savu.plugins.simulation.tomo_phantom.TomoPhantom.pre_process() - Code Metrics - Inspection of "updates to tomophantom plugin" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Pull Request — master (#734)

by Daniil

created 2021-04-13 20:17 UTC

savu.plugins.simulation.tomo_phantom.TomoPhantom.pre_process() A

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cc	1
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# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
.. module:: A wrapper for TomoPhantom software
   :platform: Unix
   :synopsis: TomoPhantom package provides an access to simulated phantom libraries and projection data 2D/3D

.. moduleauthor:: Daniil Kazantsev <[email protected]>
"""

import savu.plugins.utils as pu
from savu.plugins.plugin import Plugin
from savu.plugins.driver.cpu_plugin import CpuPlugin
from savu.plugins.utils import register_plugin

import tomophantom
from tomophantom import TomoP2D, TomoP3D
from tomophantom.supp.artifacts import _Artifacts_
import os
from savu.data.plugin_list import CitationInformation
import numpy as np

@register_plugin
class TomoPhantom(Plugin, CpuPlugin):
    """
    A plugin for TomoPhantom software which generates synthetic phantoms and \
    projection data (2D from Phantom2DLibrary.dat and 3D from Phantom3DLibrary.dat)

    :param geom_model: Select a model (integer) from the library (see TomoPhantom files). Default: 1.
    :param geom_model_size: Set the size of the phantom. Default: 256.
    :param geom_projections_total: The total number of projections. Default: 360.
    :param geom_detectors_horiz: The size of _horizontal_ detectors. Default: 300.
    :param artifacts_noise_type: Set the noise type, Poisson or Gaussian. Default: 'Poisson'.
    :param artifacts_noise_sigma: Define noise amplitude. Default: 5000.
    :param artifacts_misalignment_maxamplitude: Incorporate misalignment into projections (in pixels). Default: None.
    :param artifacts_zingers_percentage: add broken pixels to projections, e.g. 0.25. Default: None.
    :param artifacts_stripes_percentage: the amount of stripes in the data, e.g. 1.0. Default: None.
    :param artifacts_stripes_maxthickness: defines the maximal thickness of a stripe. Default: 3.0.
    :param artifacts_stripes_intensity: to incorporate the change of intensity in the stripe. Default: 0.3.
    :param artifacts_stripes_type: set the stripe type between full and partial. Default: 'full'.
    :param artifacts_stripes_variability: the intensity variability of a stripe. Default:  0.007.
    :param out_datasets: Default out dataset names. Default: ['tomo', 'model']
    """

    def __init__(self):
        super(TomoPhantom, self).__init__('TomoPhantom')

    def get_max_frames(self):
        return 'single'

    def nInput_datasets(self):
        return 1

    def nOutput_datasets(self):
        return 2

    def map_volume_dimensions(self, data):
        data._finalise_patterns()
        dim_rotAngle = data.get_data_patterns()['PROJECTION']['main_dir']
        sinogram = data.get_data_patterns()['SINOGRAM']
        dim_detY = sinogram['main_dir']

        core_dirs = sinogram['core_dims']
        dim_detX = list(set(core_dirs).difference(set((dim_rotAngle,))))[0]

        dim_volX = dim_rotAngle
        dim_volY = dim_detY
        dim_volZ = dim_detX
        return dim_volX, dim_volY, dim_volZ

    def setup(self):
        in_dataset, self.out_dataset = self.get_datasets()
        in_pData, self.out_pData = self.get_plugin_datasets()
        in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())

        [self.out_shape_sino, out_shape_phantom] = self.new_shape(in_dataset[0].get_shape(), in_dataset[0])
        self.out_dataset[0].create_dataset(patterns=in_dataset[0],
                                           axis_labels=in_dataset[0],
                                           shape=self.out_shape_sino)
        self.out_pData[0].plugin_data_setup('SINOGRAM',self.get_max_frames())

        dim_volX, dim_volY, dim_volZ = \
            self.map_volume_dimensions(in_dataset[0])

        axis_labels = [0]*3
        axis_labels = {in_dataset[0]:
                       [str(dim_volX) + '.voxel_x.voxels',
                        str(dim_volY) + '.voxel_y.voxels',
                        str(dim_volZ) + '.voxel_z.voxels']}

        self.out_dataset[1].create_dataset(axis_labels=axis_labels,
                                           shape=out_shape_phantom)
        self.out_dataset[1].add_volume_patterns(dim_volX, dim_volY, dim_volZ)

        self.out_pData[1].plugin_data_setup('VOLUME_XZ', self.get_max_frames())

        self.angles = np.linspace(0.0,179.999,self.parameters['geom_projections_total'],dtype='float32')
        self.out_dataset[0].meta_data.set('rotation_angle', self.angles)

    def new_shape(self, full_shape, data):
        # calculate a new output data shape based on the input data shape
        core_dirs = data.get_core_dimensions()
        new_shape_sino = list(full_shape)
        new_shape_phantom = list(full_shape)
        new_shape_sino= (self.parameters['geom_projections_total'], new_shape_sino[1], self.parameters['geom_detectors_horiz'])
        for dim in core_dirs:
            new_shape_phantom[dim] = self.parameters['geom_model_size']
        return [tuple(new_shape_sino), tuple(new_shape_phantom)]

    def pre_process(self):
        # set parameters for TomoPhantom:
        self.model = self.parameters['geom_model']
        self.dims = self.parameters['geom_model_size']
        self.proj_num = self.parameters['geom_projections_total']
        self.detectors_num = self.parameters['geom_detectors_horiz']
        path = os.path.dirname(tomophantom.__file__)
        self.path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
        self.path_library3D = os.path.join(path, "Phantom3DLibrary.dat")
        #print "The full data shape is", self.get_in_datasets()[0].get_shape()

    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)
            # forming dictionaries with different artifact types and noise
            _noise_ =  {'noise_type' : self.parameters['artifacts_noise_type'],
                        'noise_sigma' : self.parameters['artifacts_noise_sigma'],
                        'noise_seed' : 0}
            # misalignment dictionary
            _sinoshifts_ = {}
            if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
                _sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']}

            # adding zingers and stripes
            _zingers_ = {}
            if self.parameters['artifacts_zingers_percentage'] is not None:
                _zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage',
                             'zingers_modulus' : 10}

            _stripes_ = {}
            if self.parameters['artifacts_stripes_percentage'] is not None:
                _stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'],
                             'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'],
                             'stripes_intensity' : self.parameters['artifacts_stripes_intensity'],
                             'stripes_type' : self.parameters['artifacts_stripes_type'],
                             'stripes_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)
            # forming dictionaries with different artifact types and noise
            _noise_ =  {'noise_type' : self.parameters['artifacts_noise_type'],
                        'noise_sigma' : self.parameters['artifacts_noise_sigma'],
                        'noise_seed' : 0}
            # misalignment dictionary
            _sinoshifts_ = {}
            if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
                _sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']}

            # adding zingers and stripes
            _zingers_ = {}
            if self.parameters['artifacts_zingers_percentage'] is not None:
                _zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage',
                             'zingers_modulus' : 10}
            _stripes_ = {}
            if self.parameters['artifacts_stripes_percentage'] is not None:
                _stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'],
                             'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'],
                             'stripes_intensity' : self.parameters['artifacts_stripes_intensity'],
                             'stripes_type' : self.parameters['artifacts_stripes_type'],
                             'stripes_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]

    def get_citation_information(self):
        cite_info1 = CitationInformation()
        cite_info1.name = 'citation1'
        cite_info1.description = \
            ("TomoPhantom is a software package to generate 2D-4D analytical phantoms and their Radon transforms for various testing purposes.")
        cite_info1.bibtex = \
            ("@article{kazantsevTP2018,\n" +
             "title={TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks},\n" +
             "author={Daniil and Kazantsev, Valery and Pickalov, Srikanth and Nagella, Edoardo and Pasca, Philip and Withers},\n" +
             "journal={Software X},\n" +
             "volume={7},\n" +
             "number={--},\n" +
             "pages={150--155},\n" +
             "year={2018},\n" +
             "publisher={Elsevier}\n" +
             "}")
        cite_info1.endnote = \
            ("%0 Journal Article\n" +
             "%T TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks\n" +
             "%A Kazantsev, Daniil\n" +
             "%A Pickalov, Valery\n" +
             "%A Nagella, Srikanth\n" +
             "%A Pasca, Edoardo\n" +
             "%A Withers, Philip\n" +
             "%J Software X\n" +
             "%V 7\n" +
             "%N --\n" +
             "%P 150--155\n" +
             "%@ --\n" +
             "%D 2018\n" +
             "%I Elsevier\n")
        cite_info1.doi = "doi:10.1016/j.softx.2018.05.003"
        return [cite_info1]


1			# Copyright 2014 Diamond Light Source Ltd.
2			#
3			# Licensed under the Apache License, Version 2.0 (the "License");
4			# you may not use this file except in compliance with the License.
5			# You may obtain a copy of the License at
6			#
7			# http://www.apache.org/licenses/LICENSE-2.0
8			#
9			# Unless required by applicable law or agreed to in writing, software
10			# distributed under the License is distributed on an "AS IS" BASIS,
11			# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12			# See the License for the specific language governing permissions and
13			# limitations under the License.
14
15			"""
16			.. module:: A wrapper for TomoPhantom software
17			:platform: Unix
18			:synopsis: TomoPhantom package provides an access to simulated phantom libraries and projection data 2D/3D
19
20			.. moduleauthor:: Daniil Kazantsev <[email protected]>
21			"""
22
23			import savu.plugins.utils as pu
24			from savu.plugins.plugin import Plugin
25			from savu.plugins.driver.cpu_plugin import CpuPlugin
26			from savu.plugins.utils import register_plugin
27
28			import tomophantom
29			from tomophantom import TomoP2D, TomoP3D
30			from tomophantom.supp.artifacts import _Artifacts_
31			import os
32			from savu.data.plugin_list import CitationInformation
33			import numpy as np
34
35			@register_plugin
36			class TomoPhantom(Plugin, CpuPlugin):
37			"""
38			A plugin for TomoPhantom software which generates synthetic phantoms and \
39			projection data (2D from Phantom2DLibrary.dat and 3D from Phantom3DLibrary.dat)
40
41			:param geom_model: Select a model (integer) from the library (see TomoPhantom files). Default: 1.
42			:param geom_model_size: Set the size of the phantom. Default: 256.
43			:param geom_projections_total: The total number of projections. Default: 360.
44			:param geom_detectors_horiz: The size of _horizontal_ detectors. Default: 300.
45			:param artifacts_noise_type: Set the noise type, Poisson or Gaussian. Default: 'Poisson'.
46			:param artifacts_noise_sigma: Define noise amplitude. Default: 5000.
47			:param artifacts_misalignment_maxamplitude: Incorporate misalignment into projections (in pixels). Default: None.
48			:param artifacts_zingers_percentage: add broken pixels to projections, e.g. 0.25. Default: None.
49			:param artifacts_stripes_percentage: the amount of stripes in the data, e.g. 1.0. Default: None.
50			:param artifacts_stripes_maxthickness: defines the maximal thickness of a stripe. Default: 3.0.
51			:param artifacts_stripes_intensity: to incorporate the change of intensity in the stripe. Default: 0.3.
52			:param artifacts_stripes_type: set the stripe type between full and partial. Default: 'full'.
53			:param artifacts_stripes_variability: the intensity variability of a stripe. Default: 0.007.
54			:param out_datasets: Default out dataset names. Default: ['tomo', 'model']
55			"""
56
57			def __init__(self):
58			super(TomoPhantom, self).__init__('TomoPhantom')
59
60			def get_max_frames(self):
61			return 'single'
62
63			def nInput_datasets(self):
64			return 1
65
66			def nOutput_datasets(self):
67			return 2
68
69			def map_volume_dimensions(self, data):
70			data._finalise_patterns()
71			dim_rotAngle = data.get_data_patterns()['PROJECTION']['main_dir']
72			sinogram = data.get_data_patterns()['SINOGRAM']
73			dim_detY = sinogram['main_dir']
74
75			core_dirs = sinogram['core_dims']
76			dim_detX = list(set(core_dirs).difference(set((dim_rotAngle,))))[0]
77
78			dim_volX = dim_rotAngle
79			dim_volY = dim_detY
80			dim_volZ = dim_detX
81			return dim_volX, dim_volY, dim_volZ
82
83			def setup(self):
84			in_dataset, self.out_dataset = self.get_datasets()
85			in_pData, self.out_pData = self.get_plugin_datasets()
86			in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames())
87
88			[self.out_shape_sino, out_shape_phantom] = self.new_shape(in_dataset[0].get_shape(), in_dataset[0])
89			self.out_dataset[0].create_dataset(patterns=in_dataset[0],
90			axis_labels=in_dataset[0],
91			shape=self.out_shape_sino)
92			self.out_pData[0].plugin_data_setup('SINOGRAM',self.get_max_frames())
93
94			dim_volX, dim_volY, dim_volZ = \
95			self.map_volume_dimensions(in_dataset[0])
96
97			axis_labels = [0]*3
98			axis_labels = {in_dataset[0]:
99			[str(dim_volX) + '.voxel_x.voxels',
100			str(dim_volY) + '.voxel_y.voxels',
101			str(dim_volZ) + '.voxel_z.voxels']}
102
103			self.out_dataset[1].create_dataset(axis_labels=axis_labels,
104			shape=out_shape_phantom)
105			self.out_dataset[1].add_volume_patterns(dim_volX, dim_volY, dim_volZ)
106
107			self.out_pData[1].plugin_data_setup('VOLUME_XZ', self.get_max_frames())
108
109			self.angles = np.linspace(0.0,179.999,self.parameters['geom_projections_total'],dtype='float32')
110			self.out_dataset[0].meta_data.set('rotation_angle', self.angles)
111
112			def new_shape(self, full_shape, data):
113			# calculate a new output data shape based on the input data shape
114			core_dirs = data.get_core_dimensions()
115			new_shape_sino = list(full_shape)
116			new_shape_phantom = list(full_shape)
117			new_shape_sino= (self.parameters['geom_projections_total'], new_shape_sino[1], self.parameters['geom_detectors_horiz'])
118			for dim in core_dirs:
119			new_shape_phantom[dim] = self.parameters['geom_model_size']
120			return [tuple(new_shape_sino), tuple(new_shape_phantom)]
121
122			def pre_process(self):
123			# set parameters for TomoPhantom:
124			self.model = self.parameters['geom_model']
125			self.dims = self.parameters['geom_model_size']
126			self.proj_num = self.parameters['geom_projections_total']
127			self.detectors_num = self.parameters['geom_detectors_horiz']
128			path = os.path.dirname(tomophantom.__file__)
129			self.path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
130			self.path_library3D = os.path.join(path, "Phantom3DLibrary.dat")
131			#print "The full data shape is", self.get_in_datasets()[0].get_shape()
132
133			def process_frames(self, data):
134			# print "The input data shape is", data[0].shape
135			if (self.out_shape_sino[1] == 1):
136			# create a 2D phantom
137			model = TomoP2D.Model(self.model, self.dims, self.path_library2D)
138			# create a 2D sinogram
139			projdata_clean = TomoP2D.ModelSino(self.model, self.dims, self.detectors_num, self.angles, self.path_library2D)
140			# forming dictionaries with different artifact types and noise
141			_noise_ = {'noise_type' : self.parameters['artifacts_noise_type'],
142			'noise_sigma' : self.parameters['artifacts_noise_sigma'],
143			'noise_seed' : 0}
144			# misalignment dictionary
145			_sinoshifts_ = {}
146			if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
147			_sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']}
148
149			# adding zingers and stripes
150			_zingers_ = {}
151			if self.parameters['artifacts_zingers_percentage'] is not None:
152			_zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage',
153			'zingers_modulus' : 10}
			0 ignored issues – show introduced 2021-04-13 20:20 UTC by Report Bug Copy Issue Report invalid syntax (<unknown>, line 153) Loading history...
154			_stripes_ = {}
155			if self.parameters['artifacts_stripes_percentage'] is not None:
156			_stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'],
157			'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'],
158			'stripes_intensity' : self.parameters['artifacts_stripes_intensity'],
159			'stripes_type' : self.parameters['artifacts_stripes_type'],
160			'stripes_variability' : self.parameters['artifacts_stripes_variability']}
161
162			if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
163			[projdata, shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_)
164			else:
165			projdata = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_)
166			else:
167			# create a 3D phantom
168			frame_idx = self.out_pData[0].get_current_frame_idx()[0]
169			model = TomoP3D.ModelSub(self.model, self.dims, (frame_idx, frame_idx+1), self.path_library3D)
170			model = np.swapaxes(model,0,1)
171			model = np.flipud(model[:,0,:])
172			# create a 3D projection data
173			projdata_clean = TomoP3D.ModelSinoSub(self.model, self.dims, self.detectors_num, self.dims, (frame_idx, frame_idx+1), self.angles, self.path_library3D)
174			# forming dictionaries with different artifact types and noise
175			_noise_ = {'noise_type' : self.parameters['artifacts_noise_type'],
176			'noise_sigma' : self.parameters['artifacts_noise_sigma'],
177			'noise_seed' : 0}
178			# misalignment dictionary
179			_sinoshifts_ = {}
180			if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
181			_sinoshifts_ = {'sinoshifts_maxamplitude' : self.parameters['artifacts_misalignment_maxamplitude']}
182
183			# adding zingers and stripes
184			_zingers_ = {}
185			if self.parameters['artifacts_zingers_percentage'] is not None:
186			_zingers_ = {'zingers_percentage' : self.parameters['artifacts_zingers_percentage',
187			'zingers_modulus' : 10}
188			_stripes_ = {}
189			if self.parameters['artifacts_stripes_percentage'] is not None:
190			_stripes_ = {'stripes_percentage' : self.parameters['artifacts_stripes_percentage'],
191			'stripes_maxthickness' : self.parameters['artifacts_stripes_maxthickness'],
192			'stripes_intensity' : self.parameters['artifacts_stripes_intensity'],
193			'stripes_type' : self.parameters['artifacts_stripes_type'],
194			'stripes_variability' : self.parameters['artifacts_stripes_variability']}
195
196			if self.parameters['artifacts_misalignment_maxamplitude'] is not None:
197			[projdata, shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_)
198			else:
199			projdata = _Artifacts_(projdata_clean, _noise_, _zingers_, _stripes_, _sinoshifts_)
200			projdata = np.swapaxes(projdata,0,1)
201			return [projdata, model]
202
203			def get_citation_information(self):
204			cite_info1 = CitationInformation()
205			cite_info1.name = 'citation1'
206			cite_info1.description = \
207			("TomoPhantom is a software package to generate 2D-4D analytical phantoms and their Radon transforms for various testing purposes.")
208			cite_info1.bibtex = \
209			("@article{kazantsevTP2018,\n" +
210			"title={TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks},\n" +
211			"author={Daniil and Kazantsev, Valery and Pickalov, Srikanth and Nagella, Edoardo and Pasca, Philip and Withers},\n" +
212			"journal={Software X},\n" +
213			"volume={7},\n" +
214			"number={--},\n" +
215			"pages={150--155},\n" +
216			"year={2018},\n" +
217			"publisher={Elsevier}\n" +
218			"}")
219			cite_info1.endnote = \
220			("%0 Journal Article\n" +
221			"%T TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks\n" +
222			"%A Kazantsev, Daniil\n" +
223			"%A Pickalov, Valery\n" +
224			"%A Nagella, Srikanth\n" +
225			"%A Pasca, Edoardo\n" +
226			"%A Withers, Philip\n" +
227			"%J Software X\n" +
228			"%V 7\n" +
229			"%N --\n" +
230			"%P 150--155\n" +
231			"%@ --\n" +
232			"%D 2018\n" +
233			"%I Elsevier\n")
234			cite_info1.doi = "doi:10.1016/j.softx.2018.05.003"
235			return [cite_info1]
236

DiamondLightSource / Savu

Pull Request — master (#734)

savu.plugins.simulation.tomo_phantom.TomoPhantom.pre_process() A

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