def get_superbias(self, file):
"""Read in superbias and deal with bad pixels"""
sb_model = SuperBiasModel(file)
sb = sb_model.data
bad = np.isnan(sb)
sb[bad] = 0.
return sb
def setup_cube(ngroups, nrows, ncols):
''' Set up fake data to test.'''
nints = 1
data_model = RampModel()
data_model.data = np.zeros(shape=(nints, ngroups, nrows, ncols),
dtype=np.float32)
data_model.pixeldq = np.zeros(shape=(nrows, ncols), dtype=np.int32)
data_model.meta.subarray.xstart = 1
data_model.meta.subarray.ystart = 1
data_model.meta.subarray.xsize = ncols
data_model.meta.subarray.ysize = nrows
data_model.meta.instrument.name = 'NIRCAM'
bias_model = SuperBiasModel()
bias_model.data = np.zeros(shape=(2048, 2048), dtype=np.float32)
bias_model.dq = np.zeros(shape=(2048, 2048), dtype=np.int32)
bias_model.meta.subarray.xstart = 1
bias_model.meta.subarray.ystart = 1
bias_model.meta.subarray.xsize = 2048
bias_model.meta.subarray.ysize = 2048
bias_model.meta.instrument.name = 'NIRCAM'
bias_model.meta.description = 'Fake data.'
bias_model.meta.telescope = 'JWST'
bias_model.meta.reftype = 'SuperBiasModel'
bias_model.meta.author = 'Alicia'
bias_model.meta.pedigree = 'Dummy'
bias_model.meta.useafter = '2015-10-01T00:00:00'
return data_model, bias_model
def _cube(xstart, ystart, ngroups, nrows, ncols):
nints = 1
# create a JWST datamodel for NIRCam SUB320A335R data
data_model = RampModel((nints, ngroups, nrows, ncols))
data_model.meta.subarray.name = 'SUB320A335R'
data_model.meta.subarray.xstart = xstart
data_model.meta.subarray.ystart = ystart
data_model.meta.subarray.xsize = ncols
data_model.meta.subarray.ysize = nrows
data_model.meta.exposure.ngroups = ngroups
data_model.meta.instrument.name = 'NIRCAM'
data_model.meta.instrument.detector = 'NRCALONG'
data_model.meta.observation.date = '2019-10-14'
data_model.meta.observation.time = '16:44:12.000'
# create a superbias model for the superbias step
bias_model = SuperBiasModel((2048, 2048))
bias_model.meta.subarray.xstart = 1
bias_model.meta.subarray.ystart = 1
bias_model.meta.subarray.xsize = 2048
bias_model.meta.subarray.ysize = 2048
bias_model.meta.instrument.name = 'NIRCAM'
bias_model.meta.description = 'Fake data.'
bias_model.meta.telescope = 'JWST'
bias_model.meta.reftype = 'SuperBiasModel'
bias_model.meta.author = 'Alicia'
bias_model.meta.pedigree = 'Dummy'
bias_model.meta.useafter = '2015-10-01T00:00:00'
return data_model, bias_model
def compare(self):
#run the pipeline on the input ramp
pipeout = self.run_superbias_step()
#Manual superbias subtraction
sb = SuperBiasModel(self.sbfile)
ramp = RampModel(self.infile)
superbias = sb.data
#extract the appropriate subarray from the reference
#file if necessary
if ramp.data.shape[-2] != 2048:
xs, xe, ys, ye = ex.get_coords_rampmodel(ramp)
superbias = sb.data[ys:ye, xs:xe]
#subtract superbias
ramp.data -= superbias
#Compare pipeline output with manual output
self.test_superbias_sub(pipeout.data, ramp.data)
self.test_pixeldq_propagation(pipeout, sb)
print("Superbias testing complete")
#! /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))
def make_files(self):
#loop over detector
for det in self.detectors:
satfile = [s for s in self.satfiles if det in s][0]
sat_model = SaturationModel(satfile)
sat = sat_model.data
#pixels with saturation level of 0.
#set sat level to 65535
bad = sat == 0
sat[bad] = 65535
linfile = [s for s in self.linfiles if det in s][0]
lin_model = LinearityModel(linfile)
lin = lin_model.coeffs
#pixels with bad linearity coeffs
#set so no correction is applied
nans = np.isnan(lin[1, :, :])
tmp = lin[1, :, :]
tmp[nans] = 1.
lin[1, :, :] = tmp
for i in range(2, 7):
tmp = lin[i, :, :]
nans = np.isnan(tmp)
tmp[nans] = 0.
lin[i, :, :] = tmp
#superbias file
sbfile = [s for s in self.sbfiles if det in s][0]
sb_model = SuperBiasModel(sbfile)
superbias = sb_model.data
#linearize the saturation values
sat_lin = self.linearize(sat - superbias, lin)
#loop over readout patterns
for readpat in self.readpatts:
nframe, nskip = self.readpatts[readpat]
#optional output plot
if self.plot:
xx = 400
yy = 400
fsize = 12
f = plt.figure()
a = f.add_subplot(111)
a2 = a.twiny()
f.subplots_adjust(bottom=0.2)
xs = np.arange(self.maxgroups * (nframe + nskip))
a.plot(xs,
np.repeat(sat[yy, xx], len(xs)),
linestyle=':',
color='blue',
linewidth=2,
label='Original Saturation')
a.plot(xs,
np.repeat(sat_lin[yy, xx] + superbias[yy, xx],
len(xs)),
linestyle=':',
color='red',
linewidth=2,
label='Linearized Saturation')
a.plot(xs,
np.repeat(superbias[yy, xx], len(xs)),
linestyle=':',
color='black',
linewidth=2,
label='Superbias Level')
#loop over groups
satramp = np.zeros((self.maxgroups, 2048, 2048))
linsatramp = np.zeros((self.maxgroups, 2048, 2048))
xfmeans = []
for i in range(self.maxgroups):
#exposure time to the final frame in the group
exptime = self.frametime * (nframe + nskip) * (i + 1)
satslope = sat_lin / exptime
#now calculate signals for each frame within the
#group, by reducing exposure time by one frametime
#for each
fsigs = np.zeros((nframe, 2048, 2048))
fsigs[0, :, :] = sat_lin
for frame in range(1, nframe):
fsigs[frame, :, :] = satslope * (
exptime - (self.frametime * frame))
linsatramp[i, :, :] = np.mean(fsigs,
axis=0) + superbias
#non-linearize fsigs
fsigs_nl = self.unlinearize(fsigs, lin, sat - superbias)
#add superbias back in
fsigs_nl += superbias
satramp[i, :, :] = np.mean(fsigs_nl, axis=0)
#print("Group: {}".format(i))
#print("Exptime: {}".format(exptime))
#print("Sat: {}, Lin Sat: {}".format(sat[yy,xx],sat_lin[yy,xx]))
#print("Satslope: {}".format(satslope[yy,xx]))
#print("Frame exps: {}".format(exptime-(self.frametime*np.arange(1,nframe))))
#print("signals: {}".format(fsigs[:,yy,xx]))
#print("mean signal: {}".format(satramp[i,yy,xx]))
#if i == 1:
# stop
if self.plot:
xf = np.array([-1])
xf = np.append(
xf,
np.arange((i + 1) * (nframe + nskip) - nframe,
(i + 1) * (nframe + nskip)))
yf = np.array([superbias[yy, xx]])
yf = np.append(
yf, fsigs[:, yy, xx][::-1] + superbias[yy, xx])
yfnl = np.array([superbias[yy, xx]])
yfnl = np.append(yfnl, fsigs_nl[:, yy, xx][::-1])
if i == 9:
a.plot(xf,
yf,
mfc='red',
mec='red',
color='black',
marker='o',
linestyle='-',
label='Linearized Frames',
alpha=0.5)
#a.plot(np.mean(xf[1:]),linsatramp[i,yy,xx],color='red',marker='8',mfc='none',mec='red',markersize=10,label='Linearized Frames Mean')
a.plot(xf,
yfnl,
mfc='black',
mec='black',
color='black',
marker='o',
linestyle='-',
label='Non-Linearized Frames',
alpha=0.5)
#a.plot(np.mean(xf[1:]),linsatramp[i,yy,xx],color='red',marker='8',mfc='none',mec='red',markersize=10,label='Linearized Frames Mean')
else:
a.plot(xf,
yf,
mfc='red',
mec='red',
color='black',
marker='o',
linestyle='-',
alpha=0.5)
#a.plot(np.mean(xf[1:]),linsatramp[i,yy,xx],color='red',mfc='none',mec='red',marker='8',markersize=10)
a.plot(xf,
yfnl,
mfc='black',
mec='black',
color='black',
marker='o',
linestyle='-',
alpha=0.5)
xfmeans.append(np.mean(xf[1:]))
#optional plot
if self.plot:
new_tick_locations = np.array(xfmeans)
a.plot(xfmeans,
satramp[:, yy, xx],
color='blue',
marker='8',
markersize=10,
label='Non-Linear Frames Mean')
a.legend(loc='lower right', numpoints=1, fontsize=fsize)
a.set_xlabel('Frame Number')
a.set_ylabel('Signal (DN)')
a.set_title('NRC{}, Readpattern: {}, Pixel ({},{})'.format(
det, readpat, xx, yy))
a.set_xlim(-1, np.max(xf) + 1)
a.set_ylim(0, 60000)
# Move twinned axis ticks and label from top to bottom
a2.xaxis.set_ticks_position("bottom")
a2.xaxis.set_label_position("bottom")
# Offset the twin axis below the host
a2.spines["bottom"].set_position(("axes", -0.15))
# Turn on the frame for the twin axis, but then hide all
# but the bottom spine
a2.set_frame_on(True)
a2.patch.set_visible(False)
for sp in a2.spines.itervalues():
sp.set_visible(False)
a2.spines["bottom"].set_visible(True)
a2.set_xticks(new_tick_locations)
a2.set_xticklabels(np.arange(len(new_tick_locations)))
a2.set_xlabel("Group Number")
f.savefig(
'GroupSatPlot_forTR_{}_{}_C_filledcircs.png'.format(
det, readpat))
#save output file
self.savefile(satramp, det, readpat)