# The capability of building a subset of vertical slices out of 3D phantom (faster) import timeit from tomophantom import TomoP3D import matplotlib.pyplot as plt import tomophantom import os import numpy as np print ("Building a subset of 3D phantom using TomoPhantom software") tic=timeit.default_timer() model = 13 N_size = 256 # Define phantom dimensions using a scalar value DIM_z = (0, 150) # selected vertical (z) subset (a slab) of the phantom path = os.path.dirname(tomophantom.__file__) path_library3D = os.path.join(path, "Phantom3DLibrary.dat") phantom_tm = TomoP3D.ModelSub(model, N_size, DIM_z, path_library3D) toc=timeit.default_timer() Run_time = toc - tic print("Phantom has been built in {} seconds".format(Run_time)) sliceSel = 130 #plt.gray() plt.figure(2) plt.subplot(131) plt.imshow(phantom_tm[sliceSel,:,:],vmin=0, vmax=1) plt.title('3D Phantom, axial view') plt.subplot(132) plt.imshow(phantom_tm[:,128,:],vmin=0, vmax=1) plt.title('3D Phantom, coronal view')
def process_frames(self, data): # print "The input data shape is", data[0].shape if (self.out_shape_sino[1] == 1): # create a 2D phantom model = TomoP2D.Model(self.model, self.dims, self.path_library2D) # create a 2D sinogram projdata_clean = TomoP2D.ModelSino(self.model, self.dims, self.detectors_num, self.angles, self.path_library2D) # Adding artifacts and noise # forming dictionaries with artifact types _noise_ = { 'type': self.parameters['artifacts_noise_type'], 'sigma': self.parameters['artifacts_noise_sigma'], 'seed': 0, 'prelog': False } # misalignment dictionary _sinoshifts_ = {} if self.parameters[ 'artifacts_misalignment_maxamplitude'] is not None: _sinoshifts_ = { 'maxamplitude': self.parameters['artifacts_misalignment_maxamplitude'] } # adding zingers and stripes _zingers_ = {} if self.parameters['artifacts_zingers_percentage'] is not None: _zingers_ = { 'percentage': self.parameters['artifacts_zingers_percentage'], 'modulus': 10 } _stripes_ = {} if self.parameters['artifacts_stripes_percentage'] is not None: _stripes_ = { 'percentage': self.parameters['artifacts_stripes_percentage'], 'maxthickness': self.parameters['artifacts_stripes_maxthickness'], 'intensity': self.parameters['artifacts_stripes_intensity'], 'type': self.parameters['artifacts_stripes_type'], 'variability': self.parameters['artifacts_stripes_variability'] } if self.parameters[ 'artifacts_misalignment_maxamplitude'] is not None: [projdata, shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_) else: projdata = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_) else: # create a 3D phantom frame_idx = self.out_pData[0].get_current_frame_idx()[0] model = TomoP3D.ModelSub(self.model, self.dims, (frame_idx, frame_idx + 1), self.path_library3D) model = np.swapaxes(model, 0, 1) model = np.flipud(model[:, 0, :]) # create a 3D projection data projdata_clean = TomoP3D.ModelSinoSub( self.model, self.dims, self.detectors_num, self.dims, (frame_idx, frame_idx + 1), self.angles, self.path_library3D) # Adding artifacts and noise # forming dictionaries with artifact types _noise_ = { 'type': self.parameters['artifacts_noise_type'], 'sigma': self.parameters['artifacts_noise_sigma'], 'seed': 0, 'prelog': False } # misalignment dictionary _sinoshifts_ = {} if self.parameters[ 'artifacts_misalignment_maxamplitude'] is not None: _sinoshifts_ = { 'maxamplitude': self.parameters['artifacts_misalignment_maxamplitude'] } # adding zingers and stripes _zingers_ = {} if self.parameters['artifacts_zingers_percentage'] is not None: _zingers_ = { 'percentage': self.parameters['artifacts_zingers_percentage'], 'modulus': 10 } _stripes_ = {} if self.parameters['artifacts_stripes_percentage'] is not None: _stripes_ = { 'percentage': self.parameters['artifacts_stripes_percentage'], 'maxthickness': self.parameters['artifacts_stripes_maxthickness'], 'intensity': self.parameters['artifacts_stripes_intensity'], 'type': self.parameters['artifacts_stripes_type'], 'variability': self.parameters['artifacts_stripes_variability'] } if self.parameters[ 'artifacts_misalignment_maxamplitude'] is not None: [projdata, shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_) else: projdata = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_) projdata = np.swapaxes(projdata, 0, 1) return [projdata, model]