Updated/corrected and the wf3rej.rst and wf3rej.py files #71
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mdlpstsci
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docs/wfc3tools/wf3rej.rst
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| and WFPC2 data (`crrej`), providing a well-tested and robust procedure. | ||
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| First, `wf3rej` temporarily removes the sky background from each input image | ||
| (if requested via the SKYSUB in the CRREJTAB or by a parameter passed |
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i would reword this slightly for clarity: (if specified via the SKYSUB parameter in the CRREJTAB, or by the parameter passed to the Python...
| * a Python list of filenames | ||
| * a partial filename with wildcards (``\*raw.fits``) | ||
| * filename of an ASN table (``\*asn.fits``) | ||
| * a partial filename with wildcards (``*flt.fits``) |
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so you can't pass in an ASN table? that input option was removed from the docs here
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The option of ASN was removed because it was not actually supported by the underlying C code.
| Rejection propagation threshold. | ||
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| badinpdq : int, default=0 | ||
| Data quality flag bits to reject. | ||
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| crmask : bool, default=False | ||
| If True, flag CR in input DQ images. | ||
| crmask : bool, default=Setting to be read from CRREJTAB. |
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what is the default if not specified in CRREJTAB? I imagine all of these parameters have coded defaults that are overridden by CRREJTAB and then by user input?
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Values for the optional input parameters are expected be specified on the command line or resident in the CRREJTAB. If the parameters are not specified AND the CRREJTAB does not exist or has some other issue (i.e., missing the column for badinpdq), the executable reports an error and stops. In this case there are NO default values in the source code which are then replaced with CRREJTAB or command line input.
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| shadcorr : bool, default=False | ||
| If True, perform shading shutter correction. | ||
| shadcorr : bool, default=Setting to be read from SHADCORR keyword value in primary header of first image to process. |
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same also applies here. i think the docstring should have whatever the coded default is if there is one (in this case, seems to be none) and a note that header values will take precedence
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This is a calibration step keyword which has values of PERFORM, SKIPPED, or OMIT. This is set during the creation of the RAW files from the POD file source and keyword rules in Operations (or at least before it gets to the calibration pipeline software). A user can override the setting as desired. The specific setting of the *CORR calibration step keyword is dependent aspects of the data being process, and (again) is controlled by the "rules" external to the calibration pipeline software.
wfc3tools/wf3rej.py
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| array and is ignored when images are summed together. Surrounding pixels | ||
| within some expansion radius (CRRADIUS) are marked as ‘SPILL’ pixels and | ||
| are given less stringent detection thresholds. | ||
| Background discussion cn the wf3rej algorithm can be found in the following locations: |
| - a Python list of filenames | ||
| - a partial filename with wildcards (``*raw.fits``) | ||
| - filename of an ASN table (``*asn.fits``) | ||
| - a partial filename with wildcards (``*flt.fits``) |
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just clarifying the change here - this function does not take in associations anymore?
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This function actually could never process ASN tables as the underlying C code does not support this feature.
wfc3tools/wf3rej.py
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| within some expansion radius (CRRADIUS) are marked as ‘SPILL’ pixels and | ||
| are given less stringent detection thresholds. | ||
| Background discussion cn the wf3rej algorithm can be found in the following locations: | ||
| https://wfc3tools.readthedocs.io/en/latest/wfc3tools/wf3rej.html, |
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and Section 3.4.5 of the WFC3 Data Handbook.
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| for image in infiles: | ||
| if not os.path.exists(image): | ||
| raise IOError("Input file not found: {0}".format(image)) | ||
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| # Generate a comma-separated string of the input filenames | ||
| input = ','.join(infiles) | ||
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| call_list.append(input) | ||
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| if output: |
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For the lines below, raising errors instead of printing statements and returning errors will cut a few lines (not necessary just a little cleaner)
Removed background documentation from wf3rej.py as this text belongs in the docs. Updated/added examples for both Python and C executable usage. Provided explanatory text as to the actions taken by the underlying program when the options use their default values.
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Appropriate code review suggestions addressed in 180ba7d. |
mdlpstsci
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@cshanahan1 @FDauphin I am starting to prep for a new build release candidate which can include as many WFC3 changes that can fit. This PR needs a re-review. Thanks. |
@mdlpstsci The review was requested for @spacetelescope/wfc3tools-maintainers (which I do not think I have access to) instead of my profile. |
Both the "readthedocs" documentation, as well as the wf3rej.py routine were updated/corrected. Removed background documentation from wf3rej.py as this text belongs in the docs. Updated/added examples for both Python and C executable usage. Provided explanatory text as to the actions taken by the underlying program when the options use their default values.