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))
