MOPEX Online Manual
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Full List of Modules in MOPEX
The following tables contain a full list of all of the modules available in MOPEX, with their namelist triggers, a brief description, and the prerequisites for each module. The modules are organised in the order that you might encounter them in the MOPEX scripts. Each module name links to the relevant, more detailed, manual page.
Overlap Modules
| Module Name | Namelist Trigger | Brief Description | Module Prerequisites |
|---|---|---|---|
| S/N Estimator | compute_uncertainties_internally | internally estimates the uncertainty for each pixel in the image when no independent uncertainty estimate is available. Only use if you do not trust the uncertainty images provided with your Spitzer data download. | none |
| MedFilter | run_medfilter | performs background subtraction of the individual images. Only required if you intend to use Bright Object Masking | none |
| Fiducial Image Frame | run_fiducial_image_frame | creates the unified grid coordinate system and defines the spatial boundaries that will include all of the input data frames (the FIF table). | none |
| Detect (Outlier) | run_detect_outlier | Performs image segmentation and produces detection maps of bright objects. This identifies bright pixels that should not contribute to the background matching calculation. | none |
| Mosaic Interpolate | run_mosaic_int | performs a projection of input images onto a 2D plane defined by the FIF table and interpolates the input pixels to the output array. Also corrects for optical distortion in the input images. | Fiducial Image Frame; S/N Estimator (if S/N Estimator is turned on). |
| Compute Overlap Correction | compute-overlap-correction | computes the correction needed to set the background of all overlapping images to a constant value. Optionally applies this correction to the input images. | Mosaic Interpolate |
| Quicklook Mosaic | mosaic-corrected-images | creates a quick and dirty mosaic of the background-corrected images to check the results of the overlap correction. | Mosaic Interpolate |
Mosaic Modules
| Module Name | Namelist Trigger | Brief Description | Module Prerequisites |
|---|---|---|---|
| S/N Estimator | compute_uncertainties_internally | internally estimates the uncertainty for each pixel in the image when no independent uncertainty estimate is available. Only use if you do not trust the uncertainty images provided with your data download. | none |
| MedFilter | run_medfilter | performs background subtraction of the individual images. Only required if you intend to use Single Frame or Dual Outlier detection. | none |
| Detect RadHit | run_detect_radhit | performs single frame radhit rejection. It is the simplest of the outlier rejection schemes. | none |
| Fiducial Image Frame | run_fiducial_image_frame | creates the unified grid coordinate system and defines the spatial boundaries that will include all of the input data frames (the FIF table). | none |
| Mosaic Geometry | run_mosaic_geom | finds all of the input images that overlap with the FIF table, allowing the user to make a mosaic of a subset of the input data frames. | none, but requires a hand-edited version of the Fiducial Image Frame table. |
| Mosaic Interpolate | run_mosaic_int | performs a projection of input images onto a 2D plane defined by the FIF table and interpolates the input pixels to the output array. Also corrects for optical distortion in the input images. | Uses the output from S/N Estimator (but only if S/N Estimator is turned on). |
| Detect (Outlier) | run_detect_outlier | first of four modules run as part of dual outlier detection. Performs image segmentation and produces detection maps of point sources and radhits. | none |
| Mosaic Projection | run_mosaic_proj | second of four modules run as part of dual outlier detection. Projects the detection maps from Detect (Outlier) onto a common reference frame, and interpolates. | Detect (Outlier) |
| Mosaic Coverage | run_mosaic_covg | produces a preliminary coverage map covering the whole FIF for use in the later module Mosaic RMask. | Mosaic Interpolate |
| Mosaic Dual Outlier | run_mosaic_dual_outlier | third of four modules run as part of dual outlier detection. Applies the user-defined criteria to classify outliers using both spatial and temporal information. | Mosaic Projection |
| Level | run_level | last of four modules run as part of dual outlier detection. Corrects the dual outlier maps produced in Mosaic Dual Outlier to ensure that the edges of point sources are not accidentally rejected | Mosaic Dual Outlier |
| Mosaic Outlier | run_mosaic_outlier | runs the multiframe outlier rejection method to flag bad pixels. | Mosaic Interpolate |
| Mosaic Box Outlier | run_mosaic_box_outlier | runs the Box Outlier rejection method to flag bad pixels. | Mosaic Interpolate |
| Mosaic RMask | run_mosaic_rmask | combines outlier rejection information into a single RMask: bit 0 (single frame radhit detection), bit 1 (multiframe temporal outlier detection), bit 2 (dual outlier detection), bit 3 (box outlier detection) | Mosaic Outlier, Level, Mosaic Coverage |
| Mosaic Reinterpolate | run_mosaic_reinterp | re-runs the interpolation, this time including information from the RMasks. Only pixels flagged by the RMasks are reinterpolated. | Mosaic Interpolate, Mosaic RMask |
| Fix Coverage | run_fix_coverage | after all outlier pixels have been identified, this module gives the option to suppress the use of pixels that have very small coverage (repeated observations at the same point on the sky). Pixels whose usage is suppressed have their coverage set to 0 in new coverage maps. | Mosaic Interpolate (Mosaic Reinterpolate) |
| Mosaic Coadder | run_mosaic_coadder | co-adds the interpolated images to create one mosaic image. Co-addition can be performed on Tiles to address computer memory considerations. Several co-addition schemes are available. | Mosaic Interpolate (Mosaic Reinterpolate) |
| Mosaic Combiner | run_mosaic_combiner | combines the co-added tiles into a single mosaicked image. This module must be run, even when there is only one tile, in order to create the expected output files. | Mosaic Coadder |
| Mosaic Medfilter | run_mosaic_medfilter | performs median background subtraction of the mosaic image. | Mosaic Combine |
APEX and APEX 1Frame Modules
| Module Name | Namelist Trigger | Brief Description | Module Prerequisites |
|---|---|---|---|
| Fiducial Image Frame | run_fiducial_image_frame | creates the unified grid coordinate system and defines the spatial boundaries that will include all of the input data frames (the FIF table). | none |
| Mosaic Interpolate | run_mosaic_int | performs a projection of input images onto a 2D plane defined by the FIF table and interpolates the input pixels to the output array. Also corrects for optical distortion in the input images. Only required if you are not using the results from the Mosaic processing. | Fiducial Image Frame |
| Mosaic Coadder | run_mosaic_coadder | co-adds the interpolated images to create one mosaic image. Co-addition can be performed on Tiles to address computer memory considerations. Several co-addition schemes are available. Only required if you are not using the results from Mosaic processing | Mosaic Interpolate |
| Mosaic Combiner | run_mosaic_combiner | combines the co-added tiles into a single mosaicked image. This module must be run, even when there is only one tile, in order to create the expected output files. Only required if you are not using the results from Mosaic processing. | Mosaic Coadder |
| Detect MedFilter | run_detect_medfilter | performs background subtraction of the individual or mosaicked images that will be used for source detection. | Mosaic Combine (or the output of mosaic.pl) |
| Gaussnoise | run_gaussnoise | estimates the background flucuations in the input image for use in the signal-to-noise ratio estimation | none |
| Point Source Probability | run_pointsourcerob | filters the input coadded image to estimate the probability at each pixel of having a point source above the noise. | Mosaic Coadd (or the output of mosaic.pl) |
| Bright Detect | run_bright_detect | detects bright sources in the input images, and includes source shape information. Does not record the blends, and so generally cannot replace Detect. | Point Source Probability |
| Detect | run_bright_detect | performs image segmentation and computes the centroids for detected point sources. | Point Source Probability |
| Extract MedFilter | run_extract_medfilter | performs background subtraction of either the mosaicked image (apex_1frame.pl) or tiles (apex.pl) that will be used for point source extraction. | Detect |
| Fit Radius | run_fit_radius | determines a fitting area for each source in the detect table. This module is optional if the parameters Fitting_Area_X,Y are defined in the Source Estimate module. | Detect |
| Select Detect | run_select_detect | allows the user to select the columns and rows from the detect table to be written out to the full extract table | Detect |
| Source Estimate | run_sourcestimate | performs point source estimation using PRF-fitting. Estimates fluxes refines the positions of the point source candidates from the detect table. | Detect; Fit Radius |
| Aperture (Photometry) | run_aperture | calculates the flux(es) within the specified circular aperture(s) for each source in the extract table. The module will optionally subtract a background value calculated from a user-defined annulus. | Source Estimate |
| Select | run_select | allows the user to select the columns and rows to be written to the final extract table, based on a range of user-specified conditions. | Source Estimate; Aperture (Photometry) |
APEX QA Modules
| Module Name | Namelist Trigger | Brief Description | Module Prerequisites |
|---|---|---|---|
| Point Source Subtract | create_residual_images (with apex.pl) create_residual_mosaic (with apex_1frame.pl) |
subtracts the extracted point sources from the input images or the input mosaic to create residual images. Invaluable for testing the results of PRF-fitting. | output from either apex.pl or apex_1frame.pl |
| Contents | ~ | Previous: Appendix 2: Fatal Bit Patterns |
