Command Line Tools

Using the command line tools requires a local installation of the CRDS library. Some of the command line tools also interact with the CRDS server in order to implement their functionality.

crds master program

The original DEPRECATED command line syntax, e.g. for the list command was:

% python -m crds.list --status

This was replaced by a NEW more succinct command line syntax, e.g.:

% crds list --status

The ‘crds’ wrapper hides internal structural details of the CRDS package.

For a list of available commands do:

% crds --help

for detail on a single command do, e.g.:

% crds list --help

Specifying File Paths

The command line tools operate on CRDS reference and mapping files both inside and outside the CRDS cache. Files specified without a path are assumed to be in the CRDS cache. Files specified with an explicit absolute or relative path can be located anywhere. See examples below.

In the CRDS cache

To specify a file inside the CRDS file cache, use no path on the file:

% crds diff hst.pmap  hst_0001.pmap  # assumes paths, and nested paths, are
in CRDS cache

This is the default and aligns with the behavior of CRDS rules files.

In the current directory

To specify a file which is not located in the CRDS cache, use an explicit relative or absolute path:

% crds diff ./hst_acs_darkfile_0250.rmap  ./hst_acs_darkfile_0251.rmap

In this example, the ./ is critical for telling CRDS to use the file in the current working directory.

crds.bestrefs

The crds.bestrefs program runs the CRDS library to interpret CRDS reference file assignment rules with respect to dataset parameters.

crds.bestrefs has several use cases which have different modes for fetching input parameters, evaluating bestrefs and/or doing comparisons, and producing output.

crds.bestrefs runs in the HST archive pipeline to populate dataset headers FITS keywords (e.g. DARKFILE) with best reference files.

Other modes of crds.bestrefs are used to support CRDS reprocessing or to test new versions of CRDS rules.

The crds.bestrefs program is not normally used for JWST and best references are assigned automatically as a consequence of running the CAL code.

  • Determines best references with respect to a context or contexts.
  • Optionally updates the headers of file-based data with new recommendations.
  • Optionally compares new results to prior results.
  • Optionally prints source data names affected by the new context.

crds.bestrefs use cases

  1. File (HST Pipeline) Mode

The –files switch can be used to specify a list of FITS dataset files to process. This is used in the HST pipeline in conjunction with –update-headers to fill in dataset FITS headers with recommended best references:

% crds bestrefs  --update-headers  --files j8bt05njq_raw.fits ...

The outcome of this command is updating the best references in the FITS headers of the specified .fits files.

Omitting –update-headers can be used to evaluate bestrefs without altering the input FITS files:

% crds bestrefs --print-new-references --files  j8bt05njq_raw.fits ...

The –new-context switch can be used to choose a context which is not the current default:

% crds bestrefs --new-context hst_0457.pmap --files ...
  1. Reprocessing Mode

The bestrefs reprocessing mode is used in conjunction with archive databases to determine datasets which should be reprocessed as a consequence of the delivery of new reference files.

Reprocessing mode evaluates the same dataset parameters with respect to an old context and a new context and recommends reprocessing datasets where some reference file assignment changes.

Bestrefs reprocessing mode is run automatically on the CRDS servers whenever new reference files are delivered, after the new CRDS context is selected for use by the archive pipeline. It is run e.g. like this:

% crds bestrefs --affected-datasets --old-context  hst_0001.pmap --new-context hst_0002.pmap

—affected-datasets is a “bundle switch” that captures standard options for reprocessing. See crds bestrefs –help for more information on individual switches.

Running reprocessing mode requires setting CRDS_SERVER_URL.

  1. Context Testing Mode

CRDS bestrefs and the archive reprocessing parameters can also provide a quick way to evaluate a new context and/or residual errors. It can answer the question “what classes of errors still exist for the latest context with respect to known parameter sets?”

Context testing mode can be run like this:

% crds bestrefs --check-context --new-context jwst-edit

Context testing also requires setting CRDS_SERVER_URL to obtain archived dataset parameters. Note that during JWST pre-I&T the archive database often contains parameter sets related to obsolete test cases.

Undesired test cases can be weeded out like this:

% crds bestrefs --check-context --new-context jwst-edit --drop-ids JW93135336001_02102_00001.MIRIFUSHORT:JW93135336001_02102_00001.MIRIFUSHORT

New Context

crds.bestrefs always computes best references with respect to a context which can be explicitly specified with the –new-context parameter. If –new-context is not specified, the default operational context is determined by consulting the CRDS server or looking in the local cache.

Old Context

–old-context can be used to specify a second context for which bestrefs are dynamically computed; –old-context implies that a bestrefs comparison will be made with –new-context. If –old-context is not specified, it defaults to None. –old-context is only used for context-to-context comparisons, nominally for CRDS repro.

Lookup Parameter Sources

The following methods can be used to define parameter sets for which to compute best references:

--files can be used to specify a list of FITS files from which to load
  parameters and optionall update headers.

--instruments can be used to specify a list of instruments.  Without
  --diffs-only or --datasets-since this choice selects ALL datasets for the
  specified instruments.

--all-instruments is shorthand for all --instruments supported by the project.
  This parameter can be so memory intensive as to be infeasible.

--datasets is used to specify a list of dataset IDs as would be found under --instruments.

--load-pickles can be used to specify a list of .pkl or .json files that define parameter
  sets.  These can most easily be created using --save-pickle.

Comparison Modes

The –old-context and –compare-source-bestrefs parameters define the best references comparison mode. Each names the origin of a set of prior recommendations and implicitly requests a comparison to the recommendations from the newly computed bestrefs determined by –new-context.

–old-context CONTEXT specifies that the reference results should be computed using the named context.

–compare-source-bestrefs directs that prior reference assignments should be taken from the same stored source which provides matching parameters. These could be from FITS header keywords (e.g. DARKFILE), from live archive parameters, or from prior parameter sets that have been stored in CRDS .json or Python pickle files.

Pickle and .json saves

crds.bestrefs can load parameters and past results from a sequence of .pkl or .json files using –load-pickles. These are combined into a single parameter source in command line order.

crds.bestrefs can save the parameters obtained from various sources into .pkl or .json formatted save files using –save-pickle. The single combined result of multiple pickle or instrument parameter sources is saved. The file extension (.json or .pkl) defines the format used.

The preferred .json format defines a singleton { id: parameters} dictionary on each line as a series of isolated .json objects. Strictly speaking only each individual line is .json, but this localizes any errors.

.json format is preferred over .pkl because it is more transparent and robust across different versions of Python.

Verbosity

crds.bestrefs has –verbose and –verbosity=N parameters which can increase the amount of informational and debug output. Verbosity ranges from 0..100 where 0 means “no debug output” and 100 means “all debug output”. 50 is the default for –verbose.

Bad Files

CRDS files can be designated as scientifically invalid on the CRDS server by the CRDS team. Knowledge of bad files is synchronized to remote caches by crds.bestrefs and crds.sync. By default, attempting to use bad rules or assign bad references will generate errors and fail. crds.bestrefs supports two command line switches, —allow-bad-rules and —allow-bad-references to override the default handling of bad files and enable their use with warnings. Environment variables CRDS_ALLOW_BAD_RULES and CRDS_ALLOW_BAD_REFERENCES can also be set to 1 to establish warnings rather than errors as the default.

crds.sync

The CRDS sync tool is used to download CRDS rules and references from the CRDS server. While the sync tool can download files which are specified explicitly, it’s primary purpose is to download and manage files with respect to specified versions of CRDS rules. While the download directory of files can be explicitly specified, sync is primarily used to download files to a CRDS cache which organizes and can locate files in a standard way.

  • Dry-Running Cache Changes

    Since CRDS cache operations can involve significant network downloads, as a general note, crds.sync can be run with —readonly-cache —verbose switches to better determine what the effects of any command should be. This can be used to gauge download sizes or list files before deleting them.

  • Syncing Rules

    Typically syncing CRDS files is done with respect to particular CRDS contexts:

    Synced contexts can be explicitly listed:

    % crds sync  --contexts hst_0001.pmap hst_0002.pmap
    

    this will recursively download all the mappings referred to by .pmaps 0001 and 0002.

    Synced contexts can be specified as a numerical range:

    % crds sync --range 1:3
    

    this will also recursively download all the mappings referred to by .pmaps 0001, 002, 0003.

    Synced contexts can be specified as –all contexts:

    % crds sync --all
    

    this will recursively download all CRDS mappings for all time.

  • Syncing References By Context

    Because complete reference downloads can be enormous, you must explicitly specify when you wish to fetch the references which are enumerated in particular CRDS rules:

    % crds sync  --contexts hst_0001.pmap hst_0002.pmap  --fetch-references
    

    will download all the references mentioned by contexts 0001 and 0002.

  • Syncing Specific Files

    Downloading an explicit list of files can be done by like this:

    % crds sync  --files hst_0001.pmap hst_acs_darkfile_0037.fits
    

    this will download only those two files.

    Specific files can also be downloaded using symbolic names and output to a specified directory, for example, like this:

    % crds sync --files jwst-nircam-flat-edit --output-dir .
    

    Will download the latest NIRCAM FLAT .rmap to the current working directory, which can be useful when doing CRDS rmap adjustments.

  • Removing Unused Files

    CRDS rules from unspecified contexts can be removed like this:

    % crds sync  --contexts hst_0004.pmap hst_0005.pmap --purge-mappings
    

    while this would remove references which are not in contexts 4 or 5:

    % crds sync  --contexts hst_0004.pmap hst_0005.pmap --purge-references
    

    Again, both of these commands remove cached files which are not specified or implied.

  • References for Dataset Files

    References required by particular dataset files can be cached like this:

    % crds sync  --contexts hst_0001.pmap hst_0002.pmap --dataset-files  <dataset_files...> e.g. acs_J8D219010.fits
    

    This will fetch all the references required to support the listed datasets for contexts 0001 and 0002.

    This mode does not update dataset file headers. See also crds.bestrefs for similar functionality with header updates.

  • References for Dataset Ids

    References for particular dataset ids can be cached like this:

    % crds sync  --contexts hst_0001.pmap hst_0002.pmap --dataset-ids  <ids...>  e.g. J6M915030
    

    This will fetch all the references required to support the listed dataset ids for contexts 0001 and 0002.

  • Checking and Repairing Large Caches

    Large Institutional caches can be checked and/or repaired like this:

    % crds sync --contexts hst_0001.pmap --fetch-references --check-sha1sum --repair-files
    

    will download all the files in hst_0001.pmap not already present.

    Both mappings and references would then be checked for correct length, sha1sum, and status.

    Any files with bad length or checksum would then be deleted and re-downloaded. This is really intended for a large existing cache.

    File checksum verification is optional because it is time consuming. Verifying the contents of the current HST shared cache requires 8-10 hours. In contrast, doing simple length, existence, and status checks takes 5-10 minutes, sufficient for a quick check but not foolproof.

  • Checking Smaller Caches, Identifying Foreign Files

    The simplest approach for “repairing” a small cache is to delete it and resync. One might do this after making temporary modifications to cached files to return to the archived version:

    % rm -rf $CRDS_PATH
    % crds sync  -- ...  # repeat whatever syncs you did to cache files of interest
    

    A more complicated but also more precise approach can operate only on files already in the CRDS cache:

    % crds sync --repair-files --check-sha1sum --files `crds list --all --cached-mappings --cached-references`
    

    This approach works by using the crds.list command to dump the file names of all files in the CRDS cache and then using the crds.sync command to check exactly those files.

    Since crds.list will print the name of any file in the cache, not just files from CRDS, the second approach can also be used to detect (most likely test) files which are not from CRDS.

    For smaller caches –check-sha1sum is likekly to be less of a performance/runtime issue and should be used to detect files which have changed in contents but not in length.

  • Removing Blacklisted or Rejected Files

    crds.sync can be used to remove the files from specific contexts which have been marked as “bad”:

    % crds sync --contexts hst_0001.pmap --fetch-references --check-files --purge-rejected --purge-blacklisted
    

    would first sync the cache downloading all the files in hst_0001.pmap. Both mappings and references would then be checked for correct length. Files reported as rejected or blacklisted by the server would be removed.

  • Reorganizing Cache Structure

    CRDS now supports two cache structures for organizing references: flat and instrument. flat places all references for a telescope in a single directory, e.g. references/hst. instrument segregates references into subdirectories which name instruments or legacy environment variables, e.g. acs or jref.

    Newly created caches will default to the instrument organization. To migrate a legacy cache with a flat single directory layout to the new structure, sync with –organize=instrument:

    % crds sync --organize=instrument --verbose
    
  • Reorganizing cache structure

    CRDS now supports two cache structures for organizing references: flat and instrument. flat places all references for a telescope in a single directory, e.g. references/hst. instrument segregates references into subdirectories which name instruments or legacy environment variables, e.g. acs or jref.

    Newly created caches will default to the instrument organization. To migrate a legacy cache with a flat single directory layout to the new structure, sync with –organize=instrument:

    % crds sync --organize=instrument --verbose
    

    To migrate to the flat structure, use –organize=flat:

    % crds sync --organize=flat --verbose
    

    While reorganizing, if CRDS makes note of “junk files” in your cache which are obstructing the process of reorganizing, you can allow CRDS to delete the junk by adding –organize-delete-junk.

    The –organize switches are intended to be used only on inactive file caches when calibration software is not running and actively using CRDS.

crds.certify

crds.certify checks a reference or mapping file against constraints on legal matching parameter values. For reference files, crds.certify also performs checks of the FITS format and when given a context, and will compare the given file against the file it replaces looking for new or missing table rows.

  • crds certify –help yields:

    usage: crds certify ...
       [-h] [-d] [-r] [-a] [-e] [-p] [-x COMPARISON_CONTEXT]
       [-y COMPARISON_REFERENCE] [-s] [--dump-unique-errors]
       [--unique-errors-file UNIQUE_ERRORS_FILE]
       [--all-errors-file ALL_ERRORS_FILE] [-v] [--verbosity VERBOSITY] [-R]
       [-I] [-V] [-J] [-H] [--stats] [--profile PROFILE] [--log-time] [--pdb]
       [--debug-traps]
       files [files ...]
    
  • Checks a CRDS reference or mapping file:

    1. Verifies basic file format: .fits, .json, .yaml, .asdf, .pmap, .imap, .rmap
    2. Checks references for required keywords and values, where constraints are defined.
    3. Checks CRDS rules for permissible values with respect to defined reference constraints.
    4. Checks CRDS rules for accidental file reversions or duplicate lines.
    5. Checks CRDS rules for noteworthy version-to-version changes such as new or removed match cases.
    6. Checks tables for deleted or duplicate rows relative to a comparison table.
    7. Finds comparison references with respect to old CRDS contexts.
    
  • positional arguments:

    files
    
  • optional arguments:

    -h, --help            show this help message and exit
    -d, --deep            Certify reference files referred to by mappings have valid contents.
    -r, --dont-recurse-mappings   Do not load and validate mappings recursively,  checking only directly specified files.
    -a, --dont-parse      Skip slow mapping parse based checks,  including mapping duplicate entry checking.
    -e, --exist           Certify reference files referred to by mappings exist.
    -p, --dump-provenance  Dump provenance keywords.
    -x COMPARISON_CONTEXT, --comparison-context COMPARISON_CONTEXT   Pipeline context defining comparison files.  Defaults to operational context,  use 'none' to suppress.
    -y COMPARISON_REFERENCE, --comparison-reference COMPARISON_REFERENCE  Comparison reference for tables certification.
    -s, --sync-files      Fetch any missing files needed for the requested difference from the CRDS server.
    -v, --verbose         Set log verbosity to True,  nominal debug level.
    --verbosity VERBOSITY Set log verbosity to a specific level: 0..100.
    -R, --readonly-cache  Don't modify the CRDS cache.  Not compatible with options which implicitly modify the cache.
    
  • crds.certify is normally invoked like e.g.:

    % crds certify --comparison-context=hst_0027.pmap --run-fitsverify --dump-provenance ./some_reference.fits
    
    % crds certify ./hst_acs_darkfile_00250.rmap
    
  • To run crds.certify on a reference(s) to verify basic file format and parameter constraints:

    % crds certify --comparison-context=hst_0027.pmap   ./some_reference.fits...
    

    If some_reference.fits is a table, a comparison table will be found in the comparison context, if appropriate.

  • For recursively checking CRDS rules do this:

    % crds certify hst_0311.pmap --comparison-context=hst_0312.pmap
    

    If a comparison context is defined, checked mappings will be compared against their peers (if they exist) in the comparison context. Many classes of mapping differences will result in warnings.

  • For reference table checks, a comparison reference can also be specified directly rather than inferred from context:

    % crds certify ./some_reference.fits --comparison-reference=old_reference_version.fits --run-fitsverify --dump-provenance
    
  • For more information on the checks being performed, use –verbose or –verbosity=N where N > 50.

    % crds certify –verbose …

  • Invoking crds.certify on a context mapping recursively certifies all sub-mappings.

  • Adding –deep when specifying mappings causes CRDS to certify not just the mappings, but every reference file referred to by the mappings:

    % crds certify --deep jwst-edit
    

    asks CRDS to certify all of the latest CRDS rules and references.

crds.list

crds.list is a swiss army knife program for dumping various forms of CRDS information.

General categories of information driven by switches include:

  1. Overall CRDS configuration
  2. CRDS server file lists
  3. CRDS cache file lists and paths
  4. Cached file contents or headers
  5. CRDS reprocessing dataset ids and parameters
  6. Listing global default and installed pipeline contexts
  7. Resolving context specifiers into literal context names

Many crds list services require setting CRDS_SERVER_URL to a valid CRDS server to provide a source for the headers.

For HST:

% export CRDS_SERVER_URL=https://hst-crds.stsci.edu

or for JWST:

% export CRDS_SERVER_URL=https://jwst-crds.stsci.edu

0. Configuration information governing the behavior of CRDS for simple configurations can be dumped:

% crds list --status
CRDS Version = '7.0.7, bump-version, 7432326'
CRDS_MODE = 'auto'
CRDS_PATH = '/Users/homer/crds_cache_ops'
CRDS_SERVER_URL = 'https://jwst-crds.stsci.edu'
Effective Context = 'jwst_0204.pmap'
Last Synced = '2016-09-20 08:00:09.115330'
Python Executable = '/Users/homer/anaconda/bin/python'
Python Version = '3.5.2.final.0'
Readonly Cache = False

More comprehensive configuration information is also available for advanced configurations:

% crds list --config
... lots of info ....

1. Files known by the CRDS server to belong to specified contexts can be listed even if the files are not installed in a local CRDS Cache.

The –mappings command recursively evaluates and includes all the sub-mappings, i.e. imaps and pmaps, of the specified contexts.

Contexts to list can be specified in a variety of ways:

– To list the references contained by several contexts:

% crds list  --references --contexts hst_0001.pmap hst_0002.pmap ...
vb41935ij_bia.fits
vb41935kj_bia.fits
...

– To list the references in a numerical range of contexts:

% crds list --references --range 1:2 --references
vb41935lj_bia.fits
vb41935oj_bia.fits
...

– To list all mappings, even those not referenced by an imap or pmap:

% crds list --mappings --all
hst.pmap
hst_0001.pmap
hst_0002.pmap
hst_acs.imap
hst_acs_0001.imap
hst_acs_0002.imap
hst_acs_atodtab.rmap
...

–references, –mappings, or both can be listed.

  1. Locally cached files (files already synced to your computer) can be listed:

    % crds list --cached-mappings --full-path
    ...
    
    % crds list --cached-references --full-path
    ...
    

In both cases adding –full-path prints the path of the file within the CRDS cache.

These are merely simple directory listings which ignore the context specifiers and can be grep’ed for finer grained answers.

  1. The contents of cached mappings or references (header only) can be printed to stdout like this:

    % crds list --contexts jwst-fgs-linearity-edit jwst-nirspec-linearity-edit --cat --add-filename | grep parkey
    CRDS - INFO - Symbolic context 'jwst-fgs-linearity-edit' resolves to 'jwst_fgs_linearity_0008.rmap'
    CRDS - INFO - Symbolic context 'jwst-nirspec-linearity-edit' resolves to 'jwst_nirspec_linearity_0009.rmap'
    /cache/path/mappings/jwst/jwst_fgs_linearity_0008.rmap:     'parkey' : (('META.INSTRUMENT.DETECTOR', 'META.SUBARRAY.NAME'), ('META.OBSERVATION.DATE', 'META.OBSERVATION.TIME')),
    /cache/path/mappings/jwst/jwst_nirspec_linearity_0009.rmap:     'parkey' : (('META.INSTRUMENT.DETECTOR', 'META.SUBARRAY.NAME'), ('META.OBSERVATION.DATE', 'META.OBSERVATION.TIME')),
    

this prints the contents of the specified rmaps.

The -edit specifier above refers to mappings contained by the default starting point (.pmap) of future server submissions. It tracks on-going submission work that precedes the adoption of a new context as the default in use by the pipeline.

crds.list –cat can be applied to references and prints out the reference metadata that CRDS views abstractly as the file header.

References need to be catted explicitly by name, but the list can come from the –references command explained above:

% crds list --cat jwst_nirspec_dark_0036.fits
CRDS - INFO - Symbolic context 'jwst-operational' resolves to 'jwst_0167.pmap'
File:  '/grp/crds/jwst/references/jwst/jwst_nirspec_dark_0036.fits'
{'A1_COL_C': '8.9600000e+002',
'A1_CONF1': '2.1846000e+004',
...
}

4. Information about the dataset IDs and parameters used for CRDS reprocessing and regressions can be printed or stored.

Parameter set IDs can be listed for one or more instruments as follows:

% crds list --dataset-ids-for-instruments wfc3...
JCL403010:JCL403ECQ
... hundreds to hundreds of thousands of IDs as shown above ...

IDs can also be captured to a file using UNIX I/O redirection:

% crds list --dataset-ids-for-instruments wfc3   >wfc3.ids

IDs for HST are of the form <product>:<exposure> where many exposures feed into the construction of one product and recalibrating any component exposure suggests recalibrating the combined product.

CRDS stores dataset parameters for regression testing as a JSON dictionaries specifying one set of dataset parameters per line of the file:

% crds list --dataset-headers @wfc3.ids --json > wfc3.headers.json

NOTE: while IDs can be specified directly on the command line, CRDS has an @-notation that means “take IDs from this file”.

The JSON headers are suitable for running through crds.bestrefs to perform reprocessing checks or single context reference file coverage checks shown here:

% crds bestrefs --load-pickle wfc3.headers.json --dump-unique-errors --stats
...  errors related to looking up references for these parameter sets ...

The script crds_dataset_capture combines the process of dumping all IDs for an instrument and dumping their corresponding dataset parameters. IDs files and header files are placed in a dated regression capture directory:

% crds_dataset_capture wfc3 acs ...
... downloads IDs and headers for WFC3, ACS to dated directory ...

The default multi-line format for dataset parameters is more readable than the –json form:

% crds list --dataset-headers jcl403010 --first-id --minimize-header
CRDS - INFO - Symbolic context 'hst-operational' resolves to 'hst_0462.pmap'
CRDS - INFO - Dataset pars for 'JCL403010:JCL403ECQ' with respect to 'hst_0462.pmap'
{'APERTURE': 'WFC1',
 'ATODCORR': 'OMIT',
 'BIASCORR': 'COMPLETE',
 'CCDAMP': 'ABCD',
 'CCDCHIP': '-999.0',
 'CCDGAIN': '2.0',
 'CRCORR': 'OMIT',
 'DARKCORR': 'COMPLETE',
 'DATE-OBS': '2016-02-20',
 'DETECTOR': 'WFC',
 'DQICORR': 'COMPLETE',
 'DRIZCORR': 'COMPLETE',
 'FILTER1': 'CLEAR1L',
 'FILTER2': 'F814W',
 'FLASHCUR': 'LOW',
 'FLATCORR': 'COMPLETE',
 'FLSHCORR': 'OMIT',
 'FW1OFFST': '0.0',
 'FW2OFFST': '0.0',
 'FWSOFFST': '0.0',
 'GLINCORR': 'UNDEFINED',
 'INSTRUME': 'ACS',
 'LTV1': '0.0',
 'LTV2': '0.0',
 'NAXIS1': '4144.0',
 'NAXIS2': '4136.0',
 'OBSTYPE': 'IMAGING',
 'PCTECORR': 'UNDEFINED',
 'PHOTCORR': 'COMPLETE',
 'RPTCORR': 'UNDEFINED',
 'SHADCORR': 'OMIT',
 'SHUTRPOS': 'A',
 'TIME-OBS': '17:32:29.666665',
 'XCORNER': '0.0',
 'YCORNER': '0.0',
 'dataset_id': 'JCL403010:JCL403ECQ'}

Sometimes it’s desirable to know the individual exposures CRDS associates with a product id:

% crds list --dataset-headers jcl403010 --id-expansions-only
CRDS - INFO - Symbolic context 'hst-operational' resolves to 'hst_0462.pmap'
JCL403010:JCL403ECQ
JCL403010:JCL403EEQ
JCL403010:JCL403EGQ
JCL403010:JCL403EIQ
JCL403010:JCL403EKQ
JCL403010:JCL403EMQ
JCL403010:JCL403EOQ
JCL403010:JCL403EQQ
JCL403010:JCL403ESQ
JCL403010:JCL403EUQ
  1. Information about the default context can be printed. There are two variations and a subtle distinction:

    % python m crds.list --operational-context
    jwst_0204.pmap
    

lists the context which has been commanded as default on the CRDS server.

While:

% crds list --remote-context jwst-ops-pipeline
jwst_0101.pmap

lists the context which is in actual use in the associated archive pipeline as reported by a cache sync echo.

During the interval between commanding a new default on the CRDS server and syncing the pipeline CRDS cache, the commanded and actual pipeline contexts can differ.

  1. Resolving context specifiers

Some CRDS tools, including crds.list and crds.sync, support multiple mechanisms for specifying context. The –resolve-contexts command interprets those specifiers into a non-recursive list of literal mapping names and prints them out. –resolve-contexts differs from –mappings because it does not implicitly include all sub-mappings of the specified contexts:

% crds list --resolve-contexts --all
jwst.pmap
jwst_0000.pmap
jwst_0001.pmap
jwst_0002.pmap
jwst_0003.pmap
...

% crds list --resolve-contexts --last 5
jwst_0205.pmap
jwst_0206.pmap
jwst_0207.pmap
jwst_0208.pmap
jwst_0209.pmap

% crds list --resolve-contexts  --contexts jwst-miri-dark-operational
jwst_miri_dark_0012.rmap

% crds list --resolve-contexts --contexts jwst-niriss-superbias-2016-01-01T00:00:00
jwst_niriss_superbias_0005.rmap

crds.diff

crds.diff compares two reference or mapping files and reports differences. For references crds.diff is currently a thin wrapper around fitsdiff but may expand.

For CRDS mappings crds.diff performs a recursive logical difference which shows the full match path to each bottom level change. crds.diff –help yields:

Difference CRDS mapping or reference files.

positional arguments:
  old_file              Prior file of difference.
  new_file              New file of difference.

optional arguments:
  -h, --help            show this help message and exit
  -P, --primitive-diffs
                        Fitsdiff replaced reference files when diffing mappings.
  -T, --mapping-text-diffs
                        In addition to CRDS mapping logical differences,  run UNIX context diff for mappings.
  -K, --check-diffs     Issue warnings about new rules, deletions, or reversions.
  -N, --print-new-files
                        Rather than printing diffs for mappings,  print the names of new or replacement files.  Excludes intermediaries.
  -A, --print-all-new-files
                        Print the names of every new or replacement file in diffs between old and new.  Includes intermediaries.
  -i, --include-header-diffs
                        Include mapping header differences in logical diffs: sha1sum, derived_from, etc.
  -B, --hide-boring-diffs
                        Include mapping header differences in logical diffs: sha1sum, derived_from, etc.
  --print-affected-instruments
                        Print out the names of instruments which appear in diffs,  rather than diffs.
  --print-affected-types
                        Print out the names of instruments and types which appear in diffs,  rather than diffs.
  --print-affected-modes
                        Print out the names of instruments, types, and matching parameters,  rather than diffs.
  -v, --verbose         Set log verbosity to True,  nominal debug level.
  --verbosity VERBOSITY
                        Set log verbosity to a specific level: 0..100.
  -R, --readonly-cache  Don't modify the CRDS cache.  Not compatible with options which implicitly modify the cache.
  -V, --version         Print the software version and exit.
  -J, --jwst            Force observatory to JWST for determining header conventions.
  -H, --hst             Force observatory to HST for determining header conventions.

Reference files are nominally differenced using FITS-diff or diff.

Mapping files are differenced using CRDS machinery to recursively compare too mappings and
their sub-mappings.

Differencing two mappings will find all the logical differences between the two contexts
and any nested mappings.

By specifying --mapping-text-diffs,  UNIX diff will be run on mapping files in addition to
CRDS logical diffs.

By specifying --primitive-diffs,  FITS diff will be run on all references which are replaced
in the logical differences between two mappings.

For example:

    % crds diff hst_0001.pmap  hst_0005.pmap  --mapping-text-diffs --primitive-diffs

Will recursively produce logical, textual, and FITS diffs for all changes between the two contexts.

    NOTE: mapping logical differences (the default) do not compare CRDS mapping headers,  use
    --include-header-diffs to get those as well.

For standard CRDS filenames, crds.diff can guess the observatory. For non-standard names, the observatory needs to be specified. crds.diff can be invoked like:

% crds diff   ./jwst_nircam_dark_0010.fits  ./jwst_nircam_dark_0011.fits

% crds diff  jwst_0001.pmap   jwst_0002.pmap
(('hst.pmap', 'hst_0004.pmap'), ('hst_acs.imap', 'hst_acs_0004.imap'), ('hst_acs_darkfile.rmap', 'hst_acs_darkfile_0003.rmap'), ('WFC', 'A|ABCD|AD|B|BC|C|D', '0.5|1.0|1.4|2.0'), '2011-03-16 23:34:35', "replaced 'v441434ej_drk.fits' with 'hst_acs_darkfile_0003.fits'")

crds.rowdiff

Modules that are based on FITSDiff, such as crds.diff, compare tabular data on a column-by-column basis. Rowdiff compares tabular data on a row-by-row basis, producing UNIX diff-like output instead. Non-tabular extensions are ignored.

usage: crds rowdiff [-J] [-H]
[–ignore-fields IGNORE_FIELDS] [–fields FIELDS] [–mode-fields MODE_FIELDS] old_file new_file

Perform FITS table difference by rows

positional arguments:
old_file First FITS table to compare new_file Second FITS table to compare
optional arguments:
--ignore-fields IGNORE_FIELDS
 List of fields to ignore
--fields FIELDS
 List of fields to compare
--mode-fields MODE_FIELDS
 List of fields to do a mode compare
-J, --jwst Force observatory to JWST for determining header conventions.
-H, --hst Force observatory to HST for determining header conventions.

The FITS data to be compared are required to be similar: they must have the same number of extensions and the types of extensions must match.

The parameters –fields and –ignore-fields define which columns are compared between each table extension. These are mutually exclusive parameters and an error will generate if both are specified.

First a summary of the changes between the table extension is given. Then, row-by-row difference is given, using unified diff syntax.

The parameter –mode-fields initiates a different algorithm. Here, it is presumed the tabular data contains columns that can essentially be treated as keys upon with rows are selected. The fields specified are those key columns.

All possible coombinations of values are determined be examining both extensions. Then, each table is compared against both this list and between each other, looking for multiply specified combinations, missing combinations, and, for the common combinations between the tables, whether the rest of the rows are equivalent or not.

Examples:

% crds rowdiff s9m1329lu_off.fits s9518396u_off.fits

% crds rowdiff s9m1329lu_off.fits s9518396u_off.fits –mode-fields=detchip,obsdate

crds.uses

crds.uses searches the files in the local cache for mappings which refer to the specified files. Since the local cache is used only mappings present in the local cache will be included in the results given. crds.uses is invoked as:

% crds uses <observatory=hst|jwst> <mapping or reference>...

e.g.:

Prints out the mappings which refer to the specified mappings or references.

Prints out the datasets which historically used a particular reference as defined by DADSOPS.

IMPORTANT:
   1. You must specify references on which to operate with --files.
   2. You must set CRDS_PATH and CRDS_SERVER_URL to give crds.uses access to CRDS mappings and databases.

optional arguments:
  -h, --help            show this help message and exit
  --files FILES [FILES ...]
                        References for which to dump using mappings or datasets.
  -d, --print-datasets  Print the ids of datasets last historically using a reference.
  -i, --include-used    Include the used file in the output as the first column.
  -v, --verbose         Set log verbosity to True,  nominal debug level.
  --verbosity VERBOSITY
                        Set log verbosity to a specific level: 0..100.
  -R, --readonly-cache  Don't modify the CRDS cache.  Not compatible with options which implicitly modify the cache.
  -V, --version         Print the software version and exit.
  -J, --jwst            Force observatory to JWST for determining header conventions.
  -H, --hst             Force observatory to HST for determining header conventions.

crds.uses can be invoked like this:

% crds uses --files n3o1022ij_drk.fits --hst
hst.pmap
hst_0001.pmap
hst_0002.pmap
hst_0003.pmap
...
hst_0041.pmap
hst_acs.imap
hst_acs_0001.imap
hst_acs_0002.imap
hst_acs_0003.imap
...
hst_acs_0008.imap
hst_acs_darkfile.rmap
hst_acs_darkfile_0001.rmap
hst_acs_darkfile_0002.rmap
hst_acs_darkfile_0003.rmap
...
hst_acs_darkfile_0005.rmap

% crds uses --files n3o1022ij_drk.fits --print-datasets --hst
J8BA0HRPQ
J8BA0IRTQ
J8BA0JRWQ
J8BA0KT4Q
J8BA0LIJQ

% crds uses --files @dropped --hst --print-datasets --include-used
vb41934lj_bia.fits JA7P21A2Q
vb41934lj_bia.fits JA7P21A4Q
vb41934lj_bia.fits JA7P21A6Q

crds.matches

crds.matches reports the match patterns which are associated with the given reference files:

usage: crds matches ...
       [-h] [--contexts [CONTEXT [CONTEXT ...]]]
       [--files FILES [FILES ...]] [-b] [-o] [-t]

Prints out the selection criteria by which the specified references are matched
with respect to a particular context.

optional arguments:
  -h, --help            show this help message and exit
  --contexts [CONTEXT [CONTEXT ...]]
                        Specify a list of CRDS mappings to operate on: .pmap, .imap, or .rmap or date-based specification
  --range MIN:MAX       Operate for pipeline context ids (.pmaps) between <MIN> and <MAX>.
  --all                 Operate with respect to all known CRDS contexts.
  --last N              Operate with respect to the last N contexts.
  -i, --ignore-cache    Download required files even if they're already in the cache.
  --files FILES [FILES ...]
                        References for which to dump selection criteria.
  -b, --brief-paths     Don't the instrument and filekind.
  -o, --omit-parameter-names
                        Hide the parameter names of the selection criteria,  just show the values.
  -t, --tuple-format    Print the match info as Python tuples.
  -d DATASETS [DATASETS ...], --datasets DATASETS [DATASETS ...]
                        Dataset ids for which to dump matching parameters from DADSOPS or equivalent database.
  -c, --condition-values
                        When dumping dataset parameters, first apply CRDS value conditioning / normalization.
  -m, --minimize-header
                        When dumping dataset parameters,  limit them to matching parameters, not historical bestrefs.
  -v, --verbose         Set log verbosity to True,  nominal debug level.
  --verbosity VERBOSITY
                        Set log verbosity to a specific level: 0..100.
  -R, --readonly-cache  Don't modify the CRDS cache.  Not compatible with options which implicitly modify the cache.
  -V, --version         Print the software version and exit.
  -J, --jwst            Force observatory to JWST for determining header conventions.
  -H, --hst             Force observatory to HST for determining header conventions.

crds.matches can dump reference file match cases with respect to particular contexts:

% crds matches  --contexts hst_0001.pmap --files lc41311jj_pfl.fits
lc41311jj_pfl.fits : ACS PFLTFILE DETECTOR='WFC' CCDAMP='A|ABCD|AC|AD|B|BC|BD|C|D' FILTER1='F625W' FILTER2='POL0V' DATE-OBS='1997-01-01' TIME-OBS='00:00:00'

% crds matches --contexts hst.pmap --files lc41311jj_pfl.fits --omit-parameter-names --brief-paths
lc41311jj_pfl.fits :  'WFC' 'A|ABCD|AC|AD|B|BC|BD|C|D' 'F625W' 'POL0V' '1997-01-01' '00:00:00'

% crds matches --contexts hst.pmap --files lc41311jj_pfl.fits --tuple-format
lc41311jj_pfl.fits : (('OBSERVATORY', 'HST'), ('INSTRUMENT', 'ACS'), ('FILEKIND', 'PFLTFILE'), ('DETECTOR', 'WFC'), ('CCDAMP', 'A|ABCD|AC|AD|B|BC|BD|C|D'), ('FILTER1', 'F625W'), ('FILTER2', 'POL0V'), ('DATE-OBS', '1997-01-01'), ('TIME-OBS', '00:00:00'))

crds.matches can dump database matching parameters for specified datasets with respect to specified contexts:

% crds matches --datasets JBANJOF3Q --minimize-headers --contexts hst_0048.pmap hst_0044.pmap
JBANJOF3Q : hst_0044.pmap : APERTURE='WFC1-2K' ATODCORR='NONE' BIASCORR='NONE' CCDAMP='B' CCDCHIP='1.0' CCDGAIN='2.0' CRCORR='NONE' DARKCORR='NONE' DATE-OBS='2010-01-31' DETECTOR='WFC' DQICORR='NONE' DRIZCORR='NONE' FILTER1='F502N' FILTER2='F660N' FLASHCUR='OFF' FLATCORR='NONE' FLSHCORR='NONE' FW1OFFST='0.0' FW2OFFST='0.0' FWSOFFST='0.0' GLINCORR='NONE' INSTRUME='ACS' LTV1='-2048.0' LTV2='-1.0' NUMCOLS='UNDEFINED' NUMROWS='UNDEFINED' OBSTYPE='INTERNAL' PCTECORR='NONE' PHOTCORR='NONE' REFTYPE='UNDEFINED' SHADCORR='NONE' SHUTRPOS='B' TIME-OBS='01:07:14.960000' XCORNER='1.0' YCORNER='2072.0'
JBANJOF3Q : hst_0048.pmap : APERTURE='WFC1-2K' ATODCORR='NONE' BIASCORR='NONE' CCDAMP='B' CCDCHIP='1.0' CCDGAIN='2.0' CRCORR='NONE' DARKCORR='NONE' DATE-OBS='2010-01-31' DETECTOR='WFC' DQICORR='NONE' DRIZCORR='NONE' FILTER1='F502N' FILTER2='F660N' FLASHCUR='OFF' FLATCORR='NONE' FLSHCORR='NONE' FW1OFFST='0.0' FW2OFFST='0.0' FWSOFFST='0.0' GLINCORR='NONE' INSTRUME='ACS' LTV1='-2048.0' LTV2='-1.0' NAXIS1='2070.0' NAXIS2='2046.0' OBSTYPE='INTERNAL' PCTECORR='NONE' PHOTCORR='NONE' REFTYPE='UNDEFINED' SHADCORR='NONE' SHUTRPOS='B' TIME-OBS='01:07:14.960000' XCORNER='1.0' YCORNER='2072.0'

crds.matches can be invoked in various ways with different output formatting:

% crds matches  --contexts hst_0001.pmap --files lc41311jj_pfl.fits
lc41311jj_pfl.fits : ACS PFLTFILE DETECTOR='WFC' CCDAMP='A|ABCD|AC|AD|B|BC|BD|C|D' FILTER1='F625W' FILTER2='POL0V' DATE-OBS='1997-01-01' TIME-OBS='00:00:00'

% crds matches --contexts hst.pmap --files lc41311jj_pfl.fits --omit-parameter-names --brief-paths
lc41311jj_pfl.fits :  'WFC' 'A|ABCD|AC|AD|B|BC|BD|C|D' 'F625W' 'POL0V' '1997-01-01' '00:00:00'

% crds matches --contexts hst.pmap --files lc41311jj_pfl.fits --tuple-format
lc41311jj_pfl.fits : (('OBSERVATORY', 'HST'), ('INSTRUMENT', 'ACS'), ('FILEKIND', 'PFLTFILE'), ('DETECTOR', 'WFC'), ('CCDAMP', 'A|ABCD|AC|AD|B|BC|BD|C|D'), ('FILTER1', 'F625W'), ('FILTER2', 'POL0V'), ('DATE-OBS', '1997-01-01'), ('TIME-OBS', '00:00:00'))

crds uniqname

CRDS uniqname is used to rename references with unique official CRDS names for HST. It supports renaming both calibration and synphot reference files with modernized HST CDBS-style names.

usage::
crds uniqname [-h] [–files FILES [FILES …]] [–dry-run] [-a] [-f] [-e] [-s] [-r] [-o OUTPUT_PATH] [-b] [–fits-errors] [-v] [–verbosity VERBOSITY] [–dump-cmdline] [-R] [-I] [-V] [-J] [-H] [–stats] [–profile PROFILE] [–log-time] [–pdb] [–debug-traps]
optional arguments::
--help Show this help message and exit
–files FILES [FILES …]
Files to rename.
--dry-run Print how a file would be renamed without modifying it.
-a, --add-checksum
 Add FITS checksum. Without, checksums removed if header modified.
-f, --add-keywords
 When renaming, add FILENAME, ROOTNAME, HISTORY keywords for the generated name.
-e, --verify-file
 Verify FITS compliance and any checksums before changing each file.
-s, --standard Same as –add-keywords –verify-file, does not add checksums (add -a).
-r, --remove-original
 After renaming, remove the orginal file.
-o OUTPUT_PATH, --output-path OUTPUT_PATH
 Output renamed files to this directory path.
-b, --brief Produce less output.
--fits-errors When set, treat FITS compliance and checksum errors as fatal exceptions.
-v, --verbose Set log verbosity to True, nominal debug level.
--verbosity VERBOSITY
 Set log verbosity to a specific level: 0..100.
--dump-cmdline Dump the command line parameters used to start the script to the log.
-R, --readonly-cache
 Don’t modify the CRDS cache. Not compatible with options which implicitly modify the cache.
-I, --ignore-cache
 Download required files even if they’re already in the cache.
-V, --version Print the software version and exit.
-J, --jwst Force observatory to JWST for determining header conventions.
-H, --hst Force observatory to HST for determining header conventions.
--stats Track and print timing statistics.
--profile PROFILE
 Output profile stats to the specified file.
--log-time Add date/time to log messages.
--pdb Run under pdb.
--debug-traps Bypass exception error message traps and re-raise exception.

This program is based loosely on the CDBS program uniqname modified to support enhanced CDBS-style names with modified timestamps valid after 2016-01-01.

The CRDS uniqame is nominally run as follows:

% crds uniqname --files s7g1700gl_dead.fits --brief --standard
CRDS - INFO - Rewriting 's7g1700gl_dead.fits' --> 'zc52141pl_dead.fits'

CRDS uniqname also supports renaming synphot files not otherwise managed by CRDS:

% crds uniqname --files s7g1700gl_tmt.fits --brief --standard
CRDS - INFO - Rewriting 's7g1700gl_tmt.fits' --> 'zc52141pl_tmt.fits'

If -s or –standard is added then routinely used switches are added as a predefined bundle. Initially these are –add-keywords and –verify-file.

If –add-checksum is specified, CRDS uniqname will add FITS checksums to the file. If –add-checksum is not specified, CRDS uniqname WILL REMOVE any existing checksum.

If –verify-file is specified, CRDS uniqname will check the FITS checksum and validate the FITS format of renamed files.

If –add-keywords is specified CRDS uniqname will add/modify the FILENAME, ROOTNAME, and HISTORY to document the renaming.

If –remove-original is specified then the original file is deleted after the renamed file has been created and modified as specified (checksums, keywords, etc.)

Renamed files can be output to a different directory using –output-path.

–dry-run can be used to demo renaming by printing what the new name would be.

crds checksum

usage: crds checksum
[-h] [–remove] [–verify] [-v] [–verbosity VERBOSITY] [–dump-cmdline] [-R] [-I] [-V] [-J] [-H] [–stats] [–profile PROFILE] [–log-time] [–pdb] [–debug-traps] files [files …]

Add, remove, or verify checksums in CRDS rules or reference files.

  1. Default operation is to ADD checksums:

    % crds checksum  *.rmap
    
    % crds checksum  *.fits
    
  2. Reference files may support REMOVING checksums:

    % crds checksum --remove *.fits
    

NOTE: CRDS mapping / rules files do not support removing checksums.

  1. Checksums can be VERIFIED without attempting to update or remove:

    % crds checksum --verify  *.rmap
    
    % crds checksum --verify *.fits
    

Currently only FITS references support checksum operations. Checksums can be added or verified on all CRDS mapping types.

positional arguments:
files Files to operate on, CRDS rule or reference files.
optional arguments:
-h, --help show this help message and exit
--remove Remove checksums when specified. Invalid for CRDS mappings.
--verify Verify checksums when specified.
-v, --verbose Set log verbosity to True, nominal debug level.
--verbosity VERBOSITY
 Set log verbosity to a specific level: 0..100.
--dump-cmdline Dump the command line parameters used to start the script to the log.
-R, --readonly-cache
 Don’t modify the CRDS cache. Not compatible with options which implicitly modify the cache.
-I, --ignore-cache
 Download required files even if they’re already in the cache.
-V, --version Print the software version and exit.
-J, --jwst Force observatory to JWST for determining header conventions.
-H, --hst Force observatory to HST for determining header conventions.
--stats Track and print timing statistics.
--profile PROFILE
 Output profile stats to the specified file.
--log-time Add date/time to log messages.
--pdb Run under pdb.
--debug-traps Bypass exception error message traps and re-raise exception.

safe_bestrefs

The safe_bestrefs script is a shim around crds bestrefs which configures it for operation in the pipeline using a readonly cache and no connection to the server. Typical usage might be:

$ export CRDS_PATH=<pipeline's CRDS cache path>
$ safe_bestrefs --files <datasets FITS files...>

This script is intended to be run in parallel with multiple pipeline bestrefs and a concurrent cron_sync. The “safe” aspect refers to not modifying the CRDS cache itself, and to not stumbling into inconsistent cache states while another process is updating the cache.

To control when information is received from the server, and to prevent pipeline stalls when the CRDS server is unavailable, safe_bestrefs is configured with a bad server IP address.

Using a readonly CRDS cache enables the use of bestrefs in a multiprocessing environment where multiple copies of bestrefs are running simultaneously.

Configuring bestrefs to run with no connection to the CRDS server makes it impossible for bestrefs to do file downloads and keeps the pipeline independent of the server during routine operations. See cron_sync for more info on updating the CRDS cache in pipeline environments.

cron_sync

The cron_sync script is a wrapper around the crds sync tool that tunes it for updating the CRDS cache in a highly concurrent environment where bestrefs may be running during the cache update.

cron_sync uses file locks to prevent more than one copy of itself from running at the same time, particularly if run periodically as a cron job which may take longer than the period to fully download file updates.

Typical setup and execution is:

$ export CRDS_PATH=<pipeline's CRDS cache path>
$ export CRDS_SERVER_URL=<project's CRDS server>
$ export CRDS_LOCKS=<directory for cron_sync lock files, defaults to $CRDS_PATH>
$ cron_sync --all --check-files --fetch-references

cron_sync co-exists with an operating copy of safe_bestrefs by writing out the cache configuration information last. The cache configuration information controls the context switch. While files corresponding to the new context are downloading, the cache remains safe and continues to operate under the old context.

The HST and JWST pipeline environments currently further wrap the cron_sync script to establish the environment settings and required Python stack and eliminate all parameters:

$ crds_sync_wrapper.csh

Operators typically execute crds_sync_wrapper.csh rather than cron_sync.