def main(sensor_id, infile, output_dir='./', cti=None, do_trapping=False,
do_electronics=False):
processed_file = os.path.join(output_dir,
'{0}_processed.fits'.format(sensor_id))
corrected_file = os.path.join(output_dir,
'{0}_corrected.fits'.format(sensor_id))
## CTI parameters
if cti is None:
do_cti = False
cti = 0.0
else:
do_cti = True
cti_dict = {amp : cti for amp in range(1, 17)}
## Trapping parameters
if do_trapping:
# traps = [LinearTrap(4.0, 0.4, 1, 0.08),
# LogisticTrap(1000.0, 0.4, 1, 60000., 0.0002)]
traps = [LinearTrap(4.0, 0.4, 1, 0.08),
LogisticTrap(40.0, 0.4, 1, 17500., 0.001)]
else:
traps = None
traps_dict = {amp : traps for amp in range(1, 17)}
## Electronics parameters
if do_electronics:
scale = 0.0002
decay_time = 2.5
output_amps = {amp : FloatingOutputAmplifier(1.0, scale, decay_time) for amp in range(1, 17)}
else:
output_amps = {amp : BaseOutputAmplifier(1.0) for amp in range(1, 17)}
## Process infile
imsim = ImageSimulator.from_image_fits(infile, output_amps,
cti=cti_dict, traps=traps_dict)
imarr_results = imsim.image_readout(infile, outfile=processed_file)
ccd = MaskedCCD(processed_file)
hdulist = fits.HDUList()
with fits.open(infile) as template:
hdulist.append(template[0])
hdulist[0].header['ORIGFILE'] = hdulist[0].header['FILENAME']
hdulist[0].header['FILENAME'] = corrected_file
for amp in range(1, 17):
imarr = ccd.bias_subtracted_image(amp).getImage().getArray()
## Electronics Correction
if do_electronics:
E = electronics_operator(imarr, scale, decay_time, num_previous_pixels=15)
corrected_imarr = imarr - E
else:
corrected_imarr = imarr
## Trap Correction
if do_trapping:
T = trap_operator(imarr, *traps)
corrected_imarr = corrected_imarr - (1-cti)*T
else:
pass
## CTI Correction
if do_cti:
Dinv_cti = cti_inverse_operator(cti, imarr.shape[1])
for i in range(imarr.shape[0]):
corrected_imarr[i, :] = Dinv_cti*corrected_imarr[i, :]
else:
pass
hdulist.append(fits.ImageHDU(data=corrected_imarr,
header=template[amp].header))
with warnings.catch_warnings():
for warning in (UserWarning, AstropyWarning,
AstropyUserWarning):
warnings.filterwarnings('ignore', category=warning,
append=True)
fitsWriteto(hdulist, corrected_file, overwrite=True)
def main(sensor_id,
infile,
main_dir,
gain_file=None,
output_dir='./',
no_bias=False):
## Get existing parameter results
param_file = join(main_dir, '{0}_parameter_results.fits'.format(sensor_id))
param_results = OverscanParameterResults.from_fits(param_file)
cti_results = param_results.cti_results
drift_scales = param_results.drift_scales
decay_times = param_results.decay_times
trap_files = [
join(main_dir, '{0}_amp{1}_trap.pkl'.format(sensor_id, i))
for i in range(1, 17)
]
## Get gains
if gain_file is not None:
with open(gain_file, 'rb') as f:
gain_results = pickle.load(f)
gains = gain_results.get_amp_gains(sensor_id)
else:
gains = {i: 1.0 for i in range(1, 17)}
## Output filename
base = splitext(os.path.basename(infile))[0]
outfile = join(output_dir, '{0}_corrected.fits'.format(base))
## Include bias frame for calibration
if no_bias:
bias_frame = None
else:
bias_frame = join(main_dir, '{0}_superbias.fits'.format(sensor_id))
ccd = MaskedCCD(infile, bias_frame=bias_frame)
hdulist = fits.HDUList()
with fits.open(infile) as template:
hdulist.append(template[0])
## Perform correction amp by amp
for amp in range(1, 17):
imarr = ccd.bias_subtracted_image(
amp).getImage().getArray() * gains[amp]
## Electronics Correction
if drift_scales[amp] > 0.:
Linv = electronics_inverse_operator(imarr,
drift_scales[amp],
decay_times[amp],
num_previous_pixels=15)
corrected_imarr = imarr - Linv
else:
corrected_imarr = imarr
## Trap Correction
spltrap = pickle.load(open(trap_files[amp], 'rb'))
Tinv = trap_inverse_operator(corrected_imarr, spltrap)
corrected_imarr = corrected_imarr - (1 - cti_results[amp]) * Tinv
## Reassemble HDUList
hdulist.append(
fits.ImageHDU(data=corrected_imarr / gains[amp],
header=template[amp].header))
with warnings.catch_warnings():
for warning in (UserWarning, AstropyWarning,
AstropyUserWarning):
warnings.filterwarnings('ignore',
category=warning,
append=True)
fitsWriteto(hdulist, outfile, overwrite=True)