where <option flag> and the associated <specification> are given in Table 9.1. For example, to run Overlap using a namelist cdf/overlap_I1.nl on a list of images in /data/IRAC/bcd/ImageList.txt, you would type the following:
Mosaicking is done on the command line using the Perl wrapper script mosaic.pl. The syntax is as follows:
unix% mosaic.pl <option flag> <specification>
where <option flag> and the associated <specification> are given in Table 9.2. The default locations for all of the files except for the namelist file can be overridden by providing the full path name, for example:
APEX Multiframe is run on the command line using the perl wrapper script apex.pl. The syntax is as follows:
unix% apex.pl <option flag> <specification>
where <option flag> and the associated <specification> are given in Table 9.3. The default locations for all the files except for the namelist file can be overridden by providing the full path name. For example:
will run apex.pl using the namelist cdf/apex_I1.nl and the input image list given in /data/IRAC/ch1/bcd/ImageList.txt.
9.7.2 APEX User List Multiframe (apex_user_list.pl)
APEX User List Multiframe is run as follows:
unix% apex_user_list.pl <option> <specification>
The available options are the same as for APEX Multiframe, with the addition of one more flag,
-u.
Table 9.3: List of options that can be called from the command line when running apex.pl and apex_user_list.pl.
Option Flag
Specification File (example)
Default Location
Required/Optional
-n
namelist of input parameters (apex.nl)
./cdf/
required
-I (capital i)
list of input images (ImageList.txt)
./
required
-u
name of user input source list (user_list.tbl)
./
required for User List mode only.
-m
PRF map (PRFmap.tbl)
./cal/
either a PRF map or a PRF image is required
-p
PRF image (PRF.fits)
./cal/
either a PRF map of a PRF image is required
-P
mosaic PRF image (Mosaic_PRF.fits)
./cal/
required
-S
list of input uncertainty images (SigmaList.txt)
./
optional
-d
list of DCE status mask images (IMaskList.txt)
./
optional
-M
permanently damaged pixel mask image (pmask.fits)
./cal/
optional
-R
list of outlier mask images (RMaskList.txt)
./
optional
-F
Fiducial Image Frame file (FIF.tbl)
./<output directory>/
optional
-O
Output directory
./
optional
9.7.3 APEX QA Multiframe (apex_qa.pl)
Residual image creation for APEX Multiframe is run on the command line as follows:
unix% apex_qa.pl <option flag> <specification>
where <option flag> and the associated <specification> are given in Table 9.4. As with the apex.pl script, default locations for all of the files except for the namelist file can be overridden by providing the full path name.
Table 9.4: List of options that can be called from the command line when running apex_qa.pl in multiframe mode (i.e. with apex.pl or apex_user_list.pl)
Option Flag
Specification File (example)
Default Location
Required/Optional
-n
namelist for creating residual images (apex_qa.nl)
./cdf/
required
-u
namelist for mosaicking of residual images (mosaic_qa.nl)
./cdf/
required
-E
point source list from apex.pl (extract.tbl)
./
required
-I (capital i)
list of input images (ImageList.txt)
./
required
-m
PRF map (PRFmap.tbl)
./cal/
either a PRF map or a PRF image is required
-p
PRF image (PRF.fits)
./cal/
either a PRF map of a PRF image is required
-S
list of input uncertainty images (SigmaList.txt)
./
optional
-d
list of DCE status mask images (IMaskList.txt)
./
optional
-M
permanently damaged pixel mask image (pmask.fits)
./cal/
optional
-R
list of outlier mask images (RMaskList.txt)
./
optional
-F
Fiducial Image Frame file (FIF.tbl)
./<output directory>/
optional
-O
Output directory
./
optional
9.7.4 Single-frame mode (apex_1frame.pl)
APEX Single Frame is carried out on the command line using the Perl wrapper script apex_1frame.pl. The syntax is as follows:
where <option flag> and the associated <specification> are given in Table 9.5. The default locations for all of the files except for the namelist file can be overridden by providing the full path name, for example:
The available options are the same as for APEX Single Frame, with the addition of one more flag, -u. See Table 9.5 for the available input options.
9.7.6 Single Frame Residual Image Creation (apex_qa.pl)
Residual image creation for APEX Single Frame is run on the command line as follows:
unix% apex_qa.pl <option flag> <specification>
where <option flag> and the associated <specification> are given in Table 9.6. As with the apex_1frame.pl script, default locations for all of the files except for the namelist file can be overridden by providing the full path name.
Table 9.5: List of options that can be called from the command line when running apex_1frame.pl or apex_user_list_1frame.pl
Option Flag
Specification File (example)
Default Location
Required/Optional
-n
namelist of input parameters (apex_1frame.nl)
./cdf/
required
-i
input image (mosaic.fits)
./
required
-u
name of user input source list (user_list.tbl)
./
required for User List mode only.
-m
PRF map (PRFmap.tbl)
./cal/
either a PRF map or a PRF image is required
-p
PRF image (PRF.fits)
./cal/
either a PRF map of a PRF image is required
-s
input uncertainty image (mosaic_unc.fits)
./
optional
-C
input coverage map image (mosaic_cov.fits)
./
optional
-d
DCE status mask image (mosaic_imask.fits)
./
optional
-M
permanently damaged pixel mask image (pmask.fits)
./cal/
optional
-R
outlier mask image (mosaic_rmask.fits)
./
optional
-O
Output directory
./
optional
Table 9.6: List of options that can be called from the command line when running apex_qa.pl in single-frame mode (i.e. with apex_1frame.pl)
Option Flag
Specification File (example)
Default Location
Required/Optional
-n
namelist for creating residual images (apex_qa.nl)
./cdf/
required
-T
input image (mosaic.fits)
./
required
-E
point source list from apex_1frame.pl (extract.tbl)
./
required
-P
mosaic PRF image (PRF.fits)
./cal/
required
-F
Fiducial Image Frame file (FIF.tbl)
./<output directory>/
optional
-O
Output directory
./
optional
9.8 Running PRF Estimate on the command line
PRF Estimate is run on the command line using the script prf_estimate.pl. The script expects a list of FITS images and a namelist file as input. The format of the input list is given in §3.2 MOPEX Input List Files, and the format of the namelist is described in §9.4. The syntax for running PRF Estimate is as follows:
where <option flag> and the associated <specification> are given in Table 9.7. The default locations for all of the files except for the namelist file can be overridden by providing the full path name, for example:
