def readBOA(filename):
f = h5py.File(filename, 'r')
meta = {}
entry = f['entry']
meta['title'] = decodeHDF(entry['title'][0])
meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['start_time'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['instrument'] = 'BOA'
sample = {}
sample['name'] = decodeHDF(entry['sample/name'][0])
if pathExists(entry,'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
# TODO: check a number of files and see if you can find an entry for magnets.
# It coulkd also be that the name is magnetic_field.
if pathExists(entry,'sample/magnet'.split('/') or entry, 'sample/magnetic_field'):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
meta['user'] = decodeHDF(entry['user/name'][0])
meta['email'] = decodeHDF(entry['user/email'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
f.close()
return meta
def readAMOR(filename):
if os.path.exists(filename):
print('hdf file found')
else:
filename = filename.replace(".hdf", ".ccl")
if os.path.exists(filename):
print('ccl file found')
else:
filename = filename.replace(".ccl", ".dat")
if os.path.exists(filename):
print('dat file found')
else:
print('datatype unknown')
cclsuffix = '.ccl'
datsuffix = '.dat'
hdfsuffix = '.hdf'
print(filename)
meta = {}
dataset = ["Date", "User", "Sample Name", "Title", "ProposalID"]
if (filename.endswith(cclsuffix) or filename.endswith(datsuffix)):
f = open(filename, 'r')
x = 0
for line in f:
if line.startswith('#data'):
break
extractedData = line.split('=')
if len(extractedData) == 2:
key = extractedData[0].strip()
if key in dataset:
meta[key] = extractedData[1].strip()
meta['detector_mode'] = '1d'
f.close()
elif (filename.endswith(hdfsuffix)):
print('read data')
f = h5py.File(filename, 'r')
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['date'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['instrument'] = 'AMOR'
sample = {}
sample['name'] = decodeHDF(entry['sample/name'][0])
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
meta['user'] = decodeHDF(entry['proposal_user/name'][0])
meta['email'] = decodeHDF(entry['proposal_user/email'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
f.close()
return meta
def readHRPT(filename):
f = h5py.File(filename, 'r')
meta = {}
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
# meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['start_time'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
# meta['end_time'] = decodeHDF(entry['end_time'][0])
meta['instrument'] = 'HRPT'
meta['wavelength'] = decodeHDF(entry['HRPT/Monochromator/lambda'][0])
meta['detector two_theta start'] = decodeHDF(
entry['HRPT/HRPT-CERCA-Detector/two_theta_start'][0])
meta['proton_monitor'] = decodeHDF(
entry['HRPT/HRPT-CERCA-Detector/proton_monitor'][0])
meta['summed counts'] = decodeHDF(entry['data1/counts'][0])
meta['position_monochromator_lift'] = decodeHDF(
entry['HRPT/Monochromator/lift'][0])
sample = {}
sample['name'] = decodeHDF(entry['sample/sample_name'][0])
if pathExists(entry, 'sample/sample_changer_position'.split('/')):
sample['sample_changer position'] = decodeHDF(
entry['sample/sample_changer_position'][0])
else:
sample['sample_changer position'] = 'UNKNOWN'
sample['sample rotation'] = decodeHDF(
entry['sample/sample_table_rotation'][0])
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
meta['user'] = decodeHDF(entry['user/name'][0])
meta['email'] = decodeHDF(entry['proposal_user/email'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
f.close()
return meta
def readSANS(filename):
f = h5py.File(filename, 'r')
meta = {}
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
#meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['start_time'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['end_time'] = decodeHDF(entry['end_time'][0])
meta['instrument'] = 'SANS'
source = {}
source['type'] = 'Spallation Neutron Source'
source['probe'] = 'neutron'
source['name'] = 'SINQ at PSI'
meta['source'] = source
meta['wavelength'] = decodeHDF(entry['SANS/Dornier-VS/lambda'][0])
coll = {}
coll['shape'] = 'nxcylinder'
coll['size'] = decodeHDF(entry['SANS/collimator/length'][0])
meta['collimator'] = coll
detector = {}
# todo find proper transformation detector['sum'] = np.sum(decodeHDF(entry['SANS/detector/counts']))
detector['distance'] = decodeHDF(entry['SANS/detector/x_position'][0])
detector['polar_angle'] = 0.
detector['azimuthal_angle'] = 0.
detector['aequatorial_angle'] = 0.
detector['x_pixel_size'] = 7.5
detector['y_pixel_size'] = 7.5
if pathExists(entry, 'SANS/detector/beam_center_x'.split('/')):
detector['beam_center_x'] = decodeHDF(
entry['SANS/detector/beam_center_x'][0]) * 7.5
detector['beam_center_y'] = decodeHDF(
entry['SANS/detector/beam_center_y'][0]) * 7.5
meta['detector'] = detector
sample = {}
sample['name'] = decodeHDF(entry['sample/name'][0])
#sample['environment'] = decodeHDF(entry['sample/environment'][0])
sample['aequatorial_angle'] = 0.
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
control = {}
control['mode'] = decodeHDF(entry['SANS/detector/count_mode'][0])
control['preset'] = decodeHDF(entry['SANS/detector/preset'][0])
control['time'] = decodeHDF(entry['SANS/detector/counting_time'][0])
control['integral'] = decodeHDF(entry['SANS/monitor1/counts'][0])
control['monitor2'] = decodeHDF(entry['SANS/monitor2/counts'][0])
control['monitor3'] = decodeHDF(entry['SANS/monitor3/counts'][0])
meta['control'] = control
meta['user'] = decodeHDF(entry['user/name'][0])
if pathExists(entry, 'proposal_user/email'.split('/')):
meta['email'] = decodeHDF(entry['proposal_user/email'][0])
else:
meta['email'] = '*****@*****.**'
meta['proposal_title'] = decodeHDF(entry['proposal_title'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
# todo: commented because not existing: meta['attenuator'] = decodeHDF(entry['SANS/attenuator/selection'][0])
f.close()
return meta
def readPOLDI(filename):
f = h5py.File(filename, 'r')
meta = {}
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['start_time'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['end_time'] = decodeHDF(entry['end_time'][0])
meta['instrument'] = 'POLDI'
sample = {}
sample['name'] = decodeHDF(entry['sample/name'][0])
sample['environment'] = decodeHDF(entry['sample/environment'][0])
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
meta['user'] = decodeHDF(entry['user/name'][0])
meta['email'] = decodeHDF(entry['proposal_user/email'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
# todo: commented because not existing: meta['attenuator'] = decodeHDF(entry['SANS/attenuator/selection'][0])
meta['chopper_speed'] = decodeHDF(entry['POLDI/chopper/rotation_speed'][0])
f.close()
return meta
def readZEBRA(filename):
if os.path.exists(filename):
print('hdf file found')
else:
filename = filename.replace(".hdf", ".ccl")
if os.path.exists(filename):
print('ccl file found')
else:
filename = filename.replace(".ccl", ".dat")
if os.path.exists(filename):
print('dat file found')
else:
print('datatype unknown')
cclsuffix = '.ccl'
datsuffix = '.dat'
hdfsuffix = '.hdf'
meta = {}
if (filename.endswith(cclsuffix) or filename.endswith(datsuffix)):
f = open(filename, 'r')
dataset = [
"date", "instrument", "user", "proposal_email", "title", "sample",
"temperature", "ProposalID", "stt", "chi", "phi", "om", "nu"
]
for line in f:
if line.startswith('#data'):
break
extractedData = line.split('=')
if len(extractedData) == 2:
key = extractedData[0].strip()
if key in dataset:
meta[key] = extractedData[1].strip()
meta['detector_mode'] = '1d'
f.close()
elif (filename.endswith(hdfsuffix)):
f = h5py.File(filename, 'r')
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['date'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['instrument'] = 'ZEBRA'
meta['sample'] = decodeHDF(entry['sample/name'][0])
sample = {}
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample_directory'] = sample
meta['user'] = decodeHDF(entry['proposal_user/name'][0])
meta['proposal_email'] = decodeHDF(entry['proposal_user/email'][0])
meta['ProposalID'] = decodeHDF(entry['proposal_id'][0])
# zebra_mode
meta['detector_mode'] = '2d'
meta['stt'] = decodeHDF(entry['sample/stt'][0])
meta['chi'] = decodeHDF(entry['sample/chi'][0])
meta['phi'] = decodeHDF(entry['sample/phi'][0])
meta['om'] = decodeHDF(entry['sample/om'][0])
meta['nu'] = decodeHDF(entry['sample/nu'][0])
# om, nu
f.close()
return meta, filename
def readFOCUS(filename):
f = h5py.File(filename, 'r')
meta = {}
entry = f['entry1']
meta['title'] = decodeHDF(entry['title'][0])
meta['collection_description'] = decodeHDF(entry['comment'][0]).strip()
# todo normalize times to RFC format
meta['start_time'] = decodeHDF(entry['start_time'][0])
# todo normalize times to RFC format
meta['end_time'] = decodeHDF(entry['end_time'][0])
meta['instrument'] = 'FOCUS'
meta['wavelength'] = decodeHDF(entry['FOCUS/monochromator/lambda'][0])
if pathExists(entry, 'focus2d'):
meta['2ddetector'] = 'yes'
else:
meta['2ddetector'] = 'no'
sample = {}
sample['name'] = decodeHDF(entry['sample/name'][0])
sample['environment'] = decodeHDF(entry['sample/environment'][0])
sample['distance'] = decodeHDF(entry['sample/distance'][0])
if pathExists(entry, 'sample/temperature'.split('/')):
sample['temperature'] = decodeHDF(entry['sample/temperature'][0])
else:
sample['temperature'] = 'UNKNOWN'
# TODO: check a number of files and see if you can find an entry for magnets.
# It coulkd also be that the name is magnetic_field.
if pathExists(entry, 'sample/magnet'.split('/')):
sample['magnet'] = decodeHDF(entry['sample/magnet'][0])
else:
sample['magnet'] = 'UNKNOWN'
meta['sample'] = sample
meta['monitor'] = decodeHDF(entry['FOCUS/counter/monitor'][0])
meta['user'] = decodeHDF(entry['user/name'][0])
meta['email'] = decodeHDF(entry['proposal_user/email'][0])
meta['experiment_identifier'] = decodeHDF(entry['proposal_id'][0])
meta['disk_chopper_speed'] = decodeHDF(
entry['FOCUS/disk_chopper/rotation_speed'][0])
meta['fermi_chopper_speed'] = decodeHDF(
entry['FOCUS/fermi_chopper/rotation_speed'][0])
meta['disk_chopper_ratio'] = decodeHDF(
entry['FOCUS/disk_chopper/ratio'][0])
meta['fermi_chopper_phase'] = decodeHDF(
entry['FOCUS/fermi_chopper/phase'][0])
f.close()
return meta