def stage_isr_files(device_list, dest_dir):
"""
Stage bias frame, dark frame, and mask files for the specified
devices.
"""
run = siteUtils.getRunNumber()
fits_files = set()
ccds = CCDS.intersection(device_list)
for ccd in ccds:
fits_files = fits_files.union(get_isr_files(ccd, run))
rafts = RAFTS.intersection(device_list)
for raft in rafts:
if raft in 'R00 R04 R40 R44':
slots = 'SG0 SG1 SW0 SW1'.split()
else:
slots = 'S00 S01 S02 S10 S11 S12 S20 S21 S22'.split()
for slot in slots:
det_name = '_'.join((raft, slot))
fits_files = fits_files.union(get_isr_files(det_name, run))
for src in fits_files:
folder = os.path.basename(os.path.dirname(src))
os.makedirs(os.path.join(dest_dir, folder), exist_ok=True)
dest = os.path.join(dest_dir, folder, os.path.basename(src))
if not os.path.isfile(dest):
print('copying', src, 'to', dest)
shutil.copy(src, dest)
def run_dark_current_task(sensor_id):
"Single sensor execution of dark current analysis."
import lsst.eotest.sensor as sensorTest
import siteUtils
import eotestUtils
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
dark_files = siteUtils.dependency_glob(
'S*/%s_dark_dark_*.fits' % sensor_id,
jobname=siteUtils.getProcessName('dark_raft_acq'),
description='Dark files:')
bias_frame = siteUtils.dependency_glob('%s_sflat*median_bias.fits' %
sensor_id,
description='Super bias frame:')[0]
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
gains = eotestUtils.getSensorGains(jobname='fe55_raft_analysis',
sensor_id=sensor_id)
task = sensorTest.DarkCurrentTask()
task.config.temp_set_point = -100.
dark_curr_pixels, dark95s \
= task.run(sensor_id, dark_files, mask_files, gains,
bias_frame=bias_frame)
results_file \
= siteUtils.dependency_glob('%s_eotest_results.fits' % sensor_id,
jobname='read_noise_raft')[0]
plots = sensorTest.EOTestPlots(sensor_id, results_file=results_file)
siteUtils.make_png_file(plots.total_noise,
'%s_noise.png' % file_prefix,
dark95s=dark95s)
def validate_tearing(results, det_names):
"""Validate the tearing analysis results."""
run = siteUtils.getRunNumber()
schema = lcatr.schema.get('tearing_detection_BOT')
missing_det_names = []
for det_name in det_names:
raft, slot = det_name.split('_')
file_prefix = make_file_prefix(run, det_name)
tearing_results_file = '%s_tearing_stats.pkl' % file_prefix
if not os.path.isfile(tearing_results_file):
missing_det_names.append(det_name)
continue
with open(tearing_results_file, 'rb') as input_:
tearing_stats = pickle.load(input_)
for values in tearing_stats:
stats = dict(kv for kv in zip(('job_name', 'subset', 'sensor_id',
'detections', 'slot', 'raft'),
list(values) + [slot, raft]))
results.append(lcatr.schema.valid(schema, **stats))
png_files = sorted(glob.glob('*_tearing.png'))
results.extend(persist_tearing_png_files(png_files))
report_missing_data("validate_tearing", missing_det_names)
return results
def bias_frame_jh_task(det_name):
"""JH version of the bias_frame_task."""
import os
import siteUtils
import json
from bot_eo_analyses import glob_pattern, bias_frame_task, \
bias_stability_task
run = siteUtils.getRunNumber()
acq_jobname = siteUtils.getProcessName('BOT_acq')
bias_files \
= siteUtils.dependency_glob(glob_pattern('bias_frame', det_name),
acq_jobname=acq_jobname,
description='Bias frames:')
if not bias_files:
print("bias_frame_task: Needed data files are missing for detector",
det_name)
return None
bias_stability_files \
= siteUtils.dependency_glob(glob_pattern('bias_stability', det_name),
acq_jobname=acq_jobname,
description='Bias stability frames:')
if not bias_stability_files:
print("bias_stability_task: Needed data files are missing for detector",
det_name)
return None
bias_stability_files = sorted(bias_stability_files)
bias_stability_task(run, det_name, bias_stability_files)
return bias_frame_task(run, det_name, bias_files[1:])
def validate_overscan(results, det_names):
"""Validate the overscan analysis results."""
run = siteUtils.getRunNumber()
results = []
missing_det_names = set()
for det_name in det_names:
file_prefix = make_file_prefix(run, det_name)
results_file = f'{file_prefix}_overscan_results.fits'
if not os.path.isfile(results_file):
missing_det_names.add(det_name)
else:
md = dict(DATA_PRODUCT='overscan_task_results',
RUN=run,
DETECTOR=det_name)
results.append(siteUtils.make_fileref(results_file, metadata=md))
png_files = (glob.glob(f'{file_prefix}_*_eper_*.png') +
glob.glob(f'{file_prefix}_*_overscan_*.png') +
glob.glob(f'{file_prefix}_*_cti.png'))
md = dict(TEST_CATEGORY='EO', DETECTOR=det_name, RUN=run)
results.extend(
siteUtils.persist_png_files('',
file_prefix,
png_files=png_files,
metadata=md))
report_missing_data('validate_overscan', missing_det_names)
return results
def run_dark_pixels_task(sensor_id):
"Single sensor execution of the dark pixels task."
import lsst.eotest.sensor as sensorTest
import siteUtils
import eotestUtils
acq_jobname = siteUtils.getProcessName('sflat_raft_acq')
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
sflat_files = siteUtils.dependency_glob('S*/%s_sflat_500_flat_H*.fits' % sensor_id,
jobname=acq_jobname,
description='Superflat files:')
bias_files = siteUtils.dependency_glob('S*/%s_sflat_bias*.fits' % sensor_id,
jobname=acq_jobname,
description='Bias files:')
bias_frame = eotestUtils.make_median_bias_frame(bias_files, sensor_id,
'sflat_raft_acq')
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
task = sensorTest.DarkPixelsTask()
task.run(sensor_id, sflat_files, mask_files, bias_frame=bias_frame)
siteUtils.make_png_file(sensorTest.plot_flat,
'%s_superflat_dark_defects.png' % file_prefix,
'%s_median_sflat.fits' % sensor_id,
title='%s, superflat for dark defects analysis' % sensor_id,
annotation='ADU/pixel', flatten=True, binsize=4)
def run_bf_task(sensor_id):
import lsst.eotest.sensor as sensorTest
import siteUtils
import eotestUtils
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
flat_files = siteUtils.dependency_glob(
'S*/%s_flat*flat1*.fits' % sensor_id,
jobname=siteUtils.getProcessName('flat_pair_raft_acq'),
description='Flat files:')
bias_frame = siteUtils.dependency_glob('%s_sflat*median_bias.fits' %
sensor_id,
description='Superbias files:')[0]
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
task = sensorTest.BFTask()
task.run(sensor_id,
flat_files,
mask_files=mask_files,
bias_frame=bias_frame)
results_file = '%s_eotest_results.fits' % sensor_id
plots = sensorTest.EOTestPlots(sensor_id, results_file=results_file)
siteUtils.make_png_file(plots.bf_curves,
'%s_brighter-fatter.png' % file_prefix,
bf_file='%s_bf.fits' % sensor_id)
def validate_traps(results, det_names):
"""Validate and persist trap results."""
run = siteUtils.getRunNumber()
missing_det_names = []
for det_name in det_names:
raft, slot = det_name.split('_')
file_prefix = make_file_prefix(run, det_name)
trap_file = '%s_traps.fits' % file_prefix
if not os.path.isfile(trap_file):
missing_det_names.append(det_name)
continue
eotestUtils.addHeaderData(trap_file,
TESTTYPE='TRAP',
DATE=eotestUtils.utc_now_isoformat())
results.append(siteUtils.make_fileref(trap_file))
mask_file = '%s_traps_mask.fits' % file_prefix
results.append(siteUtils.make_fileref(mask_file))
results_file = '%s_eotest_results.fits' % file_prefix
data = sensorTest.EOTestResults(results_file)
amps = data['AMP']
num_traps = data['NUM_TRAPS']
for amp, ntrap in zip(amps, num_traps):
results.append(
lcatr.schema.valid(lcatr.schema.get('traps_BOT'),
amp=amp,
num_traps=ntrap,
slot=slot,
raft=raft))
report_missing_data("validate_traps", missing_det_names)
return results
def __init__(self, configFile, sys_paths=()):
"""
configFile contains the names of the site-specific
configuration files. File basenames are provided in
configFile, and the full paths are constructed in the
_read(...) method.
"""
super(CcsSetup, self).__init__()
self.commands = []
self['tsCWD'] = os.getcwd()
self['labname'] = siteUtils.getSiteName()
self['jobname'] = siteUtils.getJobName()
self['CCDID'] = siteUtils.getUnitId()
self['UNITID'] = siteUtils.getUnitId()
self['LSSTID'] = siteUtils.getLSSTId()
try:
self['RUNNUM'] = siteUtils.getRunNumber()
except Exception:
self['RUNNUM'] = "no_lcatr_run_number"
self['ts'] = os.getenv('CCS_TS', default='ts')
self['archon'] = os.getenv('CCS_ARCHON', default='archon')
# The following are only available for certain contexts.
if 'CCS_VAC_OUTLET' in os.environ:
self['vac_outlet'] = os.getenv('CCS_VAC_OUTLET')
if 'CCS_CRYO_OUTLET' in os.environ:
self['cryo_outlet'] = os.getenv('CCS_CRYO_OUTLET')
if 'CCS_PUMP_OUTLET' in os.environ:
self['pump_outlet'] = os.getenv('CCS_PUMP_OUTLET')
self._read(os.path.join(siteUtils.getJobDir(), configFile))
self.sys_paths = sys_paths
def dark_defects_jh_task(det_name):
"""JH version of single sensor execution of the dark defects task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
get_amplifier_gains, bias_filename, dark_defects_task, get_mask_files
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
sflat_files \
= siteUtils.dependency_glob(glob_pattern('dark_defects', det_name),
acq_jobname=acq_jobname)
if not sflat_files:
print("dark_defects_task: No high flux superflat files found for",
det_name)
return None
mask_files = sorted(glob.glob(f'{file_prefix}*mask*.fits'))
bias_frame = bias_filename(run, det_name)
return dark_defects_task(run,
det_name,
sflat_files,
mask_files=mask_files,
bias_frame=bias_frame)
def tearing_fp_heat_map(pattern='*_tearing_stats.pickle'):
"""
Plot a heat map of the tearing detections per amp over
the full focal plane. Glob the data from the tearing stats
pickle files produced by tearing_task for each CCD.
"""
channels = {amp: 'C'+_ for amp, _ in imutils.channelIds.items()}
# With lsst_distrib v20.0.0, the channel names for the WF sensors
# are of the form 'C0x'.
wf_channels = {_ + 1: f'C0{_}' for _ in range(8)}
# The following dict has the correct mapping:
#wf_channels = {_ + 1: f'C1{_}' for _ in range(8)}
amp_data = defaultdict(dict)
for item in glob.glob(pattern):
det_name = os.path.basename(item)[:len('R22_S11')]
ch = wf_channels if 'SW' in det_name else channels
with open(item, 'rb') as fd:
_, amp_counts = pickle.load(fd)
for amp, detections in amp_counts.items():
amp_data[det_name][ch[amp]] = detections
fig = plt.figure()
ax = fig.add_subplot(111)
run = siteUtils.getRunNumber()
plot_focal_plane(ax, amp_data, camera=camera_info.camera_object,
title=f'Run {run}, tearing detections')
plt.savefig(f'LCA-10134_Cryostat-0001_{run}_tearing_detections.png')
def qe_jh_task(det_name):
"""JH version of single sensor execution of the QE task."""
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
lambda_files = siteUtils.dependency_glob(glob_pattern('qe', det_name),
acq_jobname=acq_jobname)
if not lambda_files:
print("qe_task: QE scan files not found for detector", det_name)
return None
pd_ratio_file = eotestUtils.getPhotodiodeRatioFile()
if pd_ratio_file is None:
message = ("The BOT photodiode ratio file is " +
"not given in config/%s/eotest_calibrations.cfg."
% siteUtils.getSiteName())
raise RuntimeError(message)
# correction_image = eotestUtils.getIlluminationNonUniformityImage()
# if correction_image is None:
# print()
# print("WARNING: The correction image file is not given in")
# print("config/%s/eotest_calibrations.cfg." % siteUtils.getSiteName())
# print("No correction for non-uniform illumination will be applied.")
# print()
# sys.stdout.flush()
mask_files = get_mask_files(det_name)
eotest_results_file = '{}_eotest_results.fits'.format(file_prefix)
gains = get_amplifier_gains(eotest_results_file)
bias_frame = bias_filename(run, det_name)
return qe_task(run, det_name, lambda_files, pd_ratio_file, gains,
mask_files=mask_files, bias_frame=bias_frame,
mondiode_func=mondiode_value)
def validate_flat_gain_stability(results, det_names):
"""Valdiate the output files from the flat_gain_stability analysis"""
if 'gainstability' not in get_analysis_types():
return results
run = siteUtils.getRunNumber()
missing_det_names = set()
for det_name in det_names:
file_prefix = make_file_prefix(run, det_name)
results_file = f'{file_prefix}_flat_signal_sequence.pickle'
if not os.path.isfile(results_file):
missing_det_names.add(det_name)
else:
md = dict(DATA_PRODUCT='flat_gain_stability_results')
results.append(siteUtils.make_fileref(results_file, metadata=md))
report_missing_data('validate_flat_gain_stability', missing_det_names)
unit_id = siteUtils.getUnitId()
png_files = glob.glob('*flat_gain_stability.png')
for png_file in png_files:
md = dict(DATA_PRODUCT='flat_gain_stability_plot')
if unit_id in png_file:
md['LsstId'] = unit_id
results.append(siteUtils.make_fileref(png_file, metadata=md))
return results
def run_read_noise_task(sensor_id):
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
bias_files = siteUtils.dependency_glob(
'S*/%s_fe55_fe55_*.fits' % sensor_id,
jobname=siteUtils.getProcessName('fe55_raft_acq'),
description='Fe55 files for read noise:')
gains = eotestUtils.getSensorGains(jobname='fe55_raft_analysis',
sensor_id=sensor_id)
system_noise = None
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
task = sensorTest.ReadNoiseTask()
task.config.temp_set_point = -100.
task.run(sensor_id,
bias_files,
gains,
system_noise=system_noise,
mask_files=mask_files,
use_overscan=True)
# Compute amp-amp correlated noise.
_, corr_fig, _ = correlated_noise(bias_files,
target=0,
make_plots=True,
title=sensor_id)
plt.figure(corr_fig.number)
plt.savefig('%s_correlated_noise.png' % file_prefix)
def flat_gain_stability_jh_task(det_name):
"""JH version of single sensor execution of the flat pairs task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
bias_filename, flat_gain_stability_task,\
get_mask_files, medianed_dark_frame
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
flat_files = siteUtils.dependency_glob(glob_pattern('tearing', det_name),
acq_jobname=acq_jobname)
if not flat_files:
print("flat_gain_stability_task: Flat pairs files not found for",
det_name)
return None
mask_files = get_mask_files(det_name)
bias_frame = bias_filename(run, det_name)
dark_frame = medianed_dark_frame(det_name)
return flat_gain_stability_task(run,
det_name,
flat_files,
mask_files=mask_files,
bias_frame=bias_frame,
dark_frame=dark_frame)
def ptc_jh_task(det_name):
"""JH version of single sensor execution of the PTC task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
get_amplifier_gains, bias_filename, ptc_task, get_mask_files
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
flat_files = siteUtils.dependency_glob(glob_pattern('ptc', det_name),
acq_jobname=acq_jobname)
if not flat_files:
print("ptc_task: Flat pairs files not found for detector", det_name)
return None
mask_files = get_mask_files(det_name)
eotest_results_file = '{}_eotest_results.fits'.format(file_prefix)
gains = get_amplifier_gains(eotest_results_file)
bias_frame = bias_filename(run, det_name)
return ptc_task(run,
det_name,
flat_files,
gains,
mask_files=mask_files,
bias_frame=bias_frame)
def dark_current_jh_task(det_name):
"""JH version of single sensor execution of the dark current task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
get_amplifier_gains, bias_filename, dark_current_task,\
plot_ccd_total_noise, get_mask_files
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
dark_files \
= siteUtils.dependency_glob(glob_pattern('dark_current', det_name),
acq_jobname=acq_jobname,
description="Dark current frames:")
if not dark_files:
print("dark_current_task: No dark files found for detector", det_name)
return None
mask_files = get_mask_files(det_name)
eotest_results_file \
= siteUtils.dependency_glob('{}_eotest_results.fits'.format(file_prefix),
jobname='read_noise_BOT')[0]
gains = get_amplifier_gains('{}_eotest_results.fits'.format(file_prefix))
bias_frame = bias_filename(run, det_name)
dark_curr_pixels, dark95s \
= dark_current_task(run, det_name, dark_files, gains,
mask_files=mask_files, bias_frame=bias_frame)
plot_ccd_total_noise(run, det_name, dark_curr_pixels, dark95s,
eotest_results_file)
return dark_curr_pixels, dark95s
def read_noise_jh_task(det_name):
"""JH version of the single sensor read noise task."""
import os
import glob
import logging
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
get_amplifier_gains, read_noise_task, get_mask_files
logger = logging.getLogger('read_noise_jh_task')
logger.setLevel(logging.INFO)
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
nbias = os.environ.get('LCATR_NUM_BIAS_FRAMES', 10)
bias_files \
= siteUtils.dependency_glob(glob_pattern('read_noise', det_name),
acq_jobname=acq_jobname)[:nbias]
if not bias_files:
logger.info(
"read_noise_task: Needed data files are missing "
"for detector %s", det_name)
return None
eotest_results_file = '{}_eotest_results.fits'.format(file_prefix)
gains = get_amplifier_gains(eotest_results_file)
mask_files = get_mask_files(det_name)
return read_noise_task(run,
det_name,
bias_files,
gains,
mask_files=mask_files)
def bf_jh_task(det_name):
"""JH version of single sensor execution of the brighter-fatter task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
bias_filename, bf_task, find_flat2_bot, get_mask_files,\
get_amplifier_gains
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
flat_files \
= siteUtils.dependency_glob(glob_pattern('brighter_fatter', det_name),
acq_jobname=acq_jobname)
if not flat_files:
print("bf_jh_task: Flat pairs files not found for detector", det_name)
return None
flat_files = [_ for _ in flat_files if 'flat1' in _]
mask_files = get_mask_files(det_name)
eotest_results_file = '{}_eotest_results.fits'.format(file_prefix)
gains = get_amplifier_gains(eotest_results_file)
bias_frame = bias_filename(run, det_name)
return bf_task(run,
det_name,
flat_files,
gains,
mask_files=mask_files,
flat2_finder=find_flat2_bot,
bias_frame=bias_frame)
def bright_defects_jh_task(det_name):
"""JH version of single sensor bright pixels task."""
import glob
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern,\
get_amplifier_gains, bias_filename, bright_defects_task, get_mask_files
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
dark_files \
= siteUtils.dependency_glob(glob_pattern('bright_defects', det_name),
acq_jobname=acq_jobname)
if not dark_files:
print("bright_defects_task: Needed data files missing for detector",
det_name)
return None
eotest_results_file = '{}_eotest_results.fits'.format(file_prefix)
gains = get_amplifier_gains(eotest_results_file)
mask_files = sorted(glob.glob(f'{file_prefix}*mask*.fits'))
bias_frame = bias_filename(run, det_name)
return bright_defects_task(run,
det_name,
dark_files,
gains,
mask_files=mask_files,
bias_frame=bias_frame)
def persistence_jh_task(det_name):
"""JH version of the persistence_task."""
import siteUtils
from bot_eo_analyses import make_file_prefix, glob_pattern, \
bias_frame_task, get_mask_files, get_bot_eo_config, persistence_task
run = siteUtils.getRunNumber()
file_prefix = make_file_prefix(run, det_name)
acq_jobname = siteUtils.getProcessName('BOT_acq')
bias_files \
= siteUtils.dependency_glob(glob_pattern('persistence_bias', det_name),
acq_jobname=acq_jobname,
description='Persistence bias frames:')
dark_files \
= siteUtils.dependency_glob(glob_pattern('persistence_dark', det_name),
acq_jobname=acq_jobname,
description='Persistence dark frames:')
if not bias_files or not dark_files:
print("persistence_task: Needed data files are missing for detector",
det_name)
return None
# Sort by test sequence number, i.e., by filenames.
bias_files = sorted(bias_files)
dark_files = sorted(dark_files)
# Make a superbias frame using the pre-exposure persistence bias
# files, skipping the first exposure.
superbias_frame = f'{file_prefix}_persistence_superbias.fits'
bias_frame_task(run, det_name, bias_files, bias_frame=superbias_frame)
return persistence_task(run, det_name, dark_files, superbias_frame,
get_mask_files(det_name))
def validate_bias_frame(results, det_names):
"""Validate and persist medianed bias frames."""
run = siteUtils.getRunNumber()
missing_det_names = set()
for det_name in det_names:
file_prefix = make_file_prefix(run, det_name)
bias_frame = f'{file_prefix}_median_bias.fits'
rolloff_mask = f'{file_prefix}_edge_rolloff_mask.fits'
pca_bias_file = f'{file_prefix}_pca_bias.fits'
pca_superbias = f'{file_prefix}_pca_superbias.fits'
# Add/update the metadata to the primary HDU of these files.
for fitsfile in (bias_frame, rolloff_mask, pca_bias_file,
pca_superbias):
if os.path.isfile(fitsfile):
eotestUtils.addHeaderData(fitsfile,
TESTTYPE='BIAS',
DATE=eotestUtils.utc_now_isoformat())
results.append(lcatr.schema.fileref.make(fitsfile))
else:
missing_det_names.add(det_name)
# Persist the PCA bias model file.
pca_bias_model = f'{file_prefix}_pca_bias.pickle'
if os.path.isfile(pca_bias_model):
results.append(lcatr.schema.fileref.make(pca_bias_model))
else:
missing_det_names.add(det_name)
report_missing_data('validate_bias_frames', missing_det_names)
return results
def run_ptc_task(sensor_id):
import lsst.eotest.sensor as sensorTest
import siteUtils
import eotestUtils
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
flat_files = siteUtils.dependency_glob(
'S*/%s_flat*flat?_*.fits' % sensor_id,
jobname=siteUtils.getProcessName('flat_pair_raft_acq'),
description='Flat files:')
bias_frame = siteUtils.dependency_glob('%s_sflat*median_bias.fits' %
sensor_id,
description='Super bias frame:')[0]
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
gains = eotestUtils.getSensorGains(jobname='fe55_raft_analysis',
sensor_id=sensor_id)
task = sensorTest.PtcTask()
task.run(sensor_id, flat_files, mask_files, gains, bias_frame=bias_frame)
results_file = '%s_eotest_results.fits' % sensor_id
plots = sensorTest.EOTestPlots(sensor_id, results_file=results_file)
siteUtils.make_png_file(plots.ptcs,
'%s_ptcs.png' % file_prefix,
ptc_file='%s_ptc.fits' % sensor_id)
def run_dark_pixels_task(sensor_id):
print("run_dark_pixels_task: sensor_id = ", sensor_id)
# raft_id = os.environ['LCATR_UNIT_ID']
# raft = camera_components.Raft.create_from_etrav(raft_id)
# wgSlotName = siteUtils.getWGSlotNames(raft)[sensor_id];
"Single sensor execution of the dark pixels task."
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
sflat_files = siteUtils.dependency_glob(
'S*/%s_sflat_500_flat_*.fits' % sensor_id,
jobname=siteUtils.getProcessName('sflat_raft_acq'),
description='Superflat files:')
print("sflat query: ", 'S*/%s_sflat_500_flat_H*.fits' % sensor_id)
print("sflat_files = ", sflat_files)
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
task = sensorTest.DarkPixelsTask()
task.run(sensor_id, sflat_files, mask_files)
siteUtils.make_png_file(sensorTest.plot_flat,
'%s_superflat_dark_defects.png' % file_prefix,
'%s_median_sflat.fits' % sensor_id,
title='%s, superflat for dark defects analysis' %
sensor_id,
annotation='ADU/pixel')
def scan_mode_analysis_jh_task(raft_name):
"""JH version of scan mode analysis task."""
import siteUtils
from bot_eo_analyses import get_scan_mode_files, scan_mode_analysis_task
run = siteUtils.getRunNumber()
scan_mode_files = get_scan_mode_files(raft_name)
return scan_mode_analysis_task(run, raft_name, scan_mode_files)
def run_qe_task(sensor_id):
try:
if hw_objects[sensor_id] :
return
except:
hw_objects[sensor_id] = True
print("hw_objects = ",hw_objects)
"Single sensor execution of the QE task."
file_prefix = '%s_%s' % (sensor_id, siteUtils.getRunNumber())
lambda_files = siteUtils.dependency_glob('S*/%s_lambda_flat_*.fits' % sensor_id,
jobname=siteUtils.getProcessName('qe_raft_acq'),
description='Lambda files:')
pd_ratio_file = eotestUtils.getPhotodiodeRatioFile()
if pd_ratio_file is None:
message = ("The test-stand specific photodiode ratio file is " +
"not given in config/%s/eotest_calibrations.cfg."
% siteUtils.getSiteName())
raise RuntimeError(message)
correction_image = eotestUtils.getIlluminationNonUniformityImage()
if correction_image is None:
print()
print("WARNING: The correction image file is not given in")
print("config/%s/eotest_calibrations.cfg." % siteUtils.getSiteName())
print("No correction for non-uniform illumination will be applied.")
print()
sys.stdout.flush()
mask_files = \
eotestUtils.glob_mask_files(pattern='%s_*mask.fits' % sensor_id)
gains = eotestUtils.getSensorGains(jobname='fe55_raft_analysis',
sensor_id=sensor_id)
task = sensorTest.QeTask()
task.config.temp_set_point = -100.
task.run(sensor_id, lambda_files, pd_ratio_file, mask_files, gains,
correction_image=correction_image)
results_file \
= siteUtils.dependency_glob('%s_eotest_results.fits' % sensor_id,
jobname='fe55_raft_analysis',
description='Fe55 results file')[0]
plots = sensorTest.EOTestPlots(sensor_id, results_file=results_file)
siteUtils.make_png_file(plots.qe,
'%s_qe.png' % file_prefix,
qe_file='%s_QE.fits' % sensor_id)
try:
plots.flat_fields(os.path.dirname(lambda_files[0]),
annotation='e-/pixel, gain-corrected, bias-subtracted')
except Exception as eobj:
print("Exception raised while creating flat fields:")
print(str(eobj))
def stage_files(device_list, data_keys):
"""
Function to stage the needed raw image files from the specified
devices (CCDs or rafts) for the current job in the scratch area.
"""
# Gather the filenames of the needed data.
fits_files = set()
for device in device_list:
fits_files = fits_files.union(get_files(data_keys, device))
if not fits_files:
return
# Make the scratch directory for the BOT data.
run_number = siteUtils.getRunNumber()
scratch_dir = os.environ.get('LCATR_SCRATCH_DIR', '/scratch')
dest_dir = os.path.join(scratch_dir, 'bot_data', str(run_number))
os.makedirs(dest_dir, exist_ok=True)
# Glob existing files to avoid re-copying or for possible clean up.
old_files = set(glob.glob(os.path.join(dest_dir, '*', 'MC_C*.fits')))
old_files = old_files.union(
glob.glob(os.path.join(dest_dir, '*', 'Photodiode*.txt')))
# Create a dict that maps src to dest file paths. Preserve the
# folder name of the exposure so that the PTC and flat pairs tasks
# can identify the paired exposures.
new_files = dict()
frame_dirs = set()
for src in fits_files:
frame_dir = os.path.dirname(src)
frame_dirs.add(frame_dir)
folder = os.path.basename(frame_dir)
os.makedirs(os.path.join(dest_dir, folder), exist_ok=True)
new_files[src] = os.path.join(dest_dir, folder, os.path.basename(src))
# Include any Photodiode_Readings*.txt files.
for frame_dir in frame_dirs:
for src in glob.glob(os.path.join(frame_dir, 'Photodiode*.txt')):
new_files[src] = os.path.join(dest_dir,
os.path.basename(frame_dir),
os.path.basename(src))
# Clean up unneeded files.
unneeded_files = old_files.difference(new_files.values())
for item in unneeded_files:
print('removing', item)
os.remove(item)
# Copy the remaining files.
for src, dest in new_files.items():
if dest not in old_files:
print('copying', src, 'to', dest)
shutil.copy(src, dest)
stage_isr_files(device_list, dest_dir)
def validate_qe(results, det_names):
"""Validate the QE results."""
run = siteUtils.getRunNumber()
missing_det_names = []
for det_name in det_names:
raft, slot = det_name.split('_')
file_prefix = make_file_prefix(run, det_name)
qe_results_file = '%s_QE.fits' % file_prefix
if not os.path.isfile(qe_results_file):
missing_det_names.append(det_name)
continue
with fits.open(qe_results_file) as qe_results:
qe_data = qe_results['QE_BANDS'].data
QE = OrderedDict((band, []) for band in qe_data.field('BAND'))
for amp in range(1, 17):
values = qe_data.field('AMP%02i' % amp)
for band, value in zip(QE, values):
QE[band].append(value)
for band in QE:
for amp in range(1, 17):
results.append(
lcatr.schema.valid(lcatr.schema.get('qe_BOT_analysis'),
band=band,
QE=QE[band][amp - 1],
amp=amp,
slot=slot,
raft=raft))
qe_files = glob.glob('%s_*QE*.fits' % file_prefix)
for item in qe_files:
eotestUtils.addHeaderData(item,
TESTTYPE='LAMBDA',
DATE=eotestUtils.utc_now_isoformat())
results.extend([siteUtils.make_fileref(item) for item in qe_files])
# Persist the png files.
metadata = dict(DETECTOR=det_name,
RUN=run,
TESTTYPE='LAMBDA',
TEST_CATEGORY='EO')
results.extend(
siteUtils.persist_png_files('%s*qe.png' % file_prefix,
file_prefix,
metadata=metadata))
results.extend(
siteUtils.persist_png_files('%s*flat.png' % file_prefix,
file_prefix,
metadata=metadata))
report_missing_data("validate_qe", missing_det_names)
return results
def validate_brighter_fatter(results, det_names):
"""Validate the brighter-fatter results."""
run = siteUtils.getRunNumber()
missing_det_names = set()
for det_name in det_names:
raft, slot = det_name.split('_')
file_prefix = make_file_prefix(run, det_name)
bf_results = '%s_bf.fits' % file_prefix
if not os.path.isfile(bf_results):
missing_det_names.add(det_name)
continue
eotestUtils.addHeaderData(bf_results,
TESTTYPE='FLAT',
DATE=eotestUtils.utc_now_isoformat())
results.append(siteUtils.make_fileref(bf_results))
results_file = '%s_eotest_results.fits' % file_prefix
data = sensorTest.EOTestResults(results_file)
columns = (data['AMP'], data['BF_XCORR'], data['BF_XCORR_ERR'],
data['BF_YCORR'], data['BF_YCORR_ERR'], data['BF_SLOPEX'],
data['BF_SLOPEX_ERR'], data['BF_SLOPEY'],
data['BF_SLOPEY_ERR'], data['BF_MEAN'])
for amp, bf_xcorr, bf_xcorr_err, bf_ycorr, bf_ycorr_err, \
bf_slopex, bf_slopex_err, bf_slopey, bf_slopey_err, bf_mean \
in zip(*columns):
results.append(
lcatr.schema.valid(lcatr.schema.get('brighter_fatter_BOT'),
amp=amp,
bf_xcorr=bf_xcorr,
bf_xcorr_err=bf_xcorr_err,
bf_ycorr=bf_ycorr,
bf_ycorr_err=bf_ycorr_err,
bf_slopex=bf_slopex,
bf_slopex_err=bf_slopex_err,
bf_slopey=bf_slopey,
bf_slopey_err=bf_slopey_err,
bf_mean=bf_mean,
slot=slot,
raft=raft))
# Persist the png files.
metadata = dict(DETECTOR=det_name,
RUN=run,
TESTTYPE='FLAT',
TEST_CATEGORY='EO')
results.extend(
siteUtils.persist_png_files('%s*brighter-fatter.png' % file_prefix,
file_prefix,
metadata=metadata))
return results
def validate_read_noise(results, det_names):
"""Validate and persist read noise results."""
run = siteUtils.getRunNumber()
missing_det_names = set()
for det_name in det_names:
raft, slot = det_name.split('_')
file_prefix = make_file_prefix(run, det_name)
read_noise_file = '%s_eotest_results.fits' % file_prefix
if not os.path.isfile(read_noise_file):
# No data for this detector, so note that and continue
# with the others.
missing_det_names.add(det_name)
continue
data = sensorTest.EOTestResults(read_noise_file)
amps = data['AMP']
read_noise_data = data['READ_NOISE']
system_noise_data = data['SYSTEM_NOISE']
total_noise_data = data['TOTAL_NOISE']
for amp, read_noise, system_noise, total_noise \
in zip(amps, read_noise_data, system_noise_data, total_noise_data):
results.append(lcatr.schema.valid(
lcatr.schema.get('read_noise_BOT'),
amp=amp, read_noise=read_noise, system_noise=system_noise,
total_noise=total_noise, slot=slot, raft=raft))
files = glob.glob('%s_read_noise?*.fits' % file_prefix)
for fitsfile in files:
eotestUtils.addHeaderData(fitsfile, TESTTYPE='FE55',
DATE=eotestUtils.utc_now_isoformat())
data_products = [siteUtils.make_fileref(item) for item in files]
results.extend(data_products)
# Persist the png files.
metadata = dict(DETECTOR=det_name, TESTTYPE='FE55', TEST_CATEGORY='EO',
RUN=run)
filename = '%s_correlated_noise.png' % file_prefix
results.extend(siteUtils.persist_png_files(filename, file_prefix,
metadata=metadata))
# Persist the raft-level overscan correlation plots.
for raft in camera_info.get_installed_raft_names():
metadata = dict(TESTTYPE='FE55', TEST_CATEGORY='EO', RAFT=raft, RUN=run)
file_prefix = make_file_prefix(run, raft)
filename = '%s_overscan_correlations.png' % file_prefix
results.extend(siteUtils.persist_png_files(filename, file_prefix,
metadata=metadata))
report_missing_data("validate_read_noise", missing_det_names)
return results
def __init__(self, configFile):
"""
configFile contains the names of the site-specific
configuration files. File basenames are provided in
configFile, and the full paths are constructed in the
_read(...) method.
"""
super(CcsSetup, self).__init__()
if os.environ.has_key('CCS_TS8'):
self['ts8']=_quote(os.getenv('CCS_TS8'))
else:
self['ts8'] = _quote('ts8')
if os.environ.has_key('CCS_JYTH'):
self['jyth']=_quote(os.getenv('CCS_JYTH'))
else:
self['jyth'] = _quote('JythonInterpreterConsole')
if os.environ.has_key('CCS_JSON_PORT'):
self['jsonport']=os.getenv('CCS_JSON_PORT')
else:
self['jsonport'] = 4444
if os.environ.has_key('CCS_PS'):
self['ps']=_quote(os.getenv('CCS_PS'))
else:
self['ps'] = _quote('ccs-rebps')
if os.environ.has_key('CCS_TS'):
self['ts']=_quote(os.getenv('CCS_TS'))
else:
self['ts'] = _quote('ts')
if os.environ.has_key('CCS_ARCHON'):
self['archon']=_quote(os.getenv('CCS_ARCHON'))
else:
self['archon'] = _quote('archon')
if os.environ.has_key('CCS_VAC_OUTLET'):
self['vac_outlet']=os.getenv('CCS_VAC_OUTLET')
# there is no default for vac_outlet - if there is a script that needs
# it and it has not been defined then I want it to crash
if os.environ.has_key('CCS_CRYO_OUTLET'):
self['cryo_outlet']=os.getenv('CCS_CRYO_OUTLET')
# there is no default for cryo_outlet - if there is a script that needs
# it and it has not been defined then I want it to crash
if os.environ.has_key('CCS_PUMP_OUTLET'):
self['pump_outlet']=os.getenv('CCS_PUMP_OUTLET')
# there is no default for pump_outlet - if there is a script that needs
# it and it has not been defined then I want it to crash
self['tsCWD'] = _quote(os.getcwd())
self['labname'] = _quote(siteUtils.getSiteName())
self['jobname'] = _quote(siteUtils.getJobName())
self['CCDID'] = _quote(siteUtils.getUnitId())
self['UNITID'] = _quote(siteUtils.getUnitId())
self['LSSTID'] = _quote(siteUtils.getLSSTId())
unitid = siteUtils.getUnitId()
CCDTYPE = _quote(siteUtils.getUnitType())
ccdnames = {}
ccdmanunames = {}
ccdnames,ccdmanunames = siteUtils.getCCDNames()
print "retrieved the following LSST CCD names list"
print ccdnames
print "retrieved the following Manufacturers CCD names list"
print ccdmanunames
for slot in ccdnames :
print "CCD %s is in slot %s" % (ccdnames[slot],slot)
self['CCD%s'%slot] = _quote(ccdnames[slot])
if 'itl' in ccdnames[slot].lower() :
CCDTYPE = 'itl'
if 'e2v' in ccdnames[slot].lower() :
CCDTYPE = 'e2v'
for slot in ccdmanunames :
print "CCD %s is in slot %s" % (ccdmanunames[slot],slot)
self['CCDMANU%s'%slot] = _quote(ccdmanunames[slot])
try:
self['RUNNUM'] = _quote(siteUtils.getRunNumber())
except:
self['RUNNUM'] = "no_lcatr_run_number"
pass
self._read(os.path.join(siteUtils.getJobDir(), configFile))
print "CCDTYPE = %s" % CCDTYPE
self['sequence_file'] = _quote("NA")
self['acffile'] = self['itl_acffile']
# set default type
self['CCSCCDTYPE'] = _quote("ITL")
if ("RTM" in unitid.upper() or "ETU" in unitid.upper() or "RSA" in unitid.upper()) :
if ("e2v" in CCDTYPE) :
self['CCSCCDTYPE'] = _quote("E2V")
self['acffile'] = self['e2v_acffile']
self['sequence_file'] = self['e2v_seqfile']
else :
self['CCSCCDTYPE'] = _quote("ITL")
self['acffile'] = self['itl_acffile']
self['sequence_file'] = self['itl_seqfile']
os.system("export | grep -i seq")
seqdir = ""
if os.environ.has_key('SEQUENCERFILESDIR') :
seqdir = os.getenv('SEQUENCERFILESDIR')
print "seqdir=",seqdir
self['sequence_file'] = self['sequence_file'].replace('${SEQUENCERFILESDIR}',seqdir)
os.system("cp -vp %s %s" % (self['sequence_file'],self['tsCWD']))
# now use the local copy
# bb = self['sequence_file'].split("/")
# self['sequence_file'] = _quote("%s/%s" % (os.getcwd(),bb[len(bb)-1].split("'")[0]))
print "The sequence file to be used is %s" % self['sequence_file']
else :
if ("ITL" in CCDTYPE) :
self['CCSCCDTYPE'] = _quote("ITL")
self['acffile'] = self['itl_acffile']
if ("e2v" in CCDTYPE) :
self['CCSCCDTYPE'] = _quote("E2V")
self['acffile'] = self['e2v_acffile']
print "The acffile to be used is %s" % self['acffile']
#!/usr/bin/env python
import Tkinter
import glob
import shutil
import os
import matplotlib.pyplot as plt
import ccs_trending
import siteUtils
import time
import subprocess
raft_id = siteUtils.getLSSTId()
run_number = siteUtils.getRunNumber()
host = 'localhost'
jobDir = siteUtils.getJobDir()
shutil.copy("%s/ts_quantities.cfg" % jobDir ,os.getcwd())
shutil.copy("%s/ts8_quantities.cfg" % jobDir ,os.getcwd())
ccsProducer('RTM_thermo', 'ccsthermal.py')
cdir = os.getcwd()
#rtmstatelist = [
#"RTM_off_5min_stable__502",
#"REB_quiescient_record__505",
#"RTM_quies_5min_record__508",
#"RTM_biases_5min_record__510",
#"RTM_clears_5min_record__512",
