def process(self, out=None):
DATA = self.get_input()
pad = False
if len(DATA.shape) == 2:
#for 2D cases
pad = True
data_temp = numpy.expand_dims(DATA.as_array(), axis=0)
else:
data_temp = DATA.as_array()
rec_id, arr_out = astra.create_backprojection3d_gpu(
data_temp, self.proj_geom, self.vol_geom)
astra.data3d.delete(rec_id)
if pad is True:
arr_out = numpy.squeeze(arr_out, axis=0)
if out is None:
out = ImageData(arr_out,
deep_copy=False,
geometry=self.volume_geometry.copy(),
suppress_warning=True)
return out
else:
out.fill(arr_out)
def adjoint(self, x, out=None):
if self.tigre_geom.is2D:
data_temp = np.expand_dims(x.as_array(),axis=1)
arr_out = Atb.Atb(data_temp, self.tigre_geom, self.tigre_angles, krylov=self.method['adjoint'])
arr_out = np.squeeze(arr_out, axis=0)
else:
arr_out = Atb.Atb(x.as_array(), self.tigre_geom, self.tigre_angles, krylov=self.method['adjoint'])
if out is None:
out = ImageData(arr_out, deep_copy=False, geometry=self._domain_geometry.copy(), suppress_warning=True)
return out
else:
out.fill(arr_out)
def process(self, out=None):
DATA = self.get_input()
data_temp = DATA.as_array()
rec_id, arr_out = astra.create_backprojection(data_temp, self.proj_id)
astra.data2d.delete(rec_id)
if out is None:
out = ImageData(arr_out,
deep_copy=False,
geometry=self.volume_geometry.copy(),
suppress_warning=True)
return out
else:
out.fill(arr_out)
def process(self, out=None):
if self.tigre_geom.is2D:
data_temp = np.expand_dims(self.get_input().as_array(), axis=1)
arr_out = fdk(data_temp, self.tigre_geom, self.tigre_angles)
arr_out = np.squeeze(arr_out, axis=0)
else:
arr_out = fdk(self.get_input().as_array(), self.tigre_geom,
self.tigre_angles)
if out is None:
out = ImageData(arr_out,
deep_copy=False,
geometry=self.volume_geometry.copy(),
suppress_warning=True)
return out
else:
out.fill(arr_out)
def process(self, out=None):
# Get DATA
DATA = self.get_input()
pad = False
if len(DATA.shape) == 2:
#for 2D cases
pad = True
data_temp = numpy.expand_dims(DATA.as_array(), axis=0)
else:
data_temp = DATA.as_array()
rec_id = astra.data3d.create('-vol', self.vol_geom_astra)
sinogram_id = astra.data3d.create('-sino', self.proj_geom_astra,
data_temp)
cfg = astra.astra_dict('FDK_CUDA')
cfg['ReconstructionDataId'] = rec_id
cfg['ProjectionDataId'] = sinogram_id
alg_id = astra.algorithm.create(cfg)
astra.algorithm.run(alg_id)
arr_out = astra.data3d.get(rec_id)
astra.data3d.delete(rec_id)
astra.data3d.delete(sinogram_id)
astra.algorithm.delete(alg_id)
if pad == True:
arr_out = numpy.squeeze(arr_out, axis=0)
if out is None:
out = ImageData(arr_out,
deep_copy=False,
geometry=self.volume_geometry.copy(),
suppress_warning=True)
return out
else:
out.fill(arr_out)
def test_BlockDataContainer_fill(self):
ig0 = ImageGeometry(2, 3, 4)
ig1 = ImageGeometry(2, 3, 5)
data0 = ImageData(geometry=ig0)
data1 = ImageData(geometry=ig1) + 1
data2 = ImageData(geometry=ig0) + 2
data3 = ImageData(geometry=ig1) + 3
cp0 = BlockDataContainer(data0, data1)
#cp1 = BlockDataContainer(data2,data3)
cp2 = BlockDataContainer(data0 + 1, data1 + 1)
data0.fill(data2)
self.assertNumpyArrayEqual(data0.as_array(), data2.as_array())
data0 = ImageData(geometry=ig0)
cp0.fill(cp2)
self.assertBlockDataContainerEqual(cp0, cp2)
def adjoint(self, x, out=None):
data = x.as_array()
#if single angle projection add the dimension in for TIGRE
if x.dimension_labels[0] != AcquisitionGeometry.ANGLE:
data = np.expand_dims(data, axis=0)
if self.tigre_geom.is2D:
data = np.expand_dims(data, axis=1)
arr_out = self.__call_Atb(data)
arr_out = np.squeeze(arr_out, axis=0)
else:
arr_out = self.__call_Atb(data)
if out is None:
out = ImageData(arr_out,
deep_copy=False,
geometry=self._domain_geometry.copy(),
suppress_warning=True)
return out
else:
out.fill(arr_out)
def test_BlockDataContainer_fill(self):
print ("test block data container")
ig0 = ImageGeometry(2,3,4)
ig1 = ImageGeometry(2,3,5)
data0 = ImageData(geometry=ig0)
data1 = ImageData(geometry=ig1) + 1
data2 = ImageData(geometry=ig0) + 2
data3 = ImageData(geometry=ig1) + 3
cp0 = BlockDataContainer(data0,data1)
#cp1 = BlockDataContainer(data2,data3)
cp2 = BlockDataContainer(data0+1, data1+1)
data0.fill(data2)
self.assertNumpyArrayEqual(data0.as_array(), data2.as_array())
data0 = ImageData(geometry=ig0)
for el,ot in zip(cp0, cp2):
print (el.shape, ot.shape)
cp0.fill(cp2)
self.assertBlockDataContainerEqual(cp0, cp2)