def readUSANSNexus(input_file, file_obj=None, metadata_lookup=metadata_lookup, det_deadtime=0.0, trans_deadtime=0.0):
"""
Load all entries from the NeXus file into sans data sets.
"""
datasets = []
file = h5_open_zip(input_file, file_obj)
for entryname, entry in file.items():
metadata = OrderedDict([
("run.filename", _s(entry["DAS_logs/trajectoryData/fileName"][0])),
("analysis.intent", _s(entry["DAS_logs/trajectoryData/intent"][0])),
("sample.name", _s(entry["DAS_logs/sample/name"][0])),
("run.filePrefix", _s(entry["DAS_logs/trajectoryData/filePrefix"][0])),
("run.instFileNum", int(entry["DAS_logs/trajectoryData/instFileNum"][0])),
("start_time", _s(entry["start_time"][0])),
("end_time",_s(entry["end_time"][0])),
("entry", _s(entryname)),
("dQv", 0.117), # constant of the instrument. Should it be in the nexus def?
])
counts = entry['DAS_logs/linearDetector/counts'][()]
countTime = entry['DAS_logs/counter/liveTime'][()]
trans_counts = entry['DAS_logs/transDetector/counts'][()]
detCts = (counts / (1.0 - (counts*det_deadtime/countTime[:,None]))).sum(axis=1)
transCts = (trans_counts / (1.0 - (trans_counts*trans_deadtime/countTime[:,None]))).sum(axis=1)
monCts = entry['DAS_logs/counter/liveMonitor'][()]
Q = entry['DAS_logs/analyzerRotation/softPosition'][()]
dataset = USansData(metadata=metadata, countTime=countTime, detCts=detCts, transCts=transCts, monCts=monCts, Q=Q)
datasets.append(dataset)
return datasets
def readSANSNexuz(input_file, file_obj=None, metadata_lookup=metadata_lookup):
"""
Load all entries from the NeXus file into sans data sets.
"""
datasets = []
file = h5_open_zip(input_file, file_obj)
for entryname, entry in file.items():
multiplicity = 1
for i in range(multiplicity):
metadata = load_metadata(entry,
multiplicity,
i,
metadata_lookup=metadata_lookup,
unit_specifiers=unit_specifiers)
#print(metadata)
detector_keys = ['detector']
detectors = dict([(k, load_detector(entry['instrument'][k]))
for k in detector_keys])
metadata['entry'] = entryname
# hack to remove configuration from sample label (it is still stored in run.configuration)
metadata['sample.description'] = _s(
metadata["sample.labl"]).replace(
_s(metadata["run.configuration"]), "")
dataset = RawSANSData(metadata=metadata, detectors=detectors)
datasets.append(dataset)
return datasets
def readSANSNexuz_old(input_file, file_obj=None):
"""
Load all entries from the NeXus file into sans data sets.
"""
datasets = []
file = h5_open_zip(input_file, file_obj)
for entryname, entry in file.items():
areaDetector = entry['data/areaDetector'].value
shape = areaDetector.shape
if len(shape) < 2 or len(shape) > 3:
raise ValueError("areaDetector data must have dimension 2 or 3")
return
if len(shape) == 2:
# add another dimension at the front
shape = (1, ) + shape
areaDetector = areaDetector.reshape(shape)
for i in range(shape[0]):
metadata = {}
for mkey in metadata_lookup:
field = entry.get(metadata_lookup[mkey], None)
if field is not None:
if mkey in unit_specifiers:
field = data_as(field, unit_specifiers[mkey])
else:
field = field.value
if field.dtype.kind == 'f':
field = field.astype("float")
elif field.dtype.kind == 'i':
field = field.astype("int")
if len(field) == shape[0]:
metadata[mkey] = field[i]
else:
metadata[mkey] = field
else:
metadata[mkey] = field
metadata['entry'] = entryname
dataset = SansData(data=areaDetector[i].copy(), metadata=metadata)
datasets.append(dataset)
return datasets
def readVSANSNexuz(input_file, file_obj=None, metadata_lookup=metadata_lookup):
"""
Load all entries from the NeXus file into sans data sets.
"""
datasets = []
file = h5_open_zip(input_file, file_obj)
for entryname, entry in file.items():
#areaDetector = entry['data/areaDetector'].value
#shape = areaDetector.shape
#if len(shape) < 2 or len(shape) > 3:
# raise ValueError("areaDetector data must have dimension 2 or 3")
# return
#if len(shape) == 2:
# add another dimension at the front
# shape = (1,) + shape
# areaDetector = areaDetector.reshape(shape)
multiplicity = 1
for i in range(multiplicity):
metadata = load_metadata(entry,
multiplicity,
i,
metadata_lookup=metadata_lookup,
unit_specifiers=unit_specifiers)
#print(metadata)
detector_keys = [
n for n in entry['instrument'] if n.startswith('detector_')
]
detectors = dict([(k, load_detector(entry['instrument'][k]))
for k in detector_keys])
metadata['entry'] = entryname
if metadata.get('sample.labl', None) is not None and metadata.get(
'run.configuration', None) is not None:
metadata['sample.description'] = _s(
metadata["sample.labl"]).replace(
_s(metadata["run.configuration"]), "")
if metadata.get('run.filename', None) is None:
metadata['run.filename'] = input_file
dataset = RawVSANSData(metadata=metadata, detectors=detectors)
datasets.append(dataset)
return datasets
def load_nexus_entries(filename,
file_obj=None,
entries=None,
meta_only=False,
entry_loader=None):
"""
Load the summary info for all entries in a NeXus file.
"""
handle = h5_open.h5_open_zip(filename, file_obj)
measurements = []
for name, entry in handle.items():
if entries is not None and name not in entries:
continue
if _s(entry.attrs.get('NX_class', None)) == 'NXentry':
data = entry_loader(entry, name, filename)
if not meta_only:
data.load(entry)
measurements.append(data)
if file_obj is None:
handle.close()
return measurements