MOPEX Online Manual
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Point Source Extraction (APEX)
APEX performs multiframe (apex.pl) and single-frame (apex_1frame.pl) point source extraction, and can also be used to create residual mosaics by subtracting point sources from input images using the results of point source extraction (apex_qa.pl). It can do both profile-fitting and aperture photometry.
Multiframe Point Source Extraction (apex.pl)
For multi-frame point source extraction, the individual images are interpolated and co-added. Point source detection is carried out on the co-added images (i.e. the mosaic). The main components of point source detection are non-linear matched filtering and image segmentation. They produce a detection list with the potential point source position estimates. Subsequent point source estimation is performed by PRF (Point Response Function) fitting of the potential point sources from the detection list. The fitting is performed simultaneously in all the input images. The advantage of apex.pl over apex_1frame.pl is seen in data with intra-pixel variability (e.g. IRAC data) or data where the PRF varies across the array (e.g. both IRAC and MIPS). In well-sampled data with no intra-pixel variation in sensitivity or PRF variability across the array, the results will be the same as for apex_1frame.pl. APEX features passive and active deblending. Aperture photometry is always carried out on the mosaicked image, regardless of whether you run apex.pl or apex_1frame.pl
Single Frame Point Source Extraction (apex_1frame.pl)
For single-frame point source extraction, the detection and estimation as described above are performed on a single input image (e.g. a mosaic).
Residual Image Creation (apex_qa.pl)
The script apex_qa.pl creates residual images for both Multiframe and Single Frame modes by subtracting the detected point sources from the input image(s). Input requirements differ depending on whether you are running Multi- or Single-Frame mode. See below for the input options.
Basic Input Requirements
In order to carry out point source extraction, MOPEX will expect some or all of the following files as input. See the sections on Input for more information on the format of these files.- A text file containing a list of input data images or a single input image (e.g. Spitzer BCD frames; required)
- A text file containing a list of input uncertainty images or a single uncertainty image(optional)
- A text file containing a list of input status masks images or a single mask image(optional)
- A PRF image file or PRF map (e.g. PRF.fits; required)
- A permanently damaged pixel mask image (pmask; optional)
- A "namelist" file specifying the parameters to be used for mosaicking (Command-Line MOPEX only; required)
Running APEX
1.1 Multi-frame Point Source Extraction (apex.pl)Multi-frame APEX is done on the command line using the perl wrapper script apex.pl. The syntax is as follows:
prompt> apex.pl <option flag> <specification>
where <option flag> may be: -n, -I, -m, -p, -P, -S, -d, -M, -R, -F, -O, any one of which, if specified, must be followed by a blank space and a corresponding specification, as given in the following table. More than one option flag (with corresponding specification) can be included, and they can be given in any order. The only option that must be called from the command line is the namelist; the other input files can be defined as parameters within the namelist. The default locations for all of the files except for the namelist file can be overridden by providing the full path name, for example:
prompt> apex.pl -n apex_I1.nl -I /home/joe/data/IRAC/ch1/bcd/ImageList.txt
See the page on Input for more information on the input and namelist files.
| Option Flag | Specification File (example) | Default Location | Required/Optional |
|---|---|---|---|
| -n | namelist of input parameters (apex.nl) | ./cdf/ | required |
| -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 |
| -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 |
1.2 Multiframe Residual Image Creation (apex_qa.pl)
Residual image creation is run on the command line as follows:
prompt> apex_qa.pl <option flag> <specification>
where <option flag> may be: -n, -u, -E, -I, -m, -p, -S, -d, -M, -R, -F, -O, any one of which, if specified, must be followed by a blank space and a corresponding specification, as given in the following table. More than one option flag (with corresponding specification) can be included, and they can be given in any order. The only option that must be called from the command line is the namelist; the other input files can be defined as parameters within the namelist. 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. See the page on Input for more information on the input and namelist files.
| 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 | 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 |
2.1 Single-frame mode (apex_1frame.pl)
Single-frame APEX is done on the command line using the perl wrapper script apex_1frame.pl. The syntax is as follows:
prompt> apex_1frame.pl <option flag> <specification>
where <option flag> may be: -n, -i, -m, -p, -s, -C, -d, -M, -R, -O, any one of which, if specified, must be followed by a blank space and a corresponding specification, as given in the following table. More than one option flag (with corresponding specification) can be included, and they can be given in any order. The only option that must be called from the command line is the namelist; the other input files can be defined as parameters within the namelist. The default locations for all of the files except for the namelist file can be overridden by providing the full path name, for example:
prompt> apex_1frame.pl -n apex_1frame_I1.nl -i /home/joe/data/IRAC/ch1/Mosaic/mosaic_ch1.fits
See the page on Input for more information on the input and namelist files.
| 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 |
| -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 |
2.2 Single Frame Residual Image Creation (apex_qa.pl)
Residual image creation is run on the command line as follows:
prompt> apex_qa.pl <option flag> <specification>
where <option flag> may be: -n, -T, -E, -P, -F, -O, any one of which, if specified, must be followed by a blank space and a corresponding specification, as given in the following table. More than one option flag (with corresponding specification) can be included, and they can be given in any order. The only option that must be called from the command line is the namelist; the other input files can be defined as parameters within the namelist. 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. See the page on Input for more information on the input and namelist files.
| 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 |
| Contents | ~ | Previous: Mosaic Modules - Create RMask Mosaic | ~ | Next: APEX Pipeline Stages |
