-
Notifications
You must be signed in to change notification settings - Fork 17
/
msot_invision_simulation.py
217 lines (190 loc) · 10.8 KB
/
msot_invision_simulation.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
# SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
# SPDX-FileCopyrightText: 2021 Janek Groehl
# SPDX-License-Identifier: MIT
from simpa import Tags
import simpa as sp
import numpy as np
from simpa.utils.profiling import profile
from argparse import ArgumentParser
path_manager = sp.PathManager()
def run_msot_invision_simulation(spacing: float | int = 0.5, path_manager=None, visualise: bool = True):
"""
:param spacing: The simulation spacing between voxels
:param path_manager: the path manager to be used, typically sp.PathManager
:param visualise: If VISUALIZE is set to True, the reconstruction result will be plotted
:return: a run through of the example
"""
if path_manager is None:
path_manager = sp.PathManager()
SPEED_OF_SOUND = 1500
XZ_DIM = 90
Y_DIM = 40
def create_pipeline(_settings: sp.Settings):
return [
sp.ModelBasedAdapter(settings),
sp.MCXAdapter(settings),
sp.KWaveAdapter(settings),
sp.FieldOfViewCropping(settings),
sp.TimeReversalAdapter(settings)
]
def get_device():
pa_device = sp.InVision256TF(device_position_mm=np.asarray([XZ_DIM/2, Y_DIM/2, XZ_DIM/2]))
return pa_device
def create_volume():
inclusion_material = sp.Molecule(volume_fraction=1.0,
anisotropy_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
0.9),
scattering_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
100.0),
absorption_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
4.0),
speed_of_sound=SPEED_OF_SOUND,
alpha_coefficient=1e-4,
density=1000,
gruneisen_parameter=1.0,
name="Inclusion")
phantom_material = sp.Molecule(volume_fraction=1.0,
anisotropy_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
0.9),
scattering_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
100.0),
absorption_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(
0.05),
speed_of_sound=SPEED_OF_SOUND,
alpha_coefficient=1e-4,
density=1000,
gruneisen_parameter=1.0,
name="Phantom")
heavy_water = sp.Molecule(volume_fraction=1.0,
anisotropy_spectrum=sp.AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(1.0),
scattering_spectrum=sp.ScatteringSpectrumLibrary.CONSTANT_SCATTERING_ARBITRARY(0.1),
absorption_spectrum=sp.AbsorptionSpectrumLibrary.CONSTANT_ABSORBER_ARBITRARY(1e-30),
speed_of_sound=SPEED_OF_SOUND,
alpha_coefficient=1e-4,
density=1000,
gruneisen_parameter=1.0,
name="background_water")
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = (sp.MolecularCompositionGenerator()
.append(heavy_water)
.get_molecular_composition(segmentation_type=-1))
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND
phantom_material_dictionary = sp.Settings()
phantom_material_dictionary[Tags.PRIORITY] = 3
phantom_material_dictionary[Tags.STRUCTURE_START_MM] = [31, 0, 38]
phantom_material_dictionary[Tags.STRUCTURE_X_EXTENT_MM] = 28
phantom_material_dictionary[Tags.STRUCTURE_Y_EXTENT_MM] = 40
phantom_material_dictionary[Tags.STRUCTURE_Z_EXTENT_MM] = 14
phantom_material_dictionary[Tags.MOLECULE_COMPOSITION] = (sp.MolecularCompositionGenerator()
.append(phantom_material)
.get_molecular_composition(segmentation_type=0))
phantom_material_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = False
phantom_material_dictionary[Tags.STRUCTURE_TYPE] = Tags.RECTANGULAR_CUBOID_STRUCTURE
inclusion_1_dictionary = sp.Settings()
inclusion_1_dictionary[Tags.PRIORITY] = 8
inclusion_1_dictionary[Tags.STRUCTURE_START_MM] = [38, 10, 40]
inclusion_1_dictionary[Tags.STRUCTURE_X_EXTENT_MM] = 2
inclusion_1_dictionary[Tags.STRUCTURE_Y_EXTENT_MM] = 20
inclusion_1_dictionary[Tags.STRUCTURE_Z_EXTENT_MM] = 10
inclusion_1_dictionary[Tags.MOLECULE_COMPOSITION] = (sp.MolecularCompositionGenerator()
.append(inclusion_material)
.get_molecular_composition(segmentation_type=1))
inclusion_1_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = False
inclusion_1_dictionary[Tags.STRUCTURE_TYPE] = Tags.RECTANGULAR_CUBOID_STRUCTURE
inclusion_2_dictionary = sp.Settings()
inclusion_2_dictionary[Tags.PRIORITY] = 5
inclusion_2_dictionary[Tags.STRUCTURE_START_MM] = [50, 0, 43]
inclusion_2_dictionary[Tags.STRUCTURE_END_MM] = [50, 40, 43]
inclusion_2_dictionary[Tags.STRUCTURE_RADIUS_MM] = 2
inclusion_2_dictionary[Tags.MOLECULE_COMPOSITION] = (sp.MolecularCompositionGenerator()
.append(inclusion_material)
.get_molecular_composition(segmentation_type=2))
inclusion_2_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = False
inclusion_2_dictionary[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE
tissue_dict = sp.Settings()
tissue_dict[Tags.BACKGROUND] = background_dictionary
tissue_dict["phantom"] = phantom_material_dictionary
tissue_dict["inclusion_1"] = inclusion_1_dictionary
tissue_dict["inclusion_2"] = inclusion_2_dictionary
return {
Tags.STRUCTURES: tissue_dict,
Tags.SIMULATE_DEFORMED_LAYERS: False
}
def get_settings():
general_settings = {
# These parameters set the general properties of the simulated volume
Tags.RANDOM_SEED: 4711,
Tags.VOLUME_NAME: "InVision Simulation Example",
Tags.SIMULATION_PATH: path_manager.get_hdf5_file_save_path(),
Tags.SPACING_MM: spacing,
Tags.DIM_VOLUME_Z_MM: XZ_DIM,
Tags.DIM_VOLUME_X_MM: XZ_DIM,
Tags.DIM_VOLUME_Y_MM: Y_DIM,
Tags.VOLUME_CREATOR: Tags.VOLUME_CREATOR_VERSATILE,
Tags.GPU: True,
Tags.WAVELENGTHS: [700]
}
volume_settings = create_volume()
optical_settings = {
Tags.OPTICAL_MODEL_NUMBER_PHOTONS: 1e7,
Tags.OPTICAL_MODEL_BINARY_PATH: path_manager.get_mcx_binary_path(),
Tags.ILLUMINATION_TYPE: Tags.ILLUMINATION_TYPE_MSOT_INVISION,
Tags.LASER_PULSE_ENERGY_IN_MILLIJOULE: 50,
}
acoustic_settings = {
Tags.ACOUSTIC_SIMULATION_3D: False,
Tags.ACOUSTIC_MODEL_BINARY_PATH: path_manager.get_matlab_binary_path(),
Tags.KWAVE_PROPERTY_ALPHA_POWER: 0.00,
Tags.KWAVE_PROPERTY_SENSOR_RECORD: "p",
Tags.KWAVE_PROPERTY_PMLInside: False,
Tags.KWAVE_PROPERTY_PMLSize: [31, 32],
Tags.KWAVE_PROPERTY_PMLAlpha: 1.5,
Tags.KWAVE_PROPERTY_PlotPML: False,
Tags.RECORDMOVIE: False,
Tags.MOVIENAME: "visualization_log",
Tags.ACOUSTIC_LOG_SCALE: True
}
reconstruction_settings = {
Tags.RECONSTRUCTION_PERFORM_BANDPASS_FILTERING: False,
Tags.TUKEY_WINDOW_ALPHA: 0.5,
Tags.RECONSTRUCTION_BMODE_AFTER_RECONSTRUCTION: False,
Tags.RECONSTRUCTION_BMODE_METHOD: Tags.RECONSTRUCTION_BMODE_METHOD_HILBERT_TRANSFORM,
Tags.RECONSTRUCTION_APODIZATION_METHOD: Tags.RECONSTRUCTION_APODIZATION_HAMMING,
Tags.RECONSTRUCTION_MODE: Tags.RECONSTRUCTION_MODE_PRESSURE,
Tags.DATA_FIELD_SPEED_OF_SOUND: SPEED_OF_SOUND,
Tags.KWAVE_PROPERTY_SENSOR_RECORD: "p",
Tags.KWAVE_PROPERTY_PMLInside: False,
Tags.KWAVE_PROPERTY_PMLSize: [31, 32],
Tags.KWAVE_PROPERTY_PMLAlpha: 1.5,
Tags.KWAVE_PROPERTY_PlotPML: False,
Tags.RECORDMOVIE: False,
Tags.MOVIENAME: "visualization_log",
Tags.ACOUSTIC_LOG_SCALE: True,
Tags.ACOUSTIC_MODEL_BINARY_PATH: path_manager.get_matlab_binary_path(),
Tags.KWAVE_PROPERTY_ALPHA_POWER: 0.00,
Tags.SPACING_MM: 0.25,
}
_settings = sp.Settings(general_settings)
_settings.set_volume_creation_settings(volume_settings)
_settings.set_optical_settings(optical_settings)
_settings.set_acoustic_settings(acoustic_settings)
_settings.set_reconstruction_settings(reconstruction_settings)
return _settings
device = get_device()
settings = get_settings()
pipeline = create_pipeline(settings)
sp.simulate(simulation_pipeline=pipeline, digital_device_twin=device, settings=settings)
if visualise:
sp.visualise_data(settings=settings,
path_manager=path_manager,
show_absorption=True,
show_initial_pressure=True,
show_reconstructed_data=True,
show_xz_only=True)
if __name__ == "__main__":
parser = ArgumentParser(description='Run the msot invision simulation example')
parser.add_argument("--spacing", default=0.2, type=float, help='the voxel spacing in mm')
parser.add_argument("--path_manager", default=None, help='the path manager, None uses sp.PathManager')
parser.add_argument("--visualise", default=True, type=bool, help='whether to visualise the result')
config = parser.parse_args()
run_msot_invision_simulation(spacing=config.spacing, path_manager=config.path_manager, visualise=config.visualise)