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minimal_optical_simulation.py
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minimal_optical_simulation.py
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# 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
# FIXME temporary workaround for newest Intel architectures
import os
os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"
# TODO: Please make sure that you have set the correct path to MCX binary and SAVE_PATH in the file path_config.env
# located in the simpa_examples directory
@profile
def run_minimal_optical_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()
VOLUME_TRANSDUCER_DIM_IN_MM = 60
VOLUME_PLANAR_DIM_IN_MM = 30
VOLUME_HEIGHT_IN_MM = 60
RANDOM_SEED = 471
VOLUME_NAME = "MyVolumeName_"+str(RANDOM_SEED)
SAVE_REFLECTANCE = False
SAVE_PHOTON_DIRECTION = False
# If VISUALIZE is set to True, the simulation result will be plotted
def create_example_tissue():
"""
This is a very simple example script of how to create a tissue definition.
It contains a muscular background, an epidermis layer on top of the muscles
and a blood vessel.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND
muscle_dictionary = sp.Settings()
muscle_dictionary[Tags.PRIORITY] = 1
muscle_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 10]
muscle_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 100]
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.muscle()
muscle_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
muscle_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
muscle_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
vessel_1_dictionary = sp.Settings()
vessel_1_dictionary[Tags.PRIORITY] = 3
vessel_1_dictionary[Tags.STRUCTURE_START_MM] = [VOLUME_TRANSDUCER_DIM_IN_MM/2,
10,
VOLUME_HEIGHT_IN_MM/2]
vessel_1_dictionary[Tags.STRUCTURE_END_MM] = [VOLUME_TRANSDUCER_DIM_IN_MM/2,
12,
VOLUME_HEIGHT_IN_MM/2]
vessel_1_dictionary[Tags.STRUCTURE_RADIUS_MM] = 3
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.blood()
vessel_1_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_1_dictionary[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE
epidermis_dictionary = sp.Settings()
epidermis_dictionary[Tags.PRIORITY] = 8
epidermis_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 9]
epidermis_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 10]
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.epidermis()
epidermis_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
epidermis_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
epidermis_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
tissue_dict = sp.Settings()
tissue_dict[Tags.BACKGROUND] = background_dictionary
tissue_dict["muscle"] = muscle_dictionary
tissue_dict["epidermis"] = epidermis_dictionary
tissue_dict["vessel_1"] = vessel_1_dictionary
return tissue_dict
# Seed the numpy random configuration prior to creating the global_settings file in
# order to ensure that the same volume
# is generated with the same random seed every time.
np.random.seed(RANDOM_SEED)
general_settings = {
# These parameters set the general properties of the simulated volume
Tags.RANDOM_SEED: RANDOM_SEED,
Tags.VOLUME_NAME: VOLUME_NAME,
Tags.SIMULATION_PATH: path_manager.get_hdf5_file_save_path(),
Tags.SPACING_MM: spacing,
Tags.DIM_VOLUME_Z_MM: VOLUME_HEIGHT_IN_MM,
Tags.DIM_VOLUME_X_MM: VOLUME_TRANSDUCER_DIM_IN_MM,
Tags.DIM_VOLUME_Y_MM: VOLUME_PLANAR_DIM_IN_MM,
Tags.WAVELENGTHS: [798],
Tags.DO_FILE_COMPRESSION: True,
Tags.GPU: True
}
settings = sp.Settings(general_settings)
settings.set_volume_creation_settings({
Tags.SIMULATE_DEFORMED_LAYERS: True,
Tags.STRUCTURES: create_example_tissue()
})
settings.set_optical_settings({
Tags.OPTICAL_MODEL_NUMBER_PHOTONS: 5e7,
Tags.OPTICAL_MODEL_BINARY_PATH: path_manager.get_mcx_binary_path(),
Tags.COMPUTE_DIFFUSE_REFLECTANCE: SAVE_REFLECTANCE,
Tags.COMPUTE_PHOTON_DIRECTION_AT_EXIT: SAVE_PHOTON_DIRECTION
})
settings["noise_model_1"] = {
Tags.NOISE_MEAN: 1.0,
Tags.NOISE_STD: 0.1,
Tags.NOISE_MODE: Tags.NOISE_MODE_MULTIPLICATIVE,
Tags.DATA_FIELD: Tags.DATA_FIELD_INITIAL_PRESSURE,
Tags.NOISE_NON_NEGATIVITY_CONSTRAINT: True
}
if not SAVE_REFLECTANCE and not SAVE_PHOTON_DIRECTION:
pipeline = [
sp.ModelBasedAdapter(settings),
sp.MCXAdapter(settings),
sp.GaussianNoise(settings, "noise_model_1")
]
else:
pipeline = [
sp.ModelBasedAdapter(settings),
sp.MCXReflectanceAdapter(settings),
]
class ExampleDeviceSlitIlluminationLinearDetector(sp.PhotoacousticDevice):
"""
This class represents a digital twin of a PA device with a slit as illumination next to a linear detection geometry.
"""
def __init__(self):
super().__init__(device_position_mm=np.asarray([VOLUME_TRANSDUCER_DIM_IN_MM/2,
VOLUME_PLANAR_DIM_IN_MM/2, 0]))
self.set_detection_geometry(sp.LinearArrayDetectionGeometry())
self.add_illumination_geometry(sp.SlitIlluminationGeometry(slit_vector_mm=[20, 0, 0],
direction_vector_mm=[0, 0, 1]))
device = ExampleDeviceSlitIlluminationLinearDetector()
sp.simulate(pipeline, settings, device)
if Tags.WAVELENGTH in settings:
WAVELENGTH = settings[Tags.WAVELENGTH]
else:
WAVELENGTH = 700
if visualise:
sp.visualise_data(path_to_hdf5_file=path_manager.get_hdf5_file_save_path() + "/" + VOLUME_NAME + ".hdf5",
wavelength=WAVELENGTH,
show_initial_pressure=True,
show_absorption=True,
show_diffuse_reflectance=SAVE_REFLECTANCE,
log_scale=True)
if __name__ == "__main__":
parser = ArgumentParser(description='Run the minimal optical 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_minimal_optical_simulation(spacing=config.spacing, path_manager=config.path_manager, visualise=config.visualise)