.gitignore
CONTRIBUTING.md
LICENSE.md
MANIFEST.in
README.md
VERSION
requirements.txt
setup.py
LICENSES/MIT
docs/Makefile
docs/make.bat
docs/source/clean_up_rst_files.py
docs/source/conf.py
docs/source/contributing_link.md
docs/source/create_a_custom_digital_device_twin.rst
docs/source/create_custom_tissues.rst
docs/source/index.rst
docs/source/intro_link.md
docs/source/introduction.md
docs/source/linear_unmixing.rst
docs/source/minimal_optical_simulation.rst
docs/source/msot_invision_simulation.rst
docs/source/optical_and_acoustic_simulation.rst
docs/source/perform_image_reconstruction.rst
docs/source/perform_iterative_qPAI_reconstruction.rst
docs/source/segmentation_loader.rst
docs/source/simpa.core.device_digital_twins.detection_geometries.rst
docs/source/simpa.core.device_digital_twins.illumination_geometries.rst
docs/source/simpa.core.device_digital_twins.pa_devices.rst
docs/source/simpa.core.device_digital_twins.rst
docs/source/simpa.core.processing_components.monospectral.noise.rst
docs/source/simpa.core.processing_components.monospectral.rst
docs/source/simpa.core.processing_components.multispectral.rst
docs/source/simpa.core.processing_components.rst
docs/source/simpa.core.rst
docs/source/simpa.core.simulation_modules.acoustic_forward_module.rst
docs/source/simpa.core.simulation_modules.optical_simulation_module.rst
docs/source/simpa.core.simulation_modules.reconstruction_module.rst
docs/source/simpa.core.simulation_modules.rst
docs/source/simpa.core.simulation_modules.volume_creation_module.rst
docs/source/simpa.io_handling.rst
docs/source/simpa.log.rst
docs/source/simpa.rst
docs/source/simpa.utils.libraries.absorption_spectra_data.rst
docs/source/simpa.utils.libraries.anisotropy_spectra_data.rst
docs/source/simpa.utils.libraries.rst
docs/source/simpa.utils.libraries.scattering_spectra_data.rst
docs/source/simpa.utils.libraries.structure_library.rst
docs/source/simpa.utils.quality_assurance.rst
docs/source/simpa.utils.rst
docs/source/simpa.visualisation.rst
docs/source/simpa_examples.rst
docs/source/images/simpa_logo.png
simpa/__init__.py
simpa.egg-info/PKG-INFO
simpa.egg-info/SOURCES.txt
simpa.egg-info/dependency_links.txt
simpa.egg-info/requires.txt
simpa.egg-info/top_level.txt
simpa/core/__init__.py
simpa/core/simulation.py
simpa/core/device_digital_twins/__init__.py
simpa/core/device_digital_twins/digital_device_twin_base.py
simpa/core/device_digital_twins/detection_geometries/__init__.py
simpa/core/device_digital_twins/detection_geometries/curved_array.py
simpa/core/device_digital_twins/detection_geometries/detection_geometry_base.py
simpa/core/device_digital_twins/detection_geometries/linear_array.py
simpa/core/device_digital_twins/detection_geometries/planar_array.py
simpa/core/device_digital_twins/illumination_geometries/__init__.py
simpa/core/device_digital_twins/illumination_geometries/disk_illumination.py
simpa/core/device_digital_twins/illumination_geometries/gaussian_beam_illumination.py
simpa/core/device_digital_twins/illumination_geometries/illumination_geometry_base.py
simpa/core/device_digital_twins/illumination_geometries/ithera_msot_acuity_illumination.py
simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py
simpa/core/device_digital_twins/illumination_geometries/pencil_array_illumination.py
simpa/core/device_digital_twins/illumination_geometries/pencil_beam_illumination.py
simpa/core/device_digital_twins/illumination_geometries/slit_illumination.py
simpa/core/device_digital_twins/pa_devices/__init__.py
simpa/core/device_digital_twins/pa_devices/ithera_msot_acuity.py
simpa/core/device_digital_twins/pa_devices/ithera_msot_invision.py
simpa/core/device_digital_twins/pa_devices/ithera_rsom.py
simpa/core/processing_components/__init__.py
simpa/core/processing_components/monospectral/__init__.py
simpa/core/processing_components/monospectral/field_of_view_cropping.py
simpa/core/processing_components/monospectral/iterative_qPAI_algorithm.py
simpa/core/processing_components/monospectral/noise/__init__.py
simpa/core/processing_components/monospectral/noise/gamma_noise.py
simpa/core/processing_components/monospectral/noise/gaussian_noise.py
simpa/core/processing_components/monospectral/noise/poisson_noise.py
simpa/core/processing_components/monospectral/noise/salt_and_pepper_noise.py
simpa/core/processing_components/monospectral/noise/uniform_noise.py
simpa/core/processing_components/multispectral/__init__.py
simpa/core/processing_components/multispectral/linear_unmixing.py
simpa/core/simulation_modules/__init__.py
simpa/core/simulation_modules/acoustic_forward_module/__init__.py
simpa/core/simulation_modules/acoustic_forward_module/acoustic_forward_model_test_adapter.py
simpa/core/simulation_modules/acoustic_forward_module/acoustic_forward_module_k_wave_adapter.py
simpa/core/simulation_modules/acoustic_forward_module/simulate_2D.m
simpa/core/simulation_modules/acoustic_forward_module/simulate_3D.m
simpa/core/simulation_modules/optical_simulation_module/__init__.py
simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_test_adapter.py
simpa/core/simulation_modules/reconstruction_module/__init__.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_module_delay_and_sum_adapter.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_module_delay_multiply_and_sum_adapter.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_module_signed_delay_multiply_and_sum_adapter.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_module_test_adapter.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_module_time_reversal_adapter.py
simpa/core/simulation_modules/reconstruction_module/reconstruction_utils.py
simpa/core/simulation_modules/reconstruction_module/time_reversal_2D.m
simpa/core/simulation_modules/reconstruction_module/time_reversal_3D.m
simpa/core/simulation_modules/volume_creation_module/__init__.py
simpa/core/simulation_modules/volume_creation_module/volume_creation_module_model_based_adapter.py
simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
simpa/io_handling/__init__.py
simpa/io_handling/io_hdf5.py
simpa/io_handling/ipasc.py
simpa/io_handling/serialization.py
simpa/io_handling/zenodo_download.py
simpa/log/__init__.py
simpa/log/file_logger.py
simpa/utils/__init__.py
simpa/utils/calculate.py
simpa/utils/constants.py
simpa/utils/deformation_manager.py
simpa/utils/dict_path_manager.py
simpa/utils/path_manager.py
simpa/utils/serializer.py
simpa/utils/settings.py
simpa/utils/tags.py
simpa/utils/tissue_properties.py
simpa/utils/libraries/__init__.py
simpa/utils/libraries/literature_values.py
simpa/utils/libraries/molecule_library.py
simpa/utils/libraries/spectrum_library.py
simpa/utils/libraries/tissue_library.py
simpa/utils/libraries/absorption_spectra_data/Copper_Sulphide.npz
simpa/utils/libraries/absorption_spectra_data/Deoxyhemoglobin.npz
simpa/utils/libraries/absorption_spectra_data/Fat.npz
simpa/utils/libraries/absorption_spectra_data/Melanin.npz
simpa/utils/libraries/absorption_spectra_data/Nickel_Sulphide.npz
simpa/utils/libraries/absorption_spectra_data/Oxyhemoglobin.npz
simpa/utils/libraries/absorption_spectra_data/Skin_Baseline.npz
simpa/utils/libraries/absorption_spectra_data/Water.npz
simpa/utils/libraries/absorption_spectra_data/__init__.py
simpa/utils/libraries/anisotropy_spectra_data/Epidermis_Anisotropy.npz
simpa/utils/libraries/anisotropy_spectra_data/__init__.py
simpa/utils/libraries/scattering_spectra_data/__init__.py
simpa/utils/libraries/scattering_spectra_data/background_scattering.npz
simpa/utils/libraries/scattering_spectra_data/blood_scattering.npz
simpa/utils/libraries/scattering_spectra_data/bone_scattering.npz
simpa/utils/libraries/scattering_spectra_data/fat_scattering.npz
simpa/utils/libraries/scattering_spectra_data/muscle_scattering.npz
simpa/utils/libraries/structure_library/BackgroundStructure.py
simpa/utils/libraries/structure_library/CircularTubularStructure.py
simpa/utils/libraries/structure_library/EllipticalTubularStructure.py
simpa/utils/libraries/structure_library/HorizontalLayerStructure.py
simpa/utils/libraries/structure_library/ParallelepipedStructure.py
simpa/utils/libraries/structure_library/RectangularCuboidStructure.py
simpa/utils/libraries/structure_library/SphericalStructure.py
simpa/utils/libraries/structure_library/StructureBase.py
simpa/utils/libraries/structure_library/VesselStructure.py
simpa/utils/libraries/structure_library/__init__.py
simpa/utils/quality_assurance/__init__.py
simpa/utils/quality_assurance/data_sanity_testing.py
simpa/visualisation/__init__.py
simpa/visualisation/matplotlib_data_visualisation.py
simpa/visualisation/matplotlib_device_visualisation.py
simpa_examples/__init__.py
simpa_examples/create_a_custom_digital_device_twin.py
simpa_examples/create_custom_tissues.py
simpa_examples/linear_unmixing.py
simpa_examples/minimal_optical_simulation.py
simpa_examples/msot_invision_simulation.py
simpa_examples/optical_and_acoustic_simulation.py
simpa_examples/path_config.env
simpa_examples/perform_image_reconstruction.py
simpa_examples/perform_iterative_qPAI_reconstruction.py
simpa_examples/segmentation_loader.py