Marker Analysis Routines in SAOtng

As described elsewhere, each file type known to SAOtng can have user-defined analysis commands associated with it. File types also can have analysis commands that are defined for specific marker types, so that you can run analysis within an individual marker. For example, you might place a number of circular markers on an image and then retrieve the counts within each marker separately. Or, you might use a plot program on individual line markers to plot the cut of the image defined by that line. As with file-based analysis commands, these marker analysis commands are defined at start-up time by means of ASCII descriptions. The marker analysis commands associated with the currently displayed image are available for execution from the marker's menu (right mouse button inside a marker).

When activated, a marker analysis command first is macro-expanded to fill in user-defined arguments and then is executed externally using the system() function (see Macro expansion in SAOtng. As with file-based markers, results can be displayed in a separate window or even can be sent back to SAOtng. The ASCII file that defines the known image files consists of one or more file descriptors, each of which has the following format:

• A help line describing the file types
• A space-separated list of templates
• A space-separated list of markers for this command
• The command line for the analysis program

Note that in the marker analysis command, the current marker is specified by means of the $active macro. For example, the default analysis file currently contains the following:

#
# Marker Analysis command descriptions:
#	help
#	file templates
#	valid regions
#	analysis command line
display this region
*
all
echo The active region is: $active

counts -- number of events in active region
*.qp *.imh 
circle rectangle ellipse
uiraf '${xraybin}'/x_xspatial.e imcnts source='${filename}' region=$active bkgd=0 table=NONE | XText -title 'imcnts: ${filename}'

If more than one marker analysis file is supplied to SAOtng via the -manalysis command switch (or the SAOTNG_MANAL environment variable), then the user can specify how to present marker analysis routines in the marker analysis menu using the -analformat command line option (or the SAOTNG_ANALFORMAT environment variable). By default, this is set to "submenu", meaning that marker analysis routines from different analysis files will be grouped in sub-menus of the marker analysis menu. If the analformat is set to "line", then all marker analysis routines will be placed in the top level marker analysis menu, but tasks from different files will be separated by lines. If the value of "none", then no separation will be made between marker analysis tools from different files. These options are useful if a large number of analysis tools are loaded from different files.

Last Updated June 14, 1997