def test_makeAmplifierGeometry_factory(self):
e2v_geom = makeAmplifierGeometry(self.e2v_test_file)
self.assertEquals(self.e2v, e2v_geom)
itl_geom = makeAmplifierGeometry(self.itl_test_file)
self.assertEquals(self.itl, itl_geom)
self.assertNotEqual(self.e2v, itl_geom)
self.assertNotEqual(self.itl, e2v_geom)
def test_rolloff_mask(self):
amp_geom = makeAmplifierGeometry(self.input_file)
rolloff_mask(self.input_file, self.mask_file,
tmp_mask_image=self.image_file,
outer_edge_width=self.outer_edge_width,
bloom_stop_width=self.bloom_stop_width,
signal=self.signal, cleanup=False)
image = _FitsFile(self.image_file)
mask = _FitsFile(self.mask_file)
for amp in imutils.allAmps(self.input_file):
#
# Unmasked region.
#
indx = np.where(image[amp] == 0)
#
# Verify expected sensor perimeter mask along vertical sides.
#
self.assertEqual(min(indx[0]),
amp_geom.imaging.getMinY() + self.outer_edge_width)
#
# Verify that mask has zero bits set in unmasked region.
#
self.assertEqual(min(mask[amp][indx].flat), 0)
self.assertEqual(max(mask[amp][indx].flat), 0)
#
# Check that mask area is subset of mask image area.
#
indx = np.where(mask[amp] != 0)
self.assertTrue(min(image[amp][indx].flat) >= self.signal)
def make_superbias_frame(bias_files, slot, outfile):
"""
Make and save a super biasframes. Only need to do it once for each slot.
make_image will look into config['tmp_dir'] to find them.
"""
amp_geom = sensorTest.makeAmplifierGeometry(bias_files[0])
imutils.superbias_file(bias_files, amp_geom.serial_overscan, outfile)
def make_superbias_frame(raft, slot, bias_files, outdir, file_pattern='_sbias_image.fits'):
"""
Make and save a super biasframes. Only need to do it once for each slot.
make_image will look into config['tmp_dir'] to find them.
"""
amp_geom = sensorTest.makeAmplifierGeometry(bias_files[0])
outfile = raft+'_'+slot + file_pattern
imutils.superbias_file(bias_files, amp_geom.serial_overscan, os.path.join(outdir,outfile))
def __init__(self, infile):
amp_geom = makeAmplifierGeometry(infile)
xmin, xmax = amp_geom.imaging.getMinX(), amp_geom.imaging.getMaxX()
super(_FitsFile, self).__init__()
with fits.open(infile) as foo:
amps = imutils.allAmps(infile)
for amp in amps:
self[amp] = copy.deepcopy(foo[amp].data[:, xmin:xmax])
def make_median_bias_frame(bias_files, sensor_id, acq_job, skip=1):
"""Make a median bias frame from bias files."""
# Skip the initial frames since the first bias images may have
# residual signal from not having been cleared properly.
bias_files = sorted(bias_files)[skip:]
bias_frame = f'{sensor_id}_{acq_job}_median_bias.fits'
amp_geom = sensorTest.makeAmplifierGeometry(bias_files[0])
imutils.superbias_file(bias_files, amp_geom.serial_overscan, bias_frame)
return bias_frame
def bias_frame_task(run, det_name, bias_files, bias_frame=None):
"""Create a median bias file for use by downstream tasks."""
if bias_frame is None:
bias_frame = make_bias_filename(run, det_name)
amp_geom = sensorTest.makeAmplifierGeometry(bias_files[0])
imutils.superbias_file(bias_files, amp_geom.serial_overscan, bias_frame)
file_prefix = make_file_prefix(run, det_name)
rolloff_mask_file = f'{file_prefix}_edge_rolloff_mask.fits'
sensorTest.rolloff_mask(bias_files[0], rolloff_mask_file)
return bias_frame
def run_tearing_detection(sensor_id):
"""
Loop over the acquisition jobs and perform tearing analysis on each.
"""
import pickle
import lsst.eotest.image_utils as imutils
import lsst.eotest.sensor as sensorTest
import siteUtils
from tearing_detection import tearing_detection
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
tearing_stats = []
# Create a super bias frame.
bias_files = siteUtils.dependency_glob(
'S*/%s_flat_bias*.fits' % sensor_id,
jobname=siteUtils.getProcessName('flat_pair_raft_acq'),
description='Bias files:')
if bias_files:
bias_frame = '%s_superbias.fits' % sensor_id
amp_geom = sensorTest.makeAmplifierGeometry(bias_files[0])
imutils.superbias_file(bias_files[:10], amp_geom.serial_overscan,
bias_frame)
else:
bias_frame = None
acq_jobs = {
('flat_pair_raft_acq', 'N/A'): 'S*/%s_flat*flat?_*.fits',
('qe_raft_acq', 'N/A'): 'S*/%s_lambda_flat_*.fits',
('sflat_raft_acq', 'low_flux'): 'S*/%s_sflat_500_flat_L*.fits',
('sflat_raft_acq', 'high_flux'): 'S*/%s_sflat_500_flat_H*.fits'
}
for job_key, pattern in acq_jobs.items():
job_name, subset = job_key
flats = siteUtils.dependency_glob(
pattern % sensor_id,
jobname=siteUtils.getProcessName(job_name),
description='Flat files:')
tearing_found, _ = tearing_detection(flats, bias_frame=bias_frame)
tearing_stats.append((job_name, subset, sensor_id, len(tearing_found)))
with open('%s_tearing_stats.pkl' % file_prefix, 'wb') as output:
pickle.dump(tearing_stats, output)
def apply_cte(infile, pcti=None, scti=None, verbose=False,
amps=tuple(range(1, 17))):
"""
Function to apply distinct levels of parallel cte and/or serial cte
on each amplifier in an input sensor image.
"""
if pcti is None:
pcti = dict([(amp, 0) for amp in amps])
if scti is None:
scti = dict([(amp, 0) for amp in amps])
segments = {}
for amp in amps:
if verbose:
print("apply_cte: working on amp", amp)
image = afwImage.ImageF(infile, imutils.dm_hdu(amp))
geom = sensorTest.makeAmplifierGeometry(infile)
outimage = eotest_utils.ImageTools.applyCTI(image, geom.serial_overscan,
pcti[amp], scti[amp],
verbose)
segments[amp] = outimage
return fitsFile(segments, fits.open(infile))
def get_oscan_indices(target_file):
"Return the pixel indices of the overscan region."
amp_geom = sensorTest.makeAmplifierGeometry(target_file)
bbox = amp_geom.serial_overscan
return bbox.getMinY(), bbox.getMaxY(), bbox.getMinX(), bbox.getMaxX()
def ana_divisidero_tearing(sflat_files, raft_unit_id, run):
"""
Analyze a raft of corrected super-flats for Divisidero Tearing.
Parameters
----------
sflat_files: dict
Dictionary of single CCD superflat files, keyed by slot name.
raft_unit_id: str
Raft unit id, e.g., 'LCA-11021_RTM-019'
run: str
Run number
"""
my_slot = list(sflat_files)[0]
amp_geom = sensorTest.makeAmplifierGeometry(sflat_files[my_slot])
ncol = amp_geom.nx
# make x pixel values
xpixval = np.arange(ncol*8)
# dmslotorder
dmslots = ['S20', 'S21', 'S22', 'S10', 'S11', 'S12', 'S00', 'S01', 'S02']
if 'SW0' in sflat_files:
dmslots = 'SW0 SW1 SG0 SG1'.split()
# get row averages
avedict = {}
for slot in dmslots:
try:
avedict[slot] = normed_mean_response_vscol(sflat_files[slot])
except KeyError:
# This will occur if data from `slot` is not available.
pass
# make a summary plot
f = plt.figure(figsize=(20, 20))
outer = gridspec.GridSpec(3, 3, wspace=0.3, hspace=0.3)
nskip_edge = 20
for i, slot in enumerate(avedict):
max_divisidero = avedict[slot][2]
have_wf_sensor = (len(max_divisidero) == 7)
inner = gridspec.GridSpecFromSubplotSpec(2, 1, subplot_spec=outer[i],
wspace=0.1, hspace=0.0)
for j in range(2):
if have_wf_sensor and j==1:
continue
# use max of max_divisidero_tearing to set the range of plots
plot_range = np.max(max_divisidero[j*7:j*7+8])
ax = plt.Subplot(f, inner[j])
ax.plot(xpixval[nskip_edge:ncol*8 - nskip_edge],
avedict[slot][j][nskip_edge:ncol*8 - nskip_edge])
ax.set_xlabel('Col #')
try:
ax.set_ylim(1.-plot_range, 1.+plot_range)
except ValueError as eobj:
# plot_range is probably inf or NaN because of bad pixel
# data for this sensor, so just skip this plot.
print('ValueError:', str(eobj))
continue
for k in range(1, 8):
ax.axvline(x=ncol*k, color='red', ls='--', alpha=0.2)
if j == 0 and not have_wf_sensor:
ax.text(0.025, 0.9, '%s' % (slot), transform=ax.transAxes)
ax.text(0.825, 0.05, 'Seg 10-17', transform=ax.transAxes)
elif j == 1 or have_wf_sensor:
ax.text(0.825, 0.05, 'Seg 00-07', transform=ax.transAxes)
f.add_subplot(ax)
plt.suptitle('Run %s %s' % (str(run), raft_unit_id), fontsize=36)
return {slot: avedict[slot][2] for slot in avedict}