK; Jun02)
(See pro/nenh.pro)
function noismooth return the input function boxcar smoothed at varying scales such that the value at any point is determined at a sufficiently high S/N. beware that this will NOT conserve flux, and the adjacent points (or errors) of the smoothed function will no longer be statistically independent. syntax ys=noismooth(y,ysig=ysig,snrthr=thresh,snrout=snr,xsiz=xsiz,$ sdepth=sdepth,verbose=v) parameters y [INPUT; required] array that must be smoothed * note that integer count arrays are returned as integers, which may not necessarily be what is optimal. to return floats instead, simply input (y*1.0) keywords ysig [INPUT] errors on Y -- S/N on smoothed function will be calculated by square-adding * if not given, Gehrel's approximation to Poisson, sqrt(abs(Y)+0.75)+1 will be assumed * if single-element, then assumed to be -- additive constant if <0 (i.e., abs(YSIG[0]), or else -- fractional if <1, or else -- percentage if <100, and -- additive constant otherwise snrthr [INPUT] S/N threshold -- try to make every point lie above this S/N * default is 3 snrout [OUTPUT] final S/N at each point xsiz [OUTPUT] final smoothing scale at each point sdepth [INPUT] maximum smoothing scale to consider * default is n_elements(Y)/2-1, which is also the hardcoded maximum verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description akin to Harald Ebeling's adaptive smoothing of 2-D images (encoded in CIAO CSMOOTH), this program boxcar smooths the input 1-D array over a number of scales and at each bin keeps the result from the smallest scale which puts it over the specified S/N threshold. examples peasecolr & y=randomu(seed,1000,poisson=1) & y[400:499]=randomu(seed,100,poisson=5) plot,y & oplot,smooth(y,5),col=2,thick=3 & oplot,smooth(y,100),col=29,thick=3 ys=noismooth(y,ysig=ysig,snrthr=10,snrout=snr,xsiz=xsiz) plot,y & oplot,ys,col=2,thick=3 & oplot,snr,col=3 ys=noismooth(y,ysig=ysig,snrthr=3,snrout=snr,xsiz=xsiz,verbose=10) oplot,ys,col=25,thick=3 & oplot,snr,col=35 ys=noismooth(y,ysig=ysig,snrthr=13,snrout=snr,xsiz=xsiz) oplot,ys,col=29,thick=3 & oplot,snr,col=39 these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (OctMM) modified YSIG behavior to handle YSIG[0]>1 (VK; Nov'02)
(See pro/util/noismooth.pro)
procedure nrg2chan
convolves input energy spectrum with an OGIP-style response matrix
syntax
nrg2chan,nrg,flx,chan,spec,rmstr,effar=effar,nrgar=nrgar
parameters
nrg [INPUT; required] bin boundary values at which input FLX is
defined.
* usually [keV], depends on RMF file
flx [INPUT; required] fluxes in [ph/bin/(s/cm^2/sr/...)]
chan [OUTPUT; required] bin boundary values at which output SPEC
is defined
* same units as NRG
spec [OUTPUT; required] output, convolved spectrum
rmstr [INPUT; required] structure containing all the relevant
data (e.g., see output of RD_OGIP_RMF):
{NNRG,ELO,EHI,NCHAN,EMN,EMX,N_GRP,F_CHAN,N_CHAN,MATRIX}
* ELO and EHI refer to range of photon energies at which
response is valid
* EMN and EMX refer to bin boundaries for each channel
* N_GRP, F_CHAN, and N_CHAN refers to number of groups
of non-zero data, beginning channel, and number of
channels in each group
keywords
effar [INPUT] effective areas [cm^2]
nrgar [INPUT] energies at which EFFAR are defined
* same units as NRG
* sizes of EFFAR and NRGAR must match
* range of NRGAR must overlap NRG
* if EFFAR and NRGAR are legal, FLX is multiplied by
EFFAR (over intersection of NRGAR and NRG; zeroed
elsewhere) before convolving with response matrix
* of course, this multiplication makes sense only if
units on FLX are [ph/bin/cm^2/...]
_extra [JUNK] ignore - here only to prevent crashing
restrictions
requires subroutine BINERSP
requires output of RD_OGIP_RMF
history
vinay kashyap (Apr99; based on CONV_RMF)
(See pro/util/nrg2chan.pro)
FUNCTION num2str given an array of integers, prepends the appropriate number of zeros to make all the strings of the same length, equal to the maximum length needed. SYNTAX sss=num2str(nnn,len=len,nmax=nmax) PARAMETERS num [INPUT; required] array of integers KEYWORDS len [INPUT] if set, final string length = LEN. * if LEN < maximum length, defaults to maximum * if LEN < 0, overrides above setting nmax [INPUT] the maximum possible value of NUM * if set, computes LEN on the fly based on NUM * if both LEN and NMAX are set, LEN takes precedence _extra [JUNK] here only to prevent crashing the program EXAMPLE print, num2str(findgen(10),len=-4) HISTORY written by vinay kashyap (1996?) added keyword NMAX (VK; Jan2000) now takes advantage of the In.n format (VK; Jul2005)
(See pro/util/num2str.pro)
procedure ogipzip compress a numerical array to return only those elements which are above some threshold, and the means to reconstruct the full fledged array. basically this is how OGIP RMF matrix values are compressed and stored. syntax ogipzip,arr,carr,ngrp,fchan,nchan,eps=eps,chan0=chan0,cchan=cchan parameters arr [INPUT; required] input 1D array to be compressed carr [OUTPUT; required] compressed array ngrp [OUTPUT; required] number of groups into which ARR is broken fchan [OUTPUT; required] indices of first elements of each group nchan [OUTPUT; required] number of elements in each group keywords eps [INPUT] a small number, below which to ignore all values * default is 1e-6 chan0 [INPUT] index number of first channel, to determine whether FCHAN should be 0-based or 1-based * default is 1-based, because it appears that that is how Chandra RMFs are being made. set CHAN0 explicitly to 0 to make it 0-based. cchan [OUTPUT] channels corresponding to CARR _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Nov2001)
(See pro/util/ogipzip.pro)
Project : SOHO - CDS
Name : OS_FAMILY()
Purpose : Return current operating system as in !VERSION.OS_FAMILY
Category : Utilities, Operating_system
Explanation : Return the current operating system as in !VERSION.OS_FAMILY
OS_FAMILY is assumed to be 'unix' if !VERSION.OS is not 'windows',
'MacOS' or 'vms'
To make procedures from IDL V4.0 and later compatibile with earlier
versions of IDL, replace calls to !VERSION.OS_FAMILY with OS_FAMILY().
Can also be used to replace calls to !VERSION.OS if care is taken with
the change of case between 'Windows', which is what this routine
returns, and 'windows' which is what !VERSION.OS returned in versions
of IDL prior to 4.0.
Syntax : Result = OS_FAMILY()
Examples : IF OS_FAMILY() EQ 'vms' THEN ...
Inputs : None.
Outputs : The result of the function is a scalar string containing one of
the four values 'Windows','MacOS','vms' or 'unix'
Opt. Outputs: None.
Keywords : LOWER - set to return lowercase strings
NAME - return OS_NAME (if available)
Prev. Hist. : Written, W. Landsman
History : Version 1, 29-Aug-1995, William Thompson, GSFC
Incorporated into CDS library
Version 2, 15 May 2000, Zarro (SM&A/GSFC) - added /LOWER
Version 3, 22-Dec-2002, Zarro (EER/GSFC) - saved result in
common block for speed
Modifed, 2-June-2006, Zarro (L-3Com/GSFC) - removed
COMMON and added NAME keyword
Contact : WTHOMPSON
(See pro/external/os_family.pro)
procedure peasecolr set up a color table by loading in some nice colors syntax peasecolr,/white,/brewer,verbose=verbose,/help,$ oldr=oldr,oldg=oldg,oldb=oldb, XYOUTS keywords parameters NONE keywords white [INPUT] if set, chooses colors appropriate for a white background, as is the case for a postscript device * mind you, setting this does NOT force the background color to be white. it is just that colors appropriate for a white background are loaded in. * if not set, will get automatically set if the device is postscript brewer [INPUT] if set, uses single-hue 9-class color sequences from Color Brewer to fill in the 11-19, 21-29, 31-39, 51-59, 81-89, slots (Cynthia Brewer et al., http://colorbrewer2.org) verbose [INPUT] controls chatter help [INPUT] if set, prints out the calling sequence and notes which color is loaded into which index * automatically set if VERBOSE > 50 oldr [OUTPUT] old R colors oldg [OUTPUT] old G colors oldb [OUTPUT] old B colors _extra [INPUT ONLY] pass defined keywords such as CHARTHICK, CHARSIZE, and ALIGN to XYOUTS * matters only if VERBOSE.ge.10, when a plot showing all the colors and names is displayed. description this is based on Deron Pease's scheme of assigning specific colors to color table indices and more to the point, being able to remember which color goes where. Deron's idea is to have 1=BLUE, 2=RED, 3=GREEN and then have 10's to be different shades of blue, 20's to be shades of red, and 30's to be shades of greens, etc. Further, within each dex, the colors run as: X0=base, X1=dark, X9=light. This basic scheme has been enhanced as follows: -- added 4=YELLOW, 5=PINK, 6=CYAN, 7=BROWN, 8=SAFFRON, 9=GREY -- the shades are optimised for different backgrounds -- if WHITE is set, then X1=light and X9=dark, and (4) <-> (7) To obtain the complete set of color shades used, set the keyword HELP in conjunction with VERBOSE>5 color indices 100+ are not touched, but all else is overwritten. example peasecolr,verbose=10 peasecolr,/help,charthick=3 peasecolr,verbose=10,/white,/help & setkolor,'white',0 history vinay kashyap (Jul02) returns to caller on display error (VK; Sep02) !D.N_COLORS is useless on VNC? (VK; May04) added saffron (VK; May05) added grey (VK; Aug12) added keyword BREWER (VK; Sep15)
(See pro/util/peasecolr.pro)
function pickrange interactively select intervals in data -- returns a long-integer array of position indices of selected bins syntax oo=pickrange(x,y,sigmay=sigmay,xsize=xsize,ysize=ysize,wid=wid,$ /help,dynrng=dynrng,markx=markx,marky=marky,markp=markp,markc=markc,$ marks=marks,marko=marko,markl=markl,/legg,verbose=verbose,$ xo=xo,yo=yo,oxr=oxr,oyr=oyr,xtitle=xtitle,ytitle=ytitle,$ title=title,opx=opx,opy=opy,opc=opc,$ /nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol,$ stasiz=stasiz,stathk=stathk) parameters x [INPUT; required] points where "reference curve" is defined y [INPUT] the reference curve (usually data) * if not given, X is taken to be Y, and the indices of X are taken to be X! keywords sigmay [INPUT] if given, plots error bars on Y xsize [INPUT] width of window to display curve in * ignored if WID is not set ysize [INPUT] height of window to display curve in * ignored if WID is not set wid [INPUT] window ID * use current/default window if -ve/0 help [INPUT] prints out usage summary dynrng [INPUT; default: 3 dex] maximum dynamic range in log scale markx [INPUT] mark these x-coordinate points marky [INPUT] mark at these y-coordinate positions * ignored if incompatible with MARKX * if not given, labels and marks will be placed 2/3 of the way up the plot. markp [INPUT: default: 1] PSYMs for each (MARKX,MARKY) pair markc [INPUT: default: 222] COLOR for each (MARKX,MARKY) pair marks [INPUT: default: 1] SYMSIZE for each (MARKX,MARKY) pair marko [INPUT; default: 90 deg] ORIENTATION for MARKL * MARK[P,C,S,O]($) overrides the hardcoded defaults markl [INPUT] label for each (MARKX,MARKY) pair * marked only if given, unless there's only one element, in which case it is accepted as default legg [INPUT] if set, drops a leg to the X-axis xo [I/O] returns the x-position of last cursor click yo [I/O] returns the y-position of last cursor click oxr [I/O] 2-element array containing the final XRANGE oyr [I/O] 2-element array containing the final YRANGE xtitle [INPUT] passed to PLOT w/o checking ytitle [INPUT] passed to PLOT w/o checking title [INPUT] passed to PLOT w/o checking opx [INPUT] X-coords of a curve to be overplotted opy [INPUT] the curve to be overplotted * OPX and OPY may be 2-D, in which case the 1st dimension defines the number of curves to be overplotted * sizes of OPX and OPY >must< match opc [INPUT] color for the overplotting * default is 222 verbose [INPUT] controls chatter * replaces QUIET _ref_extra [INPUT ONLY] pass defined keywords to STAMPLE: NUTHIN,NODAY,NOTIME,NOUSER,NOPACK,STACOL,STASIZ,STATHK restrictions * works only under X usage summary see variable USAGE below history vinay kashyap (Oct96) added keyword SIGMA; changed to return only position indices of selected bins; modified click/drag behavior (VK; Dec96) added keyword MARKX (VK; Feb97) added keywords MARKY, MARKP, MARKC, MARKS, MARKL, MARKO, LEGG, QUIET, XO, YO, OXR, OYR; modified behavior of LEFT CLICK; added keyboard control via LEFT CLICK (VK; Aug98) allowed XO,YO,OXR,OYR to be I/O (VK; Sep98) now MARKL(0) does not act as default, XYOUTS forced to CLIP (VK; Nov98) now zoom is remembered if OXR or OYR are set on input; made XR,YR double precision; MARKY bug corrected; renamed keyword SIGMA as SIGMAY; changed _EXTRA to _REF_EXTRA (VK; Dec98) bug correction: reversed X-axis was preventing zoom (VK; Apr99) added keywords OPX,OPY,OPC (VK; Oct99) cursor changes shape when mouse button is pressed (VK; FebMM) undid cursor shape changes (VK; AprMM) MARKC can now be I*4; added extra keyboard options; added call to STAMPLE (VK; DecMM) changed MARKY default from 0.5 to 0.67 (VK; JanMMI) added keyword TITLE; improved color-scale setting for 24-bit consoles (VK; FebMMI) streamlined X,Y input behavior (VK; May02) handle color tables in 24-bit displays (VK; Jun02) replaced keyword QUIET with VERBOSE, changed color defaults (VK; Jul02) speeded up marker plots if no variations exist (VK; Dec02) button press status now stored in !MOUSE, not !ERR (VK; Apr09)
(See pro/util/pickrange.pro)
procedure plotem plots emission measures derived from the output of POTEM_TOOL (or other means) syntax plotem,logT,EM,idstr=idstr,markmin=markmin,multid=multid,lcol=lcol,$ lsiz=lsiz,tlog=tlog,wdth=wdth,xtitle=xtitle,ytitle=ytitle,title=title,$ xrange=xrange,yrange=yrange,xstyle=xstyle,ystyle=ystyle,/xlog,/ylog,$ /nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol,stasiz=stasiz,$ stathk=stathk parameters logT [INPUT] temperatures at which to plot the emission measure estimates EM [INPUT] array of emission measures at the various temperatures for each line * if EM is not given, it is assumed that EM <- "LOGT" and LOGT = default * EM is an array of the form EM(LOGT,WVL); if the size of the first dimension does not match input LOGT, the plots are interpolated keywords idstr [INPUT] ID structure, essentially to figure out labels for the curves. * if size does not match that of EM, cest la vie. markmin [INPUT] if set, plots only a single point for each curve, corresponding to the minimum in EM * the actual value of MARKMIN sets the PSYM for the points multid [INPUT] an integer array saying how many IDs there are to each component of the ID structure (comes in handy if IDSTR has all the emissivities collapsed into one) lcol [INPUT; default=200] color for the labels lsiz [INPUT; default=0.4] size of the labels tlog [I/O] if LOGT does not match size of EM, >and< EM does not match the size of the temperature grid in emissivities in ID being considered, then look for TLOG to supply the actual temperature grid. (this latter feature is not yet implemented) * default is to go from log(T)=4..8 in as equidistant steps * beware -- this will get overwritten if incorrect!! wdth [INPUT] the widths of each of the EM curves, from POTTASCH(), via POTEM_TOOL() * the size of this array must match the 2nd dimension of EM, or else it will be ignored xtitle [INPUT] passed w/o comment to PLOT ytitle [INPUT] passed w/o comment to PLOT title [INPUT] passed w/o comment to PLOT xrange [INPUT] overrides locally determined XRANGE yrange [INPUT] overrides locally determined YRANGE xstyle [INPUT] passed w/o comment to PLOT ystyle [INPUT] passed w/o comment to PLOT xlog [INPUT] passed w/o comment to PLOT, but default is 0 ylog [INPUT] passed w/o comment to PLOT, but default is 1 _extra [INPUT] pass defined keywords to subroutines STAMPLE: NUTHIN,NODAY,NOTIME,NOUSER,NOPACK,STACOL,STASIZ,STATHK history vinay kashyap (Nov98) added keyword MULTID (VK; Dec98) changed call to INITSTUFF to INICON (VK; 99May) added call to STAMPLE (VK; JanMMI) improved color-scale setting for 24-bit consoles (VK; FebMMI) added keyword WDTH (VK; SepMMVII)
(See pro/plotem.pro)
procedure plotfit takes the output of FITLINES and makes a nice plot of it with the data and the model(s) and everything. syntax plotfit,x,y,fitstr,ymod,ysig=ysig,conlev=conlev,consig=consig,$ funcs=funcs,intens=intens,scol=scol,ecol=ecol,ccol=ccol,mcol=mcol,$ ncol=ncol,imcol=imcol,clin=clin,mlin=mlin,nlin=nlin,$ missing=missing,fwhm=fwhm,betap=betap,angle=angle,submodel=submodel,$ /nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol,stasiz=stasiz,$ stathk=stathk,$ PLOT_KEYWORDS parameters x [INPUT; required] absissa, e.g., wavelength or energy y [INPUT; required] count spectrum Y(X) * size of Y must match that of X fitstr [INPUT] output of FITLINES ymod [OUTPUT] model function keywords ysig [INPUT] errors on Y * default is 0. * plotted if supplied, otherwise not. funcs [INPUT] name of user defined function that takes as input X and A (the model parameters), and returns Y(X;A) and the partial derivatives dY/dA * default is set to X3MODEL intens [INPUT] if set, Y(X) is assumed to be intensity, i.e., (counts|ergs|.../bin_unit/...) * default is to take Y(X) to be (counts|ergs|.../bin/...) * passed straight to FITLINES_EVENT * WARNING: this has >not< been road-tested! conlev [INPUT] the continuum that was taken out of the spectrum * CONLEV must match the size of X and Y else ignored * if ignored, interpolated from FITSTR.CONLEV consig [INPUT] error on CONLEV * default for CONSIG is sqrt(abs(CONLEV)+0.75)+1. * currently not implemented. i.e., it's not plotted even if given. scol [INPUT; default=6] color of spectrum plot ecol [INPUT; default=SCOL] color of error-bars ccol [INPUT; default=1] color of continuum mcol [INPUT; default=2] color of best-fit model+continuum ncol [INPUT; default=3] color of best-fit model alone imcol [INPUT; default=4] color to plot model components * individual model components are not plotted unless IMCOL is defined and non-zero clin [INPUT; default=1] line style of continuum mlin [INPUT; default=0] line style of model+continuum nlin [INPUT; default=2] line style of model alone missing [INPUT] passed w/o comment to FUNCS fwhm [INPUT] passed w/o comment to FUNCS betap [INPUT] passed w/o comment to FUNCS angle [INPUT] passed w/o comment to FUNCS submodel[OUTPUT] the model function for each component, returned as a (NCOMP,NX) sized array * calculated iff IMCOL is set _extra [INPUT ONLY] use this to pass defined keywords to PLOT and STAMPLE restrictions requires subroutines FUNCS (X3MODEL [MK_3MODEL, [MK_GAUSS, MK_LORENTZ]]) PLOT cannot handle any keyword that is either strange or undefined known bugs cannot handle spectra with varying bin sizes INTENS has not been tested history vinay kashyap (MarMM) added call to STAMPLE (VK; FebMMI) bug correction; changed default colors; added keyword IMCOL (VK; May'03) added keyword SUBMODEL (VK; NovMMVI)
(See pro/fitting/plotfit.pro)
procedure poaintsym Define useful plotting symbols not in the standard !PSYM definitions. After symbol has been defined with this routine, a plotting command should follow with either PSYM = 8 or !P.PSYM = 8 (see USERSYM). syntax poaintsym,symb,psize=psize,pthick=pthick,/pfill,color=color,$ pie=pie,/halftri,npoint=npoint,aspect=aspect,angle=angle,adent=adent,$ verbose=verbose parameters symb [INPUT; required] string describing the type of symbol to define. The following are accepted: 'circle' 'dash' 'star' 'starfish' 'asterisk' 'mercury' 'venus' 'earth' 'moon' 'mars' 'jupiter' 'saturn' 'uranus' 'neptune' 'pluto' 'square' 'diamond' 'box' 'spoke' 'triangle' 'down triangle' 'right triangle' 'left triangle' 'down arrow' 'up arrow' 'left arrow' 'right arrow' 'upper limit' 'lower limit' 'tilde ANGLE OVERFLOW' * if something unknown is specified, the program prints a list of accepted options and quits without making a change * special cases: -- STARFISH: is 5-pointed -- ASTERISK: is (NPOINT/2)-pointed and uses keyword ADENT to figure out indentation -- EARTH: forces PFILL=0 -- MOON: use ADENT to pull the horns out, and PHASE to control thickness -- URANUS: forces PFILL=0 -- PLUTO: forces PFILL=0 -- SPOKE: essentially DIAMOND with an aspect x:y::1:10 -- UPPER/LOWER LIMIT: synonyms for DOWN/UP ARROW respec. -- TILDE: set ANGLE (default=0) to rotate the symbol, and OVERFLOW (default=1) to pull the ends out a bit keywords psize [INPUT] size of the plotting symbol in multiples of the standard size (see SYMSIZE); does not need to be an integer pthick [INPUT] thickness of symbol being drawn pfill [INPUT] if set, fills the symbol * does not affect arrows or character symbols pie [INPUT] range of angles in [degrees] to include while making a circle * if scalar, includes from PIE[0] to 360. * if vector, includes from PIE[0] to PIE[1] halftri [INPUT] if set, lops off the triangle such that only the part that protrudes past the axes (above x-axis for up triangle, below x-axis for down triangle, etc.) is plotted npoint [INPUT] number of vertices in the symbol * note that usersym maximum is 49 * currently, only matters to TILDE aspect [INPUT] changes the aspect ratio of the symbols by scaling the axes prior to rotation * if +ve, scales X-axis * if -ve, scales Y-axis * if array, only the first element is used * if 0, nothing is done rotate [INPUT] angle by which to rotate the symbol [deg] adent [INPUT] the magnitude of the indentation for STARFISH and ASTERISK and the extent of the horns for MOON * default is 0.4 for STARFISH and ASTERISK, and 10 for MOON phase [INPUT] controls thickness of moon * default is 0 verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines USERSYM: COLOR method Appropiate X,Y vectors are used to define the symbol and passed to USERSYM examples Plot with filled stars as the symbol, twice the default size POAINTSYM,'star',psize=2,/pfill & PLOT,findgen(10),PSYM=8 Plot with open circle as the symbol POAINTSYM,'circle' & PLOT,findgen(10),PSYM=8 Plot filled color circles POAINTSYM,'circle',/pfil,psize=3,col=2 & PLOT,findgen(10),PSYM=8 Plot arrows all around POAINTSYM,'left arrow',pthick=2,psize=2 & plot,findgen(11),psym=8 POAINTSYM,'up arrow',pthick=3,psize=3 & oplot,findgen(11),psym=8 POAINTSYM,'right arrow',pthick=4,psize=4 & oplot,findgen(11),psym=8 POAINTSYM,'down arrow',pthick=5,psize=5 & oplot,findgen(11),psym=8 Plot tildes POAINTSYM,'tilde',pthick=5,psize=5 & plot,findgen(11),psym=8 POAINTSYM,'tilda 90',pthick=5,psize=5 & plot,findgen(11),psym=8 POAINTSYM,'tilda 90 3',pthick=5,psize=5 & plot,findgen(11),psym=8 POAINTSYM,'tilda 0 20',pthick=2,psize=5,npoint=49 & plot,findgen(11),psym=8 history modified from JDSYM (Jeremy Drake 2001; JJD added square and diamond symbols to PLOTSYM [ASTROLib; Wayne Landsman 1992]) by Vinay Kashyap (Oct03) added option TILDE and keyword NPOINT (VK; Feb04) added keywords ASPECT, ROTATE, and ADENT; added options SPOKE, MERCURY, VENUS, EARTH, MOON, MARS, JUPITER, SATURN, URANUS, NEPTUNE, PLUTO (VK; Jun05) added keyword PIE (VK; Aug12) added option DASH (VK; Jul15)
(See pro/util/poaintsym.pro)
script PoA_constructor this is a "front-end" to the initialization script INITALE of PINTofALE, needed for older versions of IDL, for which system variables need to be defined before running ANY procedure which uses them. this script defines the system variables with default values and then calls INITALE.PRO to complete the initialization. syntax @PoA_constructor variables for a complete list of the PINTofALE system variables, see the description for INITALE.PRO . calls subroutines INICON INITALE restrictions it is assumed that this is called only once per session, and that it is called _first_ history Vinay Kashyap (FebMMI; based on suggestion by A.Maggio) added !ATOMDB and !APECDIR (VK; Jun02)
(See pro/scrypt/PoA_constructor.pro)
function poplev returns the level populations at given temperature and pressure for a set of ions of a given element usage pop=poplev(temp,pres,chianti,n_e=n_e) parameters temp [INPUT; required] Temperature [K] pres [INPUT; required] pressure [cm^-3 K] chianti [INPUT; required] structure that contains all the relevant information gleaned from the CHIANTI database (type DBHELP=RD_CHIANTI() & HELP,DBHELP,/STRUCTURE for a description of what this structure contains) keywords n_e [INPUT] electron density in cm^-3 * if set, overrides PRES/TEMP requires DESCALE2_UPS, a CHIANTI routine history originally written as POPULATE.PRO, a CHIANTI routine, by Ken Dere (v2: Mar96) modified to eliminate common blocks, mesh with SCAR, and fltarr->dblarr (to remove the -ve population levels) by Vinay Kashyap (Nov96)
(See pro/mkemis/poplev.pro)
function popsol
returns the level populations at given temperature and
pressure for a set of ions of a given element as an array
of size [N(TEMP),N(PRES or DENSITY),N(N_LEVELS)]
usage
pop=popsol(temp,pres,chianti,n_e=n_e,/delec,$
radtemp=radtemp,dilute=dilute,pe_ratio=pe_ratio,$
n_levels=n_levels,data_str=data_str)
parameters
temp [INPUT; required] Temperature [K]
pres [INPUT; required] pressure [cm^-3 K]
chianti [INPUT; required] structure that contains all the relevant
information gleaned from the CHIANTI database (type
DBHELP=RD_CHIANTI() & HELP,DBHELP,/STRUCTURE
for a description of what this structure contains)
keywords
n_e [INPUT] electron density in cm^-3
* if set, overrides PRES/TEMP
delec [INPUT] if set, assumes these are DR lines
z [INPUT] atomic number of element
jon [INPUT] ionic state of species
* Z and JON are used only if DELEC is set
radtemp [INPUT] The blackbody radiation field temperature
* default is 6000 K
dilute [INPUT] a dilution factor for photoionization, based
on the distance above a star's surface -- see CHIANTI
routine R2W()
* if not set, assumed to be 0
pe_ratio [INPUT] proton-to-electron ratio
* if not given, assumed to be 1.0
n_levels [INPUT] number of levels in the model
* (from CHIANTI/idl/low_level/pop_solver.pro)
This allows the number of levels in the model to be reduced.
E.g., if the full model contains 100 levels, one could set
N_LEVELS=50. This can be useful if one is interested in
looking at the effects of cascading from higher levels.
data_str [OUTPUT] some potentially useful data
* (from CHIANTI/idl/low_level/pop_solver.pro)
If POP_SOLVER is called for just 1 temperature and density,
then the individual data arrays for each of the physical
processes can be output through DATA_STR. This allows the
user to check for the dominant processes affecting the
population of a given level. DATA_STR is a structure with
the following tags:
.aa A-values
.aax Photoexcitation/stimulated emission
.cc Electron rate coefficients
.ccp Proton rate coefficients
Each tag is a 2D array, and is such that, e.g.,
aa[0,20] corresponds to an excitation, while aa[20,0]
is a de-excitation.
A note about the default value of PE_RATIO:
The original version of this program,
CHIANTI/dbase/idl/low_level/pop_solver.pro,
set the default to be 0.83, which is the limit for a high-T
plasma with cosmic abundances. Later versions include a
calculated value passed in via a common block. Here we
exclude this factor because we want to store the emissivities
without reference to their ion balance and abundance, on which
this factor depends. The intensity of a line transition from
upper level j to lower level i is in general
dI(lam_ij) = (1/4pi)(hc/lam_ij) N_j A_ji dV [ergs/s/sr]
where lam_ij is the wavelength of the transition, A_ji is the
Einstein coefficient (the spontaneous transition probability),
dV is the emitting volume, and N_j is the number density of the
ions in level j. We can write N_j as the product
N_j = (N_j/N_XIon) (N_XIon/N_X) (N_X/N_H) (N_H/N_e) N_e
where N_XIon is the number density of the ions,
N_j/N_XIon is the population fraction of the ions at level j,
N_XIon/N_X is the ion fraction,
N_X/N_H is the relative abundance of element X wrt H, and
N_H/N_e is the H density relative to the free-electron density.
In PINTofALE, we calculate and store the emissivities as
e_ji = (hc/lam_ij) A_ji (1/N_e) (N_j/N_XIon)
and write the line intensity as
f(lam_ij) = e_ji (N_XIon/N_X) (N_X/N_H) EM (N_H/N_e)
where EM = N_e^2 V is the emission measure, and the factor
(1/4pi) is always ignored and the factor (hc/lam_ij) is usually
taken out again. This calculation is carried out in LINEFLX(),
which provides for the inclusion of the ion balance, abundance,
and the proton-to-electron ratio. Hence the use of a default of
1.0 for PE_RATIO here.
subroutines
CHIANTI routine DESCALE_ALL
NENH
history
POP_SOLVER.PRO written by Peter Young
{..
.. Ver 1, PRY 29-Mar-99
.. Ver 2, PRY 30-Apr-99, added call to get_prot_rates
.. Ver 3, PRY 15-Dec-99, added deu to upsilon common block in order
.. to be consistent with the main Chianti routines.
.. Ver 4, PRY 9-May-00, corrected problem with threshold when dealing
.. with sparse matrices. Basically values less than 1.e-30 in
.. the c-matrix were being set to zero and giving rise to
.. NaN's in certain circumstances.
.. Ver.5, PRY 14-Jul-00, changed elvl common block to the elvlc common
.. block which is now the Chianti standard. Also, when
.. descaling upsilons, the routine now uses the Delta-E from
.. the .splups file.
.. Ver.6, PRY 9-Aug-00, changed routine to deal better with the
.. dielectronic recombination files
.. Ver.7, PRY 17-Aug-00, routine does not call LINBCG now if radtemp
.. is non-zero.
.. Ver.8, PRY 29-Aug-00, the sparse matrix section has been disabled.
.. Ver.9, PRY 12-Nov-01, calls routine proton_dens() to calculate the
.. proton to electron ratio.
.. Ver.10, PRY, 6-Dec-01, corrected bug when there are more levels
.. in .splups file than in .elvlc file (ZnXXV).
.. Ver.11, PRY, 11-Jul-02, removed ION keyword
.. Ver.12, PRY, 9-Aug-02, within the equation solving section, I've set
.. the population of the ground level (rather the n_level level)
.. to 1, and this seems to stop negative populations appearing
.. in extreme conditions.
.. Ver.12, PRY, 21-Aug-02, changed exp(-1/1/a) to exp(-a) in electron
.. excitation section which caused a hang-up in some
.. circumstances. Also, the routine now uses vector ECMC
.. (combined experimental and theoretical energies) in
.. determining if a level lies above or below another level.
.. Previously only used the observed energy vector. Also, the
.. exponential in the electron excitation section now uses the
.. (accurate) .elvlc energy separation rather than the .splups
.. energy separation, which can cause significant (~20-30%)
.. differences in level populations of high-lying levels at
.. low temperatures.
.. Ver.13, PRY, 10-Sep-02, corrected bug for proton rates. The excitation
.. and de-excitation rates were being swapped.
..
.. V. 14 4-Oct-2003 Giulio Del Zanna (GDZ).
.. -removed all COMMON blocks (note that only proton_dens.pro has
.. one: COMMON elements,abund,abund_ref,ioneq,ioneq_logt,ioneq_ref)
.. -only the essential information input is passed to the routine
.. via a new input structure.
.. -fixed a bug, that affected all the satellite lines, and was
.. introduced in v.12, included in CHIANTI v.4.0.
.. basically the ionization potential was not subtracted when
.. calculating the Delta E in the exponential.
..
.. VERSION : 14, 4-Oct-2003
..}
modified to eliminate common blocks and the call to SETUP_ION,
and altered the I/O interface to mesh with PINTofALE, changed
call to PROTON_DENS() to call NENH() and changed default PE_RATIO
to 1.0 (Vinay Kashyap, Apr03)
modified to account for v14, for CHIANTI v4.2 (VK; Apr04)
(See pro/mkemis/popsol.pro)
function potem_tool return emission measures EM(LOGT,WVL) for all lines that have been ID'd (but see keyword OKMULT) for each temperature, assume a delta-function emission measure, compute line fluxes seen through some instrument, account for interstellar absorption, and scale to match the observed flux. in case of multiple IDs for a single observed line, the emissivities of the IDs are added together, and assumed for all practical purposes to be the strongest line modified by the other IDs. in case of IDs spanning different elements, the emissivities are added as before, but weighted with their relative abundances. syntax EM=potem_tool(idstr,flux,logT=logT,abund=abund,ldir=ldir,$ dwvl=dwvl,/okmult,/kettle,outid=outid,wdth=wdth, pres=pres,$ logP=logP,n_e=n_e, chifil=chifil,chidir=chidir,eqfile=eqfile,$ NH=NH,/noph,defEM=defEM, thresh=thresh,/temp,/ikev,effar=effar,$ wvlar=wvlar,fh2=fh2,He1=He1,HeII=HeII,/fano, level=level,$ verbose=verbose) parameters idstr [INPUT; required] the ID structure that comes out of LINEID flux [INPUT] observed fluxes * if not given, taken from IDSTR.(*).FLUX (if zero, forcibly set to 1 [(ph|erg)/s/cm^2]) * size is forced to match IDSTR.WVL if <, filled out with 1s if >, extra elements are ignored keywords logT [INPUT] temperatures at which to compute the emission measures * default is findgen(81)*0.05+4. abund [INPUT] abundances * default is to use Anders & Grevesse ldir [INPUT] string array containing line database directory names, one for each ID. * if given, will NOT use the embedded emissivities in IDSTR.EMIS (default is to use them) * if size < N(ALLMATCHES), the last element is replicated as often as necessary * to selectively use IDSTR.(#).EMIS, set to '0' within a string array (e.g., ['$CHIANTI','$SPEX','0','0','$SCAR'] * if set to a number, assumes "$SCAR" dwvl [INPUT; default=5e-3] search the line database for the wavelength of interest with this assumed roundoff error okmult [INPUT] if set, then multiple IDs (if any) are >not< collapsed, and the output will be of the form EM(LOGT,ALLWVL) * automatically set if size of FLUX matches the total number of matches kettle [INPUT] if set, does NOT do Pottasch corrections outid [OUTPUT] if defined on input, returns the IDs with new emissivities in an ID structure * multiple IDs are "collapsed" unless OKMULT is set multid [OUTPUT] number of IDs for each observed line (this is of use in, e.g., PLOTEM) wdth [OUTPUT] the full width in logT of the emissivity curve, as calculated by POTTASCH() verbose [INPUT] controls chatter _extra [INPUT ONLY] use to pass defined keywords to subroutines: RD_LINE: PRES,LOGP,N_E,VERBOSE FOLD_IONEQ: CHIFIL,CHIDIR,EQFILE,VERBOSE FLUX_TO_EM: NH,NOPH,DEFEM,THRESH LINEFLX: TEMP,IKEV,EFFAR,WVLAR ISMTAU: FH2,HE1,HEII,FANO POTTASCH: LEVEL subroutines INICON RD_LIST RD_LINE FOLD_IONEQ READ_IONEQ RD_IONEQ (CHIANTI routine) FLUX_TO_EM LINEFLX ISMTAU POTTASCH history vinay kashyap (Nov98; "concatenated" id_to_emis and flux_to_em) changed default behavior of FLUX; added keyword MULTID; changed OUTID.().Z and OUTID.().ION to floats in case multiple IDs have been collapsed to one emissivity (VK; Dec98) added field FLUXERR to output IDSTR (VK; Mar99) changed call to INITSTUFF to INICON (VK; 99May) no need to read in ion balance info in POTTASCH again (VK; JanMMI) added keyword WDTH to carry the emissivity width info outside (VK; SepMMVII)
(See pro/potem_tool.pro)
function pottasch
returns the Pottasch factor that is a measure of the width of
the ion emissivity in temperature space over which most of
the line emission occurs.
the Pottasch factor is the ratio
{\int [EMIS*ION_BALANCE] dlogT}/{WDTH*max([EMIS*ION_BALANCE])}
where WDTH is the range in logT where EMIS*ION_BALANCE drops to a
set fraction of the maximum.
output has as many elements as the 2nd dimension of EMIS, one point
for each line.
syntax
pot=pottasch(emis,logt,z=z,ion=ion,level=level,wdth=wdth,$
trange=trange,chifil=chifil)
parameters
emis [INPUT; required] 1- or 2-D array of line intensities as
a function of temperature
* if 1D, assumed to be EMIS(Temperature)
* if 2D, assumed to be EMIS(Temperature,{Z,ION,Wavelength})
* if Z is not specified, assumed to be the product of
line emissivity and ion balance
logt [INPUT] 1D array of log10(T[K])
* WARNING: if not given, or if size does not match 1st dim
of EMIS, makes a dumb guess
keywords
Z [INPUT] atomic numbers corresponding to the 2nd dimension
* if not set, ION is ignored and FOLD_IONEQ is not called
* if size does not match 2nd dim of EMIS,
>: ignore extra elements
<,>1: use as many as specified, take rest to be H (Z=1)
1: all are of same element
ion [INPUT; default: Z+1] ionic state
level [INPUT; default: 0.1] defines what WDTH means
wdth [OUTPUT] full width in logT at LEVEL*maximum
* minimum value at any point is the resolution in LOGT at
that point.
trange [OUTPUT] 2-column array of the boundaries of logT that
define WDTH
* trange(0,*)=lower bound, trange(1,*)=upper bound
_extra [INPUT] use to pass defined keywords
* currently, only CHIFIL to FOLD_IONEQ
subroutines
FOLD_IONEQ [WHEE, RD_IONEQ [READ_IONEQ]]
history
vinay kashyap (Apr97)
changed temperature width calculation to account for bumpy
emissivities (VK; Oct98)
(See pro/pottasch.pro)
function ppd_src
returns the posterior probability density for the source
intensity, marginalized over background intensity, assuming
gamma-function priors (see van Dyk et al., 2001, ApJ 548, 224)
D:ns,nb ; I:asrc,abkg,f ; M:s,b ; p(M|DI)=p(M|I)*p(D|MI)/p(D|I)
r = abkg/asrc & A = nb+alfa_B & B = f*(beta_B+r)
p(b|I) = ((f*beta_B)^alfa_B/Gamma(alfa_B)) * b^(alfa_B-1) * exp(-b*beta_B*f)
p(nb|b,I) = ((r*f*b)^nb/Gamma(nb+1)) * exp(-b*f*r)
p(b|nb,I) = (B^A/Gamma(A)) * b^(A-1) * exp(-b*B)
I_k = b^(ns+A-k-1) * s^(k+alfa_S-1) * exp(-s*f*(1+beta_S) -b*(f+B)) /
(Gamma(k+1)*Gamma(ns-k+1))
I_kb = (Gamma(ns+A-k)/Gamma(k+1)/Gamma(ns-k+1)) * (f+B)^(-(ns+A-k)) *
s^(k+alfa_S-1) * exp(-s*f*(1+beta_S))
I_kbs = (Gamma(ns+A-k)*Gamma(k+alfa_S)/Gamma(k+1)/Gamma(ns-k+1)) *
(f+B)^(-(ns+A-k)) * (f*(1+beta_S))^(k+alfa_S)
p(s|I) = ((f*beta_S)^alfa_S/Gamma(alfa_S)) * s^(alfa_S-1) * exp(-s*beta_S*f)
p(ns|M,I) = (f*(s+b))^ns/Gamma(ns+1) * exp(-(s+b)*f)
p(sb|D,I) = p(b|nb,I)*p(s|I)*p(ns|M,I) / p(ns|I)
= (Sum_{k=0}^{ns} I_k) / (Sum_{k=0}^{ns} I_kbs)
p(ns|I) = f^ns * (B^A/Gamma(A)) * ((f*beta_S)^alfa_S/Gamma(alfa_S)) *
Sum_{k=0}^{ns} I_kbs
p(s|D,I) = (Sum_{k=0}^{ns} I_kb) / (Sum_{k=0}^{ns} I_kbs)
syntax
ppd=ppd_src(ns,nb,sgrid,smap=smap,scred=scred,clev=clev,ppdstr=ppdstr,$
funit=funit,asrc=asrc,abkg=abkg,agamma=agamma,bgamma=bgamma,$
priorbg=priorbg,nsgrid=nsgrid,srcmin=srcmin,srcmax=srcmax,verbose=verbose)
parameters
ns [INPUT; required] observed counts in source region
nb [INPUT; required] observed counts in background region
* NS and NB must be scalar -- if vector, adds up all the elements
sgrid [OUTPUT] the output grid over which the PPD is calculated
* a regular grid that uses NSGRID, SRCMIN, and SRCMAX
keywords
smap [OUTPUT] the mode of the distribution, corresponding to the
maximum a posteriori value of the PPD
scred [OUTPUT] a two-tailed credible range on the source intensity,
defined to include CLEV/2 of the area under the PPD above
and below SMAP
* NOTE: what this means is, if the distribution is skewed,
then the total area under PPD as defined by SCRED is not
necessarily equal to CLEV
* The one-tailed credible regions, that is, the range that
encloses an area CLEV under the PPD, are returned in the
structure PPDSTR. these regions are determined such that
the mode is always _included_ within the region, but is not
necessarily at the center
clev [INPUT] a nominal level at which to determine bounds and
get credible regions
* default is 0.68
* if < 0, abs(CLEV) is used
* if > 1 and < 100, then assumed to be given as a percentage
* if > 100, then 1-1/CLEV is used
ppdstr [OUTPUT] an anonymous structure containing the fields
{
GRID : same as SGRID
MODE : mode, same as SMAP
MEAN : mean of the distribution
SIG : s.d. on the MEAN
MEDIAN : the median of the distribution
CLEV : the probability level defined by the keyword CLEV
HPD1 : the highest posterior density "1-sigma" credible range,
the interval that encloses 68% of the area and also
the highest values of the probability density
HPD2 : as HPD1, for "2-sigma", 95% of the area
HPD3 : as HPD1, for "3-sigma", 99.7% of the area
HPD0 : as HPD1, but corresponding to a fraction CLEV
CRED1 : the "1-sigma" credible range, corresponding to 68%
of the area under the PPD that _includes_ the MODE
CRED2 : as CRED1, for "2-sigma", 95% of the area
CRED3 : as CRED1, for "3-sigma", 99.7% of the area
CRED0 : as CRED1, but corresponding to a fraction CLEV of the
area under the PPD that includes the MODE
RNG1 : the two-tailed "1-sigma" range, corresponding to a
fractional area under the PPD of 0.34 above and below
the MODE
RNG2 : as for RNG1, but the "2-sigma" range, 0.475 of the area
RNG3 : as for RNG1, but the "3-sigma" range, 0.4985 of the area
RNG0 : as for RNG1, but CLEV/2 of the area, same as SCRED
lnpD : the log of the predictive probability, ALOG(p(ns|I))
}
funit [INPUT] a factor to _divide_ the counts to convert to different units
e.g., ph/cm^2/s
* assumed to be the same for both source and background counts
(any differences in exposure times can be encoded in ASRC and ABKG)
* default is 1.0
asrc [INPUT] area (or exposure time) for the background contaminated
source observation, NS
* default is 1.0
abkg [INPUT] area (or exposure time) for the background observation, NB
* default is 1.0
agamma [INPUT] alpha parameter for the source intensity prior, assumed to
be a gamma distribution (see PROB_GAMMADIST)
* default is 1.0 (also the hardcoded minimum)
* generally taken to be the number of *expected* source counts+1
bgamma [INPUT] beta parameter for the source intensity prior
* default is 0.0 (also the hardcoded minimum)
* generally the ratio of that area in which the AGAMMA-1 counts are
obtained in, to ASRC
* note that the default values of AGAMMA and BGAMMA make for a
very non-informative, but improper, prior
priorbg [INPUT] the expected number of counts due to the background,
a number that is known from prior information and NOT derived
from NB itself.
* a Gamma function prior is assumed on the background strength, with
alpha=priorbg+1; beta=abkg/asrc, but if priorbg=0, then beta=0
nsgrid [INPUT] number of points in output grid
* default=101L
srcmin [INPUT] minimum in source intensity value to consider
srcmax [INPUT] maximum in source intensity value to consider
* beware that setting [SRCMIN,SRCMAX] to too small a range will cause
it to act as a prior over and above the gamma prior. this may not be
desirable.
* the default range is the widest of:
-- NS +- 10*sqrt(NS)
-- (NS-(ASRC/ABKG)*NB) +- 10*sqrt(NS+(ASRC/ABKG)^2*NB) (if ABKG > 0)
-- (agamma/bgamma) +- 10*sqrt(agamma/bgamma^2) (if BGAMMA > 0)
as long as SRCMIN isn't -ve or SRCMAX is smaller than 20
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
subroutines
PROB_GAMMADIST
history
vinay kashyap (May02)
added keyword FUNIT (VK; Oct03)
added HPD1,HPD2,HPD3,HPD0 to the output (VK; Mar06)
(See pro/stat/ppd_src.pro)
function pred_flx return line fluxes for a given DEM and compare with observed fluxes. syntax f=pred_flx(line,logT,wvl,DEM,Z=Z,NH=NH,fobs=fobs,fsigma=fsigma,$ ulim=ulim,verbose=verbose,effar=effar,wvlar=wvlar,fH2=fH2,He1=He1,$ HeII=HeII,/fano) parameters line [INPUT; required] line cooling emissivities (T,Wvl) in units of 1e-23 erg cm^3/s, including ion balance, but not abundances. logT [INPUT; required] array of log10(Temperature [K]) at which emissivities are given. wvl [INPUT; required] wavelength of matching spectral line(s) [Ang] DEM [INPUT] Differential Emission Measure at each T [cm^-5/logK] * passed w/o change to LINEFLX keywords Z [INPUT] atomic number of element that generates each WVL * passed w/o change to LINEFLX NH [INPUT] H column density [cm^-2] fobs [INPUT] observed fluxes; if supplied, displays comparison plots of predicted v/s observed fsigma [INPUT] errors on observed fluxes; if not supplied, assumed to be 1+sqrt(abs(FOBS)+0.75) ulim [INPUT] flag to indicate whether a given FOBS is an upper limit (1: UL, 0: not) verbose [INPUT] controls chatter _extra [INPUT] allows setting defined keywords to LINEFLX [EFFAR, WVLAR, TEMP, ABUND, KEV, NOPH] ISMTAU [FH2,HE1,HEII,FANO] restrictions * requires subroutines GETABUND LINEFLX [WHEE] ISMTAU history vinay kashyap (May97) changed keyword name SIGMA to FSIGMA (VK; MMaug) changed Fobs/Fpred from /ylog to plotting alog10() (VK; MMVsep) changed Observed v/s predicted to plot psym=4 bug correction: matching up upper limit points (VK; MMVIapr) added keyword VERBOSE (VK; MMVIIjun)
(See pro/pred_flx.pro)
function prob_gammadist compute the gamma distribution, which is a continuous distribution on the real line with density function f(x) = b^a x^(a-1) exp(-bx) / Gamma(a) (see eqn 4 of van Dyk et al., 2001, ApJ 548, 224) this distribution has mean (a/b) and variance (a/b^2) for a,b>0 This is equivalent to a Poisson distribution, and is often used as a prior function, with a and b representing our prior expectation that a-1 counts should be observed in an area b*src_area; a non-informative prior therefore has a=1 and b=0, corresponding to 0 counts in 0 area. syntax g=prob_gammadist(x,agamma=agamma,bgamma=bgamma,verbose=verbose) parameters x [INPUT; required] array of abscissa values at which to compute the Gamma distribution * for x < 0, the function will return NaNs keywords agamma [INPUT; default=1] "alpha" parameter for the function * AGAMMA must be > 0, or else the function will return Infs bgamma [INPUT; default=0] "beta" parameter for the function * BGAMMA should be .GE. 0, or else who knows what will happen verbose [INPUT; default=0] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Aug01)
(See pro/stat/prob_gammadist.pro)
procedure propermotion_corrector computes proper motion and new coordinates syntax propermotion_corrector.catra,catdec,pmra,pmdec,newra,newdec,$ catyr=catyr,newyr=newyr,verbose=verbose,$ /i24,/osxg,/hrs,/idnum,/idpre,/idform,/pm,/chop,/osep parameters (all REQUIRED) catra [INPUT] catalog RA catdec [INPUT] catalog Dec * CATRA and CATDEC must have the same sizes * may be either float or string array * if float, assumed to be decimal degrees unless /I24 is set * if string, assumed to be decimal degrees unless ':' or ' ' are found pmra [INPUT] proper motion in RA [mas/yr] pmdec [INPUT] proper motion in Dec [mas/yr] * PMRA,PMDEC must be scalars, or have the same size as CATRA,CATDEC newra [OUTPUT] new RA newdec [OUTPUT] new Dec * newRA, newDEC will have the same size as CATRA,CATDEC * default is to return decimal degrees * set keyword /OSXG to return the output in sexagesimal keywords catyr [INPUT] epoch of CATRA,CATDEC * default is 2000.0 newyr [INPUT] epoch for which to compute new coordinates * default is today verbose [INPUT] controls chatter i24 [INPUT] caught and passed on to SKYPOS's first run * use iff input are _not_ in decimal degrees osxg [INPUT] caught and passed on to SKYPOS's second run * use iff you want the output in sexagesimal _extra [INPUT ONLY] pass defined keywords to subroutines SKYPOS: HRS, IDNUM, IDPRE, IDFORM, PM, CHOP, OSEP requires SKYPOS [DEG2HRS [STR_2_ARR, SYZE]] history vinay kashyap (2014sep05)
(See pro/util/propermotion_corrector.pro)
function radproject Projects a ray originating from an arbitrary point on an arbitrarily oriented sphere onto plane at \infty. Returns a structure containing the radial coordinate, and the corresponding x-coords, y-,z-offsets, the magnitude of the projection, the corresponding volume of the pillbox, as well as all the input values. syntax rstr=radproject(lat,lon,inrad=inrad,maxrad=maxrad,rrng=rrng,rdel=rdel,$ opaq=opaq,arcone=arcone,theta0=theta0,phi0=phi0,$ xout=xout,yout=yout,zout=zout,rproj=rproj,rout=rout,volout=volout,$ verbose=verbose) parameters lat [INPUT; required] latitude on sphere at which ray is anchored lon [INPUT; required] longitude on sphere at which ray is anchored * LAT,LON must be scalar * (LAT,LON)=(0,0) projects to (Y,Z)=(0,0) keywords inrad [INPUT; default=1] minimum r value of ray to consider maxrad [INPUT; default=10] maximum r value of ray to consider rrng [INPUT; default=[INRAD,MAXRAD]] filter the output by limiting the radii to consider * minmax(RRNG) is forced to not spill beyond [INRAD,MAXRAD] * use this only if you want everything outside this range to be explicitly thrown away. discarded. not zeroed, but removed from the output. rdel [INPUT; default=0.1] steps in r opaq [INPUT; default=0] decides how to treat those portions of rays that are occluded by the sphere defined by radius INRAD - by default, this is assumed to be completely transparent - set OPAQ to negative number to set the opacity as exp(-OPAQ) - any value OPAQ>0 results in a completely opaque inner sphere (so set /OPAQ to get an opaque inner sphere) arcone [INPUT; default=1] area of the opening cone at radius=1 [deg^2] theta0 [INPUT; default=0] tilt of sphere [deg] phi0 [INPUT; default=0] twist of sphere [deg] * theta0 and phi0 are defined in a coordinate frame where the projection plane is at x=\infty. * it is assumed that to get to the inclined sphere from the observer's frame, you first apply THETA0 and then PHI0. rout [OUTPUT] radii at which projections are computed xout [OUTPUT] computed X yout [OUTPUT] projected Y zout [OUTPUT] projected Z rproj [OUTPUT] projection of the radial unit vector towards the Y-Z plane, weighted by the opacity, at each ROUT volout [OUTPUT] volume of the pillbox at each ROUT verbose [INPUT; default=0] controls chatter _extra [JUNK] here only to prevent crashing the program example .run radproject history vinay kashyap (2012dec; supersedes pathrofile) added call to SPHTRIG_TRANSLB (VK; 2013feb) bug fixes (theta0,phi0=0) (VK; 2013mar)
(See pro/util/radproject.pro)
function randompow
return a sample drawn from a power-law distribution
let the power-law be defined as
f(x)=N*x^(-A)
the cumulative function,
F(X)= (N/(1-A))*(X^(1-A)-Xmin^(1-A)) if A.ne.1
= N*alog(X)-N*alog(Xmin) if A.eq.1
which may be normalized to go from 0 to 1:
G(X)=(X^(1-A)-Xmin^(1-A))/(Xmax^(1-A)-Xmin^(1-A)) if A.ne.1
=(alog(X)-alog(Xmin))/(alog(Xmax)-alog(Xmin)) if A.eq.1
given a random number 0<r==G(X)<1, solve for X:
X=(r*(Xmax^(1-A)-Xmin^(1-A))+Xmin^(1-A))^(1/(1-A)) if A.ne.1
=Xmin*exp(r*alog(Xmax/Xmin)) if A.eq.1
syntax
x=randompow(seed,num,alpha=alpha,/cumul,/outpoi,Nerr=Nerr,$
Xmin=Xmin,Xmax=Xmax,/help,verbose=verbose)
parameters
seed [INPUT; necessary] seed for random number generator
* this parameter must be present, but there is no
need for it to be defined on input.
* will be passed w/o modification to RANDOMU()
num [INPUT] this has a different meaning depending on
whether the keyword CUMUL is set or not.
* if CUMUL is not set, this is the number of random
samples that are returned, with a minimum of 1
* if CUMUL is set, this is taken to be the sum of the
numbers sampled, with a default of max{1,XMIN}
keywords
alpha [INPUT] index of power-law
* default is 1.8
cumul [INPUT] if set, generates random samples until the
sum of the values matches NUM. otherwise, the sum
is irrelevant and NUM samples are extracted
outpoi [INPUT] if set, a Poisson deviate is obtained from
the sample generated
* if CUMUL is set, the Poisson deviates are what are
summed to match against NUM
Nerr [INPUT] error on NUM. The actual SUM{X} matches a random
realization of NCT
* if given, assumed to be 1-sigma Gaussian error
* if not given, is set to sqrt(NUM+0.75)+1
Xmin [I/O] minimum value in sample
* default: 2
Xmax [I/O] maximum value in sample
* default: max{Normal(NUM,NERR),XMIN}
help [INPUT] if set, prints out usage and exits
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
example
.run randompow
history
vinay kashyap (Nov09; based loosely on samplpl.pro)
allowed XMIN,XMAX to be defined on return, modified example
calls to be self-consistent (VK; JanMMX)
allowed large photon counts by using N(mu,sqrt(mu)) to take
over as Poisson (VK; JanMMXIII)
(See pro/stat/randompow.pro)
function rdabund return abundance values read from file disk file must have one entry per line, with either atomic symbol or atomic number denoting the element (or both), and the actual abundance also. neither the order of the columns nor the order of the rows matter. the fields must be separated by "SEP", usually a <tab>. missing elements are filled out with values from Anders & Grevesse (see GETABUND). syntax abund=rdabund(filnam,comment=comment,sep=sep,inorm=inorm,norm=norm) parameters filnam [INPUT; required] name of file containing the abundances keywords comment [OUTPUT] normally, any line prefixed by ";" "%" "#" or "/" are ignored. these lines are stored as a string array and output via this variable sep [INPUT] single-character field separator * if set to "." "+" "-" or any of the alphanumerics, is ignored * if not set, tries <sp>, <tab>, "," and ":" in sequence inorm [INPUT] format of the abundances in the input file * see GETABUND for description * if INORM is defined, first converted to n(Z)/n(H), then converted back to whatever NORM is set to norm [INPUT] exactly as in GETABUND _extra [JUNK] here only to prevent crashing the program subroutines GETABUND SYZE history vinay kashyap (Dec98)
(See pro/util/rdabund.pro)
function rdarf
reads in the spectral response and associated axes from
OGIP-compliant ancillary response file
syntax
arf=rdarf(arffil,ostr,units=units)
parameters
arffil [INPUT; required] name of ARF
ostr [OUTPUT] structure containing the axes information for the
response: {NNRG, ELO, EHI}
* ELO and EHI refer to range of photon energies at which
the response is valid
keywords
units [OUTPUT] contains the units of ARF; typically 'cm**2'
_extra [INPUT] junk -- here only to prevent crashing the program
restrictions
requires IDLASTRO library routine MRDFITS
history
vinay kashyap (Jul97)
exits with 0 if ARFFIL not in fits format (VK; Apr05)
(See pro/util/rdarf.pro)
function rdb return a structure containing the output of ascii table in RDB format RDB format is assumed to be: a bunch of comments preceded by "#"s in first column a header stating the names of each column a format description specifying the type of the column (S for strings, N for numeric) and each column is separated by a "<tab>" some special things understood by this program are: -- blank lines are treated as comments -- different symbols (e.g., "%") may be used as comment characters -- output comes out as double or float or long depending on what is in the first row -- double precision may be forced by prepending a ">" to "N" syntax tab=rdb(filename,cols=cols,comm=comm,fldsep=fldsep,rdbdir=rdbdir,$ verbose=verbose) parameters rdbfil [INPUT; required] name of rdb file * the ".rdb" extension is not necessary * a trailing "." is removed, so if there's a file without an extension, set RDBFIL to "filename." * and if there's a file named "filename.", set RDBFIL to "filename.." and so on. keywords cols [INPUT] string or integer array of columns to extract * if string, column names must match *exactly*, but case is not important * if integers, remember that this is IDL, so first column is indexed as 0 * if /COLS is set, returns all columns, so if you want just the second column, remember to say COLS=[1] and not COLS=1 comm [INPUT] comment character * default is a "#" fldsep [INPUT] field separator * default is a <TAB> rdbdir [INPUT] if given, prepends RDBFIL with this pathname verbose [INPUT] if set, blabbers incoherently along the way _extra [JUNK] here only to prevent crashing the program subroutines STR_2_ARR CREATE_STRUCT KILROY LEGALVAR restrictions works only on UNIX history vinay kashyap (MIM.XII) illegal column names are now checked for (VK; MM.I) bug: preceding spaces turned values into zeros; converted all array subscripting to IDL5 (VK; JulMM) changed call to STR_2_ARR from STR2ARR (VK; MMV.IV) now looks at only the first character of format column field to decide type (VK; MMXIII.VIII) now basically returns only long integer and doubles (VK; MMXIII.XII)
(See pro/util/rdb.pro)
function rdpha return a structure containing the variables in an XSPEC style PHA file. (doesn't really have to be a PHA file. any FITS table file will do.) parameters infile [INPUT; required] name of PHA file keywords ext [INPUT] if set, only reads in the specified extension _extra [JUNK] here only to avoid crashing the program restrictions * requires the IDLASTRO library * empty extensions are treated as EOFs * can only decipher tables, not images * cannot handle Type II PHA files history vinay kashyap (Jan MM)
(See pro/util/rdpha.pro)
function rdresp
reads in an OGIP-compliant response matrix file and returns the
full response matrix
syntax
rsp=rdresp(rspfil,ostr,effar=effar,fchcol=fchcol,/shift1)
parameters
rspfil [INPUT; required] name of response file
ostr [OUTPUT] structure containing all the information for the
response matrix: {NNRG, ELO, EHI, NCHAN, EMN, EMX, N_GRP,
F_CHAN, N_CHAN, MATRIX, FIRSTCHAN}
(see RD_OGIP_RMF() for description)
* output response matrix is in the form RSP(NNRG,NCHAN)
keywords
effar [OUTPUT] returns the effective area as a function of ELO
NOTE: if an RMF file is read instead of an RSP file,
EFFAR are actually the efficiencies
_extra [INPUT ONLY] pass defined keywords to subroutines
RD_OGIP_RMF: FCHCOL,SHIFT1
restrictions
requires IDLASTRO library routine MRDFITS
requires RD_OGIP_RMF
history
vinay kashyap (Jul97)
added keyword SHIFT1 (VK; JanMMI)
removed SHIFT1, added call to RD_OGIP_RMF, cleaned up (VK; Nov2001)
(See pro/util/rdresp.pro)
function rd_aped
read in a line list from APED and return the 3D
emissivities [WVLS,TEMPS,EDENS]
syntax
emiss=rd_aped(apedfil,wvls,temps,edens,Zs,ions,levs,$
apeddir=apeddir,xtnames=xtnames)
parameters
apedfil [INPUT; required] FITS file, output of APEC
* assumed to be in following format --
[PARAMETERS][cols kT,EDensity,Nelement,Nline]
where kT is in [keV], EDensity is in [cm^-3]
[L{logT}_{logNe}][cols Lambda,Lambda_Err,Epsilon,Epsilon_Err,Element,Ion,UpperLev,LowerLev]
where {logT} and {logNe} are in '(f3.1)' or '(f4.1)',
Lambda* are in [\AA], and Epsilon* are in [ph cm^3/s]
wvls [OUTPUT; required] all the wavelengths listed in APEDFIL [\AA]
temps [OUTPUT; required] all the temperatures in APEDFIL [log[K]]
edens [OUTPUT; required] all the e-densities in APEDFIL [cm^-3]
Zs [OUTPUT; required] atomic numbers corresponding to each WVLS
ions [OUTPUT; required] ionic state of each of ZS
levs [OUTPUT; required] level designations for each line [2,N(WVLS)]
keywords
apeddir [INPUT] directory containing APEDFIL
* if not set, looks for APEDFIL in $cwd
xtnames [OUTPUT] all the extension names
_extra [JUNK] here only to prevent crashing the program
restrictions
for APED format as of Apr 2000 only
subroutines: KILROY
history
vinay kashyap (AprMM)
(See pro/mkemis/rd_aped.pro)
function rd_chandra_geom reads in the entire geometry file from Chandra's CALDB into an IDL structure and spits it out syntax geom=rd_chandra_geom(/help,caldb=caldb,version=version,verbose=verbose) parameters NONE keywords help [INPUT] if set, prints out the usage help caldb [INPUT] top level directory containing the Chandra CALDB * default is to look for environment variable CALDB * if $CALDB is not defined, then assumes /soft/ciao/CALDB/ version [INPUT] version number to use * default is 5 * the geometry file is assumed to be at $CALDB/data/chandra/tel/bcf/geom/telD1999-07-23geomN####.fits verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Oct04) changed default VERSION to 5 (VK; Jul05)
(See pro/rd_chandra_geom.pro)
function rd_chianti one stop function to read in all relevant atomic parameters from the CHIANTI v4 database and return them in a comprehensive structure (see structure variable CHELP for complete description). usage line_database=rd_chianti(Z,ion,delec=delec,chidir=chidir) parameters Z [INPUT; required] atomic number ION [INPUT] ionic state [if 0 or not given, assumes fully ionized, i.e., =Z] * Z and ION must be integer scalars keywords delec [INPUT] if set, look for the directory containing dielectronic recombination data (1/0) chidir [INPUT] path to top directory of CHIANTI installation * default: !CHIDIR * hardcoded default: /data/fubar/SCAR/CHIANTI/dbase/ _extra [INPUT] junk -- ignore restrictions * requires procedure SETSYSVAL * requires CHIANTI v4 or something very similar * requires PoA subroutine INICON and CHIANTI subroutines READ_WGFA2, READ_ELVLC, READ_SPLUPS, READ_IP history written by vinay kashyap (Nov96), based on SYNTHETIC.PRO of CHIANTI added keyword DELEC, modified default behavior of ION (VK; OctMM) modified for CHIANTI v4, incompatible with earlier versions, added call to SETSYSVAL (VK; Jun02) force a "/" at the end of CHIDIR (VK/LwL; Sep02) added call to READ_IP and output ionization potentials via CHLINE, corrected multiplicity for DR lines (VK; Apr04)
(See pro/mkemis/rd_chianti.pro)
function rd_coco reads in the ATOMDB continuum emissivities and returns it in an IDL structure syntax cocostr=rd_coco(cocofil,wrange=wrange,nbin=nbin,abund=abund,$ /noerg,/noang,cemis=cemis,wvl=wvl,wmid=wmid,logT=logT,$ verbose=verbose) parameters cocofil [INPUT; required] full path to the location of the continuum emissivities database file * if set to '$COCO', looks for /data/atomdb/apec_coco.fits * if set to '$oldAPED', looks for /data/fubar/SCAR/atomdb_1.3.1/apec_coco.fits * if set to '$APED', looks for /data/fubar/SCAR/atomdb_v2.0.0/apec_coco.fits keywords wrange [INPUT] 2-element array to define the range over which the continuum is extracted * default is [0.01,1300] nbin [INPUT] number of bins in the output array * if -ve, the bins will be in log scale, with longer widths at longer wavelengths * default is 2000 abund [INPUT] if supplied, replaces the hardcoded abundances with new ones * if not set, keeps it as Anders & Grevesse noerg [INPUT] if set, refrains from converting the units from [ph ...] to [erg ...] noang [INPUT] if set, refrains from converting the units from [... /keV] to [... /Ang] cemis [OUTPUT] emissivity array of size (TEMPERATURE,WAVELENGTH) collated from all the various extensions in COCOFIL, interpolated onto a standard wavelength grid, and with PoA style units [1e23 ergs cm^3/s/Ang] (unless NOERG and NOANG are set) wvl [OUTPUT] the standardized output wavelength grid wmid [OUTPUT] the mid-bin values of the wavelength grid logT [OUTPUT] the temperature grid over which CEMIS is defined verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Apr2009) changed default $APED to point to v2.0.0 (VK; May2011)
(See pro/mkemis/rd_coco.pro)
function rd_cont
routine to read in the output of WRT_CONT_* and return continuum
emissivities [1e-23 erg cm^3/s/Ang] for specified criteria
syntax
emis=rd_cont(root,pres=pres,logP=logP,n_e=n_e,wrange=wrange,$
dbdir=dbdir,abund=abund,metal=metal,wvl=wvl,logT=logT,fcstr=fcstr,$
chdwvl=chdwvl,/twoph,/noff,/nofb,cocofil=cocofil,/xlogT)
parameters
root [INPUT; required] prefix of files containing the emissivities
* if set to 'chianti', will carry out a real-time computation
of the continua using CHIANTI routines FREEFREE, FREEBOUND,
and TWO_PHOTON
* if set to 'apec', will read in the emissivities from the
APEC continuum database table, which includes both regular
continuum and the so-called pseudo-continuum
keywords
pres [INPUT; default: 1e15] pressure [cm^-3 K]
logP [INPUT; default: 15] log(pressure [cm^-3 K])
* LOGP takes precedence over PRES
* if no match is found, uses nearest available dataset
n_e [INPUT] electron density [cm^-3]. if set,
* overrides LOGP
* appends a "D" to DBDIR
wrange [INPUT; default: all] wavelength range
* if 2-element array, wrange==[wmin,wmax]
* if 1-element array or scalar, wrange==[wr(0),wr(0)]
dbdir [INPUT; default: "cont"] directory to look for files in
* $<whatever> : look for environment variable. if missing,
following special case is hardcoded --
-- $CONT : see variable CONT_DB
* ignored when ROOT='chianti' or ROOT='apec'
abund [INPUT; default: anders & grevesse] abundances
metal [INPUT; default: 1] metallicity
* assumes ABUND to be of metallicity 1
* if set, scales abundances from ABUND appropriately
wvl [OUTPUT] bin beginning wavelengths and final ending
wavelength [Angstroms]
logT [OUTPUT] log10(Temperatures [K])
fcstr [OUTPUT] if specified in call on input, will contain all
the output variables
{CONT_INT,LOGT,WVL,REH,TKEV,EKEV,MIDWVL}
in that order in a structure.
chdwvl [INPUT] bin size to use for ROOT='chianti'
* default is 0.005 Angstrom
twoph [INPUT] set this to _include_ two-photon continuum
noff [INPUT] set this to _exclude_ free-free continuum
nofb [INPUT] set this to _exclude_ free-bound continuum
* TWOPH, NOFF, NOFB are ignored unless ROOT='chianti'
cocofil [INPUT] full path to the location of the APEC
continuum emissivities file
* default is to use '$APED', which points to
/data/atomdb/apec_coco.fits
* used only if CEROOT points to APEC
xlogT [INPUT] if set, returns the emissivity in whatever
native logT grid as is in the databases
* the default is to rebin it with REBINX() and put
it on the grid logT=findgen(81)*0.05+4
verbose [INPUT] controls chatter
_extra [INPUT ONLY] pass defined keywords to RD_IONEQ(),
FREE_FREE_CH, FREE_BOUND_CH, and TWO_PHOTON_CH.
restrictions
* WRT_CONT_* must have been run first
* cannot handle logT arrays that change from file to file
* requires subroutines
INICON
GETABUND
SYMB2ZION [LAT2ARAB]
SETSYSVAL [LEGALVAR]
RD_IONEQ
FREE_FREE_CH [ITOH_CH,SUTHERLAND_CH]
FREE_BOUND_CH
TWO_PHOTON_CH [RD_CHIANTI]
RD_COCO
GETPOADEF
from CHIANTI: READ_IONEQ, READ_GFFGU, BILINEAR, READ_IP,
READ_KLGFB, CONCAT_DIR, GET_IEQ, FREEBOUND_ION, ZION2FILENAME,
FILE_EXIST, DATATYPE, FILE_STAT, DATA_CHK, SINCE_VERSION,
READ_FBLVL, IS_DIR, EXIST, GET_DELIM, OS_FAMILY, TAG_EXIST,
IDL_RELEASE, VERNER_XS, KARZAS_XS
history
vinay kashyap (Dec97; modified from RD_LINE)
allowed dbdir to be "$CONT" or something that may be read in
via an environmental variable (VK; Dec98)
added missing file close statement (VK; 1999Feb)
bug was preventing reading nearest available database (VK; Mar99)
bug in last bug correction, wasn't reading element files (VK; Apr99)
allowed FCSTR output if set in command line (VK; AugMM)
changes suggested by Antonio Maggio: *_DB defaults (VK; NovMM)
added byte-order check; added calls to SWAP_ENDIAN() as suggested
by Antonio Maggio; changed CONT_DB to CONT_CDB environment
variable; added call to SETSYSVAL; now deciphers default
emissivity directory location from where this file is located
(VK; FebMMI)
added keyword VERBOSE (VK; Aug01)
corrected bug where first bin was being chopped off (VK; Jan04)
check to see whether input abundances are already ratios (VK; Apr04)
added option to use chianti routines to compute continuum, added
TWO_PHOT keyword to toggle inclusion of two photon continuum when
calculating via CHIANTI to save time (LL; Feb05)
added NOFF and NOFB keywords to toggle inclusion of CHIANTI free-free
and free-bound continuum, allowed system variable !XUVTOP to be set
if not present (LL; Jun05)
changed keyword TWO_PHOT to TWOPH, added keyword CHDWVL, and
cleaned up interface and internals (VK; Jun05)
bug fix: $CONT/cont was missing the "/" on some systems (VK; May06)
added option to read in APEC_COCO files and added keyword XLOGT
(VK; Apr09)
fixed complication with abund being input as ratio (VK; Nov13)
added call to GETPOADEF (VK; Aug15)
(See pro/rd_cont.pro)
function rd_ioneq return the values of the ionization equilibrium for ions of element Z at specified temperatures as ARRAY(NLOGT,NIONS,NZ). right now this is simply a wrapper to the CHIANTI routine READ_IONEQ. someday other formats will be supported. syntax ioneq=rd_ioneq(z,logt,eqfile=eqfile,chidir=chidir,zlost=zlost,$ verbose=verbose) parameters z [INPUT; required] atomic number * must be integers logt [INPUT/OUTPUT] 1D array of log10(temperatures [K]) at which to provide ionization equilibrium values. if not defined, returns the temperatures at which the values in EQFILE are given. keywords eqfile [INPUT] pathname, relative to CHIDIR, of file containing ionization equilibrium values * default: !IONEQF * hard-coded default: ioneq/chianti.ioneq chidir [INPUT] path name to the CHIANTI installation * default: !CHIDIR * hard-coded default: /data/fubar/CHIANTI/dbase zlost [OUTPUT] average number of lost electrons at each temperature * will be of size (NLOGT,NZ) or (NLOGT) verbose [INPUT] controls chatter _extra [INPUT] junk -- here only to prevent program from crashing description reads in ionization equilibrium values a la CHIANTI and interpolates to appropriate temperatures for example, the ionization fraction of Fe XVII would be (rd_ioneq(26,logT))[*,17-1] or for that matter, (rd_ioneq([8,26,10],logT))[*,17-1,1] requires SETSYSVAL READ_IONEQ (from CHIANTI) GETPOADEF history vinay kashyap (Nov96; based on SYNTHETIC.PRO) added keyword _EXTRA (VK; Dec96) interpolation in log to avoid stepped look (VK; Feb97) smooth after interpolation to avoid segmented look (VK; Apr97) bug: force maximum IONEQ to be 1, not 10^(1)! (VK; 99Sep) added keyword VERBOSE, now takes CHIDIR and EQFILE defaults from !CHIDIR and !IONEQF if they are defined; added call to SETSYSVAL (VK; Jul01) cleaned up the interface, and allowed Z to be an array (VK; Jun02) added keyword ZLOST, converted "()" to "[]" (VK: Apr06) allowed EQFILE to be a plain filename; changed hardcoded defaults of EQFILE and CHIDIR (VK; Jul13) changed default of EQFILE to ioneq/chianti.ioneq (VK; Aug13) added call to GETPOADEF (VK; Aug15)
(See pro/rd_ioneq.pro)
function rd_line
supremely flexible routine to read in the output of WRT_LINE
and return line cooling emissivities [1e-23 erg cm^3/s] for
specified criteria in an array of size [NLOGT,NWVL]
syntax
emis=rd_line(atom,pres=pres,logP=logP,n_e=n_e,wrange=wrange,$
dbdir=dbdir,wvl=wvl,logT=logT,z=z,ion=ion,jon=jon,src=src,$
desig=desig,econf=econf,fstr=fstr,/allah,/help,verbose=verbose)
parameters
atom [INPUT] element whose line intensities are to be read.
* can specify ionic state (e.g., 'FeXX')
* may be an array (e.g., ['He', 'c 5', 'N V', 's_8'])
* default -- ALL
keywords
pres [INPUT; default: 1e15] pressure [cm^-3 K]
logP [INPUT; default: 15] log(pressure [cm^-3 K])
* LOGP takes precedence over PRES
* if no match is found, uses nearest available dataset
n_e [INPUT] electron density [cm^-3]. if set,
* overrides LOGP
* appends a "D" to DBDIR
* NOTE: PRES, LOGP, and N_E are initalized in the
system variables !GASPR, !LOGPR and !EDENS.
HOWEVER, these system variables are *not* used as
the defaults; these keywords must be explicitly set
in order to take effect.
wrange [INPUT; default: all] wavelength range
* if 2-element array, wrange==[wmin,wmax]
* if 1-element array or scalar, wrange==[wr[0],wr[0]]
dbdir [INPUT; default: !LDBDIR; hard-coded default: "$CHIANTI"]
line database directory
* if an array, only the first element is used
* WARNING: if N_E is set, a "D" is appended at the end (but
after stripping any pre-existing "D"s, mind!)
* $<whatever> : look for environment variable.
some special cases are:
-- $SPEX : from environment variable SPEX_LDB
-- $CHIANTI : from environment variable CHIANTI_LDB
-- $APED : from environment variable APED_LDB
-- $SCAR : from environment variable SCAR_LDB
if the environmental variable is undefined, then some
special cases are hardcoded:
-- SPEX : TOPDIR/emissivity/spex
-- CHIANTI : TOPDIR/emissivity/chianti
-- APED : TOPDIR/emissivity/aped
-- SCAR : TOPDIR/emissivity/xinti
wvl [OUTPUT] wavelengths [Angstroms]
logT [OUTPUT] log10(Temperatures [K])
z [OUTPUT] atomic numbers of elements generating given WVL
ion [OUTPUT] ionic state of element generating given WVL
jon [OUTPUT] the ionic state that matters, as far as ion-balance
is concerned
src [OUTPUT] reference to source of line info
* 1: SPEX, 2: CHIANTI, 3: APED
desig [I/O] level designations for lower & upper level
for each transition
* read in only if DESIG is present in call
econf [I/O] e-configurations for lower & upper level
* read in only if ECONF is present in call
fstr [OUTPUT] if present in the calling sequence, will contain all
the output variables
LINE_INT,LOGT,WVL,Z,ION,DESIG,ECONF,SRC,JON
in that order in a structure.
allah [INPUT] if set, assumes all files are available in correct
forms, and does no checking.
* quicker, but UNFORGIVING
* faith is not an option
help [INPUT] if set, prints out the calling sequence and quits
verbose [INPUT] higher the number, greater the chatter
* default is !VERBOSE
_extra [INPUT] junk -- here only to avoid crashing the program
restrictions
* WRT_LINE must have been run first
* requires subroutines
SYMB2ZION
LAT2ARAB
INICON
SETSYSVAL
IS_KEYWORD_SET
GETPOADEF
* cannot (as yet) handle logT arrays that change from atom to atom
usage examples
* f=rd_line(atom,pres=pres,logP=logP,wrange=wrange,dbdir=dbdir,$
wvl=wvl,logT=logT,z=z,ion=ion,/allah)
* f=rd_line('He',logP=20,wr=[200.,500.],wvl=wvl,logT=logT,desig=desig,$
econf=econf,fstr=fstr,/allah)
* f=rd_line(wr=16.776,wvl=wvl,logT=logT,z=z,ion=ion,desig=desig)
* econf=1 & f=rd_line(wvl=wvl,logt=logt,z=z,ion=ion,econf=econf,/allah)
oo=sort(abs(wvl)) & surface,alog10(f[*,oo]+1),logt,abs(wvl[oo]),/ylog
history
vinay kashyap (Nov96)
added keywords ECONF and FSTR, changed I/O (VK; Dec96)
corrected bug in reading in SRC (VK; Jan96)
added keyword N_E (VK; Jun97)
corrected bug that was returning nonsense labels when Z+ION was
specified (VK; Jul97)
now handles trailing "/"s and/or "D"s correctly; accepts "0"
as synonym for all atoms (VK; Jun98)
accepts '$SPEX', '$CHIANTI', and '$SCAR' as hardcoded default
values for DBDIR (VK; Oct98)
accepts DBDIR defined via environmental variable; trapped DBDIR
being input as vector; added keyword HELP (VK; Nov98)
"All" is accepted as an atom (VK; Dec98)
"_"s in DBDIR causing incorrect selections: corrected
added keyword JON, added read to ATOM_jon (VK; 1999May)
added keyword VERBOSE, allowed input of the form "ALL ion" (VK; MarMM)
added /SWAP_IF_LITTLE_ENDIAN to OPENR calls (VK; AprMM)
added $APE to list of automatic *_DB (VK; AprMM)
changed to full compatibility with IDL5+ ("()"->"[]"); allowed
read in of DESIG, ECONF and output of FSTR if present in call;
bug correction if ATOM goes past Zn (VK; AugMM)
CHIANTI 3.0 has occassional NaNs in emissivity -- put in hack to
avoid them (VK; SepMM)
changes suggested by A.Maggio: strmid params, *_DB defaults
(VK; NovMM)
changed *_DB to *_LDB environment variables; if ALLAH was set,
DBDIR was not being prepended (VK; DecMM)
added call to SETSYSVAL; now deciphers default emissivity directory
location from where this file is located; added byte-order
check; added calls to SWAP_ENDIAN() as suggested by Antonio Maggio
(VK; FebMMI)
changed defaults for DBDIR, VERBOSE to read from !LDBDIR, !VERBOSE
(VK; Jul01)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
added call to GETPOADEF (VK; 05Aug2015)
bug fix: compilation error (VK; 10Sep2015)
(See pro/rd_line.pro)
function rd_list
read in line emissivities for a list of specified lines and returns
the database in a standard structure format (RD_LINE for details)
syntax
lstr=rd_list(lnlist,/incieq,desig=desig,econf=econf,mapping=mapping,$
dbdir=dbdir,brklst=brklst,sep=sep,prefix=prefix,comment=comment,$
pres=pres,logP=logP,n_e=n_e,chifil=chifil,chidir=chidir,eqfile=eqfile,$
eps=eps,verbose=verbose)
parameters
lnlist [INPUT; required] line list
* must be a string scalar or array
* if a line contains a "/" or "./" or ".." in the first field,
assumed to be a filename unless the "/" is followed by
another "/" ("//") or a "*" ("/*"), in which case it is
assumed to be a comment.
* any line prefixed by "%", "#", ";", "/*", "*/", "//",
and PREFIX are assumed to be comments
* either the file or the direct input must describe the
line as:-
"Z ION <sep> WAVE <sep> SOURCE <sep> DESCRIPTION"
where Z is the atomic symbol, ION is the ionic state,
WAVE is in [Ang], and SOURCE is DBDIR (see RD_LINE)
* Z is required
ION is useful
WAVE, SOURCE, and DESCRIPTION are optional
but WAVE is required if SOURCE is given
and WAVE and SOURCE are required if DESCRIPTION is given
* if multiple candidates are available, DESCRIPTION may be
used to choose from among them (see MAPPING)
* <SEP> is a separator, usually a <tab>, but had better
not be any of "," "+-" "-" and "?"
* WAVE may be (any combination of):-
exact match -- "WVL"
inexact match -- "WVL +- dW" or "WVL ? dW"
range -- "WMIN,WMAX" or "WMIN-WMAX"
enclosed in brackets -- "()" "[]" "{}"
* DESCRIPTION is basically treated as a set of <SP>-separated
keywords, and if a given field is preceded by a "!" any
matches based on that field would be _excluded_ (e.g.,
"!DR" would not match any DR line)
keywords
incieq [INPUT] if set, output emissivities will include ion-balance
mapping [INPUT] this keyword controls what happens when an entry in
LNLIST matches multiple instances of (Z,ION,WAVE) in the
input database.
* if not set, or set to 0, returns all the emissivities,
exactly as found, in separate rows,
* but if not set and yet DESCRIPTION is set, then assumed
to be +ve
* if set, and is +ve, then
-- looks through the DESCRIPTION field of LNLIST, and
finds the closest match in the database and returns
only that.
-- if "closest match" is ambiguous, then default is set
to the strongest of the closest matches, and the user
is asked to verify.
-- if DESCRIPTION is not set, or the given DESCRIPTION
succeeds in eliminating >all< the matches, then asks
which one (the default being the strongest line in
the set).
* if set, and is -ve, then adds the emissivities of all
the extra lines to that of the strongest line in the
set.
* NOTE: if "WVL?dW" is set, and multiple lines are found
in the database, MAPPING is overridden and the user is
asked to choose anyway.
dbdir [I/O] directory in which to look for files
* will be used ONLY if not given in LNLIST
* if not specified, *default* will be set at run-time to
whatever was used last
* on output, will be a string array of the DBDIRs used
NOTE: this last feature will soon be eliminated -- use
keyword BRKLST instead
sep [INPUT] separator used to delineate fields in LNLIST
* the default is to separate the fields with several blanks
(<tab>)
prefix [INPUT; default='*'] any line beginning with this letter
is considered a comment
* this is in addition to "%", "#", ";", "/"
comment [OUTPUT] any commented lines are returned in this variable
as a string array
brklst [OUTPUT] structure containing a breakdown of all the
fields in LNLIST, in the form
{SPECIES, WMIN, WMAX, DBDIR, DESCRIPTION}
eps [INPUT; default=1e-5] a small number
* used as a "round-off" error for wavelength precision
if the WAVE field does not specify a range
verbose [INPUT; default=0] controls chatter
_extra [INPUT ONLY] use this to pass defined keywords to
-- RD_LINE:
N_E electron density [cm^-3], default is 1e9
_explicitly set to 0_ to use PRES/LOGP
PRES pressure [cm^-3 K]
LOGP alog10(pressure [cm^-3 K])
DESIG to read in level designations, set by default
ECONF to read in e configurations, set by default
-- FOLD_IONEQ:
CHIFIL to read in from CHIANTI style database
EQFILE name of ion balance file
-- RD_IONEQ:
CHIDIR path to CHIANTI installation
restrictions
syntax incompatible for IDL <5
function calls incompatible for idl <5.3
requires subroutines:
RD_LINE, SYMB2ZION, LAT2ARAB, FOLD_IONEQ, RD_IONEQ, READ_IONEQ,
CAT_LN, LINEFLX, GETABUND, RDABUND, SYZE, INICON, IS_KEYWORD_SET
history
vinay kashyap (Jun98)
added keyword COMMENT; changed behavior of SETASK (VK; Oct98)
DBDIR now contains all directories on output (VK; Nov98)
changed input to FOLD_IONEQ from ION to JON (VK; 99May)
allowed unfound elements to be read in also, up to a point (VK; 99Jul)
added keyword MAPPING, enhanced LNLIST, deleted SETASK, converted
to IDL5.3 (VK; MarMM)
now quits if IDL v <5.3 (VK; DecMM)
force MAPPING=1 if DESCRIPTION is set; added keyword BRKLST as
first step towards eliminating DBDIR as output; added keyword
VERBOSE and EPS; changed DESIG/ECONF behavior to be set by default
(VK; JanMMI)
changed default behavior to read in from constant-density database
at N_E=1e9 if nothing is specified (VK; Jan'03)
added ability to exclude fields via DESCRIPTION (VK; Apr'03)
changed default SEP to "any series of one or more space or tab
characters" (VK; Feb'04)
changed SEP back to <tab> (VK; Sep'05)
updated for IDL5.6 keyword_set([0]) behavior change for vectors
(VK; 20Mar2006)
(See pro/rd_list.pro)
function rd_ogip_rmf
reads in the response matrix and associated axes from OGIP-compliant
response file and returns everything in a structure of the form:
{NNRG, ELO, EHI, NCHAN, EMN, EMX, N_GRP, F_CHAN, N_CHAN, MATRIX, FIRSTCHAN}
where ELO and EHI refer to range of photon energies at which the
response is valid, EMN and EMX refer to bin boundaries for each
channel, N_GRP refers to number of groups of non-zero data, F_CHAN
refer to beginning indices of channels, N_CHAN are the number of
channels in each group, and the output response MATRIX excludes
zeros to save space. The value of FIRSTCHAN indicates whether F_CHAN
indices are 0-based or 1-based.
http://legacy.gsfc.nasa.gov/docs/heasarc/caldb/docs/memos/cal_gen_92_002/cal_gen_92_002.html
for a description of the format
WARNING: the EBOUNDS extension of RMFs, which defines EMN and EMX,
should never be used directly for scientific purposes. They
contain the nominal energy boundaries for the PHA, PI, or pixel
bins that define the MATRIX. They are never exact values, and
are useful only for plotting purposes. It is the detector bins
and their indices that are the be-all and end-all of RMFs.
syntax
rmstr=rd_ogip_rmf(rmfile,effar=effar,eqvar=eqvar,spcar=spcar,$
rmfimg=rmfimg,fchcol=fchcol,/shift1,verbose=verbose)
parameters
rmfile [INPUT; required] response matrix file
keywords
effar [OUTPUT] returns the effective area as a function of ELO
* if an RMF file is read instead of an RSP file, EFFAR are
uniformly 1, unless it is ASCA in which case it is the QEs
* EFFAR are calculated ONLY if needed. i.e., the keyword
must be present in call (IDL5+) or defined on input (IDL5-)
eqvar [OUTPUT] returns an equivalent effective area in each
detector channel, measuring the contribution to that
channel from all photon energies.
spcar [OUTPUT] a variation on EQVAR, the convolution of a really
flat intensity spectrum [ph/.../keV] with the RSP.
In other words, what a flat spectrum would look like.
* BEWARE: EQVAR and SPCAR are _not_ true effective area.
EFFAR are in _energy_ bins. EQVAR and SPCAR are in
_channel_ bins.
* CAVEAT VSVATOR!
* I will deny ever having said this, but if you _must_
use one of these fake effective areas, use SPCAR.
rmfimg [OUTPUT] returns the RMF matrix as an image of size
N(CHANNEL) x N(ENERGY)
* computed only if this keyword is present (must also
be defined to be non-zero in IDL versions prior to 5.0)
shift1 [SEMI OBSOLETE] some RMFs have position indices that are
0-based and some are 1-based. this keyword used to specify
which was what. however, this information should be in the
FITS header in the keyword TLMIN{FCHCOL}, and that is where
the program takes its value from.
* BEWARE: if SHIFT1 is set _and_ TLMIN{FCHCOL} comes out as 0
(usually if it is not defined, or perhaps it really is 0)
then FIRSTCHAN is taken to be 1, and vice versa.
* in other words, if set, overrides whatever the file
itself is saying
fchcol [INPUT] column number of F_CHAN in RMFILE
* default is 4
_extra [JUNK] here only to prevent crashing the program
restrictions
requires IDLASTRO library routine MRDFITS
history
vinay kashyap (Apr99; modified from RDRESP.PRO)
added keyword SHIFT1 (VK; JanMMI)
slight modification in defining IDL version (VK; FebMMI)
added keyword FCHCOL, overrode SHIFT1, added FIRSTCHAN to output
structure (VK; Nov2001)
commented out the "L5_MATRIX" lines (VK; Dec2001)
added keywords EQVAR, SPCAR, and VERBOSE (VK; Jul02)
bug correction: rspfil variable changed to RMFILE (LL/VK;Aug04)
added ability to handle non-OGIP Astro-E2 XIS rmf file (LL/VK:Aug04)
tweaked to speed up calculation of effar (VK; Dec04)
added keyword RMFIMG (VK; May06)
(See pro/util/rd_ogip_rmf.pro)
procedure rd_pimms_file read in the effective area values from PIMMS file syntax rd_pimms_file,pimmfl,effar,nrgar,ecol=ecol,acol=acol,/wave parameters pimmfl [INPUT; required] scalar string specifying the full pathname to PIMMS effective area file. * output of GET_PIMMS_FILE effar [OUTPUT] effective areas, usually in [cm^2] nrgar [OUTPUT] energies at which EFFAR are defined * assumed to be [keV] * if WAVE is set, converted to [Ang] keywords acol [INPUT; default=2] column number which contains EFFAR ecol [INPUT; default=1] column number which contains NRGAR wave [INPUT] if set, assumes that ECOL contains [keV] and converts to [Ang] * if columns are ALREADY in [Ang], DO NOT SET THIS KEYWORD _extra [JUNK] ignore -- here only to prevent crashing the program subroutines STR_2_ARR, WC, STR_SEP, SYZE history vinay kashyap (Mar99) changed call to STR_2_ARR from STR2ARR (VK; AprMMV)
(See pro/util/rd_pimms_file.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
astrophysical emission line spectra. It is a collaborative project
involving Ken Dere (Naval Research Laboratory, Washington DC),
Brunella Monsignori-Fossi and Enrico Landi (Arcetri Observatory,
Florence), and Helen Mason and Peter Young (DAMTP, Cambridge Univ.).
NAME:
READ_ELVLC
PURPOSE:
to read files containing observed and theoretical energy levels
CATEGORY:
science.
CALLING SEQUENCE:
READ_ELVLC, File, L1, Term, Conf, ss, ll, jj, Ecm, Eryd, Ecmth, Erydth, Ref
INPUTS:
File: the name of the file
i.e., !xuvtop+'/si/si_12/si_12.elvlc' for Si XII
OPTIONAL INPUTS:
None:
OUTPUTS: L1 - level index
Term - configuration index
Conf - configuration description
ss - 2S+1
ll - L
jj - J
Ecm - observed energy (cm^-1)
Eryd - observed energy (Rydbergs)
Ecmth - theoretical energy (cm^-1)
Erydth - theoretical energy (Rydbergs)
Ref - reference
note: the theoretical energies are usually those used in the scattering
calculation and are only useful for predicting approximate
wavelengths
EXAMPLE:
> file = !xuvtop+'/si/si_12/si_12.elvlc'
> read_elvlc,file,l1,term,conf,ss,ll,jj,ecm,eryd,ref
>
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
Ver.2, 6-Dec-2001, Peter Young
Modified the form of the "term" output. The J-value is now
represented by a fraction rather than a decimal.
(See pro/external/read_elvlc.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
READ_FBLVL
PURPOSE:
To read files containing observed free-bound energy levels
CATEGORY:
Science.
CALLING SEQUENCE:
READ_FBLVL, File, L1, Conf, pqn, ll, spd, mult, Ecm, Ecmth, Ref
INPUTS:
File: the name of the file
e.g., !xuvtop+'/si/si_12/si_12.fblvl' for Si XII
OPTIONAL INPUTS:
None:
OUTPUTS: L1 - level index
CONF - configuration description
PQN - principal quantum number of electron being ionized
LL - L-value of ionized electron
SPD - 'S', 'P', etc to denote L value
MULT - multiplicity 2J+1
ECM - energy (cm^-1)
ECMTH - energy (cm^-1)
REF - reference
EXAMPLE:
> file = !xuvtop+'/si/si_12/si_12.elvlc'
> read_fblvl,file,l1,conf,pqn,ll,mult,ecm,ecmth,ref
>
HISTORY
Ver.1, 31-Jul-2002, Peter Young
(See pro/external/read_fblvl.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is
a collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_GFFGU
PURPOSE:
Read gffgu.dat file containing free-free gaunt factors of
R. S. Sutherland, 1998, MNRAS, 300, 321
note: the file available from the web site are mislabelled
CALLING SEQUENCE:
READ_GFFGU,g2,u,gff
INPUTS:
None
OUTPUTS:
g2,u,gff defined in the paper by Sutherland
COMMON BLOCKS:
None
MODIFICATION HISTORY:
Written by: Ken Dere
April 2000: Version 3.0
October 2001: Version 4 - Ken Dere -
corrected for the fact that the original
Sutherland file was mislabelled
November 2001: Corrected the address of the gffgu.dat file - Enrico Landi
(See pro/external/read_gffgu.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
READ_IONEQ
PURPOSE:
to read files containing the ionization equilibrium values
CATEGORY:
science.
CALLING SEQUENCE:
READ_IONEQ, File, T, Ioneq, Ref
INPUTS:
File: for example, !xuvtop+'/ioneq/arnaud_rothenflug.ioneq'
OPTIONAL INPUTS:
None:
OUTPUTS:
T: array of log10 temperatures
Ioneq: 3-d array (T,element,ion)
of the fractional abundance of the ion in
ionization equilibrium.
Ref: reference in the scientific literature
EXAMPLE:
> read_ioneq,!xuvtop+'/ioneq/arnaud_rothenflug.ioneq'
> help,t,ioneq
> T FLOAT = Array(41)
> IONEQ FLOAT = Array(41, 28, 29)
> print, minmax(t)
> 4.00000 8.00000
> print,t(20)
> 6.0000
> print,ioneq(20,25,9)
> 0.269 = fractional abundance of Fe X in
ionization equilibrium
MODIFICATION HISTORY:
Written by: Ken Dere (KPD)
March 1996: Version 2.0
March 1999: KPD to read both number of temperature and number
of elements
25-Oct-2000 V. 4, Giulio Del Zanna (GDZ).
Corrected to interpret the '-1' as a reference only
if within the first 3 columns
V. 5, 21-May-2002, Giulio Del Zanna (GDZ)
generalized directory concatenation to work for
Unix, Windows and VMS.
v.6, 25-Oct-2004, Peter Young
modified format statement so that it will read any number of
temperatures.
V 7, 25-May-2005, GDZ
corrected routine header.
VERSION : 7, 25-May-2005
Aug2010: Vinay Kashyap commented out reference to !xuvtop
(See pro/external/read_ioneq.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_IP
PURPOSE:
to read values of ionization potentials
CALLING SEQUENCE:
READ_IP, File, IP, Ref
INPUTS:
File: the name of the file containing the IP values, usually
!xuvtop/ip/chianti.ip
OUTPUTS:
IP: Array values of ionization potential (cm^-1)
Ref: the reference to the IP values in the scientific literature
EXAMPLE:
> read_ip,!xuvtop+'/ip/chianti.ip',ip,ref
ip(2-1,2-1) give the ionization potential of He II (Z=2, Ion=2)
MODIFICATION HISTORY:
Written by: Ken Dere
March 1998: Version 1.0
(See pro/external/read_ip.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_KLGFB
PURPOSE:
to read CHIANTI files file containing the free-bound gaunt factors for n=1-6
from Karzas and Latter, 1961, ApJSS, 6, 167
CATEGORY:
science.
CALLING SEQUENCE:
READ_KLGFB,PE,GFB
INPUTS:
File: none
OUTPUTS:
PE: an array of natural log of 41 values of Photon Energy values relative to
the recombination edge i.e., at the recombination edge, PE=0.
GFB: an array containing the natural log of free-bound gaunt factors indexed
by energy, n and l
PROCEDURE: reads the file: '!xuvtop/continuum/klgfb.dat'
EXAMPLE:
> read_klgfb,pe,klgfb
the free-bound gaunt factor vs. energy for recombination to a hydrogen 2p state
(n=2 and l=1) is given by klgfb(*,n-1,l-1)
MODIFICATION HISTORY:
Written by: Ken Dere
July 2002: Version 1.0
Version 2, 8-Aug-02, GDZ
corrected a typo.
VERSION : V.2, 8-Aug-02
(See pro/external/read_klgfb.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_MASTERLIST
PURPOSE:
read the masterlist.ions types of file and output a list of ions
CATEGORY:
science.
CALLING SEQUENCE:
READ_MASTERLIST,filename,mlist
INPUTS:
filename: name of the masterlist file
KEYWORD PARAMETERS:
none
OUTPUTS:
mlist: list of ions
COMMON BLOCKS:
none;
EXAMPLE:
> read_masterlist,'!xuvtop/masterlist.masterlist.ions',mlist
MODIFICATION HISTORY:
Written by: Ken Dere
December 1998: first version
Ver.2, 23-Sep-2010, Peter Young
- renamed LIST to MLIST for compatibility with IDL 8
(See pro/external/read_masterlist.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It
is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_SPLUPS
PURPOSE:
to read file containing spline fits to the Burgess-Tully scaled
collision strengths
CATEGORY:
science.
CALLING SEQUENCE:
READ_SPLUPS, File, Splstr, Splref
INPUTS:
File: the name of the input file, i.e. !xuvtop/si/si_4/si_4.splups
OUTPUTS:
SPLSTR Structure containing the data from the file. The tags are
as follows:
.lvl1 lower level index
.lvl2 upper level index
.t_type transition type
.gf gf value
.de Delta-E for transition (rydbergs)
.c_ups the scaling parameter
.nspl
.spl Vector of length 9, containing spline points
OPTIONAL OUTPUTS
SPLREF String array containing references.
KEYWORDS
PROT Allows reading of .psplups files for proton rates.
PROCEDURE:
see Burgess and Tully, 1992, Astronomy and Astrophysics, 254, 436.
EXAMPLE:
> read_splups, !xuvtop+'/si/si_4/si_4.splups',splstr,splref
PROGRAMMING NOTES
This routine is marginally quicker (20-25%) reading the .splups
files than Ken's original routine. The improvement in speed is
through minimising the lines of code in the WHILE loop.
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
Ver.3, 23-Jan-01, Peter Young
completely revised. Now reads into a structure and
handles 9 point spline fits.
Ver.4, 26-Jan-01, Peter Young
speeded up routine
Ver.5, 22-Mar-01, Peter Young
now checks if file exists
Ver.6, 17-Jul-2012, Ken Dere
can handle files with 5 through 9 spline points
(See pro/external/read_splups.pro)
PROJECT: CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
NAME:
READ_WGFA2
PURPOSE:
read radiative data files
a modified version of read_wgfa
needed to take account of two types of transitions between the same 2 levels:
for example, the M1 and the 2 photon E1 transition 1s-2s in hydrogenic ions
CATEGORY:
science
CALLING SEQUENCE:
READ_WGFA2, File, Lvl1, Lvl2, Wvl, Gf, A_value, Ref
INPUTS:
File: name of the file containing the radiative data
i.e. !xuvtop/c/c_4/c_4.wgfa
OUTPUTS:
Lvl1: 1D array of indices of the lower level (starting at 1)
Lvl2: 1D array of indices of the upper level (starting at 1)
Wvl: 1D array of transition wavelengths in Angstroms
Gf: 1D array of weighted oscillator strength gf
A_value: 1D array of the total radiative transition probability (s^-1)
Ref: 1D string array of references to the data in the scientific literature
EXAMPLE:
> read_wgfa2,!xuvtop+'/c/c_4/c_4.wgfa',lvl1,lvl2,wvl,gf,a,ref
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
V.3, 3-Nov-03, Giulio Del Zanna (GDZ)
Modified size of input arrays. Now the routine can read a file up to
30 000 lines.
V.4, 26-May-09, Enrico Landi (EL)
Modified size of input arrays. Now the routine can read a file up to
100,000 lines.
Modified definition of variable index (now index=0L).
V.5, 26-May-09, Peter Young
Modified the way references are read.
VERSION : 5, 26-May-09
(See pro/external/read_wgfa2.pro)
function rebinw rebins the input array on a new grid and returns the output array. this routine is preferred over simple INTERPOL or SPLINE because this is guaranteed to e.g., conserve flux while rebinning spectra. syntax ff=rebinw(f,x,y,/perbin,numbins=numbins,nbin=nbin,wrange=wrange,$ /slowok,verbose=verbose) parameters f [INPUT; required] array values x [INPUT; required] absissae for F 1: if size matches that of F, assumed to be mid-bin values 2: if size is size(F)+1, assumed to be bin boundaries (i.e., all the bin-beginners and a final bin-ender) 3: if neither of the above, this is assumed to be the desired *output* grid, and the absissae of the input are assumed to span the linear range 1..N(F) * Y is ignored on input, but will be overwritten on output y [I/O] the new absissa values, taken from NUMBINS if it is set. 1: if scalar or 1-element vector on input, assumed to be number of bins in output * linear binning if +ve, log binning if -ve 2: if >1-element vector on input, assumed to be the desired output grid of bin boundaries, with the last element defining the final bin-ending value. 3: if not defined, takes value from NBIN NOTE: F extrapolates as zeros. keywords perbin [INPUT] if set, assumes that units of F(X) are [.../bin] nbin [I/O] number of bins in output * overwritten if defined via X or Y * linear binning if +ve, log binning if -ve * default: 1 numbins [INPUT] same as NBINS, except that if set, it overrides NBIN _and_ Y * so, just to reiterate: if NUMBINS is _not_ defined, then -- if Y is a scalar, say = NN, then output will be rebinned to have NN elements, and Y will be overwritten to contain the new grid, and NBIN will be reset to NN -- if Y is a vector, then output will be rebinned using Y as bin boundaries, and NBIN will be reset to N(Y)-1 -- if Y is not defined, but NBIN is defined, then output will be rebinned to have NBIN elements, and Y will on output contain the new grid if NUMBINS is defined, then -- output will be rebinned to have NUMBINS elements, and Y will contain the new grid on output, and NBIN will be reset to NUMBINS wrange [INPUT] output grid range * ignored if defined via array Y (or X -- case 3) * overrides if determined via X and CASE 1 of Y * default: [1.,500.] slowok [INPUT] if set, skips call to FINDEX and does it the slow IDL way verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program restrictions beware that if Y is not sorted in ascending order, on output it will be! requires external procedure FINDEX.PRO history vinay kashyap (Jan98) forced x to be required inputs (Jun98) changed call to INTERPOL to combo call to INTERPOLATE/FINDEX (VK;99Jul) corrected long-standing "feature" of NBIN being useless, changed default behavior of Y=UNDEFINED, NBIN, and X=/=F (VK; MarMM) added keyword SLOWOK (VK; Jul01) added keyword NUMBINS (VK; Dec'02) added keyword VERBOSE; now uses /CUMULATIVE in TOTAL() (VK; Feb'03) beware of /CUMULATIVE in TOTAL(), which returns an array of same size as input, and does _not_ begin with 0 (VK; Apr'03) added warning if Y gets resorted (VK; Mar04) cleaned up behavior in the case of non-unique/non-monotonic inputs (VK; Mar05)
(See pro/util/rebinw.pro)
function rebinx returns the input array suitably reformatted (resampled, stretched, constricted, what have you) to the new range. syntax f=rebinx(array,inX,outX,Xindex=Xindex,/absmin,/absmax,/norng,$ verbose=verbose) parameters array [INPUT; required] array to be reformatted inX [INPUT; required] abscissa values defining the input grid outX [INPUT] abscissa values defining the output grid * if not given, assumed to be FINDGEN(81)*0.05+4. keywords Xindex [INPUT] specifies which dimension of ARRAY corresponds to inX * if not given, picks that dimension that first matches to the number of elements in inX * e.g., if ARRAY[1000,81] and inX[81], then Xindex=1 absmin [INPUT] if set, force oARRAY to be > ABSMIN * default is min(ARRAY) absmax [INPUT] if set, force oARRAY to be < ABSMAX * default is max(ARRAY) norng [INPUT] if set, ignores ABSMIN and ABSMAX verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program example 1. rebin DEM in range logT=5..7 in 11 steps to DEM in range logT=4..8 in 81 steps: fullDEM=rebinx(DEM,findgen(11)*0.2+5,findgen(81)*0.05+4) 2. resample emissivity from full range to smaller sample: subEMIS=rebinx(EMIS,logT,sublogT,Xindex=0) restrictions * can only handle at most 2-D arrays history vinay kashyap (Oct98) bug correction with Xindex, added keyword VERBOSE, converted to IDL5 format (VK; Jul02)
(See pro/util/rebinx.pro)
REFITLINES.PRO so you ran through FITLINES and got your fits. and you are ready to publish. but wait, did you use the right model? sigh. ok, let's have a go at it again. need the spectrum, of course. should be in variables LAMBDA and SPECT[LAMBDA] and SPECTSIG[LAMBDA] need the old fit structure. should be in variable OLDFITSTR new fit structure will be in variable, what else, NEWFITSTR vinay kashyap (MMJul) included HISTERIX (VK; MMIVFeb)
(See pro/scrypt/refitlines.pro)
function regroup group an input array of counts such that each group has at least a minimum number of counts. start accumulating from one end, and keep going until the threshold is exceeded, then start on the next group, etc. syntax gct=regroup(counts,minct,grid,/newgrid,iout=iout,verbose=vv) parameters counts [INPUT; required] counts array to be regrouped minct [INPUT; required] minimum total counts in each group grid [I/O] bin indices indicating starting and ending index of each group, such that group K runs from index GRID[K] to GRID[K+1]-1 * if given as an array that contains indices from 0 to N_ELEMENTS(COUNTS) on input, uses that gridding and does not calculate a new grid, unless NEWGRID is set * if not well-defined, or if NEWGRID is set, will be overwritten on output keywords newgrid [INPUT] if set, ignores the input GRID and computes the grouping and the resulting new grid * if not set, and GRID is well-defined, GRID is used * if not set, and GRID is not well-defined, a new GRID is computed and the input is overwritten iout [OUTPUT] an integer index array designating which group each element of COUNTS has ended up in * this illustrates the essential non-destructive nature of the regrouping -- it should always be possible to go back to the original array and rearrange it. verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program example y=randomu(seed,20) & gy=regroup(y,2.5,x,/newgrid,iout=iout) print,y,iout & print,gy,x for i=0,n_elements(gy)-1 do print,i,x[i],x[i+1]-1,$ gy[i],total(y[x[i]:x[i+1]-1]),total(y[where(iout eq i)]) these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (Oct09)
(See pro/util/regroup.pro)
function regroup_rmf
Converts RMF structure created with RD_OGIP_RMF() to a
one group per photon energy RMF structure. Done so to
maximize convolution efficiency with SCRMF() e.g. for
model fitting via RMFs in FITLINES(). Will return input
if RMF is already optimal. If effective area is folded
into matrix and this is undesired, REGROUP_RMF is also
capable of returning an unfolded RMF via the NOEFFAR
keyword.
If ENRG paramater is fed, will be used to define the photon
energy grid of the reconstructed RMF.
If a spectrum SPEC is fed together with ENRG, then
the photon energy range will be constructed so that
bin-density is highest at energy ranges with largest
signal.
If NB is set, will be used as the total number of bins
for resulting photon energy grid.
syntax nrmfstr = regroup_rmf(rmfstr,enrg,spec,nb,/noeffar)
parameters
rmfstr [INPUT;required] structure containing info of
response matrix, the output of RD_OGIP_RMF()
enrg [INPUT] desired energy grid
spec [INPUT] spectrum of interest. if given, should
be on the same grid as ENRG, and is used to tweak
the energy grid in the output such that the
bin-density is correlated with SPEC.
* overrides ENRG except that the energy range in
the output is taken from ENRG.
nb [INPUT] total number of photon energy bins desired.
* is used only when SPEC is defined, and by default
is set to N(ENRG) if not given
keywords
noeffar [INPUT] if set, the LSF corresponding to each
photon energy will be normalized to 1 i.e.
effective area is unfolded.
WARNING: Because photons are _lost_ at the edges
of applicability of the RMFs, the renormalization
will not necessarily be correct in these regions.
history
liwei lin (Aug 03)
ADDED option to regrid rmf in enrgy space via
enrg, spec, and nb (LL Sep03)
BUG FIX CF handling/interpolation re-worked to avoid
shifting of grid (LL Sep03)
BUG FIX now robust to zero vavlues for N_GRP.
thanks Jan-Uwe (LL Jun06)
BUG FIX changed condition for when regroup is done
thanks Jan-Uwe (VK Dec07)
(See pro/util/regroup_rmf.pro)
function renormod given model values and data, find a normalization factor for the model that makes it a better fit to the data and return this new value. syntax norm=renormod(data,model,err,/uchisq,/uabsdev,/umaxdev,/ureldev,$ statval=statval,dstep=dstep,eps=eps,verbose=verbose) parameters data [INPUT; required] data values model [INPUT; required] model values * size must match DATA err [INPUT; optional] errors to use to determine the goodness of fit statistic. if not given, assumed to be the Gehrels approximation to Poisson, sqrt(abs(DATA+0.75)+1) * size must match DATA, or must be 1-element * if 1-element and +ve, constant value errors are assumed * if 1-element and -ve, a constant fractional value for the errors, DATA*abs(ERR) are assumed * WARNING: data points with ERR=0 are ignored when it is necessary to divide by the errors keywords uchisq [INPUT] if set, use the chi-square statistic as the measure of goodness of fit * this is the default uabsdev [INPUT] if set, use abs(DATA-MODEL) as statistic umaxdev [INPUT] if set, use min(abs(DATA-MODEL)) as statistic ureldev [INPUT] if set, use total(abs(DATA-MODEL)/ERR) as statistic * priority: UCHISQ > UABSDEV > UMAXDEV > URELDEV statval [OUTPUT] "best-fit" value of the statistic dstep [INPUT] value of the first step * default is 10% of initial value eps [INPUT] a small number * default is 1e-6 maxstep [INPUT] maximum number of iterations * default is 100 verbose [INPUT] controls chatter _extra [JUNK] here only to avoid crashing the program history vinay kashyap (Jun2001)
(See pro/fitting/renormod.pro)
function roi_selezioni simple tool to pick out a set of pixels defining a region of interest in a 2D image; returns selection as 1D index array syntax iroi=roi_selezioni(image,iseed,thresh=thresh,jitter=jitter,$ hadrian=hadrian,verbose=verbose) parameters image [INPUT; required] image from which to select region of interest iseed [INPUT] pixel indices to act as a seed selection * if given, will use these points as the selected pixels and work in batch processing mode, i.e., will NOT be interactive keywords thresh [INPUT] if given, then filters the input image such that IMAGE > THRESH * if not given, assumed to be 0 jitter [INPUT] sensitivity in distinguishing between click and drag * default is 1.5 pixels hadrian [INPUT] thus far and no further. if set, places a fixed boundary around the area selected with the cursor, i.e., connected regions are not followed out of this area. set this to pick out individual pixels, for instance. verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Aug06) added parameter ISEED and keywords THRESH, HADRIAN _EXTRA; allowed selection extending outside cursor selected areas; changed name from pickoutroi to roi_selezioni (VK; May07)
(See pro/util/roi_selezioni.pro)
function roofn returns the smallest number greater than a specified number that is a power of the specified base. output will be of same type as BASE. syntax nroof=roofn(num,base,floor=floor,pwr=pwr) parameters num [INPUT; required] number to "round up" base [INPUT; default=2] base keywords floor [INPUT] if set, returns the largest integer LESS THAN M that is a power of N. pwr [OUTPUT] the appropriate index [N^(PWR)] _extra [JUNK] here only to prevent crashing the program history vinay kashyap (April 1995) added keyword _EXTRA (VK; Mar99) cleaned up a bit (VK; Apr99) cleaned up some more (VK; Dec07) completely rewritten to be more flexible and faster (VK; Jan13)
(See pro/util/roofn.pro)
function rundens compute and return the running density of a set of measurements. syntax yrun=rundens(xpt,hwidth,/usex,/optwdt,outhwdt=outhwdt,$ yerr=yerr,xerr=xerr,nsim=nsim,ysim=ysim,yesim=yesim,xtol=xtol,$ wts=wts,dwts=dwts,lbound=lbound,rbound=rbound,cvmse=cvmse,$ verbose=verbose) parameters xpt [INPUT; required] array of points for which the running density must be calculated * a running density is calculated at each value of XPT hwidth [INPUT] the half-width on either side of a point to include in the density * this is assumed to be the number of array indices unless USEX is set * default is to use 5% of n_elements(XPT) or 5% of the range of XPT if USEX is set * if OPTWDT is set, computes the optimum width to use and treats this as just a default * actual value used is returned via keyword OUTHWDT keywords usex [INPUT] if set, assumes HWIDTH is in same units as XPT optwdt [INPUT] if set, figures out the optimum HWIDTH to use by comparing the width of the distribution of the running density estimates to the expected statistical stddev for a flat density * if this is set, HWIDTH will be overridden * the optimum HWIDTH is calculated based on the array indices -- i.e., USEX is ignored during the calculation, but if set, is used afterwards to scale the optimum HWIDTH to the units in XPT. So beware that it may not really be the optimum in this case. * if this module fails, the smallest width checked will be returned outhwdt [OUTPUT] will contain the value of HWIDTH actually used in the calculation yerr [OUTPUT] error bar on the density at each point * WARNING: adjacent values of YERR are not independent. while the error estimate at each point is fine, to get a truly independent estimate, one has to skip by 2*HWIDTH xerr [INPUT] error bars on XPT * used to compute a Monte Carlo uncertainty band on the output running density nsim [INPUT] number of simulations to carry out * default is none ysim [OUTPUT] a NSIMxN(XPT) array to contain the running density for each simulation yesim [OUTPUT] point-wise stddev based on YSIM xtol [INPUT] the tolerance for considering two points to be identical * essentially, if any two adjacent points are found to be identical, then all points are jittered by +-0.5*XTOL wts [INPUT] if given, computes the total of the WTS and returns that rather than the running density * MUST match the size of XPT, otherwise ignored dwts [INPUT] same as WTS, but the total is computed and placed in the denominator * MUST match the size of XPT, otherwise ignored * if both WTS and DWTS are given, the ratio of the totals is computed, not the average of the ratios lbound [OUTPUT] array indices of leftside bounds for all XPT rbound [OUTPUT] array indices of rightside bounds for all XPT cvmse [OUTPUT] cross-validation mean square error between estimate and leave-one-out estimate. the extra calculations are performed only if this keyword is present and are not done for the simulated data. verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines RUNDENS_OPTWDT (included here) CURVESECT EQT_INTERVAL history vinay kashyap (MMXI.VII) added keywords WTS and DWTS and corrected bug (VK; MMXI.VIII) added keywords LBOUND, RBOUND, and CVMSE (VK; MMXII.V) added keyword OPTWDT, added function RUNDENS_OPTWDT, and added calls to RUNDENS_OPTWDT(), CURVESECT(), and EQT_INTERVAL() (VK; MMXII.XII)
(See pro/util/rundens.pro)
NAME:
SCALE_VECTOR
PURPOSE:
This is a utility routine to scale the points of a vector
(or an array) into a given data range. The minimum value of
the vector (or array) is set equal to the minimum data range. And
the maximum value of the vector (or array) is set equal to the
maximum data range.
AUTHOR:
FANNING SOFTWARE CONSULTING
David Fanning, Ph.D.
1645 Sheely Drive
Fort Collins, CO 80526 USA
Phone: 970-221-0438
E-mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com
CATEGORY:
Utilities
CALLING SEQUENCE:
scaledVector = SCALE_VECTOR(vector, minRange, maxRange)
INPUT POSITIONAL PARAMETERS:
vector: The vector (or array) to be scaled.
minRange: The minimum value of the scaled vector. Set to 0 by default.
maxRange: The maximum value of the scaled vector. Set to 1 by default.
INPUT KEYWORD PARAMETERS:
DOUBLE: Set this keyword to perform scaling in double precision.
Otherwise, scaling is done in floating point precision.
MAXVALUE: Any value in the input vector greater than this value is
set to this value before scaling.
MINVALUE: Any value in the input vector less than this value is
set to this value before scaling.
NAN: Set this keyword to enable not-a-number checking. NANs
in vector will be ignored.
PRESERVE_TYPE: Set this keyword to preserve the input data type in the output.
RETURN VALUE:
scaledVector: The vector (or array) values scaled into the data range.
COMMON BLOCKS:
None.
EXAMPLE:
x = [3, 5, 0, 10]
xscaled = SCALE_VECTOR(x, -50, 50)
Print, xscaled
-20.0000 0.000000 -50.0000 50.0000
RESTRICTIONS:
Requires the following programs from the Coyote Library:
http://www.dfanning.com/programs/convert_to_type.pro
http://www.dfanning.com/programs/fpufix.pro
MODIFICATION HISTORY:
Written by: David W. Fanning, 12 Dec 1998.
Added MAXVALUE and MINVALUE keywords. 5 Dec 1999. DWF.
Added NAN keyword. 18 Sept 2000. DWF.
Removed check that made minRange less than maxRange to allow ranges to be
reversed on axes, etc. 28 Dec 2003. DWF.
Added PRESERVE_TYPE and DOUBLE keywords. 19 February 2006. DWF.
Added FPUFIX to cut down on floating underflow errors. 11 March 2006. DWF.
(See pro/external/scale_vector.pro)
procedure scrmf
Convolves input energy spectrum with the response matrix
SCRMF is a version of CONV_RMF optimized for speed.
It maximized speed at the expense of memory.
A faster version of CONV_RMF was necessary for
use with e.g., FITLINES() because the convolution procedure is
called literally tens of thousands of times.
On input, the RMF is required to be an RMF structure created
by RD_OGIP_RMF() from an OGIP-compliant FITS file AND
optimized with REGROUP_RMF().
NOTE: If the RMF is not optimized prior to
the SCRMF call, REGROUP_RMF() will be called
internally, and SCRMF will be slowed to a crawl.
syntax
scrmf,nrg,flx,chan,spec,rmf,effar=effar,nrgar=nrgar,$
rmfstr=rmfstr,fchcol=fchcol,/shift1
parameters
nrg [INPUT; required] mid-bin values at which input FLX is defined.
* preferably NRG is identical to RMF channel energy grid
* depends on the RMF, but is invariably [keV]
* if size = N(FLX)+1, assumed to be bin-boundaries
flx [INPUT; required] fluxes in [ph/bin/(s/sr/...)]
* note that this assumes that the effective areas are
already folded in. this assumption is made in order
to speed up the calculation some more
* the input should also be integrated over the bin width,
i.e., do not give [ph/keV/...] or [ph/Ang/...] as input
* also note, the units should not be [erg/...] -- be sure
to divide the input energy spectrum by the energy of
the photons corresponding to that bin before calling
the program
chan [OUTPUT; required] bin boundary values at which output SPEC
is defined.
* same energy range as NRG (so size will not necesarily match
EMN,EMX of RMF)
* same units as RMF.EMN, RMF.EMX
spec [OUTPUT; required] output, convolved spectrum
rmf [I/O; required] rmf response structure in RD_OGIP_RMF() format.
WARNING: Unlike CONV_RMF, this _cannot_ be the name of a file.
Also, the input will be overwritten if necessary.
NOTE: For most efficient use with FITLINES(), RMFs which
are defined with only one group per photon energy bin are
preferred. If RMF contains more than one group per
photon energy, the RMF will be optimized for FITLINES()
use with REGROUP_RMF().
keywords
verbose [INPUT] set verbosity level
effar [INPUT] (not implemented yet)
nrgar [INPUT] (not implemented yet)
rmfstr [OUTPUT] structure containing info of response matrix,
the output of RD_OGIP_RMF()
_extra [INPUT ONLY] pass defined keywords to subroutines
subroutines
REGROUP_RMF
these are all the smoothing tools in PINTofALE
ALALOESS() makes a loess curve
CLTSMOOTH() removes -ves from background subtracted spectra or light curves
CONV_RMF convolves with specified RMF
HAARTRAN() smoothes by filtering on Haar wavelet coefficients
LINEREM() removes lines from spectrum by iterative S/N filtering
NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth
REGROUP() accumulates from one end
SCRMF does fast convolution using optimized RMF
SMOOTHIE does peak-descent accumulation to build up S/N
SPLAC computes a segmented piecewise linear approximations
UNKINK() removes sharp kinks from a curve
VARSMOOTH() does local smoothing at specified scales
VOORSMOOTH() does fast local smoothing at specified scales
history
liwei lin (Aug 03)
BUGFIX crashed with no warning when input spectrum
not fully covered. Thanks Jan-Uwe. LL (Jun 06)
BUGFIX crashed with zero values for N_CHAN.
Thanks Jan-Uwe. LL (Jun 06)
BUGFIX crashed when FIRSTCHAN=1 for IBEG=0 (thanks Jan-Uwe; Vinay K; May 07)
(See pro/util/scrmf.pro)
function sdss2flux convert SDSS asinh magnitudes to fluxes in ergs/s/cm^2/Hz syntax fx=sdss2flux(mag,/gband,/rband,/iband,/zband,/uband,verbose=verbose) parameters mag [INPUT; required] SDSS (asinh) magnitude * could be scalar or array keywords uband [INPUT] input is u mags gband [INPUT] input is g mags rband [INPUT] input is r mags iband [INPUT] input is i mags zband [INPUT] input is z mags * default is GBAND * if multiple keywords are set, GBAND > RBAND > IBAND > ZBAND > UBAND verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program description see SDSS photometric calibration documents http://www.sdss3.org/dr10/algorithms/fluxcal.php http://www.sdss3.org/dr10/algorithms/magnitudes.php#asinh http://classic.sdss.org/dr6/algorithms/fluxcal.html example print, 'solar luminosity in g band = ',sdss2flux(4.7,/gband)*4.*!dpi*(3.1d18*10.)^2 history vinay kashyap (2014sep16)
(See pro/util/sdss2flux.pro)
function setabund widget-based editor to set abundances syntax abund=setabund(init=init,norm=norm,/help) parameters NONE keywords init [INPUT] initial set of abundances -- default is Anders & Gervasse (1989) help [INPUT] as it says norm [INPUT] same as in GETABUND, to decide whether the abundances are in normal or log format. * abs(NORM) > 1 ==> log _extra [INPUT] junk -- here only to prevent program from crashing restrictions widget-based subroutines GETABUND GETEMALL, SETEMALL (appended) history vinay kashyap (Dec96) bug correction (MULT not being set) (VK; Jan96)
(See pro/util/setabund.pro)
function setcont
interactively determine a continuum
syntax
cont=setcont(x,y,ysig,ycont=ycont,xcont=xcont,/const,$
xrange=xrange,yrange=yrange,ccol=ccol,/lock)
parameters
x [INPUT; required] abscissa values
* must be an array with at least 2 elements
y [INPUT; required] Y(X)
* length must match X
ysig [OUTPUT] errors on returned continuum (see description below)
keywords
ycont [I/O] if set on input, begins work from here
* overwritten by new values on output
xcont [I/O] if N(YCONT) .NE. N(X), then look here for the
actual abscissae values.. YCONT=YCONT(XCONT)
* if N(XCONT) .NE. N(YCONT), both are ignored
const [I/O] if set, returns piecewise >constant< continum,
as opposed to piecewise >linear< curve
* can be toggled by clicking outside the plot area
xrange [INPUT] xrange of plot -- passed with no comment to PLOT
yrange [INPUT] yrange of plot -- passed with no comment to PLOT
ccol [INPUT] color of continuum line
* default is 150*!D.N_COLORS/256
lock [INPUT] if set, locks up the relative positions of YCONT
* has an effect ONLY if YCONT is set
* side-effects:
-- does not increase number of N({XY}CONT)
-- left or middle click moves the entire curve up and down
_extra [JUNK] here only to prevent crashing the program
error calculation
since the continuum is being set interactively, there is no meaningful
way to define a statistical error on it.
restrictions
works in X. only?
history
vinay kashyap (Oct98)
increased default plotting YRANGE (VK; Nov98)
added keyword LOCK (VK; Dec98)
cursor changes shape when mouse button is pressed (VK; FebMM)
allowed return of zero errors, cleaned up error handling, added CCOL
cleaned up LOCK (VK; MarMM)
undid the cursor shape changes (VK; AprMM)
bug: wasn't holding the poisson v/s zero error toggle (VK; JulMM)
improved color-scale setting for 24-bit consoles (VK; FebMMI)
changed default to produce errors=0 rather than Poisson errors
(VK; Aug03)
(See pro/setcont.pro)
procedure setkolor loads specified colors into color table in specified indices (this used to be called "setcolor" but the name was changed to avoid a clash with JHUAPL's procedure of the same name) syntax setkolor,colors,icols,ocols,rgbfil=rgbfil,oldr=oldr,oldg=oldg,oldb=oldb parameters colors [INPUT; required] string array containing the names of the colors to be loaded icols [INPUT] integer array specifying into which index each color goes to * if size does not match COLORS, ignored * default is to go from 0:255 ocols [OUTPUT] byte array of size [3,N(COLORS)] containing the hexadecimal values determined for each COLORS, as an rgb triplet keywords rgbfil [INPUT] name of file containing (r,g,b) color values and corresponding names in same format as:- * the default, /usr/lib/X11/rgb.txt * note: some new linux systems don't seem to have this file. those users can copy over this file from another system, or use the copy provided in !ARDB+'/rgb.txt' oldr [OUTPUT] the old R colors oldg [OUTPUT] the old G colors oldb [OUTPUT] the old B colors * NOTE: to undo the setting, just do TVLCT,OLDR,OLDG,OLDB _ref_extra [JUNK] here only to prevent crashing the program example plot,findgen(10)/10.,color=1 & setkolor,'green',1 oplot,sin(findgen(10.)),color=2 & setkolor,'#ff0000',2 restrictions * requires subroutine NARY2DEC * RGBFIL bit works only on UNIX * messes with the current color table * feature, not a bug: if !D.N_COLORS < 256, and a SETKOLOR command is issued before a plot window is opened, a color table is loaded in which gets lopped off at !D.N_COLORS, and all subsequent plots appear dim. history vinay kashyap (99Jul) bug correction for ICOLS=!D.N_COLORS STRMID must have 3 args for back-compatibility (VK FebMMI/A.Maggio) changed name from SETCOLOR to SETKOLOR (VK FebMMI) added optional output OCOLS and check for UNIX (VK; Jun02) added checks to find rgb.txt in !ARDB if, as in some linux distributions, /usr/lib/X11/rgb.txt doesn't exist (VK; Mar07) bug correction: local copy was trying to override RGBFIL (JJD; May08) added switch to choose file_search() instead of findfile() for IDL 7+ (JJD/VK; Apr14)
(See pro/util/setkolor.pro)
procedure setsysval sets a system variable (the kind preceded by a "!") to the specified value syntax setsysval,sysv,val,/getval,verbose=v,/Read_Only parameters sysv [INPUT; required] a string scalar containing the name of the system variable, written out without the obligatory "!" (e.g., 'PATH') * if !SYSV does not exist, creates it using defsysv inside an execute() val [I/O] if defined on input, will set the value of !SYSV to this value, if !SYSV allows overwriting; if not defined, or is illegal (e.g., wrong type of input) then on output contains the value. * if GETVAL is set, then regardless of all above considerations VAL contains the value of !SYSV on _output_ keywords getval [INPUT] if set, returns the existing value of !SYSV in VAL verbose [INPUT; default=0] controls chatter Read_Only [INPUT] if set, defines new !SYSV as read only _extra [JUNK] here only to prevent crashing the program subroutines LEGALVAR history vinay kashyap (OctMM)
(See pro/util/setsysval.pro)
procedure show_line plot lines and label them syntax show_line,wvl,flux,Z=Z,ion=ion,lambda=lambda,spec=spec,order=order,$ wmark=wmark,fmark=fmark,lmark=lmark,cmark=cmark,xo=xo,yo=yo,oxr=oxr,$ oyr=oyr,sep=sep,/squish,dynrng=dynrng,markp=markp,markc=markc,$ marks=marks,marko=marko,/quiet,xtitle=xtitle,ytitle=ytitle,$ title=title parameters wvl [INPUT; required] wavelengths of lines flux [INPUT; optional] fluxes of lines keywords Z [INPUT] atomic number of element producing WVL ion [INPUT] ionic state of element producing WVL * Z and ION do not have to match the size of WVL: as many are used as available or necessary spec [INPUT] spectrum over which to plot the lines lambda [INPUT] as in SPEC(LAMBDA) * SPEC and LAMBDA should match in size, or else they are both ignored order [INPUT] string of comma-separated integers denoting grating orders to include in plot * default is to use just the first order * anything meaningless (including "0") defaults to first order wmark [INPUT] additional locations to mark (the output of SMUDGE, for example) fmark [INPUT] fluxes at which to mark WMARKs lmark [INPUT] labels for WMARKs * FMARK and LMARK are ignored unless they match WMARK cmark [INPUT] colors for LMARKs markc [INPUT] colors for WVLs * default is 222 xo [OUTPUT] output from PICKRANGE yo [OUTPUT] output from PICKRANGE oxr [OUTPUT] output from PICKRANGE oyr [OUTPUT] output from PICKRANGE _extra [INPUT] pass defined keywords to subroutines:- STR_2_ARR: SEP,SQUISH PICKRANGE: DYNRNG,MARKP,MARKS,MARKO,QUIET,XTITLE,YTITLE,TITLE subroutines STR_2_ARR INICON PICKRANGE history vinay kashyap (Nov98) added keywords WMARK, FMARK, LMARK (VK; Dec98) changed call to INITSTUFF to INICON (VK; 99May) added keywords MARKC and CMARK (VK; JanMMI) bug fix: if FLUX not set, 1st 2 were being marked at [0,1] (VK; Feb01) changed call to STR_2_ARR from STR2ARR (VK; AprMMV)
(See pro/show_line.pro)
Project : SOHO - CDS
Name :
SINCE_VERSION
Purpose :
Determine if current release is later than specified.
Explanation :
Determine if the current release of IDL (as given in the
!VERSION.RELEASE system variable) comes after the user specified
release.
Use :
test = SINCE_VERSION( release )
Use the /FTOXDR keyword to the BYTEORDER procedure if the current
release of IDL is 2.2.2 or later
IDL> if since_version('2.2.2') then byteorder, a, /FTOXDR
Inputs :
release - scalar string, must be formatted exactly like the
!VERSION.RELEASE system variable (e.g. '3.0.0')
Opt. Inputs :
None.
Outputs :
test - 1 if current release is identical or later than the specified
'release' else 0
Opt. Outputs: None.
Keywords : None.
Calls : None.
Common : None.
Restrictions: None.
Side effects: None.
Category : Utilities, Miscellaneous
Prev. Hist. :
Written Wayne Landsman Hughes/STX January, 1992
Corrected algorithm W. Landsman April, 1992
Written : Wayne Landsman, Hughes/STX, January 1992
Modified : Version 1, William Thompson, GSFC, 14 December 1994
Incorporated into CDS library
Version : Version 1, 14 December 1994
(See pro/external/since_version.pro)
procedure skypos process input RA and Dec and produce the appropriate output syntax skypos,ra,dec,out1,out2,/i24,/osxg,/hrs,/idnum,idpre=idpre,$ idform=idform,/PM,chop=chop,osep=osep,verbose=verbose parameters ra [INPUT; required] Right Ascension * may be a real or string array * if real, assumed to be decimal degrees unless the keyword I24 is set * if string, will check whether decimal or sexagesimal -- sexagesimal if ':' or ' ' exist, decimal otherwise dec [INPUT; required] Declination * size _must_ match RA * may be real or string array * if string, will check whether decimal or sexagesimal -- sexagesimal if ':' or ' ' or ' ' exist, decimal otherwise NOTE: all calculations are performed in double precision out1 [OUTPUT; required] output, depends on keyword (see below) out2 [OUTPUT; optional] output, depends on keyword (see below) * by default, OUT1 = RA [decimal deg] and OUT2 = Dec [decimal deg] * if keyword IDNUM is set, then OUT1 = IAU style ID number = OUT2 -- in addition, keyword IDFORM overrides keywords OSXG and HRS (see below) * if keyword OSXG is set, then OUT1 = RA [h:m:s] and OUT2 = Dec [d:m:s] * if keyword HRS is set, then OUT1 = RA [decimal hours] and OUT2 = Dec [decimal deg] keywords i24 [INPUT] set this to indicate whether the input RA is in decimal hours, not degrees osxg [INPUT] if set, output RA and Dec will be in sexagesimal units, not decimal hrs [INPUT] if set, output RA will be in hours (in sexagesimal if OSXG is set, in decimal otherwise) * if neither OSXG nor HRS is set, then RA will be in decimal degrees idnum [INPUT] if set, an IAU style name is constructed and returned as a string in OUT1 idpre [INPUT] a uniform prefix to prepend to IDNUM * default is "J" idform [INPUT] a string denoting the format for how IDNUM is written out * default is 'HMS.sXDMS' * ignored if IDNUM is not set * format rules: -- always has RA first and Dec next -- X denotes the sign of the declination (optional) -- RA is specified either as "R.r" [deg] or "HMS.s" [sexagesimal] -- Dec is specified either as "D.d" [deg] or "DMS.s" [sexagesimal] -- repetions of small letters after the period denote the number of digits, e.g., "R.rrr" is written as f7.3 -- repetitions of capital letters before the period has no effect unless they are greater than the minimum required, e.g., "R.r" == f5.1 == "RR.r" == "RRR.r", but "RRRR.r" == f6.1 PM [INPUT] if set, replaces "+/-" with "P/M" in the sign of Dec chop [INPUT] chops off the specified number of digits off the right hand end of the IDFORMatted output osep [INPUT] set the separator between fields in a sexagesimal output (see keyword OSXG) to OSEP rather than ":" verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines DEG2HRS STR_2_ARR SYZE history vinay kashyap (Jul03) bug correction when output was R.rrr, and added keyword PM (VK; Dec03) added keyword OSEP (VK; May04) updated RA and Dec outputs to ss.ssss by default and changed all internal calcs to double precision (VK; Aug15)
(See pro/util/skypos.pro)
procedure smoothie
return the input function smoothed such that a minimum required S/N
is met at each point in the function. useful for smoothing out the
weak wings and continuua in line dominated spectra. starts from
the peak of the lines and steps down the profile, accumulating the
bins as necessary.
note that unlike most adaptive smoothing algorithms, this one
conserves flux.
syntax
smoothie,y,outy,outye,ix,yerr=yerr,snrthr=snrthr,verbose=v
parameters
y [INPUT; required] array to be smoothed
outy [OUTPUT] smoothed array
outye [OUTPUT] errors on smoothed array
* WARNING: these do not include correlation errors,
and so do not represent a rigorous estimate. i.e.,
even though correctly propagated for each bin, they
cannot be used as independent errors on the values in
adjacent bins.
ix [OUTPUT] bin indices -- tells which bins are grouped
* all bins which have the same value of IX are in the same group
keywords
yerr [INPUT] error on Y
* default is 1.+sqrt(Y+0.75)
* the default is set that way for consistency with
standard PINTofALE behavior, but SQRT(Y) is a better
option for this algorithm.
snrthr [INPUT] S/N threshold below which to smooth bins
* default is 3.0
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing
example
y=50*(mk_gauss(findgen(256),128,10,1)+0.01) & yr=long(0*y)
for i=0,256-1 do yr[i]=randomu(seed,poisson=y[i])
smoothie,yr,outy,outye,ix,yerr=1+sqrt(0.75+yr),snrthr=4.0
plot,y & oplot,yr,psym=10,col=2 & oplot,outy,col=3
** notice the wings **
y=randomu(seed,1000,poisson=1)
y[400:499]=randomu(seed,100,poisson=5)
smoothie,y,outy,outye,snrthr=5
plot,y & oplot,outy,col=2,thick=3
these are all the smoothing tools in PINTofALE
ALALOESS() makes a loess curve
CLTSMOOTH() removes -ves from background subtracted spectra or light curves
CONV_RMF convolves with specified RMF
HAARTRAN() smoothes by filtering on Haar wavelet coefficients
LINEREM() removes lines from spectrum by iterative S/N filtering
NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth
REGROUP() accumulates from one end
SCRMF does fast convolution using optimized RMF
SMOOTHIE does peak-descent accumulation to build up S/N
SPLAC computes a segmented piecewise linear approximations
UNKINK() removes sharp kinks from a curve
VARSMOOTH() does local smoothing at specified scales
VOORSMOOTH() does fast local smoothing at specified scales
history
VK/LL (Nov 04)
cleaned up I/O (VK; Jan05)
now returns a flat average if total(y)/sqrt(total(ysig^2))<SNRTHR
(VK; Oct06)
bugfix: unnecessarily crashing because of a variable name mismatch
when too few counts to meet SNR threshold (VK; Oct09)
(See pro/util/smoothie.pro)
procedure smudge returns labels for features at given locations the input file is expected to be in the following format:- LOCATION <sep> UNIT <sep> LABEL <sep> KEYWORDS where <sep> is a separator, usually a <tab> LOCATION is a number, usually the wavelength in [Ang] UNIT specifies the units for LOCATION, e.g., "Ang", "keV", etc. LABEL is a string label describing the feature at LOCATION KEYWORDS are a set of keywords that facilitate pinpoint extraction, usually the instrument name, the origin of the feature, etc. Note that: LOCATION is required, and everything else is optional Lines prefixed by "%", "#", ";", "/" are ignored the following UNITs are understood: Ang, eV, keV, MeV, Hz, MHz, GHz, wave-#, /cm, cm^-1, cm**-1, mu, micron, mm, cm, meter, km syntax smudge,x,label,keys=keys,only=only,nisi=nisi,range=range,$ infile=infile,sep=sep,prefix=prefix,/okeV,/help parameters loc [OUTPUT] float array of location of features label [OUTPUT] string array of labels for features keywords keys [INPUT] string array of keywords. if given, all features answering to these keywords are returned only [INPUT] string array of keywords. while KEYS does a logical OR, ONLY does a logical AND on the keywords nisi [INPUT] return all >except< those features matching the specified keywords * KEYS is checked first, ONLY next, NISI last, and the precedence is therefore in reverse order range [INPUT] if set, returns only those LABEL(LOC)s that lie within RANGE * if 1-element vector or scalar, looks for exact match * WARNING: range check is carried out >after< conversion to keV if OKEV (see below) is set, so RANGE must then be given in units of [keV] (otherwise it should be in [Ang]) infile [INPUT] ascii file in which the features are listed * default: $SCARDIR/ardb/smudge.lst sep [INPUT] separator used to delineate fields in INFILE * default is <tab> prefix [INPUT] any line beginning with this is considered a comment * default: "*" * this is in addition to "%", "#", ";", "/" * beware: "<sp>" or "<tab>" won't work! okeV [INPUT] if set, LOC are returned in units of keV * default is to return LOC in units of Ang * KEV is accepted as a synonym for historical reasons help [INPUT] if set, prints out usage and quits ikeV [INPUT; DEFUNCT] a synonym for OKEV, still kept (temporarily) only for backward compatibility _extra [JUNK] here only to prevent crashing the program example usage smudge,/help smudge,wvl,lbl & xr=[min(wvl),max(wvl)] & plot,[0],xr=xr,/xlog xyouts,wvl,randomu(seed,n_elements(wvl)),lbl,orient=90 smudge,keys=['edge','gap'],only=['M'] smudge,keys='gap',only=['S0','S1'],/okeV smudge,keys='edge gap',range=[1,6] smudge,keys='edge gap',nisi='edge',range=[1,6] smudge,range=0.69,/okev history vinay kashyap (Nov98) added warning in case of bad SEP (VK; Dec98) changed "caldb" to "ardb" (VK; DecMM) added keyword IKEV in preparation to getting rid of KEV (VK; JanMMI) changed keyword IKEV to OKEV (VK; Jul02)
(See pro/smudge.pro)
function solar_tresp
Computes and returns temperature response for a selection of
bandpasses from a variety of solar X-Ray and EUV diagnostic
instruments. The explicitly supported instruments and bandpasses and their
corresponding ouput units (at the sun) are as follows:
TRACE 171,195,284 in [DN s-1 cm-2] per [cm-5 ln(K)-1]
EIT 171,195,284 in [DN s-1 cm-2] per [cm-5 ln(K)-1]
SXT Al1, AlMg in [DN s-1 cm-2] per [cm-5 ln(K)-1]
RHESSI GD, in [Counts s-1] per [cm-5 ln(K)-1]
CDS all GIS and NIS lines in [ergs s-1 cm-2] per [cm-5 ln(K)-1]
The user may also specify an arbitrary instrument bandpass combination
(one other than the explicitly supported ones listed above) with the
limitation that the WRANGE keyword must be set. The units in this case
would be [Counts s-1] per [cm-5 ln(K)-1] if and effective area is included and
[ph s-1 cm+2] per [cm-5 ln(K)-1] if it is not.
A choice of atomic databases, abundances, and ion equilibria
may be set via keywords LDBDIR,ABUND,and EQFILE respectively.
the temperature response calculations are made like this:
syntax
resp=solar_tresp(instrument,filter,date,tgrid=tgrid,ldbdir=ldbdir,$
abund=abund,eqfile=eqfile)
parameters
instrument [INPUT;required] name of the relevant instrument
* can be 'TRACE','EIT','SXT','CDS','RHESSI'
* may also be set to a string descrption of
arbitrary instruments e.g. 'RESIK'. keyword
wrange must be set.
bandpass [INPUT;required] select the relevant bandpass
* can be '171','195','284' for 'TRACE' and 'EIT'
* can be 'Open','Al1','AlMg','Be119','AL12','MG3' for 'SXT'
* can be 'GD' for 'RHESSI'
* for 'CDS' must be a string specifiying an ionic
state (element abbreviation and roman
numeral) and a transition wavelength.
e.g.
'Mg VII 319.03'
'Ne VI 401.14'
'Fe IX 171.07'
CDS lines are treated as very narrow
bandpasses, so that possible contributions
from weak lines are accounted for.
The transition wavelength must fall into one of
the wavelength regions covered by GIS or NIS.
If the transition wavelength is designated WVL
and the detector resolution as RES, then the
bandpass wavelength range is determined
to be [WVL-3*RES,WVL+3*RES]. RES is
hardcoded as 0.18 Ang for NIS1, 0.32A for NIS12
and 0.21 for GIS. This range may be overridden by
using keyword WRANGE.
* can be set to and arbitrary string descrption
of bandpass if instrument is set to something other
than the explicitley supported instruments. e.g.
'1.123 - 1.293 AA' for instrument 'RESIK'
keyword WRANGE must be set.
keywords
filter [INPUT] Filter wheel selection for the EIT and
TRACE passbands
* default is 'clr' for EIT can also be 'al1', 'al2'
* default is 'AO' for TRACE can also be 'OO',
'OA' or 'AA'
* ignored if instrument selection is SXT or CDS
date [INPUT] time in any Yohkoh format or a Yohkoh
index structure.
* see e.g. ANYTIME2INTS() SolarSoft function for
standard Yohkoh formats
* SXT temperature responses time variable due to an enterance
filter failiure (Oct 1992). The value of this keyword will
be passed to GET_YO_DATES to determine appropriate correction.
* if unset no correction is made.
wrange [INPUT] a two elements floating point vector which
denotes a wavelength range. overrides the internally
determined bandpass range.
tgrid [INPUT] Log(T) grid on which the ouput response
is to be defined.
* default is PoA system variable !LOGT
* if !LOGT does not exist then tgrid=4.0+findgen(41)*0.1
lstr [I/O] line emissivity structure
cstr [I/O] continuum emissivity structure
ldbdir [INPUT] line emissivity database directory
* default is '$CHIANTI' can also be '$SPEX', '$APED'
or an explicit directory specification
e.g. '/data/foo/bar/spex/' or '../foo/bar/aped' etc.
cdbdir [INPUT] continuum emissivity database directory
* default is '$CONT'
abref [INPUT] string reference to the set of abundances to use
* default is 'feldman' which will call GETABUND() to
retrieve Feldman et al. (1992) abundances
* see GETABUND() documentation for other options.
eqfile [INPUT] string reference to the ion equilibria file to use
* default is 'ioneq/mazzotta_etal.ioneq'
* see local CHIANTI database for other options
perpix [INPUT] if set, responses are returned as
[DN s-1 pixel-1] per [cm-5 ln(K)-1].
* ignored for SOHO/CDS
det [INPUT] if set then responses are computed at detector
and not at the SUN
rhessi_rmf [INPUT] RHESSI spectrometer OGIP-compliant rmf(srm) fits file from which
and effective area will be extracted via rd_ogip_rmf()
rspstr [OUTPUT] output structure containing all
ouputs and inputs as well as general info
concerning what went into response calculation.
* The structure is defined with these tags:
INSTR STRING instrument parameter
BANDPASS STRING bandpass parameter
FILTER STRING filter keyword
RESP DOUBLE computed response
TGRID FLOAT response Log(T) grid
EFFAR DOUBLE effective area
WVLAR DOUBLE effective area wavelength grid
LDBDIR STRING ldbdir keyword;
ABREF STRING abref keyword
EQFILE STRING eqfile keyword
ABUND FLOAT abund keyword
nocont [INPUT] if set, continuum will not be included in response
zresp [INPUT] if set,
_extra [INPUT] use to transmit defined keywords to called functions
restrictions
* This function uses various SolarSoft routines
and PINTofALE routines. It also employs files
from Solar Soft databases. Note also that SolarSoft
installations can vary in what missions/instruments
are supported.
* employs PINTofALE subroutines
LICOSPEC
LINEFLX
GETABUND
RD_LINE
* employs SolarSoft subroutines
SSW_INSTRUMENTS
CONCAT_DIR
RESTGEN
GET_YO_DATES
TRACE_EUV_RESP
EIT_PARMS
* If the DATE keyword is set, user cannot set the verbose keyword
due to a conflict in GET_YO_DATES
history
liwei lin (Aug 2004)
BUGFIX (Jan 2005) had assumed that licospec output emissivities were in
ergs cm-2 s-1. now /noph is fed through _extra to lineflx()
BUGFIX (LL Sep 2005) Thanks to Harry Warren who points out that upon reading the SXT
effective area file, the FILTER entry already includes ENTRANCE, CCD,
and MIRROR effective areas.
BUGFIX (LL Sep 2005) the reported units, both in documentation and
output structures were incorrect. Missing were terms 1d44 and cm^-5
EDIT (LL Sep 2005) so that there is no hard reliance on PoA system
variables. RHESSI default bandpass no longer 'G4'; user is asked
if RHESSI SRM file not fed via RHESSI_RMF keyword.
ADDED (LL Sep 2005) ZRESP keyword
BUGFIX (LL Oct 2005) wvlar returned wmid rather than wvlar
EDIT (LL Oct 2006) corrected reported UNITS
(See pro/ssw/solar_tresp.pro)
function sphtrig_translb
transform the given {theta,phi} coordinates on a sphere that
has been tilted and twisted (in that order) to {theta',phi'}
on an untwisted and untilted pov reference frame, and
returns them in a structure.
syntax
tpstr=sphtrig_translb(theta,phi,tilt=tilt,twist=twist,$
eps=eps,verbose=vv)
parameters
theta [INPUT; required] angular coordinate from Z-axis [deg]
phi [INPUT; required] azimuthal coordinate around Z-axis [deg]
* THETA,PHI may be vectors or scalars
* if vectors, assumed to be paired sets, with
values filled in with 0's if one falls short
keywords
tilt [INPUT; default=0] inclination angle of sphere
relative to pov coordinate frame [deg]
twist [INPUT; default=0] rotation angle by which the
vector going through the pole is rotated around
the Z-axis of the pov reference frame [deg]
* note that TWIST is given in the negative sense --
the angle by which the frame must be rotated to
return to 0. the program takes the -ve of the
supplied TWIST.
eps [INPUT; default=1e-6] a small number
* There are some singularities when THETA and PHI are zero.
This is added on to make sure at least something
close to the limiting value is returned in that case
verbose [INPUT] controls chatter
_extra [JUNK] here only to prevent crashing the program
example
.run sphtrig_translb
makes lines of constant latitude, constant longitude, and
draws the figure used to derive the transformation used here.
(the ultimate in self-documenting!)
subroutines
example run requires PEASECOLR
history
vinay kashyap (2013feb)
added keyword EPS (2013mar)
corrected sign error that was making PHI go clockwise instead of
counter-clockwise (2015sep)
(See pro/util/sphtrig_translb.pro)
procedure splac compute Segmented Piecewise Linear Approximation to Curve. generates piecewise linear approximations with fewest line segments within given tolerances. about the name have you heard the one about the Stanford Linear Accelerator (SLAC) and what would happen after the Big One hits? Obviously, it would have to be renamed SPLAC, the Stanford Piecewise Linear Accelerator.. syntax splac,x,y,ytol,u,v,w,/noband,/discon,verbose=verbose parameters x [INPUT; required] points at which data are defined * must be in ascending order y [INPUT; required] values of data array, Y(X) * must match size of X ytol [INPUT; required] tolerance of approximation: allowed >deviation< from the true curve * if scalar, single absolute-value tolerance for entire curve. * if vector, tolerance at each X -- size must match X * if -ve, ABS(YTOL) is taken to be the fractional factor relative to the true value. u [OUTPUT] a partition of the interval [X(0),X(N[X]-1)] with U(0)=X(0) and U(N[U]-1)=X(N[X]-1) v [OUTPUT] ordinates, V(U) * the approximating segment is (u[i],v[i]) -> (u[i+1],v[i+1]) w [OUTPUT] ordinates if the approximation may be discontinuous * the approximating segment is (u[i],w[i]) -> (u[i+1],v[i+1]) keywords noband [INPUT] indicates whether the approximation is to be restricted to the 'tolerance band' about the data (the 'tolerance band' is a piecewise linear band centered at the data whose width is determined by the tolerances at the data points.) * if set, indicates no band restriction * if not set, or set to 0, indicates apply this restriction discon [INPUT] indicates whether or not the approximation must be continuous * if set, indicates continuity not required * if not set, or set to 0, indicates continuity is required verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program examples x=findgen(100) & y=sqrt(x) splac,x,y,0.1,u,v,w,/noband,verbose=10 splac,x,y,0.3,u,v,w,/discon,verbose=10 splac,x,y,-0.1,u,v,w & plot,x,y & oplot,u,v,psym=-1,col=100 subroutines NONE restrictions Will not work with IDL versions < 5 these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history From D.G. Wilson, 1976, ACM Transactions on Mathematical Software,2,388 http://www.netlib.org/toms/510 converted to IDL by Vinay Kashyap, who is very unhappy about all those GOTOs, but doesn't have the patience to rewrite from scratch (FebMM) bug correction for when YTOL was -ve; made into IDL5 (VK; JunMM) bug correction in plotting with /DISCON (VK; AprMMVII)
(See pro/util/splac.pro)
function squishem
returns a new ID structure from the old one with all the
multiple IDs (if any) squished into a single ID pointing
to the one with the highest peak emissivity. If the IDs
include different elements, their emissivities are combined
in the ratio of their abundances.
a few more words about this combining:
o the >fluxes< are combined without regard to abundance, i.e.,
are added up directly. this is because the fluxes are assumed
to already include all info about DEMs, abundances, ion balance,
and so on. besides, UPDATID splits a measured flux value simply
on the basis of the ion-balanced emissivities.
o the >emissivities< are combined by normalizing the weaker IDs to
that of the strongest ID in the ratio of the abundances. because
the main ID itself only retains the strongest ID, the absolute
abundance on the emissivity is not set, but relative abundances
are fixed.
syntax
sqID=squishem(idstr,abund=abund)
parameters
idstr [INPUT; required] an ID structure, e.g., output of LINEID
keywords
abund [INPUT] abundances relative to H (abund(0)=1)
* abund(Z-1) contains the abundance for element Z
* if array size is smaller than the largest present Z,
the last element is replicated to fill the gap
* default: Anders & Grevesse (1989)
mproxy [OUTPUT] if set, will output 2 dimensional MPROXY string
as prescribed by MIXIE()
_extra [JUNK] here only to avoid crashing the program
subroutines
GETABUND
ZION2SYMB
INICON
history
vinay kashyap (FebMM)
bug correction with flux err (VK; MarMM)
unknown IDs were crashing at abundances; added call to ZION2SYMB
(VK; MMJul)
ADDED MPROXY keyword (Feb2004)
(See pro/squishem.pro)
procedure stample
brand existing plot. The standard format is to put
DATE (YYYY MON DD) TIME (HH:MM:SS) USER (name@host) PACKAGE
at the lower-left of a plot.
stample is a portmanteau (see Jabberwocky) of stamp and staple.
syntax
stample,package,/nuthin,/noday,/notime,/nouser,/nopack,$
stacol=stacol,stasiz=stasiz,stathk=stathk,/help
parameters
package [INPUT] name of package
* default is 'PINTofALE <version>'
keywords
nuthin [INPUT] if set, the same as setting all of
NODAY,NOTIME,NOUSER,NOPACK
noday [INPUT] if set, does not include the day
notime [INPUT] if set, does not include the time
nouser [INPUT] if set, does not include the user name
nopack [INPUT] if set, does not include the package name
stacol [INPUT] index of color in color-table to use
* default is !D.N_COLORS-10 or 1, whichever is greater
stasiz [INPUT] character size, defaults to 1.
stathk [INPUT] character thickness, defaults to 1.
help [INPUT] if set, prints usage and quits
_extra [JUNK] here only to avoid crashing the program
common
cb_stample {vname, vhost, vPoA}
restrictions
requires subroutine SETSYSVAL
history
vinay kashyap (DecMM)
added common block STAMPLE (VK; JanMMI)
added call to SETSYSVAL (VK; FebMMI)
back-compatibility fix for SYSTIME (VK FebMMI/A.Maggio)
bug corrected -- repeat use of "m" in call to CALDAT
(VK Oct01/A.Maggio)
changed name of common block from STAMPLE to CB_STAMPLE
(VK Oct02)
(See pro/util/stample.pro)
function *flux
returns total flux in the passband of interest at the specified
temperatures OR for the given DEM
syntax
flx=starflux(lstr,cstr,tlog=tlog,DEM=DEM,abund=abund,wrange=wrange,$
NH=NH,effar=effar,wvlar=wvlar,dist=dist,radius=radius,/noph,$
lflux=flux,cflux=cflux,fH2=fH2,He1=He1,HeII=HeII,/Fano)
a word on the units
the line emissivities are in [ergs cm^3/s], and the continuum
emissivities are also converted to this. the [ergs] are converted
to [ph] before output unless specified otherwise.
thus, output will have units:
[(ergs|ph) cm^3/s][EM][RADIUS^2][DIST^-2][AREA]
e.g., if EM is [cm^-3] at source, and DIST is given, then output
is [ph/cm^2/s], the flux at the telescope, which is fine.
on the other hand, if DEM is [cm^-5] (n^e*V/(4*pi*D^2) at the
telescope) and DIST are given, we'd get [ph/cm^4/s] which would
be meaningless. instead, RADIUS may be given to get [ph/s].
*******************************************************************
IT IS UP TO THE USER TO MAKE SURE THAT THE OUTPUT UNITS MAKE SENSE!
*******************************************************************
parameters
lstr [INPUT; required] structure containing line emissivity data
(see RD_LINE or RD_LIST)
* BEWARE: ion balance is assumed to be included!
cstr [INPUT; required] structure containing continuum emissivities
(see RD_CONT)
keywords
tlog [INPUT] EITHER [A] the temperatures at which to compute the
output fluxes XOR [B] the temperatures at which the DEM is
defined
* if n(DEM) < 2, then [A]
* if n(DEM) > 1 .AND. n(DEM) = n(TLOG), then [B]
DEM [INPUT] EITHER [A] volume emission measure [cm^-3 or cm^-5]
XOR [B] differential emission measure [cm^-3/logK or cm^-5/logK]
* if [B] then n(DEM) .MUST=. {n(TLOG) or n(LSTR.LOGT)}
* default is 1e14
abund [INPUT] abundances
* default: Grevesse et al. (1992)
wrange [INPUT] passband in which to compute flux
* if not given, assumes larger of range(LSTR.WVL,CSTR.WVL)
NH [INPUT] ISM column density [cm^-2]
effar [INPUT] effective area [cm^2]
wvlar [INPUT] wavelengths at which effective area is defined [Ang]
* n(EFFAR) .MUST=. n(WVLAR)
* if not given, or illegal, output will be [ph/s/cm^2]
dist [INPUT] distance to star, in [pc]
* BUT, if > 1e6, taken to be in [cm]
* if given, divides computed flux by 4*pi*DIST^2 before output
* BEWARE: no cosmological corrections are made!
radius [INPUT] radius of star, in [cm]
* BUT, if < 1e6, taken to be in [RSol]
* if given, multiplies flux by 4*pi*RADIUS^2 before output
* BEWARE: no scale-height/volume effects included!
noph [INPUT] if set, does not convert [ergs] to [ph]
lflux [OUTPUT] flux due to lines only
cflux [OUTPUT] flux due to continuum only
* LFLUX and CFLUX will >NOT< have DIST and RADIUS included!!
_extra [INPUT] pass defined keywords to
ISMTAU [fH2,He1,HeII,Fano]
ikeV [JUNK] does nothing. only to avoid passing it on to ISMTAU
restrictions
requires subroutines ISMTAU, GETABUND, MK_DEM
does not call LINEFLX or GRATFLX, so perhaps a wee bit faster,
but on the other hand, cannot handle grating effective areas either.
history
vinay kashyap (1999May)
changed KEV to IKEV (VK; DecMM)
(See pro/starflux.pro)
function str2arr converts a series of numbers written out as a string into an array. the output is an array of numbers of specified type syntax arr=str2arr(str,delim,sep=sep,/i1,/i4,/r4,/r8,/squish,$ array=array,delimit=delimit,/nomult) parameters str [INPUT; required] input string * if itself an array, is concatenated into one huge string delim [INPUT] same as SEP, put here for consistency with SSWIDL version of program with same name. * if given, is used instead of SEP * if given, the output is returned as a string array ignoring I1,I4,R4,R8 * if not given and DELIMIT is not set, and I1,I4,R4,R8 are also not set, the output is an integer array keywords sep [INPUT] separator between entries in the string * if not given as a string, first checks "," and if that doesn't seem to make any difference, then checks "<sp>" * if explicitly set, checks only for SEP * if array, uses only the first element i1 [INPUT] if set, output is a BYTARR, default is I2 i4 [INPUT] if set, output is a LONARR r4 [INPUT] if set, output is a FLTARR r8 [INPUT] if set, output is a DBLARR * precedence is R8 over R4 over I4 over I1 over I2 squish [INPUT] if set, "squishes" adjoining SEPs, e.g., "1 2" is converted to "1 2" array [OUTPUT] string array version of the output delimit [INPUT] delimiter, same as DELIM, and ignored if either DELIM or SEP are present * but if set, the output is a string array, and I1,I4,R4,R8 are ignored nomult [INPUT] same as SQUISH, just for compatibility with SSWIDL version _extra [JUNK] here only to prevent crashing the program subroutines SYZE a word yes, I know about READS. it's limitations are that you still have to define the input array first, cannot use other values for the separator (e.g., ":"), and can't handle missing data (e.g., "1,2,") history vinay kashyap (Nov98) added parameter DELIM and keywords ARRAY, DELIMIT, and NOMULT for the sake of consistency with SSWIDL version; also added call to SYZE() (VK; Jun02)
(See pro/util/str2arr.pro)
function str_2_arr converts a series of numbers written out as a string into an array. the output is an array of numbers of specified type syntax arr=str_2_arr(str,delim,sep=sep,/i1,/i4,/r4,/r8,/squish,$ array=array,delimit=delimit,/nomult) parameters str [INPUT; required] input string * if itself an array, is concatenated into one huge string delim [INPUT] same as SEP, put here for consistency with SSWIDL version of program with same name. * if given, is used instead of SEP * if given, the output is returned as a string array ignoring I1,I4,R4,R8 * if not given and DELIMIT is not set, and I1,I4,R4,R8 are also not set, the output is an integer array keywords sep [INPUT] separator between entries in the string * if not given as a string, first checks "," and if that doesn't seem to make any difference, then checks "<sp>" * if explicitly set, checks only for SEP * if array, uses only the first element i1 [INPUT] if set, output is a BYTARR, default is I2 i4 [INPUT] if set, output is a LONARR r4 [INPUT] if set, output is a FLTARR r8 [INPUT] if set, output is a DBLARR * precedence is R8 over R4 over I4 over I1 over I2 squish [INPUT] if set, "squishes" adjoining SEPs, e.g., "1 2" is converted to "1 2" array [OUTPUT] string array version of the output delimit [INPUT] delimiter, same as DELIM, and ignored if either DELIM or SEP are present * but if set, the output is a string array, and I1,I4,R4,R8 are ignored nomult [INPUT] same as SQUISH, just for compatibility with SSWIDL version _extra [JUNK] here only to prevent crashing the program subroutines SYZE a word yes, I know about READS. its limitations are that you still have to define the input array first, cannot use other values for the separator (e.g., ":"), and can't handle missing data (e.g., "1,2,") history vinay kashyap (Nov98) added parameter DELIM and keywords ARRAY, DELIMIT, and NOMULT for the sake of consistency with SSWIDL version; also added call to SYZE() (VK; Jun02) changed name from STR2ARR to STR_2_ARR to avoid conflict with SSW routine because of compilation issues with SSW (VK; Apr05)
(See pro/util/str_2_arr.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
SUTHERLAND_CH
PURPOSE:
Calculate the free-free continuum from an hot, low density plasma
Uses the free-free gaunt factor calculations of Sutherland, 1998,
MNRAS, 300, 321.
Note that Sutherland's Eq.(15) has units of erg/cm^3/s. Comparing
with Rybicki & Lightman's Eq.5.14(a) (in their book 'Radiative
Processes in Astrophysics'), suggests that Sutherland's units
should be erg/cm^3/s/sr/Hz. We are assuming the latter to be
correct in this routine.
When using the DEM_INT optional input, FREEFREE expects the
differential emission measure to have been derived from a product
of N_e*N_H rather than N_e*N_e. This can be important when dealing
with a regime (typically T < 10^4.5) where H and He are not fully
ionised.
To calculate the continuum spectrum the user should specify
whether the plasma structure is specified through a differential
emission measure (DEM) curve or through emission measure (EM)
values. For the former, the DEM values are specified through the
DEM_INT keyword and for the latter the EM values are specified
through the EM_INT keyword. If neither are specified EM_INT
values of unity are assumed.
If DEM_INT values are specifed they must be specified on a
temperature scale that has constant intervals in log10(T). EM_INT
values do not have this restriction.
Note that EM_INT must be used for isothermal plasmas.
CALLING SEQUENCE:
SUTHERLAND_CH,temperature, wavelength, intensity
INPUTS:
T Temperature in degrees Kelvin, can be a 1 D
array. If the keyword /DT is set, then the
temperatures must be specified with a fixed spacing
in logT. E.g., TEMP=10.^[4.0,4.1,4.2].
WVL Wavelength in Angstroms. If /keV is set, then WVL is
assumed to contain energies in keV units.
OPTIONAL INPUTS:
None
KEYWORD PARAMETERS:
NO_SETUP: If the procedure setup_elements has already been called
then the keyword /no_setup should be set to avoid
repeating this step.
MIN_ABUND: If set, calculates the continuum only from those
elements which have an abundance greater than min_abund.
This can speed up the calculations. ;
DEM_INT This should be the same size as TEMP and contain
differential emission measure values. Specifying
DEM_INT places a restriction on TEMP (see above). Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not.
EM_INT This should be the same size as TEMP and contain
emission measure values. Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not. If
neither EM_INT or DEM_INT are specified, then a EM_INT
vector of same size as TEMP with values of unity is
assumed.
PHOTONS The output spectrum is given in photon units rather
than ergs.
SUMT The default is to output the intensity array as an array
of size (nwvl x nT). Setting this keyword performs a sum
over the temperatures to yield a vector of same size as
the input wavelengths, thus producing the complete
free-free spectrum.
KEV If set, then WVL is assumed to contain energies in keV
units rather than wavelengths in Angstroms.
OUTPUTS:
RAD Free-free continuum intensity in units
10^-40 erg cm^3 s^-1 str^-1 angstrom^-1 per unit
emission measure [ integral (N_e N_H dh) in cm^-5 ].
If T is given as a 1-D array, then RAD will be output
as a 2-D array, with one element for each temperature
and wavelength (but also see SUMT).
If the keyword /keV is set, then the units of INT will be
10^-40 erg cm^3/s/sr/keV
PROGRAMMING NOTES
The gaunt factors from Sutherland (MNRAS 300, 321, 1998) are a
function of uu and gg (see his Eq. 14). uu is a function of both
wavelength and T, while gg is a function of T only.
The gaunt factor (gff) is tabulated for values of uu and gg at
fixed intervals in log(uu) and log(gg). The log(uu) values go from
-4 to 4 in 0.2 steps; the log(gg) values go from -4 to 4 in 0.1 steps.
A particular (input) temperature and wavelength give rise to values
uu0 and gg0, the logs of which lie between -4 and 4. To derive the
corresponding gff0 value, I use the IDL routine BILINEAR.
BILINEAR requires, not uu and gg values as input, but indices.
E.g., the indices corresponding to the tabulated values of uu are
0 (=-4.0), 1 (=-3.8), 2 (=-3.6), etc. Thus, if log(uu0)=-3.76, then
i_uu0=1.20 is the index of uu0.
In order to make significant time-savings, I give BILINEAR all of
the wavelengths and temperatures in the same call for a particular
ion. To do this, I make my i_uu and i_gg values 2-D arrays of size
(nwvl x nT), and BILINEAR then produces a (nwvl x nT) array
containing the gff values.
A problem occurred if nT=1, as BILINEAR will turn the input uu and
gg vectors into 2-D arrays of size (nwvl x nwvl). If there are a
large number of wavelengths, this uses a lot of memory. To solve
this I make a 2 element temperature vector whose values are
identical, and then change this back to a 1 element vector after
BILINEAR has been called. See the parts of the code where I use
'tst1'.
COMMON BLOCKS:
common elements,abund,abund_ref,ioneq,ioneq_t,ioneq_ref
CALLS
READ_IP, READ_GFFGU, SETUP_ELEMENTS
EXAMPLES:
IDL> freefree,1.e+6,wvl,int
IDL> freefree,1.e+6,wvl,int,min_abund=3.e-5
IDL> freefree,1.e+6,wvl,int,/no_setup,min_abund=1.e-6
IDL> wvl=findgen(5001)/10. + 50.
IDL> temp=10.^(findgen(41)/10. +4.)
IDL> freefree,temp,wvl,int
MODIFICATION HISTORY:
Written by: Ken Dere
March 1999: Version 2.0
September 1999: Version 3.0
Ver.3.1, 11-Aug-00, Peter Young
Improved call to bilinear, allowing routine to solve for
all temperatures in one go. This makes the routine quicker,
and also lowers the memory usage of the routine when dealing
with many wavelengths.
Ver.3.2, 16-Aug-00, Peter Young
Corrected expression for 'gg', replacing ip with z^2.
Ver.3.3, 16-Oct-00, Peter Young
Now deals with dem_int correctly
Ver.3.4, 10-Oct-01, Ken Dere
Corrected for labelling errors in Sutherland's gffgu.dat file
No longer reads ionization potential file
Ver.3.5, 5-Dec-01, Peter Young
Corrected expression for gamma^2
Renamed routine sutherland.pro
Restructured code to make it run quicker.
Ver.3.6, 22-May-01, Peter Young
Re-instated the MIN_ABUND optional input.
Changed ioneq_t to ioneq_logt (GDZ).
Ver.3.7, 18-Aug-03, Peter Young
Activated /PHOTONS keyword
Ver.3.8, 5-Nov-03, Peter Young
Corrected bug found by Jim McTiernan when multiple temperatures
were input. The quantity 'newfactor' was not being calculated
correctly due to indexing problems.
Ver. 4, 9-Mar-2006, Peter Young
Added /keV keyword.
Ver.5, 10-Sep-2009, Peter Young
Routine now checks that temperatures are evenly spaced
when DEM_INT is specified. Also 0.1 dex spacing is no
longer assumed.
Ver.6, 6-Oct-2009, Peter Young
Introduced EM_INT keyword for specifying emission measure
values for isothermal plasmas.
Ver.Poa, 10-Aug-2010, Vinay Kashyap
a la 18-Nov-2005, LiWei Lin
Commented out common block
Added keywords,abund, ioneq, ieq_logt, _extra
Changed ioneq_logt to ieq_logt
Renamed routine sutherland_ch
(See pro/external/sutherland_ch.pro)
procedure symb2zion convert spectroscopic symbol to atomic number and ionic state syntax symb2zion,symbol,z,ion parameters symbol [INPUT; required] string containing element designation (e.g., "he_2", "He II", "HeII", "he 2", "he", "He", whatever) z [OUTPUT] atomic number ion [OUTPUT] ionic state (0=undefined, 1=neutral, 2=singly ionized, etc.) keywords verbose [INPUT] higher the number, greater the chatter _extra [JUNK] here only to prevent crashing the program restrictions * cannot handle the "+/-" type notation (e.g., O^+5) * currently coded only up to Es requires INICON LAT2ARAB history written by vinay kashyap (Nov96), based on CHIANTI's convertname.pro modified screen dump to also show input (VK; Dec97) added call to INITSTUFF, include elements up to Es (VK; Aug98) corrected bug that was returning garbage for single-letter elements (VK; Oct98) was returning 0 for ions for, e.g., "O VII"; corrected (VK; May99) changed call to INITSTUFF to INICON (VK; 99May) added keyword VERBOSE (VK; MarMM) added various trans-Uranium symbols (VK; AugMM) now allow tab separation (VK; Mar03)
(See pro/util/symb2zion.pro)
function syze returns a vector that contains the size and type information a la IDL information routine SIZE. The diffrence is that this one operates on strings only output is always of longward type. the first element contains the number of elements in C, the next elements contain the string-length of each element, one element per element of C, the last but one element contains the type code: 0 : undefined, 1 : I*1 2 : I*2 3 : I*4 4 : R*4 5 : R*8 -1 : expression -2 : equation 7 : everything else the last element contains the total number of characters in C syntax sc=syze(c,oc=oc) parameters c [INPUT] string expression to decode keywords oc [OUTPUT] converted output, where applicable _extra [JUNK] here only to prevent crashing the program history vinay kashyap (Dec98) now catches sexagesimal (VK; Aug03)
(See pro/util/syze.pro)
Project : SOHO - CDS
Name : TAG_EXIST()
Purpose : To test whether a tag name exists in a structure.
Explanation : Routine obtains a list of tagnames and tests whether the
requested one exists or not. The search is recursive so
if any tag names in the structure are themselves structures
the search drops down to that level. (However, see the keyword
TOP_LEVEL).
Use : IDL> status = tag_exist(str, tag)
Inputs : str - structure variable to search
tag - tag name to search for
Opt. Inputs : None
Outputs : Function returns 1 if tag name exists or 0 if it does not.
Opt. Outputs: None
Keywords : INDEX = Index of matching tag
TOP_LEVEL = If set, then only the top level of the structure is
searched.
RECURSE = set to recurse on nested structures
Category : Util, structure
Written : C D Pike, RAL, 18-May-94
Modified : Version 1.1, D Zarro, ARC/GSFC, 27-Jan-95
Passed out index of matching tag
Version 2, William Thompson, GSFC, 6 March 1996
Added keyword TOP_LEVEL
Version 2.1, Zarro, GSFC, 1 August 1996
Added call to help
Version 3, Zarro, EIT/GSFC, 3 June 2000
added check for input array structure
Version 4, Zarro, EIT/GSFC, 23 Aug 2000
removed calls to DATATYPE
Version 5, Zarro, EIT/GSFC, 29 Sept 2000
added /quiet
Version 6, Zarro (EER/GSC), 22 Dec 2002
made recursion NOT the default
(See pro/external/tag_exist.pro)
function chitex
Converts spectroscopic terms and configurations to LaTeX
form, e.g.:
'1s.2p 3P2.0' to '$1s2p \; ^3P_{2}$'
'1s.2p 3P2.5' to '$1s2p \; ^3P_{5/2}$'
'(2s2.2p5) 2P_3' to '$(2s^22p^5) \; ^2P_{3}$'
'(2s2.2p5) 2P_3/2' to '$(2s^22p^5) \; ^2P_{3/2}$'
syntax
outstring = tekhi(instring)
parameters
instring [INPUT; required] single string that describes the
electron configurations and/or level designations to be
converted to LaTex form.
keywords
nodollar [INPUT] if set then output will not be wrapped with '$'s
_extra [JUNK] here only to prevent crashing the program
subroutines
STREGEX
STRJOIN
STRMID
history
LiWei Lin/Jeremy Drake (Nov04)
added keyword _EXTRA and cleaned up usage (VK; Jul05)
(See pro/util/tekhi.pro)
procedure tekku
write out a LaTeX file summary of the ID structure
syntax
tekku,id_str,fx,fxerr,texfil=texfil,fxunit=fxunit,/trance,/asku,$
fxfmt=fxfmt,fxefmt=fxefmt,/kamentu
parameters
id_str [INPUT; required] ID structure from LINEID
fx [INPUT] measured fluxes
* if size does not match number of ID components of the
number of IDs, the internally stored values are used
* if FX is set to 0, then the output will not contain
any information about fluxes.
fxerr [INPUT] errors on FX
* if size does not match FX, first element is assumed
to represent a constant >fractional< error on FX
* default is 0.01
* if FXERR is explicitly set to 0, then the output will
not report the errors.
keywords
texfil [INPUT] name of file to dump the table to
* the ".tex" extension is not needed
* if not given, dumps output to screen
* if ASKU is set, the default extension is ".txt"
fxunit [INPUT] string representing the units that the fluxes
are in, e.g., "ph s$^{-1}$"
trance [INPUT] if set, adds a column to hold transition data
(e-configuration and level designation)
trantex [INPUT] if set, e-configuration and level designation
are converted to LaTex format so that appropriate
super-scripting and sub-scripting is included. This is set
by default.
* explicitly set to zero to turn this off.
asku [INPUT] if set, writes out a plain text ascii file w/o all
the TeX commands
fxfmt [INPUT] FORTRAN-style formatting syntax for writing out
fluxes, e.g., "f10.4", "e14.4", etc.
* default is "f7.2"
fxefmt [INPUT] as FXFMT, for flux errors
* default is FXFMT
kamentu [INPUT] set this keyword to include the scracth pad notes
in the table output. if not set, the comments won't be
included.
lineu [INPUT] if set, the input structure is assumed to be a
line emissivity structure of the sort generated by RD_LINE()
* in this case, the lambda_obs column is not printed out,
and the lambda_pred column is simply labeled as lambda
_extra [JUNK] here only to prevent crashing the program
history
vinay kashyap (Dec98)
added support for scribbles (VK; Mar99)
changed call to INITSTUFF to INICON (VK; 99May)
allowed output minus flux+-fluxerr column; also transition info
column (VK; 99Nov)
added keyword ASKU (VK; MarMM)
added keywords FXFMT and FXEFMT (VK; JunMM)
corrected: what if FXFMT/FXEFMT not set (VK NovMM; viz. A.Maggio)
added keyword KAMENTU; changed transitions font to "\small";
now reads in flux and fluxerr from ID_STR; Erica asks that
wvls, and flux+error alignments be set to "r" (VK; Apr02)
now puts "..." instead of spaces for duplicates (VK; Oct03)
added support for TEKHI() via keyword TRANTEX (LL;Nov04)
added keyword LINEU, call to DUMMYID(), changed \nl to \\ (VK; Feb06)
changed \documentstyle[apjpt4]{article} to \documentclass[10pt]{article}
(VK; Mar07)
etymology
the name comes from kannadization of the "process of TeXing";
Kannada, mind you, is a language of southern India, and has
absolutely nothing to do with Quebec and surrounding regions.
(See pro/util/tekku.pro)
script tieup1 given an ID structure (IDSTR) -- sets the line width of the first component to LSFWDT, -- ties all the other widths to the first one, -- freezes all but the first width parameter, -- ties all line locations to that of the first one, but with a leeway defined by LINERR, and -- if variable POSITIVF is set, then constrains all fluxes to be +ve outputs are TIES a string array containing all the ties THAW integer array signifying frozen(0) and thawed(1) parameters POS a float array containing the initial positions WDT a float array containing the initial widths HGT a float array containing the initial heights then, if SPECT(LAMBDA) is well defined, goes ahead and calls FITLINES and makes a new copy of IDSTR -- IDSTR2 -- with the new fluxes. the fit parameters are in FPAR a structure containing everything of interest POS,WDT,FLX best-fit values [PWF]ERR[UL] upper and lower deviations on best-fit values [PWF]ERRC delta-chisq threshold for which deviations are computed vinay kashyap (MarMM) added EPITHET to call (VK; MMaug) now LINERR can be 0 (VK; MVIMaug)
(See pro/scrypt/tieup1.pro)
script tieup2 differs from TIEUP1 in that the line widths are not all identical to the first one, but are allowed some wiggle room. given an ID structure (IDSTR) -- sets the line width of the first component to LSFWDT, -- ties all other line widths to be WDT[0] +- WDTERR -- ties all line locations to that of the first one, but with a leeway defined by LINERR -- if variable POSITIVF is set, then constrains all fluxes to be +ve outputs are TIES a string array containing all the ties THAW integer array signifying frozen(0) and thawed(1) parameters POS a float array containing the initial positions WDT a float array containing the initial widths HGT a float array containing the initial heights then, if SPECT(LAMBDA) is well defined, goes ahead and calls FITLINES and makes a new copy of IDSTR -- IDSTR2 -- with the new fluxes. the fit parameters are in FPAR a structure containing everything of interest POS,WDT,FLX best-fit values [PWF]ERR[UL] upper and lower deviations on best-fit values [PWF]ERRC delta-chisq threshold for which deviations are computed vinay kashyap (MarMM) added EPITHET to call (VK; MMaug)
(See pro/scrypt/tieup2.pro)
function timevarks computes the probability that the given set of photon arrival times are obtainable as a random instance from a constant source. smaller values imply higher significances of variability. syntax vsigni=timevarks(times,dobs,pobs,tstart=tstart,tstop=tstop,$ nsim=nsim,verbose=verbose) parameters times [INPUT; required] photon arrival times * WARNING: this routine does not handle dead-time intervals, primbsching, or even GTIs dobs [OUTPUT] the deviation found in the cdfs between data and the flat lightcurve model pobs [OUTPUT] significance of DOBS, as calculated for the one-sample Kolmogorov-Smirnoff test keywords tstart [INPUT] beginning times of each segment of the good time intervals tstop [INPUT] ending times of each segment of the GTIs * array sizes of TSTART and TSTOP must match, or else they will be ignored * if in any case TSTOP < TSTART, they will be flipped nsim [INPUT; default=1000] number of simulations to run to determine the significance verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines FLAT_LC_CDF (included) KSONE (from IDLAstro) PROB_KS (from IDLAstro) TI_CLEAN (in $PINTofALE/pro/timing/ti_clean.pro) restrictions keyword values are passed on to FLAT_LC_CDF via KSONE, so make sure that KSONE allows that (post Apr 2005) description first does an one-sample K-S test on the data, compared to a flat lightcurve model, to determine the deviation and its significance. the observed deviation is then calibrated with one-sample K-S tests using randomly generated events from a flat lightcurve (also compared to a flat lightcurve model) and comparing the distribution of the deviations thus found with the observed deviation. history vinay kashyap (MMVI.VIII) added keywords TSTART and TSTOP (VK; MMVI.IX) bug: GTI filtering broken, tzero offsets incorrect, and FLAT_LC_CDF was changing TMIN,TMAX (VK; MMVII.IV)
(See pro/timing/timevarks.pro)
function timevarvk computes the probability that the given set of photon arrival times are obtainable as a random instance from a constant source. smaller values imply higher significances of variability. uses a form of Kolmogorov-Smirnoff test, as in TIMEVARKS(), but differs in an important feature: the deviations between the data cdf and the model cdf are _averaged_ over a predefined number of consecutive photons. the reasoning behind this is that the K-S statistic is a point estimate, whereas a real variability feature always shows some width, i.e., the intensities in the adjacent bins in a lightcurve are correlated. the averaging of the distance differences will suppress the random Poisson deviations but not the actual signal. syntax vsigni=timevarvk(times,dobs,pobs,tstart=tstart,tstop=tstop,$ nsim=nsim,evtavg=evtavg,verbose=verbose) parameters times [INPUT; required] photon arrival times * WARNING: this routine does not handle dead-time intervals, primbsching dobs [OUTPUT] the deviation found in the cdfs between data and the flat lightcurve model pobs [OUTPUT] significance of DOBS, as calculated for the one-sample Kolmogorov-Smirnoff test keywords tstart [INPUT] beginning times of each segment of the good time intervals tstop [INPUT] ending times of each segment of the GTIs * array sizes of TSTART and TSTOP must match, or else they will be ignored * if in any case TSTOP < TSTART, they will be flipped nsim [INPUT; default=1000] number of simulations to run to determine the significance evtavg [INPUT] the number of events on either side of the current event over which the distance deviations must be averaged over; i.e., a boxcar smoothing scale of 2*EVTAVG+1 is used * if not given, assumed to be 1 * set explicitly to 0 to avoid doing the averaging; this should produce results identical to that of TIMEVARKS() verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines FLAT_LC_CDF (included) PROB_KS (from IDLAstro) TI_CLEAN (in $PINTofALE/pro/timing/ti_clean.pro) description first does an one-sample K-S test on the data, compared to a flat lightcurve model, to determine the deviation and its significance. the observed deviation is then calibrated with one-sample K-S tests using randomly generated events from a flat lightcurve (also compared to a flat lightcurve model) and comparing the distribution of the deviations thus found with the observed deviation. history vinay kashyap (MMVI.X; modified from TIMEVARKS()) bug: GTI filtering broken, tzero offsets incorrect, and FLAT_LC_CDF was changing TMIN,TMAX (VK; MMVII.IV)
(See pro/timing/timevarvk.pro)
procedure ti_and returns the intersection of two sets of time intervals as defined by the start and stop times syntax ti_and,tstr1,tstp1,tstr2,tstp2,tstart,tstop parameters tstr1 [INPUT; required] start times for first set tstp1 [INPUT; required] stop times for first set tstr2 [INPUT; required] start times for second set tstp2 [INPUT; required] stop times for second set tstart [OUTPUT] start times of resultanat intervals tstop [OUTPUT] stop times of resultanat intervals keywords _extra [JUNK] here only to prevent crashing the program restrictions inputs are assumed to be sorted in ascending order related TI_CLEAN - cleans up intervals TI_OR - merges intervals TI_WRITE - writes intervals to file TI_COVER() - computes coverage in given bin TI_FILTER() - filter an array by GTI history vinay kashyap (May98) added keyword _EXTRA (VK; Nov98)
(See pro/timing/ti_and.pro)
procedure ti_clean given an arbitrary set of starting and stopping times of intervals, first organizes them in ascending order and then merges the various intervals that are contiguous. syntax ti_clean,tstart,tstop,leap=leap parameters tstart [I/O; required] starting times of intervals tstop [I/O; required] ending times of intervals keywords leap [INPUT; default=1.] if the difference between a stopping time and the *next* starting time of sequential intervals is < LEAP, merge the two intervals into one. _extra [JUNK] here only to prevent crashing the program related TI_OR - merges intervals TI_AND - intersection of intervals TI_WRITE - writes intervals to file TI_COVER() - computes coverage in given bin TI_FILTER() - filter an array by GTI history vinay kashyap (May98) added keyword _EXTRA (VK; Nov98) now also handles overlapping bad times (VK; Mar99)
(See pro/timing/ti_clean.pro)
function ti_cover compute and return the good time coverage fraction for each bin of a time grid, such as those used to generate lightcurves syntax tcover=ti_cover(tstart,tstop,tgrid,tmin=tmin,tmax=tmax,tbin=tbin,$ verbose=verbose,/slowok) parameters tstart [INPUT; required] array of start times of GTI's tstop [INPUT; required] array of stop times of GTI's tgrid [I/O] the bin boundaries of the grid for which the coverage must be calculated * if undefined, or has less then 2 elements, will be calculated internally using the keywords TMIN, TMAX, and TBIN, and will be overwritten on output * if legal, TMIN, TMAX, and TBIN will be ignored and the values will not have been changed on output keywords tmin [INPUT; default=min(TSTART)] time binning grid minimum tmax [INPUT; default=max(TSTOP)] time binning grid maximum tbin [INPUT; default=TMAX-TMIN] the binsize of a regular grid for binning verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords to subroutines REBINW: SLOWOK (skip call to FINDEX and use INTERPOL instead) related TI_CLEAN - cleans up intervals TI_OR - merges intervals TI_AND - intersection of intervals TI_WRITE - writes intervals to file TI_FILTER() - filter an array by GTI subroutines REBINW FINDEX history vinay kashyap (MMVI.IX)
(See pro/timing/ti_cover.pro)
function ti_degti given the event times and GTI start and stop times, removes the gaps from the input and returns a set of points that run continuously. useful for when there are large gaps in the data or large numbers of breaks, and the source does not have any periodicities syntax tx=ti_degti(tarr,tstart,tstop,tdelt,igti=igti,startt=startt,stopt=stopt,$ verbose=verbose, leap=leap) parameters tarr [INPUT; required] input time array tstart [INPUT; required] array of GTI start times tstop [INPUT; required] array of GTI stop times * TSTART and TSTOP must match in size tdelt [OUTPUT] add this to the output to get back the input keywords igti [OUTPUT] index array that says which interval each element of TARR is in * NOTE: this does not necessarily match TSTART and TSTOP indices, because this program first cleans them up, and could shrink the number of distinct intervals. startt [OUTPUT] cleaned TSTART stopt [OUTPUT] cleaned TSTOP verbose [INPUT] controls chatter _extra [JUNK] pass defined keywords to subroutines TI_CLEAN: LEAP subroutines TI_CLEAN example .run ti_degti history Vinay Kashyap (2015sep)
(See pro/timing/ti_degti.pro)
function ti_filter returns an array of locations where the input list of times fall within a given time interval defined by the start and stop times syntax it=ti_filter(time,tstart,tstop) parameters time [INPUT; required] arrival times of photons, or bin-values tstart [INPUT; required] start times of intervals tstop [INPUT; required] stop times of intervals keywords count [OUTPUT] number of elements in output array _extra [JUNK] here only to prevent crashing the program related TI_CLEAN - cleans up intervals TI_OR - merges intervals TI_AND - intersection of intervals TI_WRITE - writes intervals to file TI_COVER() - computes coverage in given bin history vinay kashyap (May98) added keyword _EXTRA (VK; Nov98)
(See pro/timing/ti_filter.pro)
procedure ti_or returns the union of two sets of time intervals as defined by the start and stop times syntax ti_or,tstr1,tstp1,tstr2,tstp2,tstart,tstop parameters tstr1 [INPUT; required] start times for first set tstp1 [INPUT; required] stop times for first set tstr2 [INPUT; required] start times for second set tstp2 [INPUT; required] stop times for second set tstart [OUTPUT] start times of resultanat intervals tstop [OUTPUT] stop times of resultanat intervals keywords _extra [JUNK] here only to prevent crashing the program restrictions inputs are assumed to be sorted in ascending order requires subroutine TI_CLEAN related TI_CLEAN - cleans up intervals TI_AND - intersection of intervals TI_WRITE - writes intervals to file TI_COVER() - computes coverage in given bin TI_FILTER() - filter an array by GTI history vinay kashyap (May98) added keyword _EXTRA (VK; Nov98)
(See pro/timing/ti_or.pro)
procedure ti_write writes out the start and stop times of a set of time intervals syntax ti_write,tstart,tstop,tifile,fitsref=fitsref,exten=exten,$ form=form,fitshdr=fitshdr,page=page parameters tstart [INPUT; required] start times tstop [INPUT; required] stop times tifile [INPUT] name of file to write to (default: STDOUT) * if name ends in .fit, .fits, .ft, or .mt then write out a FITS file with a bintable extension else an ascii file * if filename contains 'none' or 'stdout', will print to STDOUT keywords fitsref [INPUT] name of existing FITS file from which to steal the header exten [INPUT] extension of FITSREF from which steal header fitshdr [INPUT] explicitly specify the header. * if FITSHDR is set, FITSREF and EXTEN will be ignored! form [INPUT] format in case of ASCII/STDOUT output * default: '(d16.4,1x,d16.4)' * ignored for FITS output page [INPUT] number of lines to display on the screen at a time * default: 22 * ignored if not writing to STDOUT _extra [JUNK] here only to prevent crashing the program related TI_CLEAN - cleans up intervals TI_OR - merges intervals TI_AND - intersection of intervals TI_COVER() - computes coverage in given bin TI_FILTER() - filter an array by GTI history vinay kashyap (May98) added keyword _EXTRA (VK; Nov98) bug correction with setting TIFILE='STDOUT' (VK; Sep06) slightly more verbose prompt for PAGE (VK; Aug15)
(See pro/timing/ti_write.pro)
function translabel returns 2D array describing the levels involved in each transition array(0,*) are lower levels, and array(1,*) are upper levels if DR transitions, then a "(DR)" tag is appended to the lower level designations. usage trans=translabel(chianti,wmn=wmn,wmx=wmx,/tex,config=config) parameters chianti [INPUT; required] structure that contains all the relevant information gleaned from the CHIANTI database (type DBHELP=RD_CHIANTI() & HELP,DBHELP,/STRUCTURE for a description of what this structure contains) keywords wmn [INPUT; default=0 Ang] only include wavelengths > WMN wmx [INPUT; default=900 Ang] maximum wavelength to include tex [INPUT] if set, returns the levels formatted for TeX config [OUTPUT] returns the electron configurations of the lower and upper levels in 2D array * config(0,*) are for lower levels, and config(1,*) are for upper levels _extra [INPUT] junk -- ignore history vinay kashyap (Nov96; based on LATEX_WVL_DEM.PRO of CHIANTI) made loops go over long integers (VK; Jun10)
(See pro/mkemis/translabel.pro)
Project : SOHO - CDS
Name :
TRIM()
Purpose :
Converts numbers to strings, without trailing zeros.
Explanation :
Converts numbers into a string representation, and trims off leading
and/or trailing blanks. Differs from STRTRIM in that trailing zeros
after the period are also trimmed off, unless NUMBER is already a
string, or an explicit format is passed.
Use :
Result = TRIM( NUMBER [, FORMAT ] [, FLAG ] )
Inputs :
NUMBER = Variable or constant. May be of any ordinary including
string. However, structures are not allowed.
Opt. Inputs :
FORMAT - Format specification for STRING function. Must be a string
variable, start with the "(" character, end with the ")"
character, and be a valid FORTRAN format specification. If
NUMBER is complex, then FORMAT will be applied separately to
the real and imaginary parts.
FLAG - Flag passed to STRTRIM to control the type of trimming:
FLAG = 0 Trim trailing blanks.
FLAG = 1 Trim leading blanks.
FLAG = 2 Trim both leading and trailing blanks.
The default value is 2. If NUMBER is complex, then FORMAT
will be applied separately to the real and imaginary parts.
Outputs :
Function returns as a string variable representing the value NUMBER.
Opt. Outputs:
None.
Keywords :
None.
Calls :
None.
Common :
None.
Restrictions:
NUMBER must not be a structure.
FORMAT must be a valid format specification, and must not be passed
if NUMBER is of type string.
FLAG must not be of string type, or an array.
Side effects:
None.
Category :
Utilities, Strings.
Prev. Hist. :
William Thompson Applied Research Corporation
May, 1987 8201 Corporate Drive
Landover, MD 20785
William Thompson, Feb. 1992, added support for complex numbers, and
fixed Unix problem with lowercase "e".
Written :
William Thompson, GSFC, May 1987.
Modified :
Version 1, William Thompson, GSFC, 9 April 1993.
Incorporated into CDS library.
Version 2, Zarro (SAC/GSFC), 3-Jun-98
Added check for undefined input
Version 3, Zarro (SM&A/GSFC), 1-Dec-99
Returned invalid input as blank string
to avoid downstream problems.
Version 4, Zarro (SM&A/GSFC), 4-Jan-00
Added /QUIET
Version 5, Zarro (SM&A/GSFC), 20-Jan-00
Vectorized
Version 6, 24-Jan-2000, William Thompson, GSFC
Fixed bug introduced in version 5.
Version 7, 14-Mar-2000, Zarro (SM&A/GSFC)
Moved check for unsupported type ahead of recursion
Version 8, 22-Jul-2002, Zarro (LAC/GSFC)
Made loop variables LONG
Version 9, 08-Jan-2004, William Thompson, GSFC
Added support for double-precision complex, and unsigned data
types.
(See pro/external/trim.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
TWO_PHOTON_CH
PURPOSE:
Calculate the 2 photon continuum from a hot, low density plasma.
For the hydrogen isoelectronic sequence, A values
Parpia, F. A., and Johnson, W. R., 1982, Phys. Rev. A, 26, 1142.
and distribution function as a function of Z is taken from:
Goldman, S.P. and Drake, G.W.F., 1981, Phys Rev A, 24, 183
For the helium isoelectronic sequence, A values are from:
Drake, G.W.F., 1986, Phys. Rev. A, 34, 2871
and the distribution function as a function of Z is taken from:
Drake, G.W.F., Victor, G.A., Dalgarno, A., 1969, Phys.
Rev. A, 180, 25.
in this paper the distribution is only given up to Z=10 but
extrapolation to higher Z appears to be OK.
Note that, unlike the freefree and freebound routines, two_photon
requies the electron density to be specified. This is because there
is a call to pop_solver
To calculate the continuum spectrum the user should specify
whether the plasma structure is specified through a differential
emission measure (DEM) curve or through emission measure (EM)
values. For the former, the DEM values are specified through the
DEM_INT keyword and for the latter the EM values are specified
through the EM_INT keyword. If neither are specified EM_INT
values of unity are assumed.
If DEM_INT values are specifed they must be specified on a
temperature scale that has constant intervals in log10(T). EM_INT
values do not have this restriction.
Note that EM_INT must be used for isothermal plasmas.
CALLING SEQUENCE:
TWO_PHOTON_CH,temperature, density, wavelength, intensity
INPUTS:
TEMP Temperature (in K). If the keyword /DT is set, then the
temperatures must be specified with a fixed spacing in
logT. E.g., TEMP=10.^[4.0,4.1,4.2].
WAVELENGTH Wavelengths in Angstroms. If /keV is set, then WVL is
assumed to contain energies in keV units.
OPTIONAL INPUTS:
DENSITY Electron density in cm^-3, can also be a 1D array
of the same size as Temperature. If there are several
temperatures specified but only one density, then
density is assumed the same at all temperatures.
If not specified, then default densities of 10^10
electrons/cm^3 are assumed.
DEM_INT This should be the same size as TEMP and contain
differential emission measure values. Specifying
DEM_INT places a restriction on TEMP (see above). Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not.
EM_INT This should be the same size as TEMP and contain
emission measure values. Note
that DEM_INT values are multiplied by the factor dT
within the routine, whereas EM_INT values are not. If
neither EM_INT or DEM_INT are specified, then a EM_INT
vector of same size as TEMP with values of unity is
assumed.
KEYWORD PARAMETERS:
NO_SETUP: If the procedure setup_elements has already been called
then the keyword /no_setup should be set to avoid
repeating this step
MIN_ABUND: If set, calculates the continuum only from those
elements which have an abundance greater than min_abund.
Can speed up the
calculations. For example:
abundance (H) = 1.
abundance (He) = 0.085
abundance (C) = 3.3e-4
abundance (Si) = 3.3e-5
abundance (Fe) = 3.9e-5
SUMT If several temperatures have been specified, then /sumt
will sum the emissivities over the different
temperatures, giving an output INTENSITY that has the
same size as WAVELENGTH.
PHOTONS If set the continuum emissivity is output in photon
units rather than erg units.
VERBOSE If set, information is printed to screen as the routine runs.
KEV If set, then WVL is assumed to contain energies in keV units
rather than wavelengths in Angstroms.
OUTPUTS:
RAD 2 photon continuum intensity in units of
10^-40 erg cm^3/s/sr/Angstrom per unit emission measure
( integral(N_H N_e dh) in cm^-5) if a DEM is not defined.
If DEM values are defined, it is assumed that they are given
as N_H N_e dh/dT. The units are
10^-40 erg/cm^2/s/sr/Angstrom
If T is given as a 1-D array, then the output will be a 2-D
array, with one element for each temperature and wavelength
(but also see SUMT).
If the keyword /keV is set, then the units of INT will be
10^-40 erg cm^3/s/sr/keV
CALLS
POP_SOLVER, SETUP_ION, SETUP_ELEMENTS, READ_MASTERLIST,
CONVERTNAME
COMMON BLOCKS:
ELEMENTS, ELVLC, WGFA, UPSILON, PROTON
EXAMPLE:
> two_photon_ch,1.e+6,3.e+10,wvl,int
> two_photon_ch,1.e+6,3.e+10,wvl,int,min_abund=3.e-5
> two_photon_ch,1.e+6,3.e+10,wvl,int,/no_setup
PROGRAMMING NOTES
For He 2-photon decays, the distribution function is from Table II
of Drake et al. (1969), except that the values have been divided by
the A-value from Drake (1986).
MODIFICATION HISTORY:
Written by: Ken Dere
February 2001: Version 1.0
Ver.2, 19-Dec-2001, Peter Young
Now allows an array of temperatures.
Added /SUMT keyword.
Added DEM_INT= optional input.
Switched to using spl_init & spl_interp for the spline fits.
Corrected a small bug.
Ver.3, 20-Dec-2001, Peter Young
Corrected a bug related to density indices.
Ver.4, 23-Apr-2002, Peter Young
Added /photons keyword.
Ver.5, 28-May-2002, Peter Young
Corrected way in which DEM_INT is handled.
V. 6, 28-May-2002, Giulio Del Zanna (GDZ)
generalized directory concatenation to work for
Unix, Windows and VMS.
Corrected the description of the units and various
inaccuracies in the header.
V.7, 14-Aug-02, GDZ
Added keyword VERBOSE
V.8, 4-Oct-2003, GDZ
modified the input to POP_SOLVER, now it is dealt with an
input structure.
V.9, 8-Jun-2004, EL
modified the input to POP_SOLVER, now it includes ion/rec
V.10, 5-Jul-2005
corrected problems with the input structure for pop_solver
v.11 29-Jul-2005, GDZ
fixed bug, only define ioneq_ionrec when files are
there (it was failing with neutrals)
v.12, 31-Aug-2005, GDZ
missed one correct definition of ioneq_ionrec. Fixed it now.
v.13, 10-Mar-2006, Peter Young
added /keV keyword
v.14, 12-Jun-2009, Enrico Landi
Changed the definition of the temperature array for ion fractions
in the IONREC variable, now taken directly from the output of
READ_IONEQ.PRO
v.15, 11-Sep-2009, Peter Young
Routine now checks that temperatures are evenly spaced
when DEM_INT is specified. Also 0.1 dex spacing is no
longer assumed.
v.16, 6-Oct-2009, Peter Young
Introduced EM_INT keyword for specifying emission measure
values for isothermal plasmas.
VERSION : 16, 6-Oct-2009
V.PoA, 10-Aug-2010, Vinay Kashyap
a la 25-Feb-2004, LiWei Lin
Commented common block out and
Added _extra keyword
Added NeNh keyword to avoid calling proton dens
Exchanged popsol() for pop_solver for PoA convenience.
popsol() puts a_value in required 2D format while
for pop_solver this is done in a mother CHIANTI routine
e.g. ch_synthetic.
Renamed routine two_photon_ch
(See pro/external/two_photon_ch.pro)
function ulim_simplepoi compute the upper limit to the intensity of an undetected source, given the background intensity, for a specified false detection probability alpha and detection probability beta, in the Poisson regime. syntax ul=ulim_simplepoi(bkg,alpha,beta,alfa=alfa,Nthr=Nthr,verbose=v) parameters bkg [INPUT; required] background intensity over the source region alpha [INPUT] maximum false detection probability * if not given, assumed to be 0.0027 * if .GE.1, assumed to be given in units of equivalent Gaussian sigma * if .LT.0, assumed to be given as 1./abs(ALPHA) * the actual false detection probability for the selected counts threshold may be less than the specified value. beta [INPUT] probability of detecting the source of given intensity * note that some authors use the notation beta to denote the Type II error, the probability of a false negative, which is 1-beta in our notation. * if not given, assumed to 0.5 * if .LT.0 or .GE.1, assumed to be given as 1.D-1.D/abs(BETA) keywords alfa [OUTPUT] ALPHA, as noted above, is the maximum allowed false detection probability. Because of the discreteness of counts, the actual false det. probability that is used to figure out BETA will be different (though always less than ALPHA). This computed probability is returned in this array. Nthr [OUTPUT] the counts detection threshold chosen such that the false detection probability is < ALPHA verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines (all standard IDL) IGAMMA INTERPOL ERRORF description Kashyap, van Dyk, Connors, Freeman, Siemiginowska, Xu, Zezas, 2010, "On Computing Upper Limits to Source Intensities", ApJ, 719, 900 This encodes the simple Poisson case (footnotes 7 and 8) where the background intensity is known. First, ALPHA, the false detection probability, is used to determine a counts threshold for detection, and that source intensity where the source would be detected with probability BETA is returned as the upper limit. example usage bkg=2 & alpha=-1024.^2 & beta=0.5 .run ulim_simplepoi history Vinay Kashyap (Feb.MMX)
(See pro/stat/ulim_simplepoi.pro)
function unkink given a curve with kinks in it, returns a curve by sweeping line segments across that smooths out kinks syntax ys=unkink(y,n,xloc=xloc,/hires,nres=nres,/onestop,$ verbose=verbose) parameters y [INPUT; required] the ordinate values of the curve to smooth * cannot handle multi-valued functions. i.e., curve can be concave upward or downward, but not leftward or rightward n [INPUT; default=1] the number of points to cast on either side of a point to compute the smoothing line segment keywords xloc [INPUT] the abscissa values at which Y are defined * the default is to use lindgen(n_elements(Y))+1 * this is useful only if the grid is non-uniform * if specified, but size does not match that of Y, then it is ignored hires [INPUT] if set, resamples the grid into a finer resolution (with NRES additional points in each segment), linearly interpolates Y onto this finer grid, and operates on the high-resolution curve nres [INPUT] the number of additional points to include in each segment of Y(XLOC) * default is 1 onestop [INPUT] if set, the smoothed curve is returned as the value interpolated on to XLOC by a line segment that is symmetric around XLOC * if not set, an average of the interpolated Ys is computed from all the line segments that pass through the given XLOC verbose [INPUT] controls chatter _extra [JUNK] here only to prevent crashing the program subroutines none these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales example x=findgen(20) & y=abs(x-10) & plot,x,y,psym=-4 oplot,x,unkink(y,10,/hires,nres=5),thick=2 history vinay kashyap (sep08)
(See pro/util/unkink.pro)
function unlogit compute and return the inverse of the logit function. LOGIT() maps a variable in the [0,1] range to the real number line [-\infty,+\infty] by applying the transformation ln(x/(1-x)). conversely, UNLOGIT() maps the real number line to [0,1] by applying the transformation e^y/(1+e^y). syntax x=unlogit(lx,sigl,sigx=sigx) parameters lx [INPUT; required] a variable in the range [-\infty,+\infty] * can be an array * value is set to NaN in output if input falls outside valid range sigl [INPUT] standard error on LX * if <0 and >-1, then ABS(SIGL) is taken to be the fractional error * if <-1 and >-100, then ABS(SIGL) is taken to be the percentage error * if <-100, then 1/ABS(SIGL) is taken to be the fractional error keywords sigx [OUTPUT] standard error on UNLOGIT(X) * note that SIGX = SIGL*exp(LX)/(1+exp(LX))^2 == SIGL*X/(1+exp(LX)) _extra [JUNK] here only to prevent crashing the program history vinay kashyap (6jun05)
(See pro/stat/unlogit.pro)
function updatid update the values in an ID structure and return the updated structure syntax newid=updatid(idstr,fluxes,waves,emis,flxerr=flxerr,lambda=lambda,$ spec=spec,bkg=bkg,/digit,verbose=v, width=width,sigma=sigma,$ nsigma=nsigma,sigmay=sigmay,xsize=xsize,ysize=ysize,wid=wid,$ dynrng=dynrng,markx=markx,marky=marky,markp=markp,markc=markc,$ marks=marks,markl=markl,marko=marko,/legg,/quiet) parameters idstr [INPUT; required] ID structure to be updated fluxes [I/O] if given, updates the IDSTR.(#).FLUX field * size must match number of components or number of IDs * if size does not match, but is given as a scalar or a single-element vector, then if +ve, treated as a global multiplicative factor if -ve, the strongest line is normalized to abs(FLUXES) * if not single element, then gets overwritten on output using IDSTR.(#).FLUX, so will be different if DIGIT, LAMBDA, and SPEC are set waves [INPUT] if given, updates the values of the observed wavelengths in IDSTR.WVL * size must match the number of components * if size does not match, but is given as a scalar or a single-element vector, then taken to be wavelength shift * to update the wavelengths without messing with the fluxes, call UPDATID() as newid=updatid(idstr,1.,newwvl, ...) emis [INPUT] if given, updates the emissivities in IDSTR.(#).EMIS * to update only the emissivities, call UPDATID() as newid=updatid(idstr,1.,idstr.WVL,newemis, ...) keywords flxerr [I/O] if given, updates the errors in IDSTR by these values. if not given, or is illegal, no changes are made. * overwritten on output using IDSTR.(#).FLUXERR * generally taken to be 1-sigma errors * size must match that of FLUXES lambda [INPUT] wavelengths of base spectrum to be used to find the fluxes in case FLUXES is not given spec [INPUT] spectrum to use to guess at the fluxes * size of SPEC and LAMBDA must match, else both are ignored * basically, at each IDSTR.WVL, find the total counts in a small region nearby, add up the counts, and that's it. * SPEC and LAMBDA are used if 1: FLUXES is not given, OR 2: DIGIT is set bkg [INPUT] if size matches that of SPEC, subtract from SPEC prior to finding the fluxes * if single element, assumed to be global background value digit [INPUT] if set, then for each IDLSTR.WVL lets the user interactively pick the range in which to compute the fluxes * overrides FLUXES verbose [INPUT] controls chatter _extra [INPUT] pass defined keywords to subroutines GETLOCMAX: WIDTH,SIGMA,NSIGMA PICKRANGE: SIGMA,XSIZE,YSIZE,WID,DYNRNG,MARKX,MARKY,MARKP, MARKC,MARKS,MARKL,MARKO,LEGG,QUIET subroutines GETLOCMAX PICKRANGE history vinay kashyap (Dec98) added keyword FLXERR (VK; MarMM) added keyword VERBOSE; streamlined FLUXES/FLXERR output; converted to IDL5 notation (VK; JanMMI) added parameter EMIS (VK; JulMMVIII)
(See pro/updatid.pro)
Project : CHIANTI
CHIANTI is an atomic database package for the calculation of
continuum and emission line spectra from astrophysical plasmas. It is a
collaborative project involving the Naval Research Laboratory
(Washington DC, USA), the Arcetri Observatory (Firenze, Italy), and the
Cambridge University (United Kingdom).
Name : USE_CHIANTI
Purpose : Sets up system variables for use of CHIANTI routines
Explanation : The CHIANTI software uses system variables
that have to be defined. This routine is called by the
CHIANTI routines if these system variables are not defined.
** If one is using the solar-soft package, these should
already be defined*****.
** If the CHIANTI package is used as stand-alone, then
this routine can be used for the setup with e.g.:
use_chianti,'/home/data/chianti/'
if /home/data/chianti/ points to the actual place where
the CHIANTI top directory is.
Use : IDL> use_chianti, '/home/data/chianti/', $
[ioneq= , abund=]
Inputs : None
Opt. Inputs : The full pathname of the CHIANTI top directory.
Outputs : None
Opt. Outputs: None
Keywords : IONEQ - to define the default ionization eq. file to be used.
ABUND - to define the default abundance file to be used.
Calls : None
Common : None
Restrictions: None
Side effects: None
Category :
Prev. Hist. : Based on use_dere_chianti, written by C D Pike, RAL
Written : Giulio Del Zanna (GDZ) DAMTP (University of Cambridge, UK)
Modified : Version 1, GDZ 10-Oct-2000
Version 2, GDZ 10-Jan-2001
added the definition of the !abund_file
V. 3, GDZ, 2-May-2002 Modified substantially, adding a new
system variable.
V.4, 10-July-2002 GDZ
Removed the definition of !chianti_top, upon request.
V.5, 25-July-2002, GDZ
Fixed a problem with IDL versions earlier than 5.3 (the routine
would not compile). ALso, introduced the use of concat_dir for
cross-platform compatibility.
V.6, 06-Aug-02 GDZ
Changed the use of CHIANTI system variables. Added comments on
the which CHIANTI version is used.
V.7 12-Aug-02 GDZ Changed default abundance file. Removed '***'
V.8, GDZ 13-Feb-2003
Changed default ioneq file, to include ALL the elements.
V.9, 12-Aug-2005, GDZ
Changed default ioneq file from mazzotta_etal_ext to
mazzotta_etal_9.ioneq where ion fractions have been extended
up to 10^9 K. This is useful to avoid steps in the
emissivities at high-temperatures.
V.10, 19-Sept-2005, GDZ
made last version backward-compatible.
v.11, 3-Jun-2009, GDZ
made the new v.6 ioneq the default.
v.12, 6-Jul-2012, Peter Young
in preparation for the v.7.1 release, I've
changed the default abundance file.
Version : V.12, 6-Jul-2012
(See pro/external/use_chianti.pro)
function varsmooth returns a locally smoothed array by default, smooths with a boxcar of specified scale. may also smooth with gaussians, lorentzians, beta-profiles, and asymmetric beta-profiles of varying widths; or obtain stepped averages over varying widths. syntax sfunc=varsmooth(func,scale,xfunc=xfunc,weight=weight,type=type,$ steps=steps,/gauss,/boxcar,nueff=nueff,nutilde=nutilde,$ missing=missing,/fwhm,betap=betap,angle=angle) parameters func [INPUT; required] 1D array to be smoothed * if multi-D, gets converted to 1D scale [INPUT] array containing the half-length scales over which FUNC must be smoothed. * if smaller in size than FUNC, fills out with last element * must be in bin units, unless -- XFUNC and TYPE are both defined keywords xfunc [INPUT] x-coordinates for FUNC * size must match FUNC or must be bin boundaries on FUNC, else ignored. * ignored in case of boxcar smoothing weight [INPUT] allows weighting of adjacent points while boxcar smoothing * if scalar, WEIGHT(*)=(dPIX)^(-WEIGHT(0)) type [INPUT] define the 3-parameter family function to be used to smooth * may be anything accepted by X3MODEL/MK_3MODEL, e.g., "Gaussian", "Lorentizan", "Beta=<value>", "Slant=<angle>,<beta>", etc. steps [INPUT] if set, ignores the actual values of SCALE and replaces FUNC in bins with contiguous stretches of SCALE with <FUNC> averaged over this contiguous stretch. * only those values of SCALE > STEPS[0] are considered in the calculation -- those below it are held at one bin each. * NUEFF and NUTILDE are not calculated for this case gauss [INPUT] retained for backwards compatibility. if set, and TYPE is not set, then sets TYPE='Gaussian' boxcar [INPUT] if TYPE, GAUSS and STEPS are not set, the default is to carry out boxcar type smoothing. however, the default there is to limit the smoothing scale to the maximum extent of the range, i.e., N(LSCAL)/2. if BOXCAR is set, this limitation is ignored, and smoothing scales can be as large as possible. however, note that this does not handle spillage over endpoints gracefully, so _THIS OPTION IS NOT RECOMMENDED_ unless you know what you are doing. nueff [OUTPUT] the effective number of degrees of freedom in the problem, after smoothing. * the trace of the smoothing matrix nutilde [OUTPUT] correction to NUEFF * the trace of the product of the transpose of the smoothing matrix and the matrix * dof ~ 2*NUEFF-NUTILDE _extra [INPUT] pass defined keywords to MK_GAUSS: MISSING, FWHM MK_LORENTZ: BETAP, MISSING MK_SLANT: ANGLE, BETAP, MISSING restrictions input array, FUNC, must be evenly sampled. requires subroutines: X3MODEL MK_3MODEL MK_GAUSS MK_LORENTZ MK_SLANT KILROY these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (Apr97) changed gaussian smoothing to wrap around (VK; May97) corrected bug of SCALE not filling out with last element (VK; Aug98) added keywords XFUNC, STEPS, and TYPE (latter makes GAUSS obsolete) (VK; MarMM) allowed XFUNC to be bin boundaries (VK/LL; Sep02) now variable rebinning takes effect only if scales are > STEPS[0] (VK; Feb03) added keywords NUEFF and NUTILDE (VK; Jan06) corrected NUTILDE calculation; added keyword BOXCAR (VK; Mar06)
(See pro/util/varsmooth.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME
VERNER_XS()
EXPLANATION
Reads the Verner & Yakovlev (A&AS 109, 125, 1995) photoionization
cross-section data and generates the values of the cross-section at
the wavelengths WVL
INPUTS
IZ Atomic number of ion (e.g., 26 = Fe)
ION Spectroscopic number of ion (e.g., 13 = XIII)
WVL Wavelengths (in angstroms) for which cross-sections are
required (1-D array).
OPTIONAL INPUTS
DATA By default VERNER_XS reads the Verner & Yakovlev data file when
it is called. Through the DATA keyword the data array can be
sent to VERNER_XS instead.
OUTPUT
The photoionization cross-section for the ionization of the outer
electron in units of mega-barns (Mb = 10^-18 cm^2) at the input
wavelengths. E.g., for Fe XIII (ground configuration
1s2.2s2.2p6.3s2.3p2) it is the cross-section for the removal of the
3p electron.
HISTORY
Ver.1, 24-Jul-2002, Peter Young
(See pro/external/verner_xs.pro)
function voorsmooth returns an array smoothed by convolving with appropriate function this is basically a front-end to IDL's CONVOL function, and is a faster alternative to VARSMOOTH (a VARSMOOTH that goes vrooom, if you will), smooths with gaussians, lorentzians, beta-profiles, asymmetric beta-profiles, etc. syntax sy=voorsmooth(y,s,x,type=type,usekern=usekern,eps=eps,verbose=v,$ /fwhm,betap=betap,angle=angle,missing=missing,/perbin) parameters y [INPUT; required] 1D array to be smoothed s [INPUT; required] smoothing scale. if an array, only the first element is used. * assumed to be in pixel units unless X is given * the meaning of the scale depends on the function being used -- sigma for TYPE='Gauss' (unless FWHM is set), half-width for TYPE='Lorentz', etc. * >>ignored<< if USEKERN is defined, but set to some non-zero value anyway x [INPUT; optional] values at which Y=Y(X) is defined * size must match Y OR must be bin boundaries flanking Y otherwise X is ignored * if given, S is assumed to be in the same units as X * if dX is non-uniform, Y and X are rebinned to the finest possible grid and THEN convolved. keywords type [INPUT; default='Gaussian'] define the 3-parameter family function to be used to smooth * may be anything accepted by X3MODEL/MK_3MODEL, e.g., "Gaussian", "Lorentizan", "Beta=<value>", "Slant=<angle>,<beta>", etc. * >>ignored<< if USEKERN is defined usekern [I/O] if defined legally on input, will ignore parameter S and keyword TYPE and use the defined kernel to smooth the input array Y. eps [INPUT] a small number, 1e-6 by default verbose [INPUT] controls chatter _extra [INPUT ONLY] use this to pass defined keywords to subroutines -- MK_GAUSS: FWHM, MISSING -- MK_LORENTZ: BETAP, MISSING -- MK_SLANT: ANGLE, BETAP, MISSING -- REBINW: PERBIN restrictions calls subroutines: X3MODEL MK_3MODEL MK_GAUSS MK_LORENTZ MK_SLANT REBINW FINDEX example make a "spectrum": y=fltarr(500) & y[250]=2. smooth with Gaussian of sigma=10 pix ys=voorsmooth(y,10.,type='Gauss',usekern=usekern) make a new kernel: kern=0.5*(shift(usekern,-30)+shift(usekern,30)) smooth again: ys2=voorsmooth(y,10.,type='Gauss',usekern=kern) display: plot,y & peasecolr & oplot,ys,color=2 & oplot,ys2,color=3 these are all the smoothing tools in PINTofALE ALALOESS() makes a loess curve CLTSMOOTH() removes -ves from background subtracted spectra or light curves CONV_RMF convolves with specified RMF HAARTRAN() smoothes by filtering on Haar wavelet coefficients LINEREM() removes lines from spectrum by iterative S/N filtering NOISMOOTH() does boxcar accumulation a la Ebeling's asmooth REGROUP() accumulates from one end SCRMF does fast convolution using optimized RMF SMOOTHIE does peak-descent accumulation to build up S/N SPLAC computes a segmented piecewise linear approximations UNKINK() removes sharp kinks from a curve VARSMOOTH() does local smoothing at specified scales VOORSMOOTH() does fast local smoothing at specified scales history vinay kashyap (2001Jul; derived from varsmooth, but really a precursor, hence the [Noordwijk influenced] name) bug correction oo v/s o0; now reverse kernel before convol (VK; Oct01) allowed X to be bin boundaries (VK/LL; Sep02) accounted for 1-pix shift due to centering of kernel (VK; May03)
(See pro/util/voorsmooth.pro)
procedure vrdb print selected rows and columns from RDB table (see RDB.PRO) syntax vrdb,dbstr,pick,cols=cols,/row,wfield=wfield parameters dbstr [INPUT; required] structure as read in by RDB.PRO pick [INPUT] array of position indices to print out * default is [0] keywords cols [INPUT] array of column indices to print out * default is to print all except DBSTR.HEAD * if string array, then assumed to contain column names -- names do not have to be exact matches row [INPUT] if set, prints out the fields in a row * default is to print them out in a column. * -ve values will force all possible rows to be output wfield [INPUT] array of integers specifying the width at which each column must be printed * if not specified, tacks on +2 to the lengths deduced from the very first row to be printed _exra [JUNK] here only to prevent crashing the program history vinay kashyap (FebMM)
(See pro/util/vrdb.pro)
function wc obtains the number of lines, words or characters in the specified file, using the UNIX wc command syntax lines = wc(files,/word,/char,comm=comment,mat=mat,/h) parameters files [INPUT; required] name of file keywords word [INPUT] if set, returns number of words char [INPUT] if set, returns number of characters comm [INPUT] excludes lines where the first character is the comment character, as specified mat [INPUT] operate only on text containing matching string _extra [JUNK] here only to prevent crashing the program notes if input is an array, the output is also an array, but with one extra element at the end, containing the total number of lines, words, or characters found. restrictions IDL wrapper to the UNIX wc command, so obviously works only for UNIX. history vinay kashyap (3/25/93)
(See pro/util/wc.pro)
function wee_paramesran,img computes and returns the sharpness of an image (see Wee, C.-Y., and Paramesran, R., 2008, ICSP 2008) http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&tp=&arnumber=4697259 parameters img [INPUT; required] 2D image keywords firstk [INPUT] how many of the eigenvalues to include in measure of sharpness * default is to include all of them verbose [INPUT] controls chatter _extra [JUNK] here to prevent program from crashing history vinay kashyap (2014jul)
(See pro/util/wee_paramesran.pro)
procedure whee emulates a wheel rolling in place by printing the characters "|", "/", "-", "\", "|", "/", "-", "\" in succession syntax whee,spoke=spoke,/moveit parameters NONE keywords spoke [I/O] a +ve integer that on input says at what state the spoke in the wheel is in. if not given, set to 1. contains this value on output (see MOVEIT) * if > 8, wraps back to 1 moveit [INPUT] if set, increments SPOKE by 1 prior to output usage IDL> for i=0,3000 do whee,spoke=spoke,/moveit history vinay kashyap (Feb97)
(See pro/util/whee.pro)
function whereis apes the csh command `which` in the IDL environment, and finds the path to the specified file by looking through all the directories specified in the !PATH variable. NOTE: it is possible to use ROUTINE_INFO to get the path to a compiled subroutine directly: help,routine_info(routine,/source,/function),/structure but clearly you need to know the exact name of the routine (can't use wildcards) as well as whether what you need is a procedure or a function beforehand. also, they have to be compiled procedures, not, for example, command files or scripts or datafiles lurking under the horizon. and what if there are duplicates in different directories? btw, FILEPATH() is completely uselss for this purpose and FINDFILE() is of limited use because you still need to explicitly say which directory to look in. syntax fpath=whereis(file,lookin=lookin,/dironly,/nospawn,verbose=verbose) parameters file [INPUT; required] name(s) of file to search for * may include shell wildcards, regexps, etc. (but remember to prepend the escape character "\") * may also be an array. path [OUTPUT] full path to the requested file(s) * there is no reason to expect that the array sizes of FILE and PATH will match. keywords lookin [INPUT] path specification in which to look for FILE * this will be passed without comment to EXPAND_PATH() dironly [INPUT] if set, returns only the name(s) of the directory(ies) containing the specified file(s) nospawn [INPUT] if set, acts as wrapper for FINDFILE() even on UNIX systems, i.e., does spawn find verbose [INPUT] if set, spits out informational messages _extra [JUNK] here only to prevent crashing the program notes spawns "find" on UNIX systems, and calls FINDFILE() otherwise history vinay kashyap (Dec2001)
(See pro/util/whereis.pro)
procedure wrt_ln_aped writes out line intensities computed from an APED-type database in a form that is easier to access. usage wrt_ln_aped,apedfil,logT,outdir=outdir,apeddir=apeddir parameters apedfil [INPUT; required] FITS file, output of APEC * passed w/o comment to RD_APED logT [INPUT] log_10(T[K]) at which to store the emissivities * default is FINDGEN(81)*0.05+4 keywords outdir [INPUT; default: aped] directory tree under which to store the output files * WARNING: do not append a "/" (will crash if N_E is set) apeddir [INPUT] directory containing APEDFIL * passed w/o comment to RD_APED abund [INPUT] APED includes abundances, so "undo" by dividing by the abundances * default is to use Anders & Grevesse _extra [JUNK] here only to avoid crashing the program side effects deposits (possibly large) files in OUTDIR * ATOM_wvl wavelengths of all the transitions * ATOM_tem temperatures * ATOM_##.# line intensities I(tem,wvl)@logP * ATOM_ion ionic states corresponding to wvl * ATOM_src source of line information 3: APED * ATOM_lvl level designations of each transition * ATOM_ecn e-configurations of each level restrictions requires APED-style datafile subroutines: RD_APED, KILROY, INICON history vinay kashyap (AprMM)
(See pro/mkemis/wrt_ln_aped.pro)
procedure wrt_ln_chianti writes out line intensities computed from a CHIANTI-type database in a form that is easier to access. usage wrt_ln_chianti,logP,logT,Z=Z,N_e=N_e,outdir=outdir,$ wmn=wmn,wmx=wmx,istate=istate,chidir=chidir parameters logP [INPUT; required] log10(Pressure [cm^-3 K]) logT [INPUT] array of log10(Temperature [K]) at which to compute line intensities. default: logT=findgen(81)*0.05+4. * best keep delta(logT) constant keywords Z [INPUT; default: ALL] element, ionic state (e.g.:'He','Fe XII') n_e [INPUT] if set, computes line emissivities at the specified electron density [cm^-3] * overrides LOGP * appends a "D" to OUTDIR outdir [INPUT; default: emisschianti] directory tree under which to store the output files * WARNING: do not append a "/" (will crash if N_E is set) _extra [INPUT ONLY] allows passing defined keywords (WMN,WMX,N_E, ISTATE,CHIDIR) to LINE_CHIANTI side effects deposits (possibly large) files in OUTDIR * ATOM_wvl wavelengths of all the transitions * ATOM_tem temperatures * ATOM_##.# line intensities I(tem,wvl)@logP * ATOM_ion ionic states corresponding to wvl * ATOM_jon ionic states that matter to the ion balance * ATOM_src source of line information 2: CHIANTI * ATOM_lvl level designations of each transition * ATOM_ecn e-configurations of each level restrictions requires CHIANTI-style database requires LINE_CHIANTI and associated subroutines input LOGP must be uniquely writeable in format f4.1 (e.g.,14.5) history vinay kashyap (Nov96) forced output filenames to not have spaces, changed output file names and format, esp. of e-configurations (VK; Dec96) changed ATOM_src CHIANTI code from 0 to 2 (VK; Jan96) added keyword N_E (VK; Jun97) modified to account for dielectronic recombination lines in CHIANTIv3 (VK; OctMM)
(See pro/mkemis/wrt_ln_chianti.pro)
procedure wrt_ln_generic writes out line intensities to a PoA style database from a PoA style line emissivities structure. usage wrt_ln_generic,linstr,outdir,tag,abund=abund,excieq=excieq,$ eps=eps,chidir=chidir,eqfile=eqfile parameters linstr [INPUT; required] line emissivities structure, of the same form output by RD_LINE() * NOTE: the emissivities must be in units of [1e-23 ergs cm^3/s] outdir [INPUT; required] directory to deposit the database files * WARNING: the PINTofALE convention is to automatically append a "D" while reading from emissivities derived at constant density. so if the emissivities being written out were derived at constant density, then please makes sure that OUTDIR has an extra "D" at the end. this is not checked for, because a priori this program can have no idea of the nature of the emissivities being input. tag [INPUT; required] a value (such as pressure, or density) defining the emissivities. see description of output files below for where it is used. * MUST BE writeable in the format (f4.1) * if > 99, the alog10 value is used * if < 0, forced to be 00.0 keywords abund [INPUT] if given, assumes that the input emissivities have been multiplied by these abundance values, and that you don't want this factor stored in the database files, and divides them out. excieq [INPUT] if set, assumes that the input emissivities have been multiplied by the ion balance defined by the keywords CHIDIR and EQFILE, and that you don't want them to be included in the stored database, and divides them out over the range where the ion balance is > EPS eps [INPUT] a small number * default is 1e-6 verbose [INPUT] controls chatter _extra [INPUT ONLY] pass defined keywords CHIDIR and EQFILE to RD_IONEQ() side effects deposits (possibly large) files in OUTDIR * ATOM_wvl wavelengths of all the transitions * ATOM_tem temperatures * ATOM_##.# line emissivities [tem,wvl]_TAG * ATOM_ion ionic states corresponding to wvl * ATOM_jon ionic states that matter to the ion balance * ATOM_src source of line information * ATOM_lvl level designations of each transition * ATOM_ecn e-configurations of each level subroutines: ARRAYEQ INICON SETSYSVAL, LEGALVAR() RD_IONEQ(), READ_IONEQ history vinay kashyap (Jun02) Antonio Maggio discovered that ion, jon, and src files were writing out float rather than long (VK; Aug02)
(See pro/mkemis/wrt_ln_generic.pro)
procedure wrt_ogip_rmf write out a response matrix into an OGIP-compatible FITS file syntax wrt_ogip_rmf,rmf,rmfile,hdrfil=hdrfil,matext=matext,ebext=ebext,$ telescop=telescop,instrume=instrume,filter=filter,detnam=detnam,$ grating=grating,chantype=chantype,detchans=detchans,$ hduclass=hduclass,hduclas1=hduclas1,hduclas2_rm=hduclas2_rm,$ hduclas2_eb=hduclas2_eb,hduclas3=hduclas3,hduvers=hduvers,$ tlmin4=tlmin4,numgrp=numgrp,numelt=numelt,lo_thres=lo_thres,$ /ccls,/ccnm,/cdtp,cvsd=cvsd,cvst=cvst,cdes=cdes,$ rmfversn=rmfversn,hduvers1=hduvers1,hduvers2=hduvers2,$ origin=origin,creator=creator,revision=revision,mission=mission parameters rmf [INPUT; required] response matrix structure, in the same format as is read in by, e.g., RD_OGIP_RMF() rmfile [INPUT; required] name of output file keywords hdrfil [INPUT] name of existing OGIP-style response matrix file from which to copy the headers as far as possible the following are header keywords recommended by OGIP, along with a brief description of what they mean. the default values used by this program are also listed. see http://legacy.gsfc.nasa.gov/docs/heasarc/caldb/docs/memos/cal_gen_92_002/cal_gen_92_002.html matext = 'MATRIX' /MATRIX or SPECRESP MATRIX, name of extension ebext = 'EBOUNDS' /name of extension telescop = 'TELESCOP' /telescope used instrume = 'INSTRUME' /instrument used filter = 'NONE' /the instrument filter in use (if any) detnam = 'DETNAM' /detector used grating = 'GRATING' /grating used (if any) chantype = 'PHA' /PHA or PI, uncorrected or corrected for gain detchans = n_elements(rmf.EMN) /number of raw detector channels hduclass = 'OGIP' /file format is OGIP standard hduclas1 = 'RESPONSE' /extension contains response data hduclas2_rm = 'RSP_MATRIX' /extension contains a response matrix hduclas2_eb = 'EBOUNDS' /extension contains a response matrix hduvers = '1.3.0' /version of the file format tlmin4 = rmf.FIRSTCHAN /first channel in the response numgrp = total(rmf.N_GRP) /number of channel subsets numelt = total(rmf.N_CHAN) /number of response elements lo_thres = 0.000001 /lower threshold used to construct the matrix hduclas3 = 'DETECTOR' /REDIST (RMF) or DETECTOR (with QE, no ARF) or FULL (everything) rmfversn = '1992a' /obsolete hduvers1 = '1.1.0' /obsolete hduvers2 = '1.2.0' /obsolete ccls = 'CPF' /the OGIP-class of this calibration file ccnm = 'MATRIX' or 'EBOUNDS' /CIF codename for this type of calibration dataset cdtp = 'DATA' /OGIP code for the form of the contents of the file cvsd = YYYY-MM-DD /UTC date of beginning applicability cvst = HH:MM:SS /UTC time of beginning applicability cdes = 'RSP' /brief descriptive summary of this dataset origin = whoami@host /source of FITS file creator = 'PINTofALE' /program creating this file revision = 1 mission = 'MISSION' /mission _extra [JUNK] here only to prevent crashing the program restrictions * requires the IDL-Astro library * if not a UNIX system, keyword ORIGIN must be explicitly set side-effects writes out a FITS file to disk history vinay kashyap (Nov2001) force variable length arrays even when N_GRP=1 (VK; Jul02)
(See pro/util/wrt_ogip_rmf.pro)
function findscale returns the lengthscale in pixels at each point on the given curve using the MexHat Wavelet Transforms as a guide syntax ls=wvlt_scale(curve,/coarse) parameters curve [INPUT; required] regularly gridded 1D array of function values to be used to compute the length scales * if scalar, returns 0 * if >1D, convert to 1D keywords coarse [INPUT; default=2] explore scales at specified coarseness e.g.: if COARSE=1, every scale from 1 to N(CURVE)-1 will be tested _extra [INPUT] junk; ignore. here only to prevent crashing program. history vinay kashyap (Apr97) fixed bug when N(CURVE) was a power of 2 (LiWei Lin/VK; Jan'03)
(See pro/util/wvlt_scale.pro)
procedure x3model
procedure written to be compatible with FIT_LEVMAR, and also
with IDL's CURVEFIT, GHRS-IDL's WFIT, etc.
computes F(X;A) and partial derivatives as needed for a
combination of 3-parameter family of curves
syntax
x3model,x,a,f,pder, group=group,delp=delp,type=type,/asis,/allcomp,$
missing=missing,/fwhm,/norm,betap=betap,vrot=vrot
parameters
x [INPUT; required] points at which to generate models
a [INPUT; required] array of parameter values
* N_ELEMENTS(A) must be a multiple of 3
* expected to be sequential triples of (position, width, height)
f [OUTPUT; required] output f=f(x;a)
pder [OUTPUT; optional] partial derivatives for each parameter
keywords
rmfstr [INPUT] structure w/ OGIP standard rmf with which to
convolve model. SEE: RD_OGIP_RMF.PRO
x_seg [INPUT] x-axis wavelength grid on which to construct
the model spectrum; used when RMFSTR is set, and X is
then ignored
_extra [INPUT] pass defined keywords to subroutines
MK_3MODEL: GROUP, DELP, TYPE, ASIS, ALLCOMP
MK_GAUSS: MISSING, FWHM, NORM
MK_LORENTZ: BETAP, MISSING, NORM
MK_SLANT: ANGLE, BETAP, MISSING, NORM
MK_ROGAUSS: VROT, FWHM, NORM, MISSING
MK_SINUSOID: PHASE, MISSING
requires
MK_3MODEL
MK_GAUSS
MK_LORENTZ
MK_SLANT
MK_ROGAUSS
MK_POWLAM
MK_SINUSOID
SCRMF
REGROUP_RMF
history
vinay kashyap (Oct98; modified from GMODEL.PRO)
added MK_SLANT (VK; MarMM)
added MK_ROGAUSS,MK_POWLAM (VK; JunMM)
added keywords RMFSTR and X_SEG and call to SCRMF (LL; Aug03)
added MK_SINUSOID (VK; Sep04)
(See pro/fitting/x3model.pro)
function x3model_f function written to be compatible with MPFIT, and is identical in all respects to X3MODEL, except that this is a function and not a procedure. returns F(X;A) and computes partial derivatives as needed for a combination of 3-parameter family of curves syntax f=x3model_f(x,a,pder, group=group,delp=delp,type=type,/asis,/allcomp,$ missing=missing,/fwhm,/norm,betap=betap,vrot=vrot) parameters x [INPUT; required] points at which to generate models a [INPUT; required] array of parameter values * N_ELEMENTS(A) must be a multiple of 3 * expected to be sequential triples of (position, width, height) pder [OUTPUT; optional] partial derivatives for each parameter keywords _extra [INPUT] pass defined keywords to subroutines MK_3MODEL: GROUP, DELP, TYPE, ASIS, ALLCOMP MK_GAUSS: MISSING, FWHM, NORM MK_LORENTZ: BETAP, MISSING, NORM MK_SLANT: ANGLE, BETAP, MISSING, NORM MK_ROGAUSS: VROT, FWHM, NORM, MISSING MK_SINUSOID: PHASE, MISSING requires MK_3MODEL MK_GAUSS MK_LORENTZ MK_SLANT MK_ROGAUSS MK_POWLAM MK_SINUSOID history converted from X3MODEL (VK/LL; Oct02) added MK_SINUSOID (VK; Sep04)
(See pro/fitting/x3model_f.pro)
procedure xspecplot plot two curves in two panels the way XSPEC does spectra and residuals syntax xspecplot,x,y1,y2,y1err=y1err,y2err=y2err,xerr=xerr,$ y1over=y1over,y2over=y2over,$ fraclow=fraclow,verbose=verbose,outfile=outfile,$ Ulstyl=Ulstyl,Upsym=Upsym,Ucol=Ucol,Uylog=Uylog,Uytitle=Uytitle,Uyr=Uyr,$ Llstyl=Llstyl,Lpsym=Lpsym,Lcol=Lcol,Lylog=Lylog,Lytitle=Lytitle,Lyr=Lyr,$ oUlstyl=oUlstyl,oUpsym=oUpsym,oUcol=oUcol,oLlstyl=oLlstyl,oLpsym=oLpsym,oLcol=oLcol,$ [PLOT keywords] parameters x [INPUT; required] abscissa array y1 [INPUT; required] array that goes in the top panel y2 [INPUT; required] array that goes in the bottom panel * sizes of all arrays _must_ match keywords y1err [INPUT] error bar on Y1 y2err [INPUT] error bar on Y2 xerr [INPUT] error bar on Y2 * if scalar and +ve, assumed to be a fractional error if between 0 and 1, and %error if greater than 1 * if scalar and -ve, abs value is assumed to be a constant error * if array of same size as X, assumed to be symmetric * if array of size [2,NX] or [NX,2], assumed to be upper and lower bounds * ignored if array size doesn't match X y1over [INPUT] additional arrays to overplot in upper panel y2over [INPUT] additional arrays to overplot in lower panel * size must be [m,NX] or [NX,m] * if not set, both assumed to be 0*NX fraclow [INPUT] what fraction of the plot should the lower panel take up? * default is 0.35 * hard minimum of 0.05 and hard maximum of 0.95 verbose [INPUT] controls chatter outfile [INPUT] if set, makes a postscript plot * if set to a string, assumes that that is the name of the file, otherwise writes to ./xspecplot.ps Ulstyl [INPUT] line style for upper panel Llstyl [INPUT] line style for lower panel linestyle [INPUT] caught and discarded Upsym [INPUT] PSYM for upper panel Lpsym [INPUT] PSYM for lower panel psym [INPUT] caught and discarded Ucol [INPUT] COLOR for upper panel Lcol [INPUT] COLOR for lower panel color [INPUT] caught and discarded Uylog [INPUT] YLOG for upper panel Lylog [INPUT] YLOG for lower panel ylog [INPUT] caught and discarded Uytitle [INPUT] YTITLE for upper panel Lytitle [INPUT] YTITLE for lower panel ytitle [INPUT] caught and discarded Uyr [INPUT] YRANGE for upper panel Lyr [INPUT] YRANGE for lower panel oUlstyl [INPUT] line styles of Y1OVER (must be array of size M) oLlstyl [INPUT] line styles of Y2OVER (must be array of size M) oUpsym [INPUT] PSYM for Y1OVER (must be array of size M) oLpsym [INPUT] PSYM for Y2OVER (must be array of size M) oUcol [INPUT] COLOR for Y1OVER (must be array of size M) oLcol [INPUT] COLOR for Y2OVER (must be array of size M) yrange [INPUT] caught and discarded _extra [INPUT ONLY] pass defined keywords to PLOT history vinay kashyap (2012-jun)
(See pro/util/xspecplot.pro)
procedure xsplot make XSPEC like double-panel plots for given counts spectrum and associated model syntax xsplot,data,model,egrid,dataerror,linecolor,/perbin,minct=minct,$ dataN=dataN,modN=modN,eeN=eeN,dsigN=dsigN,lcolN=lcolN,$ ;N=0..9 /resid,/fracres,/delchi,/ratio,verbose=vv,wsplit=wsplit,$ /ylog,xtitle=xtitle,ytitle=ytitle,xthick=xthick,ythick=ythick,$ title=title,subtitle=subtitle,charsize=charsize,charthick=charthick,$ yrange=yrange,zrange=zrange, /xlog,xrange=xrange,thick=thick,$ /halfit,eps=eps, /nuthin,/noday,/notime,/nouser,/nopack,stacol=stacol parameters data [INPUT; required] array of observed counts model [INPUT] array of model counts * must match size of DATA - extra bins are ignored - missing bins are assumed to be 0 ee [INPUT] x-axis grid defining DATA and MODEL * if size is N(DATA), assumed to be mid-bin values * if size is N(DATA)+1, assumed to be bin boundaries * if not given, 1-based integer indices are used dsig [INPUT] error bars on DATA * if not given, assumed to be Gehrels' approximation of Poisson counts error, sqrt(DATA+0.75)+1 * if set to a scalar, then - if -ve, errors are assumed constant = abs(DSIG) - if integer, assumed to be in units of SIGMAs, i.e., DSIG*default are plotted - if not integer and 0<DSIG<0.5, then assumed to be a fractional error DSIG*abs(DATA) - if not integer and 0.5<DSIG<10, then assumed to be in units of SIGMAs, i.e., DSIG*default are plotted - if not integer and DSIG>10, assumed to be a percentage error, (DSIG/100)*abs(DATA) lcol [INPUT] 3-element byte array specifying the line colors for MODEL, DATA, DSIG in that order * if incompletely given, missing elements are assumed to be [0,10,20] or [255,245,235] depending on whether !p.background is 255 or 0. keywords perbin [INPUT] if set, will treat the input as counts/bin and plot accordingly. if not set, will compute the bin widths and plot the density instead * if EE is not given, the bin widths will be 1 and this has no relevance except to the YTITLE minct [INPUT] if given, regroups the input DATA on the fly to have a minimum number of counts in each bin, and then regroups all the other arrays to the same grid * forces PERBIN to be ignored verbose [INPUT] controls chatter dataN [INPUT] for N=0..9, additional DATA arrays * size must match DATA modN [INPUT] for N=0..9, additional MODEL arrays * size must match DATA eeN [INPUT] for N=0..9, additional EE arrays * if not given, default is to use EE dsigN [INPUT] for N=0..9, additional DSIG arrays * size must match DATA lcolN [INPUT] for N=0..9, line colors, by default, N*25+[25,35,45] resid [INPUT] if set, plots (DATA-MODEL) in lower panel fracres [INPUT] if set, plots (DATA-MODEL)/MODEL in lower panel delchi [INPUT] if set, plots (DATA-MODEL)/DSIG in lower panel ratio [INPUT] if set, plots DATA/MODEL in lower panel * if more than one of RESID,FRACRES,DELCHI,RATIO are set, the priority is in that order. i.e., the later ones in the list override anything given before it. * if none are set, assumes /DELCHI wsplit [INPUT] fraction by which to split the upper and lower windows * default is 0.35 * ignored if <0.05 or > 0.95 ylog [INPUT] catch and release to upper PLOT xtitle [INPUT] catch and release to lower PLOT ytitle [INPUT] catch and release to upper PLOT xthick [INPUT] catch and release to PLOT ythick [INPUT] catch and release to PLOT title [INPUT] catch and release to upper PLOT charsize [INPUT] catch and release to PLOT charthick [INPUT] catch and release to PLOT subtitle [INPUT] catch and release to lower OPLOT yrange [INPUT] catch and release to upper PLOT zrange [INPUT] yrange catch and release to lower PLOT xstyle [INPUT] catch and discard psym [INPUT] catch and discard color [INPUT] catch and discard _extra [INPUT ONLY] pass defined keywords to subroutines: PLOT: XLOG, XRANGE, THICK STAMPLE: NUTHIN, NODAY, NOTIME, NOUSER, NOPACK, STACOL MID2BOUND: HALFIT, EPS examples xsplot,data,model xsplot,data,model,/verbose ;to stamp creator name and time xsplot,data,model,wvl ;to include physical x-axis grid xsplot,data,model,wvl,0 ;to not plot error bars xsplot,counts,model,minct=25 ;adaptively group the counts on the fly xsplot,data,model,wvl,1,150 ;to change color of model curve xsplot,data,model,data3=data3,mod3=mod3 ;overplot another set xsplot,data,model,mod0=mod0,mod1=mod1 ;overplot alternate models xsplot,data,model,mod9=mod9,lcol9=5 ;alt model with specific color xsplot,counts,model,keV,/perbin ;plot counts/bin rather than counts/keV xsplot,data,model,/ratio ;plot data/model in lower panel xsplot,data,model,/delchi ;plot delta chi in lower panel xsplot,data,model,/resid ;plot data-model in lower panel xsplot,data,model,/fracres ;plot (data-model)/model in lower panel xsplot,data,model,wvl,/xlog,/ylog,xrange=xr,yrange=yr,zrange=zr x=findgen(100)+1 & y=50*(sin(x/10)+1.1) & d=0*y & plot,x,y for i=0,99 do d[i]=randomu(seed,poisson=y[i]) & xsplot,d,y,x subroutines STAMPLE [SETSYSVAL, LEGALVAR()] MID2BOUND() REGROUP() history vinay kashyap (Oct09)
(See pro/util/xsplot.pro)
PROJECT: CHIANTI
CHIANTI is an Atomic Database Package for Spectroscopic Diagnostics of
Astrophysical Plasmas. It is a collaborative project involving the Naval
Research Laboratory (USA), the University of Florence (Italy), the
University of Cambridge and the Rutherford Appleton Laboratory (UK).
NAME:
ZION2FILENAME
PURPOSE:
help locate CHIANTI database files
CATEGORY:
database.
CALLING SEQUENCE:
ZION2FILENAME, Iz, Ion, Filename
INPUTS:
Iz: nuclear charge of ion of interest, i.e. 26 for Fe
Ion: charge state of ion of interest, i.e. 2 for Fe II
KEYWORDS:
diel: set if excitation of this ion is by dielectronic
recombination
OUTPUTS:
Filename: the complete filename and path specification for generic
CHIANTI database file, i.e. '.elvlc' suffix is not included
RESTRICTIONS:
!xuvtop must be set
EXAMPLE:
> zion2filename,26,2,filename
> print,filename
> /data1/xuv/fe/fe_2/fe_2 assuming !xuvtop = '/data1/xuv'
MODIFICATION HISTORY:
Written by: Ken Dere
March 1996: Version 2.0
Sept 1996: Modified for use with VMS
December 1998: Modified to diel keyword
V.5, 29-May-2002, Giulio Del Zanna (GDZ)
generalized directory concatenation to work for
Unix, Windows and VMS. Added keyword name to output just
the name of the file and changed the dielectronic keyword.
VERSION : 5, 29-May-2002
(See pro/external/zion2filename.pro)
procedure zion2symb convert atomic number and ionic state to spectroscopic symbol syntax zion2symb,z,ion,symbol,ziform=ziform parameters z [INPUT; required] atomic number ion [INPUT] ionic state (0=undefined, 1=neutral, 2=singly ionized, etc.) symbol [OUTPUT] string containing element designation (e.g., "he_2", "He II", "HeII", "he 2", "he", "He", depending on ZIFORM) keywords ziform [INPUT] string containing "Z" and "ION" to describe the output format:- if "Z" is capitalized, symbol as is (e.g., "He", not "he"). if "z", symbol in small letters (e.g., "fe", "ca", etc). if "ion" is in lower case, ion in arabic numerals. if "ION" or "Ion", ion in roman numerals. symbol and ion separated by whatever "Z" and "Ion" are separated by. * default is "ZION" oform [INPUT] kept here only for backwards-compatibility * WARNING -- will be phased out >>very<< soon _extra [JUNK] here only to prevent crashing the system restrictions cannot return the "+-" format (e.g., "O^+5") requires INICON history vinay kashyap (Nov98) OFORM bug correction (VK; Apr99) changed call to INITSTUFF to INICON (VK; 99May) allowed OFORM to be "Z<sep>number" and "Z<sep>ion" (VK; MMJul) changed keyword OFORM to ZIFORM; converted to IDL5 notation (VK; AugMM)
(See pro/util/zion2symb.pro)