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