def test_astropy_return():
hrcI_file = os.path.abspath(
os.path.dirname(os.path.abspath(__file__)) +
'/data/hrcI_evt1_testfile.fits.gz')
hrcI_evt1_df = hypercore.HRCevt1(hrcI_file)
hrcI_evt1_table = hypercore.HRCevt1(hrcI_file, as_astropy_table=True)
assert isinstance(hrcI_evt1_df.data, pd.DataFrame)
assert type(hrcI_evt1_table.data) is astropy.table.table.Table
def hrcS_evt1():
print("Loading test HRC-S EVT1 File as a pytest Fixture")
hrcS_file = os.path.abspath(
os.path.dirname(os.path.abspath(__file__)) +
'/data/hrcS_evt1_testfile.fits.gz')
hrcS_evt1 = hypercore.HRCevt1(hrcS_file)
return hrcS_evt1
def hrcS_evt1_sparsetap():
print(
"Loading test HRC-S EVT1 File, which includes some sparsely rung taps, as a pytest Fixture"
)
hrcS_file = os.path.abspath(
os.path.dirname(os.path.abspath(__file__)) +
'/data/hrcS_evt1_sparsetap_testfile.fits.gz')
hrcS_evt1_sparsetap = hypercore.HRCevt1(hrcS_file)
return hrcS_evt1_sparsetap
def screenHRCevt1(input_fits_file, hyperscreen_results_dict=None, comparison_products=True, savepath=None, verbose=True, backup=True):
obsid = fits.getheader(input_fits_file)['OBS_ID']
# Get the root string to use as our naming convention
file_name = input_fits_file.split('/')[-1] # Split off the path
# Split off the .fits (or .fits.gz)
file_root = file_name.split('.fits')[0].split('_')[0]
file_path = os.path.realpath(os.path.dirname(input_fits_file))
print(file_path)
if savepath is None:
savepath = file_path
backup_dir = os.path.join(
savepath, '{}_hyperscreen_report'.format(obsid))
if not os.path.exists(backup_dir):
os.makedirs(backup_dir)
if verbose is True:
print("Made HyperScreen Products Directory {}".format(backup_dir))
# Check if the passed input file is a string ending with .fits or .fits.gz
if isinstance(input_fits_file, str):
filetype_match = input_fits_file.split(
'.')[-1] == 'fits' or input_fits_file.split('.')[-1] == 'gz'
if filetype_match is False:
raise Exception(
'ERROR: Input given ({}) is not recognized as a .fits[.gz] or HRCevt1 object.'.format(input_fits_file))
if hyperscreen_results_dict is None:
# Then you need to make it!
if verbose is True:
print("Applying HyperScreen algorithm to {}".format(file_name))
obs = hypercore.HRCevt1(input_fits_file)
hyperscreen_results = obs.hyperscreen()
else:
hyperscreen_results = hyperscreen_results_dict
# if backup is True:
# if not os.path.exists(backup_dir):
# os.makedirs(backup_dir)
# if verbose is True:
# print("Made backup directory {}".format(backup_dir))
# if verbose is True:
# print("Backing up (copying) input fits file {} to {}".format(
# input_fits_file.split('/')[-1], backup_dir))
# copyfile(input_fits_file, os.path.join(
# file_path, '{}_original_event_list.fits'.format(obsid)))
# hyperscreen_fits_file = file_path + '/hyperscreen_' + file_name
hyperscreen_fits_file = os.path.join(file_path, 'hyperscreen_' + file_name)
rejected_events_file = os.path.join(
backup_dir, '{}_hyperscreen_rejected_events.fits'.format(obsid))
# difference_map_file = file_path + '/hyperscreen_DIFFERENCE_MAP_' + file_name
survival_mask = hyperscreen_results['All Survivals (boolean mask)']
failure_mask = hyperscreen_results['All Failures (boolean mask)']
with fits.open(input_fits_file) as hdul:
original_data = hdul[1].data
hdul[1].data = hdul[1].data[survival_mask]
if verbose is True:
print("Masking data with HyperScreen Results")
hdul.writeto(hyperscreen_fits_file, overwrite=True)
if verbose is True:
print(
"Wrote new HyperScreen-filtered evt1 file to {}".format(hyperscreen_fits_file))
if comparison_products is True:
hdul[1].data = original_data[failure_mask]
hdul.writeto(rejected_events_file, overwrite=True)
if verbose is True:
print("Wrote Rejected Events Map {}".format(rejected_events_file))
original_evt1_file_path = os.path.join(
file_path, '{}_original_event_list.fits'.format(obsid))
os.rename(input_fits_file, original_evt1_file_path)
print("Backed up original evt1 file to {}".format(original_evt1_file_path))
def screener(evt1file,
verbose=False,
savepath=None,
make_reportCard=True,
make_fitsfiles=False,
save_json=True,
show=False,
overwrite=False): # pragma: no cover
obs = hypercore.HRCevt1(evt1file)
if verbose is True:
print(
"Gathering HyperScreen performance statistics for {} | {}, {} ksec, {:,} counts"
.format(obs.obsid, obs.detector, round(obs.exptime / 1000., 2),
obs.numevents))
# if make_reportCard is True:
# reportCard(obs, show=show, savepath=savepath)
# if verbose is True:
# print("Report Card generated for {} | {}, {} ksec, {} counts".format(
# obs.obsid, obs.detector, round(obs.exptime/1000.,2), obs.numevents))
try:
results_dict = obs.hyperscreen()
if save_json is True:
json_savepath = os.path.join(
savepath, '{}_{}_{}_hyperResults.json'.format(
obs.obsid, obs.target.replace(' ', '_'), obs.detector))
if os.path.exists(json_savepath) and overwrite is False:
print("{} exists and overwrite=False. Skipping.".format(
json_savepath.split('/')[-1]))
else:
if os.path.exists(json_savepath) and verbose is True:
print("Overwriting existing {}".format(
json_savepath.split('/')[-1]))
# We don't want JSONify the full results dictionary (which includes embedded dictionaries!)
json_reduced_results_dict = {
"ObsID":
results_dict['ObsID'],
"Target":
results_dict['Target'],
"Exposure Time":
results_dict['Exposure Time'],
"Detector":
results_dict['Detector'],
"Number of Events":
results_dict['Number of Events'],
"Number of Good Time Events":
results_dict['Number of Good Time Events'],
# YOU CAN'T JSONIFY AN NDARRAY. MUST MAKE IT A LIST!
"All Survivals (event indices)":
results_dict['All Survivals (event indices)'].tolist(),
"All Survivals (boolean mask)":
results_dict['All Survivals (boolean mask)'].tolist(),
"All Failures (boolean mask)":
results_dict['All Failures (boolean mask)'].tolist(),
"Percent rejected by Tapscreen":
results_dict['Percent rejected by Tapscreen'],
"Percent rejected by Hyperbola":
results_dict['Percent rejected by Hyperbola'],
"Percent improvement":
results_dict['Percent improvement']
}
with open(json_savepath, 'w') as json_file:
json.dump(json_reduced_results_dict,
json_file,
sort_keys=True,
indent=4)
if verbose is True:
print("Created {}".format(json_savepath.split('/')[-1]))
if make_reportCard is True:
reportCard_savepath = os.path.join(
savepath,
'{}_{}_{}_hyperReport.pdf'.format(obs.obsid,
obs.target.replace(' ', '_'),
obs.detector))
if os.path.exists(reportCard_savepath) and overwrite is False:
print("{} exists and overwrite=False. Skipping.".format(
reportCard_savepath.split('/')[-1]))
else:
if os.path.exists(reportCard_savepath) and verbose is True:
print("Overwriting existing {}".format(
reportCard_savepath.split('/')[-1]))
reportCard(obs,
hyperscreen_results_dict=results_dict,
show=show,
reportCard_savepath=reportCard_savepath)
if verbose is True:
print(
"Report Card generated for {} | {}, {} ksec, {:,} counts"
.format(obs.obsid, obs.detector,
round(obs.exptime / 1000., 2), obs.numevents))
if make_fitsfiles is True:
evtscreen.screenHRCevt1(evt1file,
hyperscreen_results_dict=results_dict,
savepath=savepath,
comparison_products=True,
verbose=True)
except Exception as exception_message:
print(
"ERROR on {} ({} | {} ksec | {:,} events | {:,} good time events), pressing on"
.format(obs.obsid, obs.detector, round(obs.exptime / 1000, 2),
obs.numevents, obs.goodtimeevents))
print("Exception message is: {}".format(exception_message))