def _start(self):
# Read the file structure
self._reader = reader = NXmxReader(self._image_file)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(
reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples
) == 1, "Currently only supports 1 NXsample"
assert (len(reader.entries[0].samples[0].beams) == 1
or len(reader.entries[0].instruments[0].beams)
== 1), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0] if sample.beams else instrument.beams[0]
data = entry.data[0]
# Construct the models
self._beam_factory = BeamFactory(beam)
self._beam_factory.load_model(0)
self._setup_gonio_and_scan(sample, detector)
if self._scan_model:
array_range = self._scan_model.get_array_range()
num_images = array_range[1] - array_range[0]
else:
num_images = 0
if len(instrument.detector_groups) == 0:
assert (
len(reader.entries[0].instruments[0].detectors) == 1
), "Currently only supports 1 NXdetector unless in a detector group"
assert (
len(reader.entries[0].instruments[0].detectors[0].modules) == 1
), "Currently only supports 1 NXdetector_module unless in a detector group"
self._raw_data = DataFactory(data, max_size=num_images)
self._detector_model = DetectorFactory(
detector,
self._beam_factory.model,
shape=self._raw_data.shape()).model
else:
self._raw_data = detectorgroupdatafactory(data, instrument)
self._detector_model = DetectorFactoryFromGroup(
instrument, self._beam_factory.model).model
def _start(self):
# Read the file structure
temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
fixer = EigerNXmxFixer(self._image_file, temp_file)
reader = NXmxReader(handle=fixer.handle)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (
len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples) == 1, "Currently only supports 1 NXsample"
assert (
len(reader.entries[0].instruments[0].detectors) == 1
), "Currently only supports 1 NXdetector"
assert (
len(reader.entries[0].instruments[0].detectors[0].modules) == 1
), "Currently only supports 1 NXdetector_module"
assert (
len(reader.entries[0].samples[0].beams) == 1
or len(reader.entries[0].instruments[0].beams) == 1
), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0] if sample.beams else instrument.beams[0]
# Use data from original master file
data = NXdata(fixer.handle_orig[entry.data[0].handle.name])
self._raw_data = DataFactory(data, cached_information=fixer.data_factory_cache)
# Construct the models
self._beam_factory = BeamFactory(beam)
self._beam_factory.load_model(0)
self._detector_model = DetectorFactory(
detector, self._beam_factory.model, shape=self._raw_data.shape()
).model
# Override the minimum trusted value - for Eiger should be -1
for panel in self._detector_model:
trusted = panel.get_trusted_range()
panel.set_trusted_range((-1, trusted[1]))
self._goniometer_model = GoniometerFactory(sample).model
self._scan_model = generate_scan_model(sample, detector)
# update model for masking Eiger detectors
for f0, f1, s0, s1 in determine_eiger_mask(self._detector_model):
self._detector_model[0].add_mask(f0 - 1, s0 - 1, f1, s1)
def _start(self):
# Read the file structure
import uuid
temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
fixer = EigerNXmxFixer(self._image_file, temp_file)
reader = NXmxReader(handle=fixer.handle)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (
len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples) == 1, "Currently only supports 1 NXsample"
assert (
len(reader.entries[0].instruments[0].detectors) == 1
), "Currently only supports 1 NXdetector"
assert (
len(reader.entries[0].instruments[0].detectors[0].modules) == 1
), "Currently only supports 1 NXdetector_module"
assert (
len(reader.entries[0].samples[0].beams) == 1
), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0]
# Use data from original master file
data = NXdata(fixer.handle_orig[entry.data[0].handle.name])
# Construct the models
self._beam_model = BeamFactory(beam).model
self._detector_model = DetectorFactory(detector, self._beam_model).model
self._goniometer_model = GoniometerFactory(sample).model
self._scan_model = ScanFactory(sample, detector).model
self._raw_data = DataFactory(data).model
# update model for masking Eiger detectors
from dxtbx.format.FormatPilatusHelpers import determine_eiger_mask
for f0, f1, s0, s1 in determine_eiger_mask(self._detector_model):
self._detector_model[0].add_mask(f0 - 1, s0 - 1, f1, s1)
def _start(self):
# Read the file structure
import uuid
temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
fixer = EigerNXmxFixer(self._image_file, temp_file)
reader = NXmxReader(handle=fixer.handle)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, \
"Currently only supports 1 NXmx entry"
assert len(reader.entries[0].data) == 1, \
"Currently only supports 1 NXdata"
assert len(reader.entries[0].instruments) == 1, \
"Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples) == 1, \
"Currently only supports 1 NXsample"
assert len(reader.entries[0].instruments[0].detectors) == 1, \
"Currently only supports 1 NXdetector"
assert len(reader.entries[0].instruments[0].detectors[0].modules) == 1, \
"Currently only supports 1 NXdetector_module"
assert len(reader.entries[0].samples[0].beams) == 1, \
"Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0]
# Use data from original master file
data = NXdata(fixer.handle_orig[entry.data[0].handle.name])
# Construct the models
self._beam_model = BeamFactory(beam).model
self._detector_model = DetectorFactory(detector,
self._beam_model).model
self._goniometer_model = GoniometerFactory(sample).model
self._scan_model = ScanFactory(sample, detector).model
self._raw_data = DataFactory(data).model
self._mask = MaskFactory([detector]).mask
def _start(self):
# Read the file structure
self._reader = reader = NXmxReader(self._image_file)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(
reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples
) == 1, "Currently only supports 1 NXsample"
assert (len(reader.entries[0].samples[0].beams) == 1
), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0]
data = entry.data[0]
# Construct the models
self._beam_model = BeamFactory(beam).model
self._setup_detector(detector, self._beam_model)
self._setup_gonio_and_scan(sample, detector)
if self._scan_model:
array_range = self._scan_model.get_array_range()
num_images = array_range[1] - array_range[0]
else:
num_images = 0
self._raw_data = DataFactory(data, max_size=num_images).model
class FormatHDF5EigerNearlyNexus(FormatHDF5):
@staticmethod
def understand(image_file):
try:
return is_eiger_nearly_nexus_file(image_file)
except IOError:
return False
def _start(self):
# Read the file structure
temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
fixer = EigerNXmxFixer(self._image_file, temp_file)
reader = NXmxReader(handle=fixer.handle)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (
len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples) == 1, "Currently only supports 1 NXsample"
assert (
len(reader.entries[0].instruments[0].detectors) == 1
), "Currently only supports 1 NXdetector"
assert (
len(reader.entries[0].instruments[0].detectors[0].modules) == 1
), "Currently only supports 1 NXdetector_module"
assert (
len(reader.entries[0].samples[0].beams) == 1
or len(reader.entries[0].instruments[0].beams) == 1
), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0] if sample.beams else instrument.beams[0]
# Use data from original master file
data = NXdata(fixer.handle_orig[entry.data[0].handle.name])
self._raw_data = DataFactory(data, cached_information=fixer.data_factory_cache)
# Construct the models
self._beam_factory = BeamFactory(beam)
self._beam_factory.load_model(0)
self._detector_model = DetectorFactory(
detector, self._beam_factory.model, shape=self._raw_data.shape()
).model
# Override the minimum trusted value - for Eiger should be -1
for panel in self._detector_model:
trusted = panel.get_trusted_range()
panel.set_trusted_range((-1, trusted[1]))
self._goniometer_model = GoniometerFactory(sample).model
self._scan_model = generate_scan_model(sample, detector)
# update model for masking Eiger detectors
for f0, f1, s0, s1 in determine_eiger_mask(self._detector_model):
self._detector_model[0].add_mask(f0 - 1, s0 - 1, f1, s1)
def _end(self):
return
def _goniometer(self):
return self._goniometer_model
def _detector(self):
return self._detector_model
def _beam(self, index=None):
self._beam_model, _ = self._beam_factory.read_models(index)
return self._beam_model
def _scan(self):
return self._scan_model
def get_goniometer(self, index=None):
return self._goniometer()
def get_detector(self, index=None):
return self._detector()
def get_beam(self, index=None):
return self._beam(index)
def get_scan(self, index=None):
if index is None:
return self._scan()
return self._scan()[index]
def get_raw_data(self, index):
return self._raw_data[index]
def get_static_mask(self, index=None, goniometer=None):
return MaskFactory(self.instrument.detectors, index).mask
def get_num_images(self):
scan = self._scan()
if isinstance(scan, list):
return sum(s.get_num_images() for s in scan)
return scan.get_num_images()
def get_image_file(self, index=None):
return self._image_file
def detectorbase_start(self, index=0):
self.detectorbase = EIGERImage(self._image_file, index=index)
self.detectorbase.readHeader(dxtbx_instance=self)
def model_get_raw_data(ptr, index):
return self.get_raw_data(index)
self.detectorbase.get_raw_data_callback = model_get_raw_data
def get_detectorbase(self, index=0):
self.detectorbase_start(index)
return self.detectorbase
def get_vendortype(self):
return gv(self.get_detector())
class FormatNexus(FormatHDF5):
@staticmethod
def understand(image_file):
try:
return is_nexus_file(image_file)
except IOError:
return False
def _start(self):
# Read the file structure
self._reader = reader = NXmxReader(self._image_file)
# Only support 1 set of models at the moment
assert len(reader.entries) == 1, "Currently only supports 1 NXmx entry"
assert len(
reader.entries[0].data) == 1, "Currently only supports 1 NXdata"
assert (len(reader.entries[0].instruments) == 1
), "Currently only supports 1 NXinstrument"
assert len(reader.entries[0].samples
) == 1, "Currently only supports 1 NXsample"
assert (len(reader.entries[0].samples[0].beams) == 1
or len(reader.entries[0].instruments[0].beams)
== 1), "Currently only supports 1 NXbeam"
# Get the NXmx model objects
entry = reader.entries[0]
self.instrument = instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0] if sample.beams else instrument.beams[0]
data = entry.data[0]
# Construct the models
self._beam_factory = BeamFactory(beam)
self._beam_factory.load_model(0)
self._setup_gonio_and_scan(sample, detector)
if self._scan_model:
array_range = self._scan_model.get_array_range()
num_images = array_range[1] - array_range[0]
else:
num_images = 0
if len(instrument.detector_groups) == 0:
assert (
len(reader.entries[0].instruments[0].detectors) == 1
), "Currently only supports 1 NXdetector unless in a detector group"
assert (
len(reader.entries[0].instruments[0].detectors[0].modules) == 1
), "Currently only supports 1 NXdetector_module unless in a detector group"
self._raw_data = DataFactory(data, max_size=num_images)
self._detector_model = DetectorFactory(
detector,
self._beam_factory.model,
shape=self._raw_data.shape()).model
else:
self._raw_data = detectorgroupdatafactory(data, instrument)
self._detector_model = DetectorFactoryFromGroup(
instrument, self._beam_factory.model).model
def _setup_gonio_and_scan(self, sample, detector):
"""Set up rotation-specific models"""
self._goniometer_model = GoniometerFactory(sample).model
self._scan_model = generate_scan_model(sample, detector)
def _end(self):
return
def _goniometer(self):
return self._goniometer_model
def _detector(self):
return self._detector_model
def _beam(self, index=None):
self._beam_model, _ = self._beam_factory.read_models(index)
return self._beam_model
def _scan(self):
return self._scan_model
def get_goniometer(self, index=None):
return self._goniometer()
def get_detector(self, index=None):
return self._detector()
def get_beam(self, index=None):
return self._beam(index)
def get_spectrum(self, index=None):
self._beam_model, _ = self._beam_factory.read_models(index)
return self._beam_factory.spectrum
def get_scan(self, index=None):
if index is None:
return self._scan()
scan = self._scan()
if scan is not None:
return scan[index]
return scan
def get_raw_data(self, index):
return self._raw_data[index]
def get_static_mask(self, index=None, goniometer=None):
return MaskFactory(self.instrument.detectors, index).mask
def get_num_images(self):
if self._scan() is not None:
return self._scan().get_num_images()
return len(self._raw_data)
def get_image_file(self, index=None):
return self._image_file
def get_detectorbase(self, index=None):
raise NotImplementedError
@staticmethod
def get_instrument_name(handle):
if "short_name" in handle["/entry/instrument"].attrs:
name = handle["/entry/instrument"].attrs["short_name"]
elif "/entry/instrument/name" in handle:
if "short_name" in handle["/entry/instrument/name"].attrs:
name = handle["/entry/instrument/name"].attrs["short_name"]
else:
name = handle["/entry/instrument/name"][()]
else:
name = None
return name