def test_calculate_magnification(self):
AG = AcquisitionGeometry.create_Parallel2D()
out = AG.config.system.calculate_magnification()
self.assertEqual(out, [None, None, 1])
def get_geometry(self):
'''
Parse NEXUS file and returns either ImageData or Acquisition Data
depending on file content
'''
with h5py.File(self.file_name,'r') as dfile:
if np.string_(dfile.attrs['creator']) != np.string_('NEXUSDataWriter.py'):
raise Exception('We can parse only files created by NEXUSDataWriter.py')
ds_data = dfile['entry1/tomo_entry/data/data']
if ds_data.attrs['data_type'] == 'ImageData':
self._geometry = ImageGeometry(voxel_num_x = int(ds_data.attrs['voxel_num_x']),
voxel_num_y = int(ds_data.attrs['voxel_num_y']),
voxel_num_z = int(ds_data.attrs['voxel_num_z']),
voxel_size_x = ds_data.attrs['voxel_size_x'],
voxel_size_y = ds_data.attrs['voxel_size_y'],
voxel_size_z = ds_data.attrs['voxel_size_z'],
center_x = ds_data.attrs['center_x'],
center_y = ds_data.attrs['center_y'],
center_z = ds_data.attrs['center_z'],
channels = ds_data.attrs['channels'])
if ds_data.attrs.__contains__('channel_spacing') == True:
self._geometry.channel_spacing = ds_data.attrs['channel_spacing']
# read the dimension_labels from dim{}
dimension_labels = self.read_dimension_labels(ds_data.attrs)
else: # AcquisitionData
if ds_data.attrs.__contains__('dist_source_center') or dfile['entry1/tomo_entry'].__contains__('config/source/position'):
geom_type = 'cone'
else:
geom_type = 'parallel'
if ds_data.attrs.__contains__('num_pixels_v'):
num_pixels_v = ds_data.attrs.get('num_pixels_v')
elif ds_data.attrs.__contains__('pixel_num_v'):
num_pixels_v = ds_data.attrs.get('pixel_num_v')
else:
num_pixels_v = 1
if num_pixels_v > 1:
dim = 3
else:
dim = 2
if self.is_old_file_version():
num_pixels_h = ds_data.attrs.get('pixel_num_h', 1)
num_channels = ds_data.attrs['channels']
ds_angles = dfile['entry1/tomo_entry/data/rotation_angle']
if geom_type == 'cone' and dim == 3:
self._geometry = AcquisitionGeometry.create_Cone3D(source_position=[0, -ds_data.attrs['dist_source_center'], 0],
detector_position=[0, ds_data.attrs['dist_center_detector'],0])
elif geom_type == 'cone' and dim == 2:
self._geometry = AcquisitionGeometry.create_Cone2D(source_position=[0, -ds_data.attrs['dist_source_center']],
detector_position=[0, ds_data.attrs['dist_center_detector']])
elif geom_type == 'parallel' and dim == 3:
self._geometry = AcquisitionGeometry.create_Parallel3D()
elif geom_type == 'parallel' and dim == 2:
self._geometry = AcquisitionGeometry.create_Parallel2D()
else:
num_pixels_h = ds_data.attrs.get('num_pixels_h', 1)
num_channels = ds_data.attrs['num_channels']
ds_angles = dfile['entry1/tomo_entry/config/angles']
rotation_axis_position = list(dfile['entry1/tomo_entry/config/rotation_axis/position'])
detector_position = list(dfile['entry1/tomo_entry/config/detector/position'])
ds_detector = dfile['entry1/tomo_entry/config/detector']
if ds_detector.__contains__('direction_x'):
detector_direction_x = list(dfile['entry1/tomo_entry/config/detector/direction_x'])
else:
detector_direction_x = list(dfile['entry1/tomo_entry/config/detector/direction_row'])
if ds_detector.__contains__('direction_y'):
detector_direction_y = list(dfile['entry1/tomo_entry/config/detector/direction_y'])
elif ds_detector.__contains__('direction_col'):
detector_direction_y = list(dfile['entry1/tomo_entry/config/detector/direction_col'])
ds_rotate = dfile['entry1/tomo_entry/config/rotation_axis']
if ds_rotate.__contains__('direction'):
rotation_axis_direction = list(dfile['entry1/tomo_entry/config/rotation_axis/direction'])
if geom_type == 'cone':
source_position = list(dfile['entry1/tomo_entry/config/source/position'])
if dim == 2:
self._geometry = AcquisitionGeometry.create_Cone2D(source_position, detector_position, detector_direction_x, rotation_axis_position)
else:
self._geometry = AcquisitionGeometry.create_Cone3D(source_position,\
detector_position, detector_direction_x, detector_direction_y,\
rotation_axis_position, rotation_axis_direction)
else:
ray_direction = list(dfile['entry1/tomo_entry/config/ray/direction'])
if dim == 2:
self._geometry = AcquisitionGeometry.create_Parallel2D(ray_direction, detector_position, detector_direction_x, rotation_axis_position)
else:
self._geometry = AcquisitionGeometry.create_Parallel3D(ray_direction,\
detector_position, detector_direction_x, detector_direction_y,\
rotation_axis_position, rotation_axis_direction)
# for all Aquisition data
#set angles
angles = list(ds_angles)
angle_unit = ds_angles.attrs.get('angle_unit','degree')
initial_angle = ds_angles.attrs.get('initial_angle',0)
self._geometry.set_angles(angles, initial_angle=initial_angle, angle_unit=angle_unit)
#set panel
pixel_size_v = ds_data.attrs.get('pixel_size_v', ds_data.attrs['pixel_size_h'])
origin = ds_data.attrs.get('panel_origin','bottom-left')
self._geometry.set_panel((num_pixels_h, num_pixels_v),\
pixel_size=(ds_data.attrs['pixel_size_h'], pixel_size_v),\
origin=origin)
# set channels
self._geometry.set_channels(num_channels)
dimension_labels = []
dimension_labels = self.read_dimension_labels(ds_data.attrs)
#set labels
self._geometry.set_labels(dimension_labels)
return self._geometry
def test_get_centre_slice(self):
AG = AcquisitionGeometry.create_Parallel2D()
AG2 = AG.copy()
AG2.config.system.get_centre_slice()
self.assertEqual(AG.config.system, AG2.config.system)
