def test_cone3D_simple(self):
ag = AcquisitionGeometry.create_Cone3D(source_position=[0,-2,0], detector_position=[0,1,0])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
ig = ag.get_ImageGeometry()
ig.voxel_num_y = 50
ig.voxel_size_y /= 2
angles_rad = np.array([-np.pi / 2, -np.pi, -3 * np.pi / 2])
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(ig, ag)
np.testing.assert_allclose(
tg_geometry.DSD, ag.dist_center_detector + ag.dist_source_center)
np.testing.assert_allclose(tg_geometry.DSO, ag.dist_source_center)
np.testing.assert_allclose(tg_angles, angles_rad)
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.rotDetector, 0)
np.testing.assert_allclose(tg_geometry.offDetector, 0)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
mag = ag.magnification
np.testing.assert_allclose(tg_geometry.nVoxel, [3, 50, 128])
np.testing.assert_allclose(tg_geometry.dVoxel,
[0.2 / mag, 0.05 / mag, 0.1 / mag])
def test_parallel3D_offset(self):
ag = AcquisitionGeometry.create_Parallel3D(detector_position=[2,0,0], rotation_axis_position=[3,0, 0])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
self.assertTrue(ag.system_description == 'offset')
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
det_offset = np.array([0, -1, 0])
np.testing.assert_allclose(tg_geometry.offDetector, det_offset)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'parallel')
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
np.testing.assert_allclose(
tg_geometry.nVoxel,
[self.ig.voxel_num_z, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(
tg_geometry.dVoxel,
[self.ig.voxel_size_z, self.ig.voxel_size_y, self.ig.voxel_size_x])
def test_parallel3D_simple(self):
ag = AcquisitionGeometry.create_Parallel3D()\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'parallel')
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.rotDetector, 0)
np.testing.assert_allclose(tg_geometry.offDetector, 0)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
np.testing.assert_allclose(
tg_geometry.nVoxel,
[self.ig.voxel_num_z, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(
tg_geometry.dVoxel,
[self.ig.voxel_size_z, self.ig.voxel_size_y, self.ig.voxel_size_x])
def __init__(self, volume_geometry, sinogram_geometry):
DataOrder.check_order_for_engine('tigre', volume_geometry)
DataOrder.check_order_for_engine('tigre', sinogram_geometry)
tigre_geom, tigre_angles = CIL2TIGREGeometry.getTIGREGeometry(volume_geometry,sinogram_geometry)
super(FBP, self).__init__( volume_geometry = volume_geometry, sinogram_geometry = sinogram_geometry,\
tigre_geom=tigre_geom, tigre_angles=tigre_angles)
def __init__(self,
image_geometry,
aquisition_geometry,
direct_method='interpolated',
adjoint_weights='matched'):
'''
This class creates a configured TIGRE ProjectionOperator
Please refer to the TIGRE documentation for futher descriptions
https://github.com/CERN/TIGRE
https://iopscience.iop.org/article/10.1088/2057-1976/2/5/055010
:param image_geometry: A description of the ImageGeometry of your data
:type image_geometry: ImageGeometry
:param aquisition_geometry: A description of the AcquisitionGeometry of your data
:type aquisition_geometry: AcquisitionGeometry
:param direct_method: The method used by the forward projector, 'Siddon' for ray-voxel intersection, 'interpolated' for interpolated projection
:type direct_method: str, default 'interpolated'
:param adjoint_weights: The weighting method used by the cone-beam backward projector, 'matched' for weights to approximatly match the 'interpolated' forward projector, 'FDK' for FDK weights, default 'matched'
:type adjoint_weights: str
'''
DataOrder.check_order_for_engine('tigre', image_geometry)
DataOrder.check_order_for_engine('tigre', aquisition_geometry)
super(ProjectionOperator,self).__init__(domain_geometry=image_geometry,\
range_geometry=aquisition_geometry)
if direct_method not in ['interpolated', 'Siddon']:
raise ValueError(
"direct_method expected 'interpolated' or 'Siddon' got {}".
format(direct_method))
if adjoint_weights not in ['matched', 'FDK']:
raise ValueError(
"adjoint_weights expected 'matched' or 'FDK' got {}".format(
adjoint_weights))
self.method = {'direct': direct_method, 'adjoint': adjoint_weights}
#set up TIGRE geometry
tigre_geom, tigre_angles = CIL2TIGREGeometry.getTIGREGeometry(
image_geometry, aquisition_geometry)
#TIGRE bug workaround, when voxelgrid and panel are aligned ray tracing fails
if direct_method == 'Siddon' and aquisition_geometry.geom_type == AcquisitionGeometry.PARALLEL:
for i, angle in enumerate(tigre_angles):
if abs(angle / np.pi) % 0.5 < 1e-4:
tigre_angles[i] += 1e-5
tigre_geom.check_geo(tigre_angles)
tigre_geom.cast_to_single()
self.tigre_geom = tigre_geom
#set up TIGRE GPU targets (from 2.2)
if has_gpu_sel:
self.gpuids = GpuIds()
def __init__(self, image_geometry, aquisition_geometry, direct_method='Siddon',adjoint_method='matched'):
DataOrder.check_order_for_engine('tigre', image_geometry)
DataOrder.check_order_for_engine('tigre', aquisition_geometry)
super(ProjectionOperator,self).__init__(domain_geometry=image_geometry,\
range_geometry=aquisition_geometry)
self.tigre_geom, self.tigre_angles= CIL2TIGREGeometry.getTIGREGeometry(image_geometry,aquisition_geometry)
self.method = {'direct':direct_method,'adjoint':adjoint_method}
def test_cone3D_advanced(self):
ag = AcquisitionGeometry.create_Cone3D(source_position=[0,-10,0], detector_position=[0,10,0], rotation_axis_position=[0,0, 0],rotation_axis_direction=[0,-1,1])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
self.assertTrue(ag.system_description == 'advanced')
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
self.assertAlmostEqual(tg_geometry.DSO,
ag.dist_source_center * np.sin(np.pi / 4), 5)
s2o = ag.dist_source_center * np.cos(np.pi / 4)
np.testing.assert_allclose(tg_geometry.DSO, s2o)
s2d = (ag.dist_center_detector + ag.dist_source_center) * np.cos(
np.pi / 4)
np.testing.assert_allclose(tg_geometry.DSD, s2d)
det_rot = np.array([0, -np.pi / 4, 0])
np.testing.assert_allclose(tg_geometry.rotDetector, det_rot)
det_offset = np.array([-s2d, 0, 0])
np.testing.assert_allclose(tg_geometry.offDetector, det_offset)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'cone')
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
height = 10 / np.sqrt(2)
np.testing.assert_allclose(tg_geometry.offOrigin, [-height, 0, 0])
np.testing.assert_allclose(
tg_geometry.nVoxel,
[self.ig.voxel_num_z, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(
tg_geometry.dVoxel,
[self.ig.voxel_size_z, self.ig.voxel_size_y, self.ig.voxel_size_x])
def test_cone3D_offset(self):
#3, 4, 5 triangle for source + object
ag = AcquisitionGeometry.create_Cone3D(source_position=[0,-4,0], detector_position=[0,4,0], rotation_axis_position=[3,0, 0])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
self.assertTrue(ag.system_description == 'offset')
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
np.testing.assert_allclose(tg_geometry.DSO, ag.dist_source_center)
yaw = np.arcsin(3. / 5.)
det_rot = np.array([0, 0, yaw])
np.testing.assert_allclose(tg_geometry.rotDetector, det_rot)
offset = 4 * 6 / 5
det_offset = np.array([0, -offset, 0])
np.testing.assert_allclose(tg_geometry.offDetector, det_offset)
s2d = ag.dist_center_detector + ag.dist_source_center - 6 * 3 / 5
np.testing.assert_allclose(tg_geometry.DSD, s2d)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2 + yaw)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'cone')
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
np.testing.assert_allclose(
tg_geometry.nVoxel,
[self.ig.voxel_num_z, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(
tg_geometry.dVoxel,
[self.ig.voxel_size_z, self.ig.voxel_size_y, self.ig.voxel_size_x])
def test_cone3D_cofr(self):
#3, 4, 5 triangle for source + object
ag = AcquisitionGeometry.create_Cone3D(source_position=[0,-4,0], detector_position=[0,4,0], rotation_axis_position=[3,0, 0])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
ig = ag.get_ImageGeometry()
ig.voxel_num_y = 50
ig.voxel_size_y /= 2
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(ig, ag)
np.testing.assert_allclose(tg_geometry.DSO, ag.dist_source_center)
yaw = np.arcsin(3. / 5.)
det_rot = np.array([0, 0, yaw])
np.testing.assert_allclose(tg_geometry.rotDetector, det_rot)
offset = 4 * 6 / 5
det_offset = np.array([0, -offset, 0])
np.testing.assert_allclose(tg_geometry.offDetector, det_offset)
s2d = ag.dist_center_detector + ag.dist_source_center - 6 * 3 / 5
np.testing.assert_allclose(tg_geometry.DSD, s2d)
angles_rad = np.array([-np.pi / 2, -np.pi, -3 * np.pi / 2]) - yaw
np.testing.assert_allclose(tg_angles, angles_rad)
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
mag = ag.magnification
np.testing.assert_allclose(tg_geometry.nVoxel, [3, 50, 128])
np.testing.assert_allclose(tg_geometry.dVoxel,
[0.2 / mag, 0.05 / mag, 0.1 / mag])
def test_cone3D_simple(self):
ag = AcquisitionGeometry.create_Cone3D(source_position=[0,-6,0], detector_position=[0,16,0])\
.set_angles(self.angles_deg, angle_unit='degree')\
.set_labels(['vertical', 'angle','horizontal'])\
.set_panel((self.num_pixels_x,self.num_pixels_y), (self.pixel_size_x,self.pixel_size_y))
self.assertTrue(ag.system_description == 'simple')
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'cone')
np.testing.assert_allclose(
tg_geometry.DSD, ag.dist_center_detector + ag.dist_source_center)
np.testing.assert_allclose(tg_geometry.DSO, ag.dist_source_center)
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.rotDetector, 0)
np.testing.assert_allclose(tg_geometry.offDetector, 0)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
np.testing.assert_allclose(
tg_geometry.nVoxel,
[self.ig.voxel_num_z, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(
tg_geometry.dVoxel,
[self.ig.voxel_size_z, self.ig.voxel_size_y, self.ig.voxel_size_x])
def test_cone2D(self):
ag = AcquisitionGeometry.create_Cone2D(source_position=[0,-6], detector_position=[0,16])\
.set_angles(self.angles_rad, angle_unit='radian')\
.set_labels(['angle','horizontal'])\
.set_panel(self.num_pixels_x, self.pixel_size_x)
#2D cone
tg_geometry, tg_angles = CIL2TIGREGeometry.getTIGREGeometry(
self.ig, ag)
for i, ang in enumerate(tg_angles):
ang2 = -(self.angles_rad[i] + np.pi / 2)
self.compare_angles(ang, ang2, 1e-6)
self.assertTrue(tg_geometry.mode == 'cone')
np.testing.assert_allclose(
tg_geometry.DSD, ag.dist_center_detector + ag.dist_source_center)
np.testing.assert_allclose(tg_geometry.DSO, ag.dist_source_center)
np.testing.assert_allclose(tg_geometry.dDetector,
ag.config.panel.pixel_size[::-1])
np.testing.assert_allclose(tg_geometry.nDetector,
ag.config.panel.num_pixels[::-1])
np.testing.assert_allclose(
tg_geometry.sDetector,
tg_geometry.dDetector * tg_geometry.nDetector)
np.testing.assert_allclose(tg_geometry.rotDetector, 0)
np.testing.assert_allclose(tg_geometry.offDetector, 0)
np.testing.assert_allclose(tg_geometry.offOrigin, 0)
np.testing.assert_allclose(
tg_geometry.nVoxel, [1, self.ig.voxel_num_y, self.ig.voxel_num_x])
np.testing.assert_allclose(tg_geometry.dVoxel, [
ag.config.panel.pixel_size[1] / ag.magnification,
self.ig.voxel_size_y, self.ig.voxel_size_x
])