def save_final_map(bad_pix_map, instrument, detector, hdulist, files, author,
description, pedigree, useafter, history_text, outfile):
"""Save a bad pixel map into a CRDS-formatted reference file
Parameters
----------
bad_pix_map : numpy.ndarray
2D bad pixel array
instrument : str
Name of instrument associated with the bad pixel array
detector : str
Name of detector associated with the bad pixel array
hdulist : astropy.fits.HDUList
HDUList containing "extra" fits keywords
files : list
List of files used to create ``bad_pix_map``
author : str
Author of the bad pixel mask reference file
description : str
CRDS description to use in the final bad pixel file
pedigree : str
CRDS pedigree to use in the final bad pixel file
useafter : str
CRDS useafter string for the bad pixel file
history_text : list
List of strings to add as HISTORY entries to the bad pixel file
outfile : str
Name of the output bad pixel file
"""
yd, xd = bad_pix_map.shape
# Initialize the MaskModel using the hdu_list, so the new keywords will
# be populated
model = MaskModel(hdulist)
model.dq = bad_pix_map
# Create dq_def data
dq_def = badpix_from_flats.create_dqdef()
model.dq_def = dq_def
model.meta.reftype = 'MASK'
model.meta.subarray.name = 'FULL'
model.meta.subarray.xstart = 1
model.meta.subarray.xsize = xd
model.meta.subarray.ystart = 1
model.meta.subarray.ysize = yd
model.meta.instrument.name = instrument.upper()
model.meta.instrument.detector = detector
# Get the fast and slow axis directions from one of the input files
fastaxis, slowaxis = badpix_from_flats.get_fastaxis(files[0])
model.meta.subarray.fastaxis = fastaxis
model.meta.subarray.slowaxis = slowaxis
model.meta.author = author
model.meta.description = description
model.meta.pedigree = pedigree
model.meta.useafter = useafter
# Add information about parameters used
# Parameters from badpix_from_flats
package_note = (
'This file was created using the bad_pixel_mask.py module within the '
'jwst_reffiles package.')
software_dict = {
'name': 'jwst_reffiles.bad_pixel_mask.bad_pixel_mask.py',
'author': 'STScI',
'homepage': 'https://github.com/spacetelescope/jwst_reffiles',
'version': '0.0.0'
}
entry = util.create_history_entry(package_note, software=software_dict)
model.history.append(entry)
model.history.append(
util.create_history_entry('Parameter values and descriptions:'))
dead_search_descrip = (
'dead_search: Boolean, whether or not to run the dead pixel search '
'using flat field files. The value is stored in the {} keyword.'.
format(dead_search_kw))
model.history.append(util.create_history_entry(dead_search_descrip))
low_qe_search_descrip = (
'low_qe_and_open_search: Boolean, whether or not to run the low QE '
'and open pixel search using flat field files. The value is stored in the {} '
'keyword.'.format(low_qe_search_kw))
model.history.append(util.create_history_entry(low_qe_search_descrip))
dead_type_descrip = (
'dead_search_type: Method used to identify dead pixels. The value is stored in the '
'{} keyword.'.format(dead_search_type_kw))
model.history.append(util.create_history_entry(dead_type_descrip))
sigma_descrip = (
'flat_mean_sigma_threshold: Number of standard deviations to use when sigma-clipping to '
'calculate the mean slope image or the mean across the detector. The value '
'used is stored in the {} keyword.'.format(mean_sig_threshold_kw))
model.history.append(util.create_history_entry(sigma_descrip))
norm_descrip = (
'flat_mean_normalization_method: Specify how the mean image is normalized prior to searching '
'for bad pixels. The value used is stored in the {} keyword.'.format(
norm_method_kw))
model.history.append(util.create_history_entry(norm_descrip))
smooth_descrip = (
'smoothing_box_width: Width in pixels of the box kernel to use to compute the '
'smoothed mean image. The value used is stored in the {} keyword.'.
format(smooth_box_width_kw))
model.history.append(util.create_history_entry(smooth_descrip))
smooth_type_descrip = (
'smoothing_type: Type of smoothing to do: Box2D or median filtering. The value used '
'is stored in the {} keyword.'.format(smoothing_type_kw))
model.history.append(util.create_history_entry(smooth_type_descrip))
dead_sig_descrip = (
'Number of standard deviations below the mean at which a pixel is considered dead. '
'The value used is stored in the {} keyword.'.format(
dead_sig_thresh_kw))
model.history.append(util.create_history_entry(dead_sig_descrip))
max_dead_descrip = (
'Maximum normalized signal rate of a pixel that is considered dead. The value '
'used is stored in the {} keyword.'.format(max_dead_sig_kw))
model.history.append(util.create_history_entry(max_dead_descrip))
run_dead_flux_descrip = (
'run_dead_flux_check: Boolean, if True, search for pixels erroneously flagged '
'as dead because they are saturated in all groups. The value used is stored '
'in the {} keyword.'.format(dead_flux_check_kw))
model.history.append(util.create_history_entry(run_dead_flux_descrip))
dead_flux_limit_descrip = (
'Signal limit in raw data above which the pixel is considered not dead. The '
'value used is stored in the {} keyword.'.format(max_dead_sig_kw))
model.history.append(util.create_history_entry(dead_flux_limit_descrip))
max_low_qe_descrip = (
'The maximum normalized signal a pixel can have and be considered low QE. The '
'value used is stored in the {} keyword.'.format(max_low_qe_kw))
model.history.append(util.create_history_entry(max_low_qe_descrip))
max_open_adj_descrip = (
'The maximum normalized signal a pixel adjacent to a low QE pixel can have '
'in order for the low QE pixel to be reclassified as OPEN. The value used '
'is stored in the {} keyword.'.format(max_open_adj_kw))
model.history.append(util.create_history_entry(max_open_adj_descrip))
flat_do_not_use_descrip = (
'List of bad pixel types (from flats) where the DO_NOT_USE flag is also applied. '
'The values used are stored in the {} keyword.'.format(
flat_do_not_use_kw))
model.history.append(util.create_history_entry(flat_do_not_use_descrip))
manual_file_descrip = (
'Name of the ascii file containing a list of pixels to be added manually. The '
'value used is stored in the {} keyword.'.format(manual_flag_kw))
model.history.append(util.create_history_entry(manual_file_descrip))
# Parameters from badpix_from_darks
bad_from_dark_descrip = (
'badpix_from_dark: Boolean, whether or not the bad pixel from dark search '
'has been run. The value is stored in the {} keyword.'.format(
bad_from_dark_kw))
model.history.append(util.create_history_entry(bad_from_dark_descrip))
dark_clip_sig_descrip = (
'Number of sigma to use when sigma-clipping 2D stdev image. The value used '
'is stored in the {} keyword.'.format(dark_clip_sigma_kw))
model.history.append(util.create_history_entry(dark_clip_sig_descrip))
dark_clip_iter_descrip = (
'Max number of iterations to use when sigma clipping mean and stdev values. '
'The value used is stored in the {} keyword.'.format(
dark_clip_iters_kw))
model.history.append(util.create_history_entry(dark_clip_iter_descrip))
dark_noisy_thresh_descrip = (
'Number of sigma above mean noise for noisy pix threshold. The value '
'used is stored in the {} keyword.'.format(dark_noisy_thresh_kw))
model.history.append(util.create_history_entry(dark_noisy_thresh_descrip))
max_sat_frac_descrip = (
'Fraction of integrations within which a pixel must be fully saturated before '
'flagging it as HOT. The value used is stored in the {} keyword.'.
format(max_sat_frac_kw))
model.history.append(util.create_history_entry(max_sat_frac_descrip))
jump_limit_descrip = (
'Maximum number of jumps a pixel can have in an integration before it is flagged as a '
'"high jump" pixel. The value used is stored in the {} keyword.'.
format(jump_limit_kw))
model.history.append(util.create_history_entry(jump_limit_descrip))
jump_ratio_descrip = (
'Cutoff for the ratio of jumps early in the ramp to jumps later in the ramp when '
'looking for RC pixels. The value used is stored in the {} keyword.'.
format(jump_ratio_thresh_kw))
model.history.append(util.create_history_entry(jump_ratio_descrip))
cutoff_frac_descrip = (
'Fraction of the integration to use when comparing the jump rate early in the integration to '
'that across the entire integration. The value used is stored in the {} keyword.'
.format(cutoff_frac_kw))
model.history.append(util.create_history_entry(cutoff_frac_descrip))
ped_sigma_descrip = (
'Pixels with pedestal values more than this limit above the mean are flagged as RC. '
'The value used is stored in the {} keyword.'.format(
pedestal_sig_thresh_kw))
model.history.append(util.create_history_entry(ped_sigma_descrip))
rc_thresh_descrip = (
'Fraction of input files within which a pixel must be identified as an RC pixel before '
'it will be flagged as a permanent RC pixel. The value used is stored in the {} '
'keyword.'.format(rc_frac_thresh_kw))
model.history.append(util.create_history_entry(rc_thresh_descrip))
low_ped_descrip = (
'Fraction of input files within which a pixel must be identified as a low pedestal '
'pixel before it will be flagged as a permanent low pedestal pixel. The value used '
'is stored in the {} keyword.'.format(low_ped_frac_kw))
model.history.append(util.create_history_entry(low_ped_descrip))
high_cr_descrip = (
'Fraction of input files within which a pixel must be flagged as having a high number '
'of jumps before it will be flagged as permanently noisy. The value used '
'is stored in the {} keyword.'.format(high_cr_frac_kw))
dark_do_not_use_descrip = (
'List of bad pixel types (from darks) where the DO_NOT_USE flag is also applied. '
'The values used are stored in the {} keyword.'.format(
dark_do_not_use_kw))
model.history.append(util.create_history_entry(dark_do_not_use_descrip))
# Add the list of input files used to create the map
model.history.append('DATA USED:')
for file in files:
totlen = len(file)
div = np.arange(0, totlen, 60)
for val in div:
if totlen > (val + 60):
model.history.append(
util.create_history_entry(file[val:val + 60]))
else:
model.history.append(util.create_history_entry(file[val:]))
# Add the do not use lists, pixel flag mappings, and user-provided
# history text
for history_entry in history_text:
if history_entry != '':
model.history.append(util.create_history_entry(history_entry))
model.save(outfile, overwrite=True)
print('Final bad pixel mask reference file save to: {}'.format(outfile))
def save_readnoise(readnoise,
instrument='',
detector='',
subarray='GENERIC',
readpatt='ANY',
outfile='readnoise_jwst_reffiles.fits',
author='jwst_reffiles',
description='CDS Noise Image',
pedigree='GROUND',
useafter='2015-10-01T00:00:00',
history='',
fastaxis=-1,
slowaxis=2,
substrt1=1,
substrt2=1,
filenames=[]):
"""Saves a CRDS-formatted readnoise reference file.
Parameters
----------
readnoise : numpy.ndarray
The 2D readnoise 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 readnoise reference file to save the final
readnoise 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.
"""
r = ReadnoiseModel()
r.data = readnoise
r.meta.bunit_data = 'DN'
r.meta.instrument.name = instrument
r.meta.instrument.detector = detector
r.meta.subarray.name = subarray
r.meta.exposure.readpatt = readpatt
r.meta.author = author
r.meta.description = description
r.meta.pedigree = pedigree
r.meta.useafter = useafter
r.meta.subarray.fastaxis = fastaxis
r.meta.subarray.slowaxis = slowaxis
r.meta.reftype = 'READNOISE'
yd, xd = readnoise.shape
r.meta.subarray.xstart = substrt1
r.meta.subarray.xsize = xd
r.meta.subarray.ystart = substrt2
r.meta.subarray.ysize = yd
package_note = ('This file was created using the readnoise.py module '
'within the jwst_reffiles package.')
software_dict = {
'name': 'jwst_reffiles.readnoise.py',
'author': 'STScI',
'homepage': 'https://github.com/spacetelescope/jwst_reffiles',
'version': '0.0.0'
}
entry = util.create_history_entry(package_note, software=software_dict)
r.history.append(entry)
# Add the list of input files used to create the readnoise reference file
r.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):
r.history.append(util.create_history_entry(f[val:val + 60]))
else:
r.history.append(util.create_history_entry(f[val:]))
if history != '':
r.history.append(util.create_history_entry(history))
r.save(outfile, overwrite=True)
print('Final CRDS-formatted readnoise map saved to {}'.format(outfile))
def save_final_map(datamap, dq, err, dqdef, instrument, detector, hdulist, filterdir, grism, files,
author, description, pedigree,useafter, fpatemp, history_text, pomoutlineoffsetx, pomoutlineoffsety, ngrow, outfile):
"""Save a flat field or POM transmission map into a CRDS-formatted reference file
Parameters
----------
datamap : numpy.ndarray
2D flat-field array
dq : numpy.ndarray
2D flat-field DQ array
err : numpy.ndarray
2D flat-field error array
dqdef : numpy.ndarray
binary table of DQ definitions
instrument : str
Name of instrument associated with the flat-field array
detector : str
Name of detector associated with the flat-field array
hdulist : astropy.fits.HDUList
HDUList containing "extra" fits keywords
filterdir : str
filter of flat file
grism : str
grism of flat file
files : list
List of files used to create reference file
author : str
Author of the reference file
description : str
CRDS description to use in the final reference file
pedigree : str
CRDS pedigree to use in the final reference file
useafter : str
CRDS useafter string for the reference file
history_text : list
List of strings to add as HISTORY entries to the reference file
outfile : str
Name of the output reference file
"""
yd, xd = datamap.shape
# For now use FlatModel for the POM transmission as well so don't have to define a new model.
# Initialize the FlatModel using the hdu_list, so the new keywords will
# be populated
if 'flat' in description:
model = FlatModel(hdulist)
model.meta.reftype = 'FLAT'
elif 'transmission' in description:
model = FlatModel(hdulist)
model.meta.reftype = 'TRANSMISSION'
model.data = datamap
model.dq = dq
model.err = err
model.dq_def = dqdef
#Load a file to get some header info
primaryheader=fits.getheader(os.path.join(filterdir,files[0]))
filterwheel=primaryheader['FILTER']
pupilwheel=primaryheader['PUPIL']
model.meta.subarray.name = 'FULL'
model.meta.subarray.xstart = 1
model.meta.subarray.xsize = xd
model.meta.subarray.ystart = 1
model.meta.subarray.ysize = yd
model.meta.instrument.name = instrument.upper()
model.meta.instrument.detector = detector
if grism=='GR700XD':
model.meta.instrument.filter='CLEAR'
model.meta.instrument.pupil=grism
else:
model.meta.instrument.filter=grism
model.meta.instrument.pupil=pupilwheel
# Get the fast and slow axis directions from one of the input files
fastaxis, slowaxis = bad_pixel_mask.badpix_from_flats.get_fastaxis(os.path.join(filterdir,files[0]))
model.meta.subarray.fastaxis = fastaxis
model.meta.subarray.slowaxis = slowaxis
if 'transmission' in description:
model.meta.offsetx=pomoutlineoffsetx
model.meta.offsety=pomoutlineoffsety
model.meta.author = author
model.meta.description = description
model.meta.pedigree = pedigree
model.meta.useafter = useafter
# Add HISTORY information
package_note = ('This file was created using https://github.com/chriswillott/jwst/blob/master/makenirissgrismflats.py')
entry = util.create_history_entry(package_note)
model.history.append(entry)
package_note = ('FPA Temperature={}K'.format(fpatemp))
entry = util.create_history_entry(package_note)
model.history.append(entry)
package_note = ('Number of pixels to grow POM features={}'.format(ngrow))
entry = util.create_history_entry(package_note)
model.history.append(entry)
# Add the list of input files used to create the map
model.history.append('DATA USED:')
for file in files:
totlen = len(file)
div = np.arange(0, totlen, 60)
for val in div:
if totlen > (val+60):
model.history.append(util.create_history_entry(file[val:val+60]))
else:
model.history.append(util.create_history_entry(file[val:]))
# Add the do not use lists, pixel flag mappings, and user-provided
# history text
for history_entry in history_text:
if history_entry != '':
model.history.append(util.create_history_entry(history_entry))
model.save(outfile, overwrite=True)
print('Final reference file save to: {}'.format(outfile))
#Add the offsetx and offsety values manually since no schema yet for transmission files
if 'transmission' in description:
fits.setval(outfile, 'OFFSETX', value=pomoutlineoffsetx, ext=0, after='SLOWAXIS', comment='Transmision map-detector offset in x pixels')
fits.setval(outfile, 'OFFSETY', value=pomoutlineoffsety, ext=0, after='OFFSETX', comment='Transmision map-detector offset in y pixels')
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))
def save_final_map(flat_map, flat_dq, flat_err, dqdef, instrument, detector,
hdulist, filterdir, files, author, description, pedigree,
useafter, fpatemp, history_text, outfile):
"""Save a flat field map into a CRDS-formatted reference file
Parameters
----------
flat_map : numpy.ndarray
2D flat-field array
flat_dq : numpy.ndarray
2D flat-field DQ array
flat_err : numpy.ndarray
2D flat-field error array
dqdef : numpy.ndarray
binary table of DQ definitions
instrument : str
Name of instrument associated with the flat-field array
detector : str
Name of detector associated with the flat-field array
hdulist : astropy.fits.HDUList
HDUList containing "extra" fits keywords
files : list
List of files used to create reference file
author : str
Author of the reference file
description : str
CRDS description to use in the final reference file
pedigree : str
CRDS pedigree to use in the final reference file
useafter : str
CRDS useafter string for the reference file
history_text : list
List of strings to add as HISTORY entries to the reference file
outfile : str
Name of the output reference file
"""
yd, xd = flat_map.shape
# Initialize the MaskModel using the hdu_list, so the new keywords will
# be populated
model = FlatModel(hdulist)
model.data = flat_map
model.dq = flat_dq
model.err = flat_err
model.dq_def = dqdef
#Load a file to get some header info
primaryheader = fits.getheader(os.path.join(filterdir, files[0]))
filterwheel = primaryheader['FILTER']
pupilwheel = primaryheader['PUPIL']
model.meta.reftype = 'FLAT'
model.meta.subarray.name = 'FULL'
model.meta.subarray.xstart = 1
model.meta.subarray.xsize = xd
model.meta.subarray.ystart = 1
model.meta.subarray.ysize = yd
model.meta.instrument.name = instrument.upper()
model.meta.instrument.detector = detector
model.meta.instrument.filter = filterwheel
model.meta.instrument.pupil = pupilwheel
# Get the fast and slow axis directions from one of the input files
fastaxis, slowaxis = bad_pixel_mask.badpix_from_flats.get_fastaxis(
os.path.join(filterdir, files[0]))
model.meta.subarray.fastaxis = fastaxis
model.meta.subarray.slowaxis = slowaxis
model.meta.author = author
model.meta.description = description
model.meta.pedigree = pedigree
model.meta.useafter = useafter
# Add HISTORY information
package_note = (
'This file was created using https://github.com/chriswillott/jwst/blob/master/makenirissimagingflats.py'
)
entry = util.create_history_entry(package_note)
model.history.append(entry)
package_note = ('FPA Temperature={}K'.format(fpatemp))
entry = util.create_history_entry(package_note)
model.history.append(entry)
# Add the list of input files used to create the map
model.history.append('DATA USED:')
for file in files:
totlen = len(file)
div = np.arange(0, totlen, 60)
for val in div:
if totlen > (val + 60):
model.history.append(
util.create_history_entry(file[val:val + 60]))
else:
model.history.append(util.create_history_entry(file[val:]))
# Add the do not use lists, pixel flag mappings, and user-provided
# history text
for history_entry in history_text:
if history_entry != '':
model.history.append(util.create_history_entry(history_entry))
model.save(outfile, overwrite=True)
print('Final flat reference file save to: {}'.format(outfile))
def save_final_map(bad_pix_map, instrument, detector, files, author, description, pedigree, useafter,
history_text, sigma_thresh, smooth_width, dead_sigma_thresh, max_dead_rate,
max_low_qe_rate, max_open_adj_rate, do_not_use_list, outfile):
"""Save a bad pixel map into a CRDS-formatted reference file
Parameters
----------
"""
# Define the non-standard fits header keywords by placing them in a
# fits HDU List
sig_thresh_keyword = 'BPMSIGMA'
smooth_keyword = 'BPMSMOTH'
dead_sigma_keyword = 'BPMDEDSG'
max_dead_keyword = 'BPMMXDED'
max_low_qe_keyword = 'BPMMXLQE'
max_open_adj_keyword = 'BPMMXOAD'
hdu = fits.PrimaryHDU()
hdu.header[sig_thresh_keyword] = sigma_thresh
hdu.header[smooth_keyword] = smooth_width
hdu.header[dead_sigma_keyword] = dead_sigma_thresh
hdu.header[max_dead_keyword] = max_dead_rate
hdu.header[max_low_qe_keyword] = max_low_qe_rate
hdu.header[max_open_adj_keyword] = max_open_adj_rate
hdu_list = fits.HDUList([hdu])
yd, xd = bad_pix_map.shape
# Initialize the MaskModel using the hdu_list, so the new keywords will
# be populated
model = MaskModel(hdu_list)
model.dq = bad_pix_map
# Create dq_def data
dq_def = create_dqdef()
model.dq_def = dq_def
model.meta.reftype = 'MASK'
model.meta.subarray.name = 'FULL'
model.meta.subarray.xstart = 1
model.meta.subarray.xsize = xd
model.meta.subarray.ystart = 1
model.meta.subarray.ysize = yd
model.meta.instrument.name = instrument.upper()
model.meta.instrument.detector = detector
# Get the fast and slow axis directions from one of the input files
fastaxis, slowaxis = get_fastaxis(files[0])
model.meta.subarray.fastaxis = fastaxis
model.meta.subarray.slowaxis = slowaxis
model.meta.author = author
model.meta.description = description
model.meta.pedigree = pedigree
model.meta.useafter = useafter
# Populate "extra" header keywords that will contain parameters used
# in this module
package_note = ('This file was created using the bad_pixel_mask.py module within the '
'jwst_reffiles package.')
software_dict = {'name': 'jwst_reffiles.bad_pixel_mask.py', 'author': 'STScI',
'homepage': 'https://github.com/spacetelescope/jwst_reffiles',
'version': '0.0.0'}
entry = util.create_history_entry(package_note, software=software_dict)
model.history.append(entry)
model.history.append(util.create_history_entry('Parameter values and descriptions:'))
sigma_descrip = ('sigma_thresh: Number of standard deviations to use when sigma-clipping to '
'calculate the mean slope image or the mean across the detector. The value '
'used is stored in the {} keyword.'.format(sig_thresh_keyword))
model.history.append(util.create_history_entry(sigma_descrip))
smooth_descrip = ('smoothing_box_width: Width in pixels of the box kernel to use to compute the '
'smoothed mean image. The value used is stored in the {} keyword.'.format(smooth_keyword))
model.history.append(util.create_history_entry(smooth_descrip))
dead_sig_descrip = ('Number of standard deviations below the mean at which a pixel is considered dead. '
'The value used is stored in the {} keyword.'.format(dead_sigma_keyword))
model.history.append(util.create_history_entry(dead_sig_descrip))
max_dead_descrip = ('Maximum normalized signal rate of a pixel that is considered dead. The value '
'used is stored in the {} keyword.'.format(max_dead_keyword))
model.history.append(util.create_history_entry(max_dead_descrip))
max_low_qe_descrip = ('The maximum normalized signal a pixel can have and be considered low QE. The '
'value used is stored in the {} keyword.'.format(max_low_qe_keyword))
model.history.append(util.create_history_entry(max_low_qe_descrip))
max_open_adj_descrip = ('The maximum normalized signal a pixel adjacent to a low QE pixel can have '
'in order for the low QE pixel to be reclassified as OPEN. The value used '
'is stored in the {} keyword.'.format(max_open_adj_keyword))
model.history.append(util.create_history_entry(max_open_adj_descrip))
do_not_use_descrip = ('List of bad pixel types where the DO_NOT_USE flag is also applied. '
'Values used are: {}'.format(do_not_use_list))
model.history.append(util.create_history_entry(do_not_use_descrip))
# Add the list of input files used to create the map
model.history.append('DATA USED:')
for file in files:
totlen = len(file)
div = np.arange(0, totlen, 60)
for val in div:
if totlen > (val+60):
model.history.append(util.create_history_entry(file[val:val+60]))
else:
model.history.append(util.create_history_entry(file[val:]))
if history_text is not None:
model.history.append(util.create_history_entry(history_text))
model.save(outfile, overwrite=True)
print('Final bad pixel mask reference file save to: {}'.format(outfile))
def create_nircam_distortion(detector, aperture, outname, sci_pupil,
sci_subarr, sci_exptype, history_entry):
"""
Create an asdf reference file with all distortion components for the NIRCam imager.
NOTE: The IDT has not provided any distortion information. The files are constructed
using ISIM transformations provided/(computed?) by the TEL team which they use to
create the SIAF file.
These reference files should be replaced when/if the IDT provides us with distortion.
Parameters
----------
detector : str
NRCB1, NRCB2, NRCB3, NRCB4, NRCB5, NRCA1, NRCA2, NRCA3, NRCA4, NRCA5
aperture : str
Name of the aperture/subarray. (e.g. FULL, SUB160, SUB320, SUB640, GRISM_F322W2)
outname : str
Name of output file.
Examples
--------
"""
degree = 5 # distotion in pysiaf is a 5th order polynomial
numdet = detector[-1]
module = detector[-2]
channel = 'SHORT'
if numdet == '5':
channel = 'LONG'
full_aperture = detector + '_' + aperture
# Get Siaf instance for detector/aperture
inst_siaf = pysiaf.Siaf('nircam')
siaf = inst_siaf[full_aperture]
# Find the distance between (0,0) and the reference location
xshift, yshift = get_refpix(inst_siaf, full_aperture)
# *****************************************************
# "Forward' transformations. science --> ideal --> V2V3
label = 'Sci2Idl'
#from_units = 'distorted pixels'
#to_units = 'arcsec'
xcoeffs, ycoeffs = get_distortion_coeffs(label, siaf)
sci2idlx = Polynomial2D(degree, **xcoeffs)
sci2idly = Polynomial2D(degree, **ycoeffs)
# Get info for ideal -> v2v3 or v2v3 -> ideal model
parity = siaf.VIdlParity
v3_ideal_y_angle = siaf.V3IdlYAngle * np.pi / 180.
idl2v2v3x, idl2v2v3y = v2v3_model('ideal', 'v2v3', parity, v3_ideal_y_angle)
# Finally, we need to shift by the v2,v3 value of the reference
# location in order to get to absolute v2,v3 coordinates
v2shift, v3shift = get_v2v3ref(siaf)
# *****************************************************
# 'Reverse' transformations. V2V3 --> ideal --> science
label = 'Idl2Sci'
#from_units = 'arcsec'
#to_units = 'distorted pixels'
xcoeffs, ycoeffs = get_distortion_coeffs(label, siaf)
idl2scix = Polynomial2D(degree, **xcoeffs)
idl2sciy = Polynomial2D(degree, **ycoeffs)
# Get info for ideal -> v2v3 or v2v3 -> ideal model
parity = siaf.VIdlParity
v3_ideal_y_angle = siaf.V3IdlYAngle * np.pi / 180.
v2v32idlx, v2v32idly = v2v3_model('v2v3', 'ideal', parity, v3_ideal_y_angle)
##"Forward' transformations. science --> ideal --> V2V3
#sci2idlx, sci2idly, sciunit, idlunit = read_siaf_table.get_siaf_transform(coefffile,full_aperture,'science','ideal', 5)
#idl2v2v3x, idl2v2v3y = read_siaf_table.get_siaf_v2v3_transform(coefffile,full_aperture,from_system='ideal')
##'Reverse' transformations. V2V3 --> ideal --> science
#v2v32idlx, v2v32idly = read_siaf_table.get_siaf_v2v3_transform(coefffile,full_aperture,to_system='ideal')
#idl2scix, idl2sciy, idlunit, sciunit = read_siaf_table.get_siaf_transform(coefffile,full_aperture,'ideal','science', 5)
# Now create a compound model for each with the appropriate inverse
sci2idl = Mapping([0, 1, 0, 1]) | sci2idlx & sci2idly
sci2idl.inverse = Mapping([0, 1, 0, 1]) | idl2scix & idl2sciy
idl2v2v3 = Mapping([0, 1, 0, 1]) | idl2v2v3x & idl2v2v3y
idl2v2v3.inverse = Mapping([0, 1, 0, 1]) | v2v32idlx & v2v32idly
# Now string the models together to make a single transformation
# We also need
# to account for the difference of 1 between the SIAF
# coordinate values (indexed to 1) and python (indexed to 0).
# Nadia said that this shift should be present in the
# distortion reference file.
core_model = sci2idl | idl2v2v3
# Now add in the shifts to create the full model
# including the shift to go from 0-indexed python coords to
# 1-indexed
# SIAF coords
index_shift = Shift(1)
model = index_shift & index_shift | xshift & yshift | core_model | v2shift & v3shift
# Since the inverse of all model components are now defined,
# the total model inverse is also defined automatically
# In the reference file headers, we need to switch NRCA5 to
# NRCALONG, and same for module B.
if detector[-1] == '5':
detector = detector[0:4] + 'LONG'
# Save using the DistortionModel datamodel
d = DistortionModel(model=model, input_units=u.pix,
output_units=u.arcsec)
#Populate metadata
# Keyword values in science data to which this file should
# be applied
p_pupil = ''
for p in sci_pupil:
p_pupil = p_pupil + p + '|'
p_subarr = ''
for p in sci_subarr:
p_subarr = p_subarr + p + '|'
p_exptype = ''
for p in sci_exptype:
p_exptype = p_exptype + p + '|'
d.meta.instrument.p_pupil = p_pupil
d.meta.subarray.p_subarray = p_subarr
d.meta.exposure.p_exptype = p_exptype
#d.meta.instrument.p_pupil = "CLEAR|F162M|F164N|F323N|F405N|F470N|"
#d.meta.p_subarray = "FULL|SUB64P|SUB160|SUB160P|SUB320|SUB400P|SUB640|SUB32TATS|SUB32TATSGRISM|SUB8FP1A|SUB8FP1B|SUB96DHSPILA|SUB96DHSPILB|SUB64FP1A|SUB64FP1B|"
#d.meta.exposure.p_exptype = "NRC_IMAGE|NRC_TSIMAGE|NRC_FLAT|NRC_LED|NRC_WFSC|"
# metadata describing the reference file itself
d.meta.title = "NIRCam Distortion"
d.meta.instrument.name = "NIRCAM"
d.meta.instrument.module = module
d.meta.instrument.channel = channel
d.meta.instrument.detector = detector
d.meta.telescope = 'JWST'
d.meta.subarray.name = 'FULL'
d.meta.pedigree = 'GROUND'
d.meta.reftype = 'DISTORTION'
d.meta.author = 'B. Hilbert'
d.meta.litref = "https://github.com/spacetelescope/jwreftools"
d.meta.description = "Distortion model from SIAF coefficients in pysiaf version 0.6.1"
#d.meta.exp_type = exp_type
d.meta.useafter = "2014-10-01T00:00:00"
# To be ready for the future where we will have filter-dependent solutions
d.meta.instrument.filter = 'N/A'
# Create initial HISTORY ENTRY
sdict = {'name': 'nircam_distortion_reffiles_from_pysiaf.py',
'author': 'B.Hilbert',
'homepage': 'https://github.com/spacetelescope/jwreftools',
'version': '0.8'}
entry = util.create_history_entry(history_entry, software=sdict)
d.history = [entry]
#Create additional HISTORY entries
#entry2 = util.create_history_entry(history_2)
#d.history.append(entry2)
d.save(outname)
print("Output saved to {}".format(outname))