#! /usr/bin/env python ''' Modify a superbias reference file for pipeline testing. Currently all we should need to do is make sure that the reference file contains at least one pixel flagged with UNRELIABLE_BIAS, so that in testing we can make sure that the superbias is still subtracted from this pixel ''' from jwst.datamodels import SuperBiasModel infile = '../reffiles/A1_superbias_from_list_of_biasfiles.list.fits' outfile = 'modified_superbias_reffile.fits' #read in reffile sb = SuperBiasModel(infile) #set the unreliable_bias flag for one pixel sb.dq[50, 50] = 2 #save sb.save(outfile)
def save_superbias(superbias, error, dq, instrument='', detector='',
subarray='GENERIC', readpatt='ANY',
outfile='superbias_jwst_reffiles.fits',
author='jwst_reffiles', description='Super Bias Image',
pedigree='GROUND', useafter='2000-01-01T00:00:00',
history='', fastaxis=-1, slowaxis=2, substrt1=1, substrt2=1,
filenames=[]):
"""Saves a CRDS-formatted superbias reference file.
Parameters
----------
superbias : numpy.ndarray
The 2D superbias image.
error : numpy.ndarray
The 2D superbias error image.
dq : numpy.ndarray
The 2D superbias data quality image.
instrument : str
CRDS-required instrument for which to use this reference file for.
detector : str
CRDS-required detector for which to use this reference file for.
subarray : str
CRDS-required subarray for which to use this reference file for.
readpatt : str
CRDS-required read pattern for which to use this reference file for.
outfile : str
Name of the CRDS-formatted superbias reference file to save the final
superbias map to.
author : str
CRDS-required name of the reference file author, to be placed in the
referece file header.
description : str
CRDS-required description of the reference file, to be placed in the
reference file header.
pedigree : str
CRDS-required pedigree of the data used to create the reference file.
useafter : str
CRDS-required date of earliest data with which this referece file
should be used. (e.g. '2019-04-01T00:00:00').
history : str
CRDS-required history section to place in the reference file header.
fastaxis : int
CRDS-required fastaxis of the reference file.
slowaxis : int
CRDS-required slowaxis of the reference file.
substrt1 : int
CRDS-required starting pixel in axis 1 direction.
substrt2 : int
CRDS-required starting pixel in axis 2 direction.
filenames : list
List of dark current files that were used to generate the reference
file.
"""
s = SuperBiasModel()
s.data = superbias
s.err = error
s.dq = dq
s.dq_def = [(0, 0, 'GOOD', ''),
(0, 1, 'DO_NOT_USE', ''),
(1, 2, 'UNRELIABLE_BIAS', '')]
s.meta.instrument.name = instrument
s.meta.instrument.detector = detector
s.meta.subarray.name = subarray
s.meta.exposure.readpatt = readpatt
s.meta.author = author
s.meta.description = description
s.meta.pedigree = pedigree
s.meta.useafter = useafter
s.meta.subarray.fastaxis = fastaxis
s.meta.subarray.slowaxis = slowaxis
s.meta.reftype = 'SUPERBIAS'
yd, xd = superbias.shape
s.meta.subarray.xstart = substrt1
s.meta.subarray.xsize = xd
s.meta.subarray.ystart = substrt2
s.meta.subarray.ysize = yd
package_note = ('This file was created using the superbias.py module '
'within the jwst_reffiles package.')
software_dict = {'name': 'jwst_reffiles.superbias.py', 'author': 'STScI',
'homepage': 'https://github.com/spacetelescope/jwst_reffiles',
'version': '0.0.0'}
entry = util.create_history_entry(package_note, software=software_dict)
s.history.append(entry)
# Add the list of input files used to create the superbias reference file
s.history.append('DATA USED:')
for f in filenames:
f = os.path.basename(f)
totlen = len(f)
div = np.arange(0, totlen, 60)
for val in div:
if totlen > (val+60):
s.history.append(util.create_history_entry(f[val:val+60]))
else:
s.history.append(util.create_history_entry(f[val:]))
if history != '':
s.history.append(util.create_history_entry(history))
s.save(outfile, overwrite=True)
print('Final CRDS-formatted superbias map saved to {}'.format(outfile))