from __future__ import division from dxtbx.format.Format import Format from dxtbx.format.FormatHDF5 import FormatHDF5 class FormatHDF5Nexus(FormatHDF5): @staticmethod def understand(image_file): try: tag = FormatHDF5.open_file(image_file, 'rb').read(8) except IOError, e: return False # check that this is a HDF5 file (should not have got here if not # anyway...) if tag != "\211HDF\r\n\032\n": return False # now look to see if this is a pukka NeXus file accoring to # http://download.nexusformat.org/doc/html/classes/ # contributed_definitions/NXmx.html import h5py h5_handle = h5py.File(image_file, 'r') if not 'entry' in h5_handle: return False if not 'definition' in h5_handle['entry']: h5_handle.close() return False definition = h5_handle['entry']['definition'].value version = h5_handle['entry']['definition'].attrs.get('version') h5_handle.close() if not version: return False if definition == 'NXmx' and float(version) >= 1.0: return True return False def __init__(self, image_file): assert(self.understand(image_file)) FormatHDF5.__init__(self, image_file) def _start(self): import h5py self._h5_handle = h5py.File(self.get_image_file(), 'r') # names change as to what the sample positioner is called - originally was # 'pose' now is 'transformations' - FIXME I should be using the depends_on # attribute then I would not care what this is called... # compute coordinate frame transformation to imgCIF frame, just for kicks entry = self._h5_handle['entry'] sample = entry['sample'] if 'pose' in sample: self._pose_name = 'pose' elif 'transformations' in sample: self._pose_name = 'transformations' else: raise RuntimeError, 'cannot find pose or transformations' axis = tuple(sample[self._pose_name]['CBF_axis_omega'].attrs['vector']) # NeXus coordinate frame: Z is canonical from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame self._R = align_reference_frame(axis, (1, 0, 0), (0, 0, -1), (0, 0, 1)) return def _goniometer(self): ''' Get the rotation axis. ''' entry = self._h5_handle['entry'] sample = entry['sample'] pose = sample[self._pose_name] axis = tuple(pose['CBF_axis_omega'].attrs['vector']) return self._goniometer_factory.known_axis(self._R * axis) def _detector(self): from scitbx import matrix # Get the detector geometry stuff entry = self._h5_handle['entry'] instrument = entry['instrument'] detector = instrument['detector'] pose = detector[self._pose_name] translation = pose['translation'] rotation = pose['rotation'] # Get the translation offset = translation.attrs['offset'] trans = translation[0] vector = matrix.col(translation.attrs['vector']).normalize() # Initialise detector frame fast = matrix.col((1.0, 0.0, 0.0)) slow = matrix.col((0.0, 1.0, 0.0)) orig = 1000 * matrix.col((offset[0] + trans * vector[0], offset[1] + trans * vector[1], offset[2] + trans * vector[2])) # Next comes a rotation about an axis vector = matrix.col(rotation.attrs['vector']).normalize() angle = rotation[0] m_rot = vector.axis_and_angle_as_r3_rotation_matrix(angle, deg=True) # Transform detector frame - also to imgCIF fast = self._R * (m_rot * fast).normalize() slow = self._R * (m_rot * slow).normalize() orig = self._R * m_rot * orig # Get the pixel and image size pixel_size = 1000 * detector['x_pixel_size'].value, \ 1000 * detector['y_pixel_size'].value image_size = len(detector['x_pixel_offset']), \ len(detector['y_pixel_offset']) trusted_range = (-1, detector['saturation_value'][0]) # Make the detector return self._detector_factory.make_detector( "", fast, slow, orig, pixel_size, image_size, trusted_range) def _beam(self): ''' Nexus defines beam along z axis, i.e. from source to sample (i.e. reversed w.r.t. imgCIF convention).''' from scitbx import matrix entry = self._h5_handle['entry'] sample = entry['sample'] beam = sample['beam'] # seems to be two different syntax options for this if 'wavelength' in beam: wavelength = beam['wavelength'] elif 'incident_wavelength' in beam: wavelength = beam['incident_wavelength'] return self._beam_factory.simple_directional( self._R * matrix.col((0,0,-1)), wavelength[0]) def _scan(self): ''' Get the scan. ''' import time entry = self._h5_handle['entry'] sample = entry['sample'] pose = sample[self._pose_name] angles = pose['CBF_axis_omega'] oscillation = (angles[0], angles[1] - angles[0]) image_range = (1, len(angles)) instrument = entry['instrument'] detector = instrument['detector'] exposure_times = detector['count_time'] # Create the epochs frame_time = detector['frame_time'] start_time = entry['start_time'] time_ssec = start_time.value.split('.') time_struct = time.strptime(time_ssec[0], "%Y-%m-%dT%H:%M:%S") start_time = time.mktime(time_struct) + float('0.%s' % time_ssec[1]) epochs = {0 : start_time} for i, t in enumerate(frame_time[:-1]): epochs[i+1] = epochs[i] + t # Create the scan return self._scan_factory.make_scan( image_range, list(exposure_times), oscillation, list(epochs), deg=True) def get_num_images(self): entry = self._h5_handle['entry'] data = entry['data']['data'] return data.shape[0] def get_goniometer(self, index=None): return Format.get_goniometer(self) def get_detector(self, index=None): return Format.get_detector(self) def get_beam(self, index=None): return Format.get_beam(self) def get_scan(self, index=None): if index == None: return Format.get_scan(self) else: scan = Format.get_scan(self) return scan[index] def get_raw_data(self, index): from scitbx.array_family import flex entry = self._h5_handle['entry'] data = entry['data']['data'] return flex.int(data[index,:,:]) def get_image_file(self, index=None): return Format.get_image_file(self)