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))