def test_ImageGeometry_allocate(self):
vgeometry = ImageGeometry(voxel_num_x=4, voxel_num_y=3, channels=2)
image = vgeometry.allocate()
self.assertEqual(0,image.as_array()[0][0][0])
image = vgeometry.allocate(1)
self.assertEqual(1,image.as_array()[0][0][0])
default_order = ['channel' , 'horizontal_y' , 'horizontal_x']
self.assertEqual(default_order[0], image.dimension_labels[0])
self.assertEqual(default_order[1], image.dimension_labels[1])
self.assertEqual(default_order[2], image.dimension_labels[2])
order = [ 'horizontal_x' , 'horizontal_y', 'channel' ]
vgeometry.set_labels(order)
image = vgeometry.allocate(0)
self.assertEqual(order[0], image.dimension_labels[0])
self.assertEqual(order[1], image.dimension_labels[1])
self.assertEqual(order[2], image.dimension_labels[2])
ig = ImageGeometry(2,3,2)
try:
z = ImageData(numpy.random.randint(10, size=(2,3)), geometry=ig)
self.assertTrue(False)
except ValueError as ve:
print (ve)
self.assertTrue(True)
class NEXUSDataReader(object):
def __init__(self, **kwargs):
'''
Constructor
Input:
file_name full path to NEXUS file
'''
self.file_name = kwargs.get('file_name', None)
if self.file_name is not None:
self.set_up(file_name=self.file_name)
def set_up(self, file_name=None):
self.file_name = os.path.abspath(file_name)
# check that h5py library is installed
if (h5pyAvailable == False):
raise Exception('h5py is not available, cannot load NEXUS files.')
if self.file_name == None:
raise Exception('Path to nexus file is required.')
# check if nexus file exists
if not (os.path.isfile(self.file_name)):
raise Exception('File\n {}\n does not exist.'.format(
self.file_name))
self._geometry = None
def read_dimension_labels(self, attrs):
dimension_labels = [None] * 4
for k, v in attrs.items():
if k in ['dim0', 'dim1', 'dim2', 'dim3']:
dimension_labels[int(k[3:])] = v
# remove Nones
dimension_labels = [i for i in dimension_labels if i]
if len(dimension_labels) == 0:
dimension_labels = None
return dimension_labels
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 read(self):
if self._geometry is None:
self.get_geometry()
with h5py.File(self.file_name, 'r') as dfile:
ds_data = dfile['entry1/tomo_entry/data/data']
data = np.array(ds_data, dtype=np.float32)
# handle old files?
if self.is_old_file_version():
if isinstance(self._geometry, AcquisitionGeometry):
return AcquisitionData(data,
True,
geometry=self._geometry,
suppress_warning=True)
elif isinstance(self._geometry, ImageGeometry):
return ImageData(data,
True,
geometry=self._geometry,
suppress_warning=True)
else:
raise TypeError("Unsupported geometry. Expected ImageGeometry or AcquisitionGeometry, got {}"\
.format(type(self._geometry)))
output = self._geometry.allocate(None)
output.fill(data)
return output
def load_data(self):
'''alias of read'''
return self.read()
def is_old_file_version(self):
#return ds_data.attrs.__contains__('geom_type')
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']
return 'geom_type' in ds_data.attrs.keys()
class TestSubset(unittest.TestCase):
def setUp(self):
self.ig = ImageGeometry(2, 3, 4, channels=5)
angles = numpy.asarray([90., 0., -90.], dtype=numpy.float32)
self.ag_cone = AcquisitionGeometry.create_Cone3D([0,-500,0],[0,500,0])\
.set_panel((20,2))\
.set_angles(angles)\
.set_channels(4)
self.ag = AcquisitionGeometry.create_Parallel3D()\
.set_angles(angles)\
.set_channels(4)\
.set_panel((20,2))
def test_ImageDataAllocate1a(self):
data = self.ig.allocate()
default_dimension_labels = [
ImageGeometry.CHANNEL, ImageGeometry.VERTICAL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X
]
self.assertTrue(
default_dimension_labels == list(data.dimension_labels))
def test_ImageDataAllocate1b(self):
data = self.ig.allocate()
self.assertTrue(data.shape == (5, 4, 3, 2))
def test_ImageDataAllocate2a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.VERTICAL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.CHANNEL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
self.assertTrue(
non_default_dimension_labels == list(data.dimension_labels))
def test_ImageDataAllocate2b(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.VERTICAL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.CHANNEL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
self.assertTrue(data.shape == (2, 4, 3, 5))
def test_ImageDataSubset1a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.CHANNEL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.VERTICAL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
sub = data.subset(horizontal_y=1)
self.assertTrue(sub.shape == (2, 5, 4))
def test_ImageDataSubset2a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.CHANNEL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.VERTICAL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
sub = data.subset(horizontal_x=1)
self.assertTrue(sub.shape == (5, 3, 4))
def test_ImageDataSubset3a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.CHANNEL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.VERTICAL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
sub = data.subset(channel=1)
self.assertTrue(sub.shape == (2, 3, 4))
def test_ImageDataSubset4a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.CHANNEL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.VERTICAL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
sub = data.subset(vertical=1)
self.assertTrue(sub.shape == (2, 5, 3))
def test_ImageDataSubset5a(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.HORIZONTAL_Y
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
sub = data.subset(horizontal_y=1)
self.assertTrue(sub.shape == (2, ))
def test_ImageDataSubset1b(self):
non_default_dimension_labels = [
ImageGeometry.HORIZONTAL_X, ImageGeometry.CHANNEL,
ImageGeometry.HORIZONTAL_Y, ImageGeometry.VERTICAL
]
self.ig.set_labels(non_default_dimension_labels)
data = self.ig.allocate()
new_dimension_labels = [
ImageGeometry.HORIZONTAL_Y, ImageGeometry.CHANNEL,
ImageGeometry.VERTICAL, ImageGeometry.HORIZONTAL_X
]
sub = data.subset(dimensions=new_dimension_labels)
self.assertTrue(sub.shape == (3, 5, 4, 2))
def test_ImageDataSubset1c(self):
data = self.ig.allocate()
sub = data.subset(channel=0, horizontal_x=0, horizontal_y=0)
self.assertTrue(sub.shape == (4, ))
def test_AcquisitionDataAllocate1a(self):
data = self.ag.allocate()
default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.ANGLE,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.HORIZONTAL
]
self.assertTrue(
default_dimension_labels == list(data.dimension_labels))
def test_AcquisitionDataAllocate1b(self):
data = self.ag.allocate()
self.assertTrue(data.shape == (4, 3, 2, 20))
def test_AcquisitionDataAllocate2a(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
self.assertTrue(
non_default_dimension_labels == list(data.dimension_labels))
def test_AcquisitionDataAllocate2b(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
self.assertTrue(data.shape == (4, 20, 2, 3))
def test_AcquisitionDataSubset1a(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sub = data.subset(vertical=0)
self.assertTrue(sub.shape == (4, 20, 3))
def test_AcquisitionDataSubset1b(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sub = data.subset(channel=0)
self.assertTrue(sub.shape == (20, 2, 3))
def test_AcquisitionDataSubset1c(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sub = data.subset(horizontal=0, force=True)
self.assertTrue(sub.shape == (4, 2, 3))
def test_AcquisitionDataSubset1d(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sliceme = 1
sub = data.subset(angle=sliceme)
#print (sub.shape , sub.dimension_labels)
self.assertTrue(sub.shape == (4, 20, 2))
self.assertTrue(
sub.geometry.angles[0] == data.geometry.angles[sliceme])
def test_AcquisitionDataSubset1e(self):
non_default_dimension_labels = [
AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL,
AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE
]
self.ag.set_labels(non_default_dimension_labels)
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sliceme = 1
sub = data.subset(angle=sliceme)
self.assertTrue(
sub.geometry.angles[0] == data.geometry.angles[sliceme])
def test_AcquisitionDataSubset1f(self):
data = self.ag.allocate()
#self.assertTrue( data.shape == (4,20,2,3))
sliceme = 1
sub = data.subset(angle=sliceme)
self.assertTrue(
sub.geometry.angles[0] == data.geometry.angles[sliceme])
def test_AcquisitionDataSubset1g(self):
data = self.ag_cone.allocate()
sliceme = 1
sub = data.subset(angle=sliceme)
self.assertTrue(
sub.geometry.angles[0] == data.geometry.angles[sliceme])
def test_AcquisitionDataSubset1h(self):
data = self.ag_cone.allocate()
sub = data.subset(vertical='centre')
self.assertTrue(sub.geometry.shape == (4, 3, 20))
def test_AcquisitionDataSubset1i(self):
data = self.ag_cone.allocate()
sliceme = 1
sub = data.subset(vertical=sliceme, force=True)
self.assertTrue(sub.shape == (4, 3, 20))
def test_AcquisitionDataSubset1j(self):
data = self.ag.allocate()
sub = data.subset(angle=0)
sub = sub.subset(vertical=0)
sub = sub.subset(horizontal=0, force=True)
self.assertTrue(sub.shape == (4, ))