GO Primer
Getting your dataFirst things first--Paper Products
Matching the file name with exposures
Looking at your data headers
Displaying your data
Plotting your data
Extracting and plotting your spectrum
Further Information
A Very Small IRAF Cheat Sheet
We recommend that you use the HST Data Archive to retrieve your data prior to your visit so that you can look at it. If you have received a data tape and wish to read your data off of it, use the STSDAS command "strfits"; you will need to set the image type to fits. This will copy the FITS files from the tape onto the specified disk; to keep the original file names, set the "Use old IRAF name" to "yes". As an example:
set imtype = fits
strfits mta 1-3 oldiraf=yes
This will copy the first 3 files from the IRAF device named mta to the current working directory with the original file name used.. Alternately, if the tape was written as a UNIX tar, the FITS files can be accessed directly by:
tar xvf /dev/rmtx
which will dump the contents of the tape to the present directory. Note that as STIS datasets are quite large (over 2MB mimimum a piece), directories should be chosen appropriately.
Data on your tape includes: raw, calibrated, data quality,and OMS files. Note that the first file on the tape is a log file giving the tape contents.
NOTE:As of August 1, 2000 the archive will no longer automatically generate tapes for any proposal. This extends the policy now in place for cycle 9 to all older proposals. Tapes will only be made available by making a specific request to archive@stsci.edu.
First things first--Paper Products:
The fastest and easiest way to look at your data is to look at the paper products. These were carefully designed to help you get a quick look at your data and assess it. You can generate the paper products using the HST PDF Products Page. Or produce them yourself using the following steps in IRAF:
1. Place all of your data in one directory
2. Load the IRAF packages, stsdas, hst_calib and paperprod
(simply by typing them).
3. Run the task pp_dads type: pp_dads *.fits
Matching the file name with exposures:
The easiest way to learn about your exposures is to use an IRAF task called infostis.
Simply type:
infostis o3ura2060_raw.fits
and a table of keywords will be displayed for you; among them, Exposure ID which will tell you the visit and exposure number that you can then match to your proposal if you wish. For example, an exposure ID of 2.018 translates to visit 2, exposure 18.
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S T I S
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Rootname: O3URA2060 Detector: CCD
Proposal ID: 7075 Obs Type: IMAGING
Exposure ID: 2.018 Obs Mode: ACCUM
Lamp: NONE
Target Name: G191B2B Aperture: F28X50OII
Rigth Ascension: 05:05:30.6 Filter: OII
Declination: +52:49:52.8 Opt Element: MIRVIS
Equinox: 2000.0 CCD amp: D
Gain: 4
Axis 1 binning: 1 CR-split: 2
Axis 2 binning: 1
Subarray: no
Total Exp. Time: 24.0 sec
Number of imsets: 2
An alternative method is to read the instrument parameters from the header
(see below) to determine the instrument configuration.
To work with your data you're going to need the proper software. You'll need the latest version of IRAF (version 2.11.3) that contains the new "fits kernel". You will also want to download the latest version of the STSDAS (version 2.2) STIS package, as calstis and the accompanying tools are evolving rapidly. (Please note that these programs are available only for Sun/OS and Solaris 2.5 platforms).
Once you have the proper software, start by looking at your data headers. The format of STIS data is very different from other HST data you may have had experience with. It's in a type of fits format, either fits with image extensions for two-dimentional data or 3-D binary tables for extracted spectra and time-tag series. Go into IRAF and run the task, catfits, on one of your datasets, e.g.:
catfits o3ura2060_raw.fits long-
EXT# FITSNAME FILENAME EXTVE DIMENS BITPI OBJECT 0 o3ura2060_raw 16 1 IMAGE SCI 1 1062x1044 16 2 IMAGE ERR 1 16 3 IMAGE DQ 1 16 4 IMAGE SCI 2 1062x1044 16 5 IMAGE ERR 2 16 6 IMAGE DQ 2 16You'll note there are 3 types of extensions: SCI, ERR, and DQ. SCI stands for "science" and contains the actual data. ERR stands for "error" and contains statistical errors. DQ stands for "data quality" and contains data quality values which flag suspect pixels. Details about data format can be found in the Data Handbook.
You may want to look at the header of your calibrated data. To do this use the IRAF task imheader:
imhead o42701010_sx2.fits[1] long+
This will give you the long version of the primary header of your 2-D calibrated extracted spectra. Naturally, what mode you used to take your data will determine what the final, calibrated image will contain (see Table 1). A complete description of file naming conventions and various suffixes (Table 2) is available.
Some useful keywords found in the header include:
PROPOSID, TDATEOBS, TARGNAME, TEXPTIME, OBSTYPE, OBSMODE, DETECTOR, CCDGAIN, SCLAMP, OPT_ELEM, APERTURE, FILTER, APER_FOV, MIRROR.
For an explanation of what each of these means in detail please refer to the Data Handbook.
Table 1: Typical STIS Output Products by Observation Type*
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Observation Type Uncalibrated Files Calibrated
Files+
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ACQ, ACQ/PEAK _raw none
IMAGING _raw, _spt, _asn _flt, _crj (CCD),
(CR-SPLIT or repeatobs) _sfl(MAMA)
IMAGING (single exposure) _raw, _spt, _asn _flt
FIRST ORDER SPECTROSCOPY _raw, _wav, _asn _flt, _crj (CCD),
(CR-SPLIT or repeatobs) _spt, _wsp _sx1 (CCD), _sx2
FIRST ORDER SPECTROSCOPY _raw, _wav, _asn _flt, _x2d
(single exposure) _spt, _wsp
ECHELLE SPECTROSCOPY _raw, _wav, _asn _flt, _x1d
(single or repeatobs) _spt, _wsp
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* for ACCUM mode. The file names are the same for TIME-TAG with the addition of
the uncalibrated _tag file.+ the file in boldface is the most processed file
Table 2: Data File Naming Conventions
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Product Suffix Type Contents
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Uncalibrated _raw image Raw sciencea
_tag table Timetag event list
_spt image Support file (header)
_wav image Associate wavecal exposure
_wsp image Wavecal support file
_asn table Association file
_trl table Trailer file (input)
_lrc image Local rate check image
_lsp text LRC support file (header)
_jit See Chapter 2
_jif image See Chapter 2
_pdq table See Chapter 2
Calibrated _flt image Flat-fielded science
_crj image CR-rejected, flat-fielded science
_sfl image Summed flat-fielded science
_x1d table 1-D extracted spectra
_x2d image 2-D extracted spectra or
geometrically corrected images
_sx1 table Summed 1-D extracted spectra
_sx2 image Summed 2-D extracted spectra
_trl table Trailer file (output)
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a Raw data from isolated wavecals, biases, darks, and flats, as well as from ACQs and ACQ/Peaks, have the _raw suffix.
For information on various modes see the STIS Instrument Handbook:
Detailed information on how to look at your data is contained in the HST Data Handbook in section 3.5.2 COS and STIS Spectra. Below we give some short examples.
Before attempting to display or plot your data you may find it useful to run catfits on it. For example:
catfits file_sx2.fits
EXT# FITSNAME FILENAME EXTVE DIMENS BITPI OBJECT 0 file_sx2 file_sx2.fits 16 1 IMAGE SCI 1 1201x1201 -32 2 IMAGE ERR 1 1201x1201 -32 3 IMAGE DQ 1 1201x1201 16
catfits file_x1d.fits
EXT# FITSNAME FILENAME EXTVE DIMENS BITPI OBJECT 0 file_x1d file_x1d.fits 16 1 BINTABLE SCI 1 9Fx1RYou can display any data that is an IMAGE, but you will have to plot such things as binary tables, (BINTABLE), or use tprint to read the table. Tprint can also be used to read fits tables (TABLE).
To display your data bring up your favorite display tool (saoimage or ximtool). Then simply use the IRAF task display:
display yourfile.fits[1] 1
You can display any image data (see table above).
You can plot any image data or binary table data with sgraph. In many cases only a small portion of your image will contain the data you wish to look at. You should display your two-dimensional spectra to determine the pixel range you wish to plot. An example of plotting a range of data is:
sgraph data_x2d.fits[1][*,100:1000]
This will plot the science extension of your dataset for the entire x range, but only pixel 100 through 1000 averaged together for the y range.
Extracting and plotting your spectrum:
To extract a 1-dimensional spectrum from your 2-dimensional image, you need to determine the AXIS2 (Y) position of the object. Use the IRAF task implot:
implot data_crj.fits[1] (CCD observations)
implot data_flt.fits[1] (MAMA observations)
This will give you a line plot through your data. Issue the command:
:c 512
to get a column plot through your data, which should show a peak at the Y location of your spectrum. Expand the plot around your line (place the cursor to the left of the line, hit "e", then the right of the line, and hit "e" again), and measure the middle of the line by placing the cursor on the peak and hitting the spacebar. You will also need to measure the width of your spectrum by placing the cursor at the edges of the profile. You can then use the STSDAS task x1d (part of the calstis pipeline) to extract a 1-dimension spectrum:
x1d data_crj.fits output=data_x1d.fits a2center=MIDDLE extrsize=WIDTH
where MIDDLE is a real value that provides the center of the search range for finding
the spectrum, and WIDTH is a real value with the size of the extraction box, in
reference pixels.
Note that you must have the calibration reference files on-line, and have
properly set the oref parameter
(see section 3.5.1
in the Data Handbook).
This spectrum is a FITS binary table. To convert this to an 1-dimensional
image, use the STSDAS task tomultispec:
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TOMULTISPEC work around for STIS Data
The IRAF task TOMULTISPEC does not currently work on STIS Data. While this problem is being resolved, please use the following work around:
In the pyraf command line type the following three commands:
- tprint input_x1d.fits showrow- showhdr- row=1 column="wavelength,flux" > tprint_output.txt
- rspec tprint_output.txt rspec_output.fits
- splot rspec_output.fits
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You can now use the standard IRAF 1-dimensional tasks (such as splot) to plot and analyze your spectrum. If you have echelle spectra, echplot is an excellent task for plotting extracted spectral orders (see section 23.1 in the Data Handbook).
You can now use the standard IRAF 1-dimensional tasks (such as splot) to plot and analyze your spectrum. If you have echelle spectra, echplot is an excellent task for plotting extracted spectral orders (see section 23.1 in the Data Handbook).
Note that the STIS pipeline automatically extracts a one-dimensional spectrum for you. To determine the position of the extracted spectrum on the crj (CCD) or flt (MAMA) image, look at the trl file with the tread command for the x1d analysis section:
tread data_trl.fits
or alternately (to create an ascii file which is searchable):
strfits data_trl.fits "" data.trl
grep "spectrum extracted" data.trl
Further Information: We recommend reading sections of the STIS Instrument Handbook and/or the STIS Web Site that are relevant to your data to familiarize yourself with how your data was taken:
Some particularly relevant sections of the Data Handbook include:-
Instrument Capabilities and Design
- Data Structure and naming conventions
- Output products
- Headers keywords
- Paper Products
- Calibration switches
- Calstis structure
- Pipeline flowchart
- Recalibration
- Error Sources
- Analysis Tools
- Time Tag data
- Target Acquisitions
- Data Structure and naming conventions
A Very Small IRAF Cheat Sheet:
There are just a handful of IRAF and UNIX tasks that you need to get started looking at your data.
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Command Meaning
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lpr filename To print a file
cd To change directories,
e.g.- cd /where/you/want/to/go
ls To list files in that directory
apropos To find tasks relating to what you want to do,
e.g.- apropos
plot will give you many plotting package options
display To display an image
splot To plot a spectra
epar To edit a task parameter file
lpar To look at a task parameter file
imhead To look at a data header
catfits To list the header extensions in a .fits file
implot Plot lines and columns of images
sgraph To plot spectra
(in either image form or binary tables)
echplot Generate plots of STIS extracted spectral orders
x1d Extract a colelction of 1-D spectra from a
calibrated 2-D ACCUM image
tomultispec Converts spectra from rows of a FITS 2-D
binary table to an IRAF multispec image
infostis To get information about your dataset
help To get help on a task, e.g.- help splot
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