def _beam(self, index=None):
if index is None:
index = 0
entry = self._reader.entries[0]
sample = entry.samples[0]
beam = sample.beams[0]
self._beam_model = BeamFactory(beam, index).model
return self._beam_model
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
def tst_dxtbx_eiger():
print "Testing eiger hdf5 geometry recognition.."
try:
# due to https://github.com/cctbx/cctbx_project/issues/282
import dxtbx.format.FormatHDFEigerNearlyNexus
except ImportError:
print " FormatHDFEigerNearlyNexus does not exist. This implies h5-recorded geometry can be no longer extracted using dxtbx. I hope it works. OK"
return True
try:
import h5py
import uuid
from dxtbx.format.nexus import NXmxReader
from dxtbx.format.FormatHDFEigerNearlyNexus import EigerNXmxFixer
from dxtbx.format.nexus import BeamFactory
from dxtbx.format.nexus import DetectorFactory
from dxtbx.format.nexus import GoniometerFactory
import numpy
tmpfd, tmpf = tempfile.mkstemp()
os.close(tmpfd)
h = h5py.File(tmpf, "w")
h.create_group("/entry/instrument/detector/")
h["/entry/instrument/detector/description"] = "Dectris Eiger"
h["/entry/"].attrs["NX_class"] = "NXentry"
g = h.create_group(
"entry/instrument/detector/detectorSpecific/detectorModule_000")
g["countrate_correction_count_cutoff"] = 10
g = h.create_group("/entry/instrument/beam")
g["incident_wavelength"] = 1.
g["incident_wavelength"].attrs["units"] = "angstrom"
h["/entry/instrument"].attrs["NX_class"] = "NXinstrument"
h["/entry/instrument/beam"].attrs["NX_class"] = "NXbeam"
g = h.create_group("/entry/data")
g.create_dataset("data_000001", (1, 3269, 3110), dtype=numpy.uint16)
h["/entry/data"].attrs["NX_class"] = "NXdata"
g = h.create_group("/entry/instrument/detector/geometry/orientation")
g["value"] = (-1, 0, 0, 0, -1, 0)
g = h.create_group("/entry/instrument/detector/geometry/translation")
g["distances"] = (0.11737501, 0.11992501, -0.18)
h["/entry/instrument/detector"].attrs["NX_class"] = "NXdetector"
h["/entry/instrument/detector/x_pixel_size"] = h[
"/entry/instrument/detector/y_pixel_size"] = 7.5e-5
h["/entry/instrument/detector/sensor_material"] = "Si"
h["/entry/instrument/detector/sensor_thickness"] = 4.5e-4
h["/entry/instrument/detector/sensor_thickness"].attrs["units"] = "m"
h["/entry/instrument/detector/count_time"] = 0.99998
g = h.create_group("/entry/sample/goniometer")
g["omega_range_average"] = 1.
h["/entry/sample"].attrs["NX_class"] = "NXsample"
h.close()
temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
fixer = EigerNXmxFixer(tmpf, temp_file)
reader = NXmxReader(handle=fixer.handle)
entry = reader.entries[0]
instrument = entry.instruments[0]
detector = instrument.detectors[0]
sample = entry.samples[0]
beam = sample.beams[0]
beam_model = BeamFactory(beam).model
detector_model = DetectorFactory(detector, beam_model).model
goniometer_model = GoniometerFactory(sample).model
_test = detector_model[0].get_fast_axis(
) + detector_model[0].get_slow_axis() + beam_model.get_direction(
) + goniometer_model.get_rotation_axis()
os.remove(tmpf)
if _test == (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0,
0.0):
print " OK"
return True
elif _test == (1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0,
0.0):
print " OK"
return True
else:
print " vectors=", _test
except:
print traceback.format_exc()
print " NG! You are using old cctbx. Use latest cctbx or environment of DIALS v1.6 or PHENIX 1.12 or newer."
return False