Library Use

This section describes the formal top level interfaces for CRDS intended as the main entry points for the calibration software or basic use. Functions at this level should be assumed to require network connectivity with the CRDS server.

To function correctly, these API calls may require the user to set the environment variables CRDS_SERVER_URL and CRDS_PATH. See the section on Installation for more details.

crds.getrecommendations()

Given dataset header containing parameters required to determine best references, and optionally a specific .pmap to use as the best references context, and optionally a list of the reference types for which reference files are to be determined, getrecommendations() will determine best references and return a mapping from reference types to reference file basenames:

def getrecommendations(parameters, reftypes=None, context=None, ignore_cache=False,
                     observatory="jwst", fast=False):
  """
  getrecommendations() returns the best references for the specified `parameters`
  and pipeline `context`.   Unlike getreferences(),  getrecommendations() does
  not attempt to cache the files locally.

  parameters      { str:  str,int,float,bool, ... }

    `parameters` should be a dictionary-like object mapping best reference
    matching parameters to their values for this dataset.

  reftypes        [ str, ... ]

    If `reftypes` is None,  return all possible reference types.   Otherwise
    return the reference types specified by `reftypes`.

  context         str

    Specifies the pipeline context, i.e. specific version (.pmap) of CRDS
    rules used to do the best references match.  If `context` is None, use
    the latest available context.

  ignore_cache    bool

    If `ignore_cache` is True,  download files from server even if already present.

  observatory     str

     nominally 'jwst' or 'hst'.

  fast            bool

    If fast is True, skip verbose output, parameter screening, implicit
    config update, and bad reference checking.

  Returns { reftype : bestref_basename, ... }

    returns a mapping from types requested in `reftypes` to the path for each
    cached reference file.
  """

crds.getreferences()

Given dataset header containing parameters required to determine best references, and optionally a specific .pmap to use as the best references context, and optionally a list of the reference types for which reference files are to be determined, getreferences() will determine best references, cache them on the local file system, and return a mapping from reference types to reference file paths:

def getreferences(parameters, reftypes=None, context=None, ignore_cache=False,
                  observatory="jwst"):
    """Return the mapping from the requested `reftypes` to their
    corresponding best reference file paths appropriate for a dataset
    described by `parameters` with CRDS rules defined by `context`::

    parameters :    A mapping of parameter names to parameter value
            strings for parameters which define best reference file matches.

            { str  :   str, int, float, bool }

           e.g.  {
                   'INSTRUME' : 'ACS',
                   'CCDAMP' : 'ABCD',
                   'CCDGAIN' : '2.0',
                   ...
                }

    reftypes :    A list of reference type names.   For HST these are the keywords
                 used to record reference files in dataset headers.   For JWST,  these
                 are the identifiers which will appear in instrument contexts and
                 reference mappings.

                e.g.  [ 'darkfile', 'biasfile']

                If reftypes is None,  return all reference types defined by
                the instrument mapping for the instrument specified in
                `parameters`.

    context :   The name of the pipeline context mapping which should be
            used to define best reference lookup rules,  or None.  If
            `context` is None,  use the latest operational pipeline mapping.

            str

            e.g. 'hst_0037.pmap'

    ignore_cache :   If True,  download all required mappings and references
            from the CRDS server.  If False,  download only those files not
            already in the local caches.

    observatory :  The name of the observatory this query applies to,  needed
            to support both 'hst' and 'jwst' from a single server.

    Returns
    -------
            a mapping from reftypes to cached best reference file paths.

            { str : str }

            e.g.   {
                'biasfile' : '/path/to/file/hst_acs_biasfile_0042.fits',
                'darkfile' : '/path/to/file/hst_acs_darkfile_0056.fits',
                }
    """

crds.assign_bestrefs()

The assign_bestrefs() higher level function call simulates the behavior of the crds bestrefs program used in the archive pipeline for HST. Essentially, it populates the headers of FITS dataset files with the best choice for each reference type:

def assign_bestrefs(filepaths, context=None, reftypes=(),
                  sync_references=False, verbosity=-1):
  """Assign best references to FITS files specified by `filepaths`
  filling in appropriate reference type keywords.

  Define best references using either .pmap `context` or the default
  CRDS operational context if context=None.

  If `reftypes` is defined, assign bestrefs to only the listed
  reftypes, otherwise assign all reftypes.

  If `sync_references` is True, download any missing reference files
  to the CRDS cache.

  Verbosity defines the level of CRDS log output:

  verbosity=-3    feeling lucky, no output
  verbosity=-2    only errors
  verbosity=-1    only warnings and errors
  verbosity=0     info, warnings, and errors
  verbosity=10    info + minimal progress output
  verbosity=30    info + simplified bestref assignments
  verbosity=50    info + keywords + exact values (standard)
  verbosity=60    info + bestrefs elimination
  ...
  -3 <= verbosity <= 100

  NOTE: While assign_bestrefs() may work for JWST, it is primarily intended
  for HST and does not precisely simulate the actions performed by the JWST
  CAL s/w to handle reference files.  The underlying machinery is the same,
  but header updates are not guaranteed to be identical, particularly
  regarding the reference types which are assigned values.

  Returns  count of errors
  """

crds.get_default_context()

get_default_context() returns the name of the pipeline mapping which is currently in operational use. When no

The default context defines the matching rules used to determine best reference files for a given set of parameters:

def get_default_context():
    """Return the name of the latest pipeline mapping in use for processing
    files.

    Returns
    -------
    pipeline context name

        e.g.   'hst_0007.pmap'
    """

Basic Operations on Mappings

Loading Rmaps

Perhaps the most fundamental thing you can do with a CRDS mapping is create an active object version by loading the file:

% python
>>> import crds.rmap as rmap
>>> hst = rmap.load_mapping("hst.pmap")

The load_mapping() function will take any mapping and instantiate it and all of it’s child mappings into various nested Mapping subclasses: PipelineContext, InstrumentContext, or ReferenceMapping.

Loading an rmap implicitly screens it for invalid syntax and requires that the rmap’s checksum (sha1sum) be valid by default.

Since HST has on the order of 70 mappings, this is a fairly slow process requiring a couple seconds to execute. In order to speed up repeated access to the same Mapping, there’s a mapping cache maintained by the rmap module and accessed like this:

>>> hst = rmap.get_cached_mapping("hst.pmap")

The behavior of the cached mapping is identical to the “loaded” mapping and subsequent calls are nearly instant.

Seeing Referenced Names

CRDS Mapping classes all know how to show you the files referenced by themselves and their descendents. The ACS instrument context has a reference mapping for each of it’s associated file kinds:

>>> acs = rmap.get_cached_mapping("hst_acs.imap")
>>> acs.mapping_names()
['hst_acs.imap',
 'hst_acs_idctab.rmap',
 'hst_acs_darkfile.rmap',
 'hst_acs_atodtab.rmap',
 'hst_acs_cfltfile.rmap',
 'hst_acs_spottab.rmap',
 'hst_acs_mlintab.rmap',
 'hst_acs_dgeofile.rmap',
 'hst_acs_bpixtab.rmap',
 'hst_acs_oscntab.rmap',
 'hst_acs_ccdtab.rmap',
 'hst_acs_crrejtab.rmap',
 'hst_acs_pfltfile.rmap',
 'hst_acs_biasfile.rmap',
 'hst_acs_mdriztab.rmap']

The ACS atod reference mapping (rmap) refers to 4 different reference files:

>>> acs_atod = rmap.get_cached_mapping("hst_acs_atodtab.rmap")
>>> acs_atod.reference_names()
['j4d1435hj_a2d.fits',
 'kcb1734hj_a2d.fits',
 'kcb1734ij_a2d.fits',
 't3n1116mj_a2d.fits']

Computing Best References

The primary function of CRDS is the computation of best reference files based upon a dictionary of dataset metadata. Hence, both an InstrumentContext and a ReferenceMapping can meaningfully return the best references for a dataset based upon a parameter dictionary. It’s possible define a header as any Python dictionary provided you have sufficient knowledge of the parameters:

>>>  hdr = { ... what matters most ... }

On the other hand, if your dataset is a FITS file and you want to do something quick and dirty, you can ask CRDS what dataset metadata may matter for determining best references:

>>> hdr = acs.get_minimum_header("test_data/j8bt05njq_raw.fits")
{'CCDAMP': 'C',
 'CCDGAIN': '2.0',
 'DATE-OBS': '2002-04-13',
 'DETECTOR': 'HRC',
 'FILTER1': 'F555W',
 'FILTER2': 'CLEAR2S',
 'FW1OFFST': '0.0',
 'FW2OFFST': '0.0',
 'FWSOFFST': '0.0',
 'LTV1': '19.0',
 'LTV2': '0.0',
 'NAXIS1': '1062.0',
 'NAXIS2': '1044.0',
 'OBSTYPE': 'IMAGING',
 'TIME-OBS': '18:16:35'}

Here I say may matter because CRDS is currently dumb about specific instrument configurations and is returning metadata about filekinds which may be inappropriate.

Once you have your dataset parameters, you can ask an InstrumentContext for the best references for all filekinds for that instrument:

>>> acs.get_best_references(hdr)
{'atodtab': 'kcb1734ij_a2d.fits',
'biasfile': 'm4r1753rj_bia.fits',
'bpixtab': 'm8r09169j_bpx.fits',
'ccdtab': 'o1515069j_ccd.fits',
'cfltfile': 'NOT FOUND n/a',
'crrejtab': 'n4e12510j_crr.fits',
'darkfile': 'n3o1059hj_drk.fits',
'dgeofile': 'o8u2214mj_dxy.fits',
'flshfile': 'NOT FOUND n/a',
'idctab': 'p7d1548qj_idc.fits',
'imphttab': 'vbb18105j_imp.fits',
'mdriztab': 'ub215378j_mdz.fits',
'mlintab': 'NOT FOUND n/a',
'oscntab': 'm2j1057pj_osc.fits',
'pfltfile': 'o3u1448rj_pfl.fits',
'shadfile': 'kcb1734pj_shd.fits',
'spottab': 'NOT FOUND n/a'}

In the above results, FITS files are the recommended best references, while a value of “NOT FOUND n/a” indicates that no result was expected for the current instrument mode as defined in the header. Other values of “NOT FOUND xxx” include an error message xxx which hints at why no result was found, such as an invalid dataset parameter value or simply a matching failure.

You can ask a ReferenceMapping for the best reference for single the filekind it manages:

>>> acs_atod.get_best_ref(hdr)
>>> 'kcb1734ij_a2d.fits'

Often it is convenient to simply refer to a pipeline/observatory context file, and hence PipelineContext can also return the best references for a dataset, but this is really just shorthand for returning the best references for the instrument of that dataset:

>>> hdr = hst.get_minimum_header("test_data/j8bt05njq_raw.fits")
>>> hst.get_best_references(hdr)
... for this hdr, same as acs.get_best_references(hdr) ...

Here it is critical to call get_minimum_header on the pipeline context, hst, because this will make it include the “INSTRUME” parameter needed to choose the ACS instrument.

Mapping Checksums

CRDS mappings contain sha1sum checksums over the entire contents of the mapping, with the exception of the checksum itself. When a CRDS Mapping of any kind is loaded, the checksum is transparently verified to ensure that the Mapping contents are intact.

Ignoring Checksums!

Ordinarily, during pipeline operations, ignoring checksums should not be done. Ironically though, the first thing you may want to do as a developer is ignore the checksum while you load a mapping you’ve edited:

>>> pipeline = rmap.load_mapping("hst.pmap", ignore_checksum=True)

Alternately you can set an environment variable to ignore the mapping checksum while you iterate on new versions of the mapping:

% setenv CRDS_IGNORE_MAPPING_CHECKSUM 1

Adding Checksums

Once you’ve finished your masterpiece ReferenceMapping, it can be sealed with a checksum like this:

% crds checksum /where/it/really/is/hst_acs_my_masterpiece.rmap