def test_equal(self): AG = AcquisitionGeometry.create_Parallel3D() AG.set_channels(4, ['a','b','c','d']) AG.set_panel([2,3]) AG.set_angles([0,1,2,3,5]) AG.set_labels(('horizontal','angle','vertical','channel')) AG2 = AcquisitionGeometry.create_Parallel3D() AG2.set_channels(4, ['a','b','c','d']) AG2.set_panel([2,3]) AG2.set_angles([0,1,2,3,5]) AG2.set_labels(('horizontal','angle','vertical','channel')) self.assertTrue(AG == AG2) #test not equal AG3 = AG2.copy() AG3.config.system.ray.direction = [1,0,0] self.assertFalse(AG == AG3) AG3 = AG2.copy() AG3.config.panel.num_pixels = [1,2] self.assertFalse(AG == AG3) AG3 = AG2.copy() AG3.config.channels.channel_labels = ['d','b','c','d'] self.assertFalse(AG == AG3) AG3 = AG2.copy() AG3.config.angles.angle_unit ='radian' self.assertFalse(AG == AG3) AG3 = AG2.copy() AG3.config.angles.angle_data[0] = -1 self.assertFalse(AG == AG3)
def test_get_centre_slice(self): #returns the 2D version AG = AcquisitionGeometry.create_Parallel3D() AG2 = AcquisitionGeometry.create_Parallel2D() cs = AG.config.system.get_centre_slice() self.assertEqual(cs, AG2.config.system) #returns the 2D version AG = AcquisitionGeometry.create_Parallel3D( rotation_axis_direction=[-1, 0, 1], detector_direction_x=[1, 0, 1], detector_direction_y=[-1, 0, 1]) AG2 = AcquisitionGeometry.create_Parallel2D() cs = AG.config.system.get_centre_slice() self.assertEqual(cs, AG2.config.system) #raise error if cannot extract a cnetre slice AG = AcquisitionGeometry.create_Parallel3D(ray_direction=[0, 1, 1]) with self.assertRaises(ValueError): cs = AG.config.system.get_centre_slice() AG = AcquisitionGeometry.create_Parallel3D( detector_direction_x=[1, 0, 1], detector_direction_y=[-1, 0, 1]) with self.assertRaises(ValueError): cs = AG.config.system.get_centre_slice()
def test_system_description(self): AG = AcquisitionGeometry.create_Parallel3D() self.assertTrue(AG.system_description == 'simple') AG = AcquisitionGeometry.create_Parallel3D( detector_position=[5, 0, 0], rotation_axis_position=[5, 0, 0]) self.assertTrue(AG.system_description == 'simple') AG = AcquisitionGeometry.create_Parallel3D( rotation_axis_position=[5, 0, 0]) self.assertTrue(AG.system_description == 'offset') AG = AcquisitionGeometry.create_Parallel3D(ray_direction=[1, 1, 0]) self.assertTrue(AG.system_description == 'advanced')
def setUp(self): #%% Setup Geometry voxel_num_xy = 16 voxel_num_z = 4 pix_size = 0.2 det_pix_x = voxel_num_xy det_pix_y = voxel_num_z num_projections = 36 angles = np.linspace(0, 360, num=num_projections, endpoint=False) self.ag = AcquisitionGeometry.create_Parallel2D()\ .set_angles(angles)\ .set_panel(det_pix_x, pix_size)\ .set_labels(['angle','horizontal']) self.ig = self.ag.get_ImageGeometry() self.ag3D = AcquisitionGeometry.create_Parallel3D()\ .set_angles(angles)\ .set_panel((det_pix_x,det_pix_y), (pix_size,pix_size))\ .set_labels(['angle','vertical','horizontal']) self.ig3D = self.ag3D.get_ImageGeometry() self.ad3D = self.ag3D.allocate('random') self.ig3D = self.ag3D.get_ImageGeometry()
def test_fill_dimension_AcquisitionData(self): ag = AcquisitionGeometry.create_Parallel3D() ag.set_channels(4) ag.set_panel([2,3]) ag.set_angles([0,1,2,3,5]) ag.set_labels(('horizontal','angle','vertical','channel')) u = ag.allocate(0) a = numpy.ones((4,2)) # default_labels = [ImageGeometry.VERTICAL, ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] data = u.as_array() axis_number = u.get_dimension_axis('horizontal_y') u.fill(a, horizontal_y=0) numpy.testing.assert_array_equal(u.subset(horizontal_y=0).as_array(), a) u.fill(2, horizontal_y=1) numpy.testing.assert_array_equal(u.subset(horizontal_y=0).as_array(), 2 * a) u.fill(2, horizontal_y=1) numpy.testing.assert_array_equal(u.subset(horizontal_y=1).as_array(), 2 * a) b = u.subset(horizontal_y=2) b.fill(3) u.fill(b, horizontal_y=2) numpy.testing.assert_array_equal(u.subset(horizontal_y=2).as_array(), 3 * a) # slice with 2 axis a = numpy.ones((2,)) u.fill(a, horizontal_y=1, vertical=0) numpy.testing.assert_array_equal(u.subset(horizontal_y=1, vertical=0).as_array(), a)
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_fill_dimension_AcquisitionData(self): ag = AcquisitionGeometry.create_Parallel3D() ag.set_channels(4) ag.set_panel([2,3]) ag.set_angles([0,1,2,3,5]) ag.set_labels(('horizontal','angle','vertical','channel')) u = ag.allocate(0) print (u.shape) # (2, 5, 3, 4) a = numpy.ones((2,5)) # default_labels = [ImageGeometry.VERTICAL, ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] b = u.subset(channel=0, vertical=0) print(b.shape) data = u.as_array() u.fill(a, channel=0, vertical=0) print(u.shape) numpy.testing.assert_array_equal(u.subset(channel=0, vertical=0).as_array(), a) u.fill(2, channel=0, vertical=0) numpy.testing.assert_array_equal(u.subset(channel=0, vertical=0).as_array(), 2 * a) u.fill(2, channel=0, vertical=0) numpy.testing.assert_array_equal(u.subset(channel=0, vertical=0).as_array(), 2 * a) b = u.subset(channel=0, vertical=0) b.fill(3) u.fill(b, channel=1, vertical=1) numpy.testing.assert_array_equal(u.subset(channel=1, vertical=1).as_array(), 3 * a)
def test_AcquisitionData(self): ag = AcquisitionGeometry.create_Parallel3D().set_panel( [5, 4]).set_angles([0, 1, 2]).set_channels(2).set_labels( ['channel', 'angle', 'vertical', 'horizontal']) data = ag.allocate(None) data_new = data.get_slice(angle=2) self.assertEquals(data_new.shape, (2, 4, 5)) self.assertEquals(data_new.geometry.dimension_labels, ('channel', 'vertical', 'horizontal')) #won't return a geometry for un-reconstructable slice ag = AcquisitionGeometry.create_Cone3D( [0, -200, 0], [0, 200, 0]).set_panel([5, 4]).set_angles( [0, 1, 2]).set_channels(2).set_labels( ['channel', 'angle', 'vertical', 'horizontal']) data = ag.allocate('random') data_new = data.get_slice(vertical=1, force=True) self.assertEquals(data_new.shape, (2, 3, 5)) self.assertTrue(isinstance(data_new, (DataContainer))) self.assertIsNone(data_new.geometry) self.assertEquals(data_new.dimension_labels, ('channel', 'angle', 'horizontal')) #if 'centre' is between pixels interpolates data_new = data.get_slice(vertical='centre') self.assertEquals(data_new.shape, (2, 3, 5)) self.assertEquals(data_new.geometry.dimension_labels, ('channel', 'angle', 'horizontal')) numpy.testing.assert_allclose( data_new.array, (data.array[:, :, 1, :] + data.array[:, :, 2, :]) / 2)
def setUp(self): N = 128 angles = np.linspace(0, np.pi, 180, dtype='float32') ag = AcquisitionGeometry.create_Parallel2D()\ .set_angles(angles, angle_unit='radian')\ .set_panel(N, 0.1)\ .set_labels(['angle', 'horizontal']) ig = ag.get_ImageGeometry() ag3 = AcquisitionGeometry.create_Parallel3D()\ .set_angles(angles, angle_unit='radian')\ .set_panel((N, N), (0.1, 0.1))\ .set_labels(['vertical', 'angle', 'horizontal']) ig3 = ag3.get_ImageGeometry() self.ig = ig self.ag = ag self.ig3 = ig3 self.ag3 = ag3 self.norm = 14.85
def test_align_reference_frame_tigre(self): ag = AcquisitionGeometry.create_Parallel3D( ray_direction=[0, -1, 0], detector_position=[0., -100., 0], rotation_axis_position=[10., 5., 0], rotation_axis_direction=[0, 0, -1]) ag.config.system.align_reference_frame('tigre') numpy.testing.assert_allclose(ag.config.system.ray.direction, [0, 1, 0], rtol=1E-6) numpy.testing.assert_allclose(ag.config.system.detector.position, [-10, 105, 0], rtol=1E-6) numpy.testing.assert_allclose(ag.config.system.detector.direction_x, [1, 0, 0], rtol=1E-6) numpy.testing.assert_allclose(ag.config.system.detector.direction_y, [0, 0, -1], rtol=1E-6) numpy.testing.assert_allclose(ag.config.system.rotation_axis.position, [0, 0, 0], rtol=1E-6) numpy.testing.assert_allclose(ag.config.system.rotation_axis.direction, [0, 0, 1], rtol=1E-6)
def test_get_ImageGeometry(self): AG = AcquisitionGeometry.create_Parallel2D()\ .set_panel(num_pixels=[512,1],pixel_size=[0.1,0.1]) IG = AG.get_ImageGeometry() IG_gold = ImageGeometry(512,512,0,0.1,0.1,1,0,0,0,1) self.assertEqual(IG, IG_gold) AG = AcquisitionGeometry.create_Parallel3D()\ .set_panel(num_pixels=[512,3],pixel_size=[0.1,0.2]) IG = AG.get_ImageGeometry() IG_gold = ImageGeometry(512,512,3,0.1,0.1,0.2,0,0,0,1) self.assertEqual(IG, IG_gold) AG = AcquisitionGeometry.create_Cone2D(source_position=[0,-500], detector_position=[0.,500.])\ .set_panel(num_pixels=[512,1],pixel_size=[0.1,0.2]) IG = AG.get_ImageGeometry() IG_gold = ImageGeometry(512,512,0,0.05,0.05,1,0,0,0,1) self.assertEqual(IG, IG_gold) AG = AcquisitionGeometry.create_Cone3D(source_position=[0,-500,0], detector_position=[0.,500.,0])\ .set_panel(num_pixels=[512,3],pixel_size=[0.1,0.2]) IG = AG.get_ImageGeometry() IG_gold = ImageGeometry(512,512,3,0.05,0.05,0.1,0,0,0,1) self.assertEqual(IG, IG_gold) AG = AcquisitionGeometry.create_Cone3D(source_position=[0,-500,0], detector_position=[0.,500.,0])\ .set_panel(num_pixels=[512,3],pixel_size=[0.1,0.2]) IG = AG.get_ImageGeometry(resolution=0.5) IG_gold = ImageGeometry(256,256,2,0.025,0.025,0.05,0,0,0,1) self.assertEqual(IG, IG_gold)
def test_filtering(self): ag = AcquisitionGeometry.create_Parallel3D()\ .set_panel([64,3],[0.1,0.1])\ .set_angles([0,90]) ad = ag.allocate('random', seed=0) reconstructor = FBP(ad) out1 = ad.copy() reconstructor._pre_filtering(out1) #by hand filter = reconstructor.get_filter_array() reconstructor._calculate_weights(ag) pad0 = (len(filter) - ag.pixel_num_h) // 2 pad1 = len(filter) - ag.pixel_num_h - pad0 out2 = ad.array.copy() out2 *= reconstructor._weights for i in range(2): proj_padded = np.zeros((ag.pixel_num_v, len(filter))) proj_padded[:, pad0:-pad1] = out2[i] filtered_proj = fft(proj_padded, axis=-1) filtered_proj *= filter filtered_proj = ifft(filtered_proj, axis=-1) out2[i] = np.real(filtered_proj)[:, pad0:-pad1] diff = (out1 - out2).abs().max() self.assertLess(diff, 1e-5)
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 test_get_centre_slice(self): AG = AcquisitionGeometry.create_Parallel3D(detector_direction_y=[0,1,1]) AG.set_panel([1000,2000],[1,1]) AG_cs = AG.get_centre_slice() AG2 = AcquisitionGeometry.create_Parallel2D() AG2.set_panel([1000,1],[1,math.sqrt(0.5)]) self.assertEqual(AG2, AG_cs)
def test_copy(self): AG = AcquisitionGeometry.create_Parallel3D() AG.set_channels(4) AG.set_panel([2,3]) AG.set_angles([0,1,2,3,5]) AG.set_labels(('horizontal','angle','vertical','channel')) AG2 = AG.copy() self.assertEqual(AG2, AG)
def test_AcquisitionData(self): ag = AcquisitionGeometry.create_Parallel3D().set_panel( [5, 4]).set_angles([0, 1, 2]).set_channels(2).set_labels( ['channel', 'angle', 'vertical', 'horizontal']) data = ag.allocate(None) new_order = ['horizontal', 'vertical', 'angle', 'channel'] data.reorder(new_order) self.assertEquals(data.shape, (5, 4, 3, 2)) self.assertEquals(data.geometry.dimension_labels, tuple(new_order))
def test_update_reference_frame(self): #translate origin AG = AcquisitionGeometry.create_Parallel3D(detector_position=[0.,1000.,0], rotation_axis_position=[5.,2.,4.]) AG.config.system.update_reference_frame() numpy.testing.assert_allclose(AG.config.system.ray.direction, [0,1,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.position, [-5,998,-4], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_x, [1,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.position, [0,0,0], rtol=1E-6) #align Z axis with rotate axis AG = AcquisitionGeometry.create_Parallel3D(detector_position=[0.,1000.,0], rotation_axis_position=[0.,0.,0.], rotation_axis_direction=[0,1,0]) AG.config.system.update_reference_frame() numpy.testing.assert_allclose(AG.config.system.ray.direction, [0,0,1], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.position, [0,0,1000], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_x, [1,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_y, [0,-1,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.position, [0,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.direction, [0,0,1], rtol=1E-6)
def test_allocate(self): AG = AcquisitionGeometry.create_Parallel3D() AG.set_channels(4) AG.set_panel([2,3]) AG.set_angles([0,1,2,3,5]) AG.set_labels(('horizontal','angle','vertical','channel')) test = AG.allocate() test2 = numpy.ndarray([2,5,3,4]) self.assertEqual(test.shape, test2.shape)
def test_read_as_AcquisitionData1(self): ag = AcquisitionGeometry.create_Parallel3D() ag.set_panel([10, 11]) ag.set_angles([i for i in range(12)]) ag.set_channels(3) print(ag.shape) # print (glob.glob(os.path.join(self.data_dir, '*'))) reader = TIFFStackReader(file_name=self.data_dir) acq = reader.read_as_AcquisitionData(ag) np.testing.assert_array_equal(acq.as_array(), self.data.as_array())
def test_AcquisitionData_fortigre(self): ag = AcquisitionGeometry.create_Parallel3D().set_panel( [5, 4]).set_angles([0, 1, 2]).set_channels(2).set_labels( ['horizontal', 'vertical', 'angle', 'channel']) data = ag.allocate(None) data.reorder('tigre') self.assertTrue( list(data.dimension_labels) == ['channel', 'angle', 'vertical', 'horizontal']) self.assertTrue(data.shape == (2, 3, 4, 5))
def setUp(self): #%% Setup Geometry voxel_num_xy = 255 voxel_num_z = 15 self.cs_ind = (voxel_num_z-1)//2 src_to_obj = 500 src_to_det = src_to_obj pix_size = 0.2 det_pix_x = voxel_num_xy det_pix_y = voxel_num_z num_projections = 360 angles = np.linspace(0, 2*np.pi, num=num_projections, endpoint=False) self.ag_cone = AcquisitionGeometry.create_Cone3D([0,-src_to_obj,0],[0,src_to_det-src_to_obj,0])\ .set_angles(angles, angle_unit='radian')\ .set_panel((det_pix_x,det_pix_y), (pix_size,pix_size))\ .set_labels(['vertical','angle','horizontal']) self.ag_parallel = AcquisitionGeometry.create_Parallel3D()\ .set_angles(angles, angle_unit='radian')\ .set_panel((det_pix_x,det_pix_y), (pix_size,pix_size))\ .set_labels(['vertical','angle','horizontal']) self.ig_3D = self.ag_parallel.get_ImageGeometry() #%% Create phantom kernel_size = voxel_num_xy kernel_radius = (kernel_size - 1) // 2 y, x = np.ogrid[-kernel_radius:kernel_radius+1, -kernel_radius:kernel_radius+1] circle1 = [5,0,0] #r,x,y dist1 = ((x - circle1[1])**2 + (y - circle1[2])**2)**0.5 circle2 = [5,100,0] #r,x,y dist2 = ((x - circle2[1])**2 + (y - circle2[2])**2)**0.5 circle3 = [25,0,100] #r,x,y dist3 = ((x - circle3[1])**2 + (y - circle3[2])**2)**0.5 mask1 =(dist1 - circle1[0]).clip(0,1) mask2 =(dist2 - circle2[0]).clip(0,1) mask3 =(dist3 - circle3[0]).clip(0,1) phantom = 1 - np.logical_and(np.logical_and(mask1, mask2),mask3) self.golden_data = self.ig_3D.allocate(0) for i in range(4): self.golden_data.fill(array=phantom, vertical=7+i) self.golden_data_cs = self.golden_data.subset(vertical=self.cs_ind)
def test_SystemConfiguration(self): #SystemConfiguration error handeling AG = AcquisitionGeometry.create_Parallel3D() #vector wrong length with self.assertRaises(ValueError): AG.config.system.detector.position = [-0.1,0.1] #detector xs and yumns should be perpendicular with self.assertRaises(ValueError): AG.config.system.detector.set_direction([1,0,0],[-0.1,0.1,1])
def test_read_as_AcquisitionData2(self): # with this data will be scrambled but reshape is possible ag = AcquisitionGeometry.create_Parallel3D() ag.set_panel([11, 10]) ag.set_angles([i for i in range(12)]) ag.set_channels(3) reader = TIFFStackReader(file_name=self.data_dir) acq = reader.read_as_AcquisitionData(ag) np.testing.assert_array_equal(acq.as_array().flatten(), self.data.as_array().flatten())
def test_read_as_AcquisitionData_Exceptions1(self): ag = AcquisitionGeometry.create_Parallel3D() ag.set_panel([11, 12]) ag.set_angles([i for i in range(12)]) ag.set_channels(3) reader = TIFFStackReader(file_name=self.data_dir) try: acq = reader.read_as_AcquisitionData(ag) assert False except ValueError as ve: print(ve) assert True
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 setUp(self): self.acq_data = dataexample.SIMULATED_PARALLEL_BEAM_DATA.get() self.img_data = dataexample.SIMULATED_SPHERE_VOLUME.get() self.acq_data = np.log(self.acq_data) self.acq_data *= -1.0 self.ig = self.img_data.geometry self.ag = self.acq_data.geometry self.ag_small = AcquisitionGeometry.create_Parallel3D() self.ag_small.set_panel((16, 16)) self.ag_small.set_angles([0])
def test_weights(self): ag = AcquisitionGeometry.create_Parallel3D()\ .set_panel([3,4],[0.1,0.2])\ .set_angles([0,90]) ad = ag.allocate(0) reconstructor = FBP(ad) reconstructor._calculate_weights(ag) weights = reconstructor._weights scaling = (2 * np.pi / ag.num_projections) / (4 * ag.pixel_size_h) weights_new = np.ones_like(weights) * scaling np.testing.assert_allclose(weights, weights_new)
def test_create_Parallel3D(self): #default AG = AcquisitionGeometry.create_Parallel3D() numpy.testing.assert_allclose(AG.config.system.ray.direction, [0,1,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.position, [0,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_x, [1,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_y, [0,0,1], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.position, [0,0,0], rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.direction, [0,0,1], rtol=1E-6) #values ray_direction = [0.1, 3.0, 0.2] detector_position = [-1.3,1000.0, -1.0] detector_direction_x = [1,0.2, 0] detector_direction_y = [0.0,0,1] rotation_axis_position=[0.1, 2,-0.4] rotation_axis_direction=[-0.1,-0.3,1] AG = AcquisitionGeometry.create_Parallel3D(ray_direction, detector_position, detector_direction_x,detector_direction_y, rotation_axis_position,rotation_axis_direction) ray_direction = numpy.asarray(ray_direction) detector_direction_x = numpy.asarray(detector_direction_x) detector_direction_y = numpy.asarray(detector_direction_y) rotation_axis_direction = numpy.asarray(rotation_axis_direction) ray_direction /= numpy.sqrt((ray_direction**2).sum()) detector_direction_x /= numpy.sqrt((detector_direction_x**2).sum()) detector_direction_y /= numpy.sqrt((detector_direction_y**2).sum()) rotation_axis_direction /= numpy.sqrt((rotation_axis_direction**2).sum()) numpy.testing.assert_allclose(AG.config.system.ray.direction, ray_direction, rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.position, detector_position, rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_x, detector_direction_x, rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.detector.direction_y, detector_direction_y, rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.position, rotation_axis_position, rtol=1E-6) numpy.testing.assert_allclose(AG.config.system.rotation_axis.direction, rotation_axis_direction, rtol=1E-6)
def test_set_panel(self): AG = AcquisitionGeometry.create_Parallel3D() #default AG.set_panel([1000,2000]) self.assertEqual(AG.config.panel.num_pixels, [1000,2000]) self.assertEqual(AG.config.panel.pixel_size, [1.,1.]) #values AG.set_panel([1000,2000],[0.1,0.2]) self.assertEqual(AG.config.panel.num_pixels, [1000,2000]) self.assertEqual(AG.config.panel.pixel_size, [0.1,0.2]) #set 2D panel with 3D geometry with self.assertRaises(ValueError): AG.config.panel.num_pixels = [5]
def test_set_labels(self): AG = AcquisitionGeometry.create_Parallel3D() AG.set_channels(4) AG.set_panel([2,3]) AG.set_angles([0,1,2,3,5]) #default self.assertEqual(AG.dimension_labels, ('channel','angle','vertical','horizontal')) self.assertEqual(AG.shape, (4,5,3,2)) #values AG.set_angles([0]) AG.set_labels(('horizontal','channel','vertical')) self.assertEqual(AG.dimension_labels, ('horizontal','channel','vertical')) self.assertEqual(AG.shape, (2,4,3))