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SIMPA toolkit

  • Getting started
    • SIMPA installation instructions
    • External tools installation instructions
      • mcx (Optical Forward Model)
      • k-Wave (Acoustic Forward Model)
    • Path management
      • Option 1:
      • Option 2:
    • Run manual tests
  • Simulation examples
  • Reproducibility
  • Understanding SIMPA
    • Understanding Tags
      • What are Tags?
      • Purpose of Tags
      • How Tags Work
      • What Tags are Available?
    • Concept of Settings
      • Global Settings
        • Example of Global Settings
      • Component Settings
        • Difference Between Global and Component Settings
        • Implementation
    • Available Component Settings
      • 1. Volume Creation
        • Examples of Volume Creation Settings
      • 2. Acoustic Model
        • Examples of Acoustic Settings
      • 3. Optical Model
        • Examples of Optical Settings
      • 4. Reconstruction model
        • Examples of Reconstruction Settings
  • Benchmarking SIMPA
    • Overview
    • Usage
      • Benchmarking for contributions
    • Options
    • Default Values
    • Examples
  • Line Profiler (more advanced - for specific function profiling)
    • Example Usage
  • Contributing to SIMPA
    • How to contribute
      • Contribution process
      • Contribution origin, rights, and sign-off
      • Install pre-commit hooks
        • git config user email address checking
      • Contribution review and integration
      • Contact
    • Coding style
    • Documenting your code
  • List of Contributors

SIMPA examples

  • simpa_examples
    • create_a_custom_digital_device_twin
    • create_custom_tissues
    • linear_unmixing
    • minimal_optical_simulation
    • minimal_optical_simulation_heterogeneous_tissue
    • minimal_optical_simulation_uniform_cube
    • msot_invision_simulation
    • optical_and_acoustic_simulation
    • perform_image_reconstruction
    • perform_iterative_qPAI_reconstruction
    • segmentation_loader

Package reference

  • core
    • device_digital_twins
      • detection_geometries
        • CurvedArrayDetectionGeometry
        • DetectionGeometryBase
        • LinearArrayDetectionGeometry
        • PlanarArrayDetectionGeometry
      • illumination_geometries
        • DiskIlluminationGeometry
        • GaussianBeamIlluminationGeometry
        • IlluminationGeometryBase
        • MSOTAcuityIlluminationGeometry
        • MSOTInVisionIlluminationGeometry
        • PencilArrayIlluminationGeometry
        • PencilBeamIlluminationGeometry
        • RectangleIlluminationGeometry
        • RingIlluminationGeometry
        • SlitIlluminationGeometry
      • pa_devices
        • MSOTAcuityEcho
        • InVision256TF
        • RSOMExplorerP50
        • PhotoacousticDevice
      • DigitalDeviceTwinBase
        • DigitalDeviceTwinBase.__eq__()
        • DigitalDeviceTwinBase.check_settings_prerequisites()
        • DigitalDeviceTwinBase.deserialize()
        • DigitalDeviceTwinBase.generate_uuid()
        • DigitalDeviceTwinBase.get_field_of_view_mm()
        • DigitalDeviceTwinBase.serialize()
        • DigitalDeviceTwinBase.update_settings_for_use_of_model_based_volume_creator()
    • processing_components
      • monospectral
        • noise
        • FieldOfViewCropping
        • IterativeqPAI
      • multispectral
        • LinearUnmixing
        • MultispectralProcessingAlgorithm
      • ProcessingComponentBase
    • simulation_modules
      • reconstruction_module
        • create_reconstruction_settings()
        • DelayAndSumAdapter
        • reconstruct_delay_and_sum_pytorch()
        • DelayMultiplyAndSumAdapter
        • reconstruct_delay_multiply_and_sum_pytorch()
        • ReconstructionAdapterBase
        • ReconstructionTestAdapter
        • apply_b_mode()
        • bandpass_filter_with_settings()
        • butter_bandpass_filtering()
        • butter_bandpass_filtering_with_settings()
        • compute_delay_and_sum_values()
        • compute_image_dimensions()
        • get_apodization_factor()
        • preparing_reconstruction_and_obtaining_reconstruction_settings()
        • reconstruction_mode_transformation()
        • tukey_bandpass_filtering()
        • tukey_bandpass_filtering_with_settings()
        • tukey_window_function()
        • SignedDelayMultiplyAndSumAdapter
        • reconstruct_signed_delay_multiply_and_sum_pytorch()
        • TimeReversalAdapter
      • volume_creation_module
        • ModelBasedAdapter
        • SegmentationBasedAdapter
        • VolumeCreationAdapterBase
      • SimulationModuleBase
        • SimulationModuleBase.get_additional_flags()
        • SimulationModuleBase.load_component_settings()
    • PipelineElementBase
      • PipelineElementBase.run()
    • simulate()
  • io_handling
    • load_data_field()
    • load_hdf5()
    • save_data_field()
    • save_hdf5()
    • IpascSimpaAdapter
      • IpascSimpaAdapter.generate_binary_data()
      • IpascSimpaAdapter.generate_device_meta_data()
      • IpascSimpaAdapter.set_metadata_value()
    • export_to_ipasc()
    • download_from_zenodo()
  • log
    • Logger
      • Logger.critical()
      • Logger.debug()
      • Logger.deserialize()
      • Logger.error()
      • Logger.info()
      • Logger.serialize()
      • Logger.warning()
  • utils
    • libraries
      • absorption_spectra_data
      • anisotropy_spectra_data
      • scattering_spectra_data
      • structure_library
        • priority_sorted_structures()
        • Background
        • define_background_structure_settings()
        • CircularTubularStructure
        • define_circular_tubular_structure_settings()
        • EllipticalTubularStructure
        • define_elliptical_tubular_structure_settings()
        • HorizontalLayerStructure
        • define_horizontal_layer_structure_settings()
        • ParallelepipedStructure
        • define_parallelepiped_structure_settings()
        • RectangularCuboidStructure
        • define_rectangular_cuboid_structure_settings()
        • SphericalStructure
        • define_spherical_structure_settings()
        • GeometricalStructure
        • VesselStructure
        • define_vessel_structure_settings()
      • BlobHeterogeneity
      • HeterogeneityGeneratorBase
        • HeterogeneityGeneratorBase.get_map()
        • HeterogeneityGeneratorBase.normalise_map()
      • ImageHeterogeneity
        • ImageHeterogeneity.map
        • ImageHeterogeneity.change_resolution()
        • ImageHeterogeneity.crop_image()
        • ImageHeterogeneity.upsize_to_fill_area()
      • RandomHeterogeneity
      • MorphologicalTissueProperties
        • MorphologicalTissueProperties.ACCOMPANYING_VEIN_DEPTH_STD_MM
        • MorphologicalTissueProperties.ACCOMPANYING_VEIN_DISTANCE_MEAN_MM
        • MorphologicalTissueProperties.ACCOMPANYING_VEIN_DISTANCE_STD_MM
        • MorphologicalTissueProperties.ACCOMPANYING_VEIN_MEDIAN_DISTANCE_MEAN_MM
        • MorphologicalTissueProperties.ACCOMPANYING_VEIN_MEDIAN_DISTANCE_STD_MM
        • MorphologicalTissueProperties.ARTERY_X_POSITION_UNCERTAINTY_MM
        • MorphologicalTissueProperties.DERMIS_THICKNESS_MEAN_MM
        • MorphologicalTissueProperties.DERMIS_THICKNESS_STD_MM
        • MorphologicalTissueProperties.DISTANCE_RADIAL_AND_ULNA_ARTERY_MEAN_MM
        • MorphologicalTissueProperties.DISTANCE_RADIAL_AND_ULNA_ARTERY_STD_MM
        • MorphologicalTissueProperties.EPIDERMIS_THICKNESS_MEAN_MM
        • MorphologicalTissueProperties.EPIDERMIS_THICKNESS_STD_MM
        • MorphologicalTissueProperties.MEDIAN_ARTERY_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.MEDIAN_ARTERY_DEPTH_STD_MM
        • MorphologicalTissueProperties.MEDIAN_ARTERY_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.MEDIAN_ARTERY_DIAMETER_STD_MM
        • MorphologicalTissueProperties.MEDIAN_ARTERY_X_POSITION_MEAN_MM
        • MorphologicalTissueProperties.MEDIAN_VEIN_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.MEDIAN_VEIN_DIAMETER_STD_MM
        • MorphologicalTissueProperties.RADIAL_ARTERY_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.RADIAL_ARTERY_DEPTH_STD_MM
        • MorphologicalTissueProperties.RADIAL_ARTERY_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.RADIAL_ARTERY_DIAMETER_STD_MM
        • MorphologicalTissueProperties.RADIAL_ARTERY_X_POSITION_MEAN_MM
        • MorphologicalTissueProperties.RADIAL_VEIN_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.RADIAL_VEIN_DIAMETER_STD_MM
        • MorphologicalTissueProperties.RADIUS_BONE_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.RADIUS_BONE_DEPTH_STD_MM
        • MorphologicalTissueProperties.RADIUS_BONE_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.RADIUS_BONE_DIAMETER_STD_MM
        • MorphologicalTissueProperties.RADIUS_ULNA_BONE_POSITION_STD_MM
        • MorphologicalTissueProperties.RADIUS_ULNA_BONE_SEPARATION_MEAN_MM
        • MorphologicalTissueProperties.SUBCUTANEOUS_VEIN_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.SUBCUTANEOUS_VEIN_DEPTH_STD_MM
        • MorphologicalTissueProperties.SUBCUTANEOUS_VEIN_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.SUBCUTANEOUS_VEIN_DIAMETER_STD_MM
        • MorphologicalTissueProperties.ULNAR_ARTERY_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.ULNAR_ARTERY_DEPTH_STD_MM
        • MorphologicalTissueProperties.ULNAR_ARTERY_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.ULNAR_ARTERY_DIAMETER_STD_MM
        • MorphologicalTissueProperties.ULNAR_ARTERY_X_POSITION_MEAN_MM
        • MorphologicalTissueProperties.ULNAR_VEIN_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.ULNAR_VEIN_DIAMETER_STD_MM
        • MorphologicalTissueProperties.ULNA_BONE_DEPTH_MEAN_MM
        • MorphologicalTissueProperties.ULNA_BONE_DEPTH_STD_MM
        • MorphologicalTissueProperties.ULNA_BONE_DIAMETER_MEAN_MM
        • MorphologicalTissueProperties.ULNA_BONE_DIAMETER_STD_MM
      • OpticalTissueProperties
        • OpticalTissueProperties.ARTERIAL_OXYGENATION
        • OpticalTissueProperties.ARTERIAL_OXYGENATION_VARIATION
        • OpticalTissueProperties.BACKGROUND_OXYGENATION
        • OpticalTissueProperties.BACKGROUND_OXYGENATION_VARIATION
        • OpticalTissueProperties.BLOOD_ANISOTROPY
        • OpticalTissueProperties.BLOOD_PLASMA_FRACTION
        • OpticalTissueProperties.BLOOD_VOLUME_FRACTION_LYMPH_NODE
        • OpticalTissueProperties.BLOOD_VOLUME_FRACTION_LYMPH_NODE_VARIATION
        • OpticalTissueProperties.BLOOD_VOLUME_FRACTION_MUSCLE_TISSUE
        • OpticalTissueProperties.BMIE_BACKGROUND_TISSUE
        • OpticalTissueProperties.BMIE_BLOOD
        • OpticalTissueProperties.BMIE_BONE
        • OpticalTissueProperties.BMIE_DERMIS
        • OpticalTissueProperties.BMIE_EPIDERMIS
        • OpticalTissueProperties.BMIE_FAT
        • OpticalTissueProperties.BMIE_MUSCLE_TISSUE
        • OpticalTissueProperties.BONE_ABSORPTION
        • OpticalTissueProperties.DERMIS_ANISOTROPY
        • OpticalTissueProperties.FRAY_BACKGROUND_TISSUE
        • OpticalTissueProperties.FRAY_BLOOD
        • OpticalTissueProperties.FRAY_BONE
        • OpticalTissueProperties.FRAY_DERMIS
        • OpticalTissueProperties.FRAY_EPIDERMIS
        • OpticalTissueProperties.FRAY_FAT
        • OpticalTissueProperties.FRAY_MUSCLE_TISSUE
        • OpticalTissueProperties.LYMPH_NODE_OXYGENATION
        • OpticalTissueProperties.LYMPH_NODE_OXYGENATION_VARIATION
        • OpticalTissueProperties.MELANIN_VOLUME_FRACTION_MEAN
        • OpticalTissueProperties.MELANIN_VOLUME_FRACTION_STD
        • OpticalTissueProperties.MUS500_BACKGROUND_TISSUE
        • OpticalTissueProperties.MUS500_BLOOD
        • OpticalTissueProperties.MUS500_BONE
        • OpticalTissueProperties.MUS500_DERMIS
        • OpticalTissueProperties.MUS500_EPIDERMIS
        • OpticalTissueProperties.MUS500_FAT
        • OpticalTissueProperties.MUS500_MUSCLE_TISSUE
        • OpticalTissueProperties.STANDARD_ANISOTROPY
        • OpticalTissueProperties.VENOUS_OXYGENATION
        • OpticalTissueProperties.VENOUS_OXYGENATION_VARIATION
        • OpticalTissueProperties.WATER_VOLUME_FRACTION_BONE_MEAN
        • OpticalTissueProperties.WATER_VOLUME_FRACTION_BONE_STD
        • OpticalTissueProperties.WATER_VOLUME_FRACTION_HUMAN_BODY
        • OpticalTissueProperties.WATER_VOLUME_FRACTION_SKIN
      • StandardProperties
        • StandardProperties.AIR_G
        • StandardProperties.AIR_MUA
        • StandardProperties.AIR_MUS
        • StandardProperties.ALPHA_COEFF_AIR
        • StandardProperties.ALPHA_COEFF_BLOOD
        • StandardProperties.ALPHA_COEFF_BONE
        • StandardProperties.ALPHA_COEFF_FAT
        • StandardProperties.ALPHA_COEFF_GEL_PAD
        • StandardProperties.ALPHA_COEFF_GENERIC
        • StandardProperties.ALPHA_COEFF_LYMPH_NODE
        • StandardProperties.ALPHA_COEFF_MUSCLE
        • StandardProperties.ALPHA_COEFF_SKIN
        • StandardProperties.ALPHA_COEFF_WATER
        • StandardProperties.BODY_TEMPERATURE_CELCIUS
        • StandardProperties.DENSITY_AIR
        • StandardProperties.DENSITY_BLOOD
        • StandardProperties.DENSITY_BONE
        • StandardProperties.DENSITY_FAT
        • StandardProperties.DENSITY_GEL_PAD
        • StandardProperties.DENSITY_GENERIC
        • StandardProperties.DENSITY_HEAVY_WATER
        • StandardProperties.DENSITY_LYMPH_NODE
        • StandardProperties.DENSITY_MUSCLE
        • StandardProperties.DENSITY_SKIN
        • StandardProperties.DENSITY_WATER
        • StandardProperties.GELPAD_G
        • StandardProperties.GELPAD_MUA
        • StandardProperties.GELPAD_MUS
        • StandardProperties.HEAVY_WATER_MUA
        • StandardProperties.SPEED_OF_SOUND_AIR
        • StandardProperties.SPEED_OF_SOUND_BLOOD
        • StandardProperties.SPEED_OF_SOUND_BONE
        • StandardProperties.SPEED_OF_SOUND_FAT
        • StandardProperties.SPEED_OF_SOUND_GEL_PAD
        • StandardProperties.SPEED_OF_SOUND_GENERIC
        • StandardProperties.SPEED_OF_SOUND_HEAVY_WATER
        • StandardProperties.SPEED_OF_SOUND_LYMPH_NODE
        • StandardProperties.SPEED_OF_SOUND_MUSCLE
        • StandardProperties.SPEED_OF_SOUND_SKIN
        • StandardProperties.SPEED_OF_SOUND_WATER
        • StandardProperties.WATER_G
        • StandardProperties.WATER_MUS
      • MolecularComposition
        • MolecularComposition.segmentation_type
        • MolecularComposition.internal_properties
        • MolecularComposition.deserialize()
        • MolecularComposition.get_properties_for_wavelength()
        • MolecularComposition.serialize()
        • MolecularComposition.update_internal_properties()
      • MolecularCompositionGenerator
        • MolecularCompositionGenerator.append()
        • MolecularCompositionGenerator.get_molecular_composition()
      • Molecule
        • Molecule.name
        • Molecule.spectrum
        • Molecule.volume_fraction
        • Molecule.scattering_spectrum
        • Molecule.anisotropy_spectrum
        • Molecule.gruneisen_parameter
        • Molecule.density
        • Molecule.speed_of_sound
        • Molecule.alpha_coefficient
        • Molecule.__eq__()
        • Molecule.deserialize()
        • Molecule.get_volume_fraction()
        • Molecule.serialize()
      • MoleculeLibrary
        • MoleculeLibrary.air()
        • MoleculeLibrary.bone()
        • MoleculeLibrary.constant_scatterer()
        • MoleculeLibrary.deoxyhemoglobin()
        • MoleculeLibrary.dermal_scatterer()
        • MoleculeLibrary.epidermal_scatterer()
        • MoleculeLibrary.fat()
        • MoleculeLibrary.heavy_water()
        • MoleculeLibrary.mediprene()
        • MoleculeLibrary.melanin()
        • MoleculeLibrary.muscle_scatterer()
        • MoleculeLibrary.oxyhemoglobin()
        • MoleculeLibrary.soft_tissue_scatterer()
        • MoleculeLibrary.water()
      • AbsorptionSpectrumLibrary
        • AbsorptionSpectrumLibrary.CONSTANT_ABSORBER_ARBITRARY()
      • AnisotropySpectrumLibrary
        • AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY()
      • ScatteringSpectrumLibrary
        • ScatteringSpectrumLibrary.CONSTANT_SCATTERING_ARBITRARY()
        • ScatteringSpectrumLibrary.scattering_from_rayleigh_and_mie_theory()
      • SpectraLibrary
        • SpectraLibrary.spectra
        • SpectraLibrary.add_spectra_from_folder()
        • SpectraLibrary.get_spectra_names()
        • SpectraLibrary.get_spectrum_by_name()
      • Spectrum
        • Spectrum.spectrum_name
        • Spectrum.wavelengths
        • Spectrum.max_wavelength
        • Spectrum.min_wavelength
        • Spectrum.values
        • Spectrum.values_interp
        • Spectrum.__eq__()
        • Spectrum.deserialize()
        • Spectrum.get_value_for_wavelength()
        • Spectrum.get_value_over_wavelength()
        • Spectrum.serialize()
      • get_simpa_internal_absorption_spectra_by_names()
      • view_saved_spectra()
      • TissueLibrary
        • TissueLibrary.blood()
        • TissueLibrary.bone()
        • TissueLibrary.constant()
        • TissueLibrary.dermis()
        • TissueLibrary.epidermis()
        • TissueLibrary.generic_tissue()
        • TissueLibrary.get_blood_volume_fractions()
        • TissueLibrary.heavy_water()
        • TissueLibrary.lymph_node()
        • TissueLibrary.mediprene()
        • TissueLibrary.muscle()
        • TissueLibrary.soft_tissue()
        • TissueLibrary.subcutaneous_fat()
        • TissueLibrary.ultrasound_gel()
    • quality_assurance
      • assert_array_well_defined()
      • assert_equal_shapes()
    • are_equal()
    • calculate_bvf()
    • calculate_gruneisen_parameter_from_temperature()
    • calculate_oxygenation()
    • create_spline_for_range()
    • extract_hemoglobin_fractions()
    • min_max_normalization()
    • positive_gauss()
    • randomize_uniform()
    • rotation()
    • rotation_matrix_between_vectors()
    • rotation_x()
    • rotation_y()
    • rotation_z()
    • round_x5_away_from_zero()
    • spline_evaluator2d_voxel()
    • EPS
    • SegmentationClasses
      • SegmentationClasses.AIR
      • SegmentationClasses.BLOOD
      • SegmentationClasses.BONE
      • SegmentationClasses.COUPLING_ARTIFACT
      • SegmentationClasses.DERMIS
      • SegmentationClasses.EPIDERMIS
      • SegmentationClasses.FAT
      • SegmentationClasses.GENERIC
      • SegmentationClasses.HEAVY_WATER
      • SegmentationClasses.LYMPH_NODE
      • SegmentationClasses.MEDIPRENE
      • SegmentationClasses.MUSCLE
      • SegmentationClasses.SOFT_TISSUE
      • SegmentationClasses.ULTRASOUND_GEL
      • SegmentationClasses.WATER
    • create_deformation_settings()
    • get_functional_from_deformation_settings()
    • generate_dict_path()
    • get_data_field_from_simpa_output()
    • generate_matlab_cmd()
    • PathManager
      • PathManager.detect_local_path_config()
      • PathManager.get_hdf5_file_save_path()
      • PathManager.get_matlab_binary_path()
      • PathManager.get_mcx_binary_path()
      • PathManager.get_path_from_environment()
    • get_processing_device()
    • profile()
    • SerializableSIMPAClass
      • SerializableSIMPAClass.deserialize()
      • SerializableSIMPAClass.serialize()
    • Settings
      • Settings.deserialize()
      • Settings.get_acoustic_settings()
      • Settings.get_optical_settings()
      • Settings.get_reconstruction_settings()
      • Settings.get_volume_creation_settings()
      • Settings.get_volume_dimensions_voxels()
      • Settings.serialize()
      • Settings.set_acoustic_settings()
      • Settings.set_optical_settings()
      • Settings.set_reconstruction_settings()
      • Settings.set_volume_creation_settings()
    • Tags
      • Tags.ACOUSTIC_LOG_SCALE
      • Tags.ACOUSTIC_MODEL
      • Tags.ACOUSTIC_MODEL_BINARY_PATH
      • Tags.ACOUSTIC_MODEL_K_WAVE
      • Tags.ACOUSTIC_MODEL_OUTPUT_NAME
      • Tags.ACOUSTIC_MODEL_SETTINGS
      • Tags.ACOUSTIC_MODEL_TEST
      • Tags.ACOUSTIC_SIMULATION_3D
      • Tags.ADDITIONAL_FLAGS
      • Tags.ADHERE_TO_DEFORMATION
      • Tags.BACKGROUND
      • Tags.BANDPASS_CUTOFF_HIGHPASS_IN_HZ
      • Tags.BANDPASS_CUTOFF_LOWPASS_IN_HZ
      • Tags.BANDPASS_FILTER_METHOD
      • Tags.BUTTERWORTH_BANDPASS_FILTER
      • Tags.BUTTERWORTH_FILTER_ORDER
      • Tags.CHILD_STRUCTURES
      • Tags.CIRCULAR_TUBULAR_STRUCTURE
      • Tags.COMPUTE_DIFFUSE_REFLECTANCE
      • Tags.COMPUTE_PHOTON_DIRECTION_AT_EXIT
      • Tags.CONSIDER_PARTIAL_VOLUME
      • Tags.CONSIDER_PARTIAL_VOLUME_IN_DEVICE
      • Tags.CONTINUE_SIMULATION
      • Tags.CROP_POSITION_BOTTOM
      • Tags.CROP_POSITION_CENTRE
      • Tags.CROP_POSITION_LEFT
      • Tags.CROP_POSITION_RANDOM
      • Tags.CROP_POSITION_RIGHT
      • Tags.CROP_POSITION_TOP
      • Tags.DATA_FIELD
      • Tags.DATA_FIELD_ABSORPTION_PER_CM
      • Tags.DATA_FIELD_ALPHA_COEFF
      • Tags.DATA_FIELD_ANISOTROPY
      • Tags.DATA_FIELD_BLOOD_VOLUME_FRACTION
      • Tags.DATA_FIELD_DENSITY
      • Tags.DATA_FIELD_DIFFUSE_REFLECTANCE
      • Tags.DATA_FIELD_DIFFUSE_REFLECTANCE_POS
      • Tags.DATA_FIELD_FLUENCE
      • Tags.DATA_FIELD_GRUNEISEN_PARAMETER
      • Tags.DATA_FIELD_INITIAL_PRESSURE
      • Tags.DATA_FIELD_OXYGENATION
      • Tags.DATA_FIELD_PHOTON_EXIT_DIR
      • Tags.DATA_FIELD_PHOTON_EXIT_POS
      • Tags.DATA_FIELD_RECONSTRUCTED_DATA
      • Tags.DATA_FIELD_SCATTERING_PER_CM
      • Tags.DATA_FIELD_SEGMENTATION
      • Tags.DATA_FIELD_SPEED_OF_SOUND
      • Tags.DATA_FIELD_TIME_SERIES_DATA
      • Tags.DEFORMATION_X_COORDINATES_MM
      • Tags.DEFORMATION_Y_COORDINATES_MM
      • Tags.DEFORMATION_Z_ELEVATIONS_MM
      • Tags.DEFORMED_LAYERS_SETTINGS
      • Tags.DETECTOR_ELEMENT_WIDTH_MM
      • Tags.DIGITAL_DEVICE
      • Tags.DIGITAL_DEVICE_MSOT_ACUITY
      • Tags.DIGITAL_DEVICE_MSOT_INVISION
      • Tags.DIGITAL_DEVICE_POSITION
      • Tags.DIGITAL_DEVICE_RSOM
      • Tags.DIGITAL_DEVICE_SLIT_ILLUMINATION_LINEAR_DETECTOR
      • Tags.DIM_VOLUME_X_MM
      • Tags.DIM_VOLUME_Y_MM
      • Tags.DIM_VOLUME_Z_MM
      • Tags.DOWNSCALE_FACTOR
      • Tags.DO_FILE_COMPRESSION
      • Tags.DO_IPASC_EXPORT
      • Tags.ELLIPTICAL_TUBULAR_STRUCTURE
      • Tags.GPU
      • Tags.HORIZONTAL_LAYER_STRUCTURE
      • Tags.IGNORE_QA_ASSERTIONS
      • Tags.ILLUMINATION_DIRECTION
      • Tags.ILLUMINATION_PARAM1
      • Tags.ILLUMINATION_PARAM2
      • Tags.ILLUMINATION_POSITION
      • Tags.ILLUMINATION_TYPE
      • Tags.ILLUMINATION_TYPE_DISK
      • Tags.ILLUMINATION_TYPE_DKFZ_PAUS
      • Tags.ILLUMINATION_TYPE_FOURIER
      • Tags.ILLUMINATION_TYPE_FOURIER_X
      • Tags.ILLUMINATION_TYPE_FOURIER_X_2D
      • Tags.ILLUMINATION_TYPE_GAUSSIAN
      • Tags.ILLUMINATION_TYPE_IPASC_DEFINITION
      • Tags.ILLUMINATION_TYPE_MSOT_ACUITY_ECHO
      • Tags.ILLUMINATION_TYPE_MSOT_INVISION
      • Tags.ILLUMINATION_TYPE_PATTERN
      • Tags.ILLUMINATION_TYPE_PATTERN_3D
      • Tags.ILLUMINATION_TYPE_PENCIL
      • Tags.ILLUMINATION_TYPE_PENCILARRAY
      • Tags.ILLUMINATION_TYPE_PLANAR
      • Tags.ILLUMINATION_TYPE_RING
      • Tags.ILLUMINATION_TYPE_SLIT
      • Tags.IMAGE_PROCESSING
      • Tags.IMAGE_SCALING_CONSTANT
      • Tags.IMAGE_SCALING_EDGE
      • Tags.IMAGE_SCALING_STRETCH
      • Tags.IMAGE_SCALING_SYMMETRIC
      • Tags.IMAGE_SCALING_WRAP
      • Tags.INPUT_SEGMENTATION_VOLUME
      • Tags.ITERATIVE_RECONSTRUCTION_CONSTANT_REGULARIZATION
      • Tags.ITERATIVE_RECONSTRUCTION_MAX_ITERATION_NUMBER
      • Tags.ITERATIVE_RECONSTRUCTION_REGULARIZATION_SIGMA
      • Tags.ITERATIVE_RECONSTRUCTION_SAVE_INTERMEDIATE_RESULTS
      • Tags.ITERATIVE_RECONSTRUCTION_SAVE_LAST_FLUENCE
      • Tags.ITERATIVE_RECONSTRUCTION_STOPPING_LEVEL
      • Tags.ITERATIVE_qPAI_RESULT
      • Tags.KWAVE_PROPERTY_ALPHA_POWER
      • Tags.KWAVE_PROPERTY_DIRECTIVITY_ANGLE
      • Tags.KWAVE_PROPERTY_INITIAL_PRESSURE_SMOOTHING
      • Tags.KWAVE_PROPERTY_INTRINSIC_EULER_ANGLE
      • Tags.KWAVE_PROPERTY_PMLAlpha
      • Tags.KWAVE_PROPERTY_PMLInside
      • Tags.KWAVE_PROPERTY_PMLSize
      • Tags.KWAVE_PROPERTY_PlotPML
      • Tags.KWAVE_PROPERTY_SENSOR_MASK
      • Tags.KWAVE_PROPERTY_SENSOR_RECORD
      • Tags.K_WAVE_SPECIFIC_DT
      • Tags.K_WAVE_SPECIFIC_NT
      • Tags.LASER_PULSE_ENERGY_IN_MILLIJOULE
      • Tags.LINEAR_UNMIXING_COMPUTE_SO2
      • Tags.LINEAR_UNMIXING_NON_NEGATIVE
      • Tags.LINEAR_UNMIXING_RESULT
      • Tags.LINEAR_UNMIXING_SPECTRA
      • Tags.MATLAB_BINARY_PATH_VARNAME
      • Tags.MAX_DEFORMATION_MM
      • Tags.MCX_ASSUMED_ANISOTROPY
      • Tags.MCX_BINARY_PATH_VARNAME
      • Tags.MCX_SEED
      • Tags.MEDIUM_TEMPERATURE_CELCIUS
      • Tags.MODEL_SENSOR_FREQUENCY_RESPONSE
      • Tags.MOLECULE_COMPOSITION
      • Tags.MOVIENAME
      • Tags.NOISE_FREQUENCY
      • Tags.NOISE_MAX
      • Tags.NOISE_MEAN
      • Tags.NOISE_MIN
      • Tags.NOISE_MODE
      • Tags.NOISE_MODE_ADDITIVE
      • Tags.NOISE_MODE_MULTIPLICATIVE
      • Tags.NOISE_NON_NEGATIVITY_CONSTRAINT
      • Tags.NOISE_SCALE
      • Tags.NOISE_SHAPE
      • Tags.NOISE_STD
      • Tags.OPTICAL_MODEL
      • Tags.OPTICAL_MODEL_BINARY_PATH
      • Tags.OPTICAL_MODEL_ILLUMINATION_GEOMETRY_JSON_FILE
      • Tags.OPTICAL_MODEL_MCX
      • Tags.OPTICAL_MODEL_NUMBER_PHOTONS
      • Tags.OPTICAL_MODEL_OUTPUT_NAME
      • Tags.OPTICAL_MODEL_SETTINGS
      • Tags.OPTICAL_MODEL_TEST
      • Tags.OPTICAL_MODEL_UNITS
      • Tags.ORIGINAL_DATA
      • Tags.PARALLELEPIPED_STRUCTURE
      • Tags.PRIORITY
      • Tags.RANDOM_SEED
      • Tags.RECONSTRUCTION_ALGORITHM
      • Tags.RECONSTRUCTION_ALGORITHM_DAS
      • Tags.RECONSTRUCTION_ALGORITHM_DMAS
      • Tags.RECONSTRUCTION_ALGORITHM_SDMAS
      • Tags.RECONSTRUCTION_ALGORITHM_TEST
      • Tags.RECONSTRUCTION_ALGORITHM_TIME_REVERSAL
      • Tags.RECONSTRUCTION_APODIZATION_BOX
      • Tags.RECONSTRUCTION_APODIZATION_HAMMING
      • Tags.RECONSTRUCTION_APODIZATION_HANN
      • Tags.RECONSTRUCTION_APODIZATION_METHOD
      • Tags.RECONSTRUCTION_BMODE_AFTER_RECONSTRUCTION
      • Tags.RECONSTRUCTION_BMODE_BEFORE_RECONSTRUCTION
      • Tags.RECONSTRUCTION_BMODE_METHOD
      • Tags.RECONSTRUCTION_BMODE_METHOD_ABS
      • Tags.RECONSTRUCTION_BMODE_METHOD_HILBERT_TRANSFORM
      • Tags.RECONSTRUCTION_INVERSE_CRIME
      • Tags.RECONSTRUCTION_MITK_BINARY_PATH
      • Tags.RECONSTRUCTION_MITK_SETTINGS_XML
      • Tags.RECONSTRUCTION_MODE
      • Tags.RECONSTRUCTION_MODEL_SETTINGS
      • Tags.RECONSTRUCTION_MODE_DIFFERENTIAL
      • Tags.RECONSTRUCTION_MODE_FULL
      • Tags.RECONSTRUCTION_MODE_PRESSURE
      • Tags.RECONSTRUCTION_OUTPUT_NAME
      • Tags.RECONSTRUCTION_PERFORM_BANDPASS_FILTERING
      • Tags.RECONSTRUCTION_PERFORM_RESAMPLING_FOR_FFT
      • Tags.RECORDMOVIE
      • Tags.RECTANGULAR_CUBOID_STRUCTURE
      • Tags.SEGMENTATION_CLASS_MAPPING
      • Tags.SENSOR_BANDWIDTH_PERCENT
      • Tags.SENSOR_CENTER_FREQUENCY_HZ
      • Tags.SENSOR_CONCAVE
      • Tags.SENSOR_DIRECTIVITY_PATTERN
      • Tags.SENSOR_DIRECTIVITY_SIZE_M
      • Tags.SENSOR_ELEMENT_POSITIONS
      • Tags.SENSOR_LINEAR
      • Tags.SENSOR_NUM_ELEMENTS
      • Tags.SENSOR_NUM_USED_ELEMENTS
      • Tags.SENSOR_PITCH_MM
      • Tags.SENSOR_RADIUS_MM
      • Tags.SENSOR_SAMPLING_RATE_MHZ
      • Tags.SETTINGS
      • Tags.SIGNAL_THRESHOLD
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_COPPER_SULPHIDE
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_DEOXYHEMOGLOBIN
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_FAT
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_MELANIN
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_NICKEL_SULPHIDE
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_OXYHEMOGLOBIN
      • Tags.SIMPA_NAMED_ABSORPTION_SPECTRUM_WATER
      • Tags.SIMPA_OUTPUT_FILE_PATH
      • Tags.SIMPA_OUTPUT_NAME
      • Tags.SIMPA_SAVE_DIRECTORY_VARNAME
      • Tags.SIMPA_VERSION
      • Tags.SIMULATE_DEFORMED_LAYERS
      • Tags.SIMULATIONS
      • Tags.SIMULATION_PATH
      • Tags.SIMULATION_PIPELINE
      • Tags.SIMULATION_PROPERTIES
      • Tags.SPACING_MM
      • Tags.SPHERICAL_STRUCTURE
      • Tags.STRUCTURES
      • Tags.STRUCTURE_BIFURCATION_LENGTH_MM
      • Tags.STRUCTURE_CURVATURE_FACTOR
      • Tags.STRUCTURE_DIRECTION
      • Tags.STRUCTURE_ECCENTRICITY
      • Tags.STRUCTURE_END_MM
      • Tags.STRUCTURE_FIRST_EDGE_MM
      • Tags.STRUCTURE_RADIUS_MM
      • Tags.STRUCTURE_RADIUS_VARIATION_FACTOR
      • Tags.STRUCTURE_SECOND_EDGE_MM
      • Tags.STRUCTURE_SEGMENTATION_TYPE
      • Tags.STRUCTURE_START_MM
      • Tags.STRUCTURE_THIRD_EDGE_MM
      • Tags.STRUCTURE_TYPE
      • Tags.STRUCTURE_X_EXTENT_MM
      • Tags.STRUCTURE_Y_EXTENT_MM
      • Tags.STRUCTURE_Z_EXTENT_MM
      • Tags.TIME_STEP
      • Tags.TISSUE_PROPERTIES_OUPUT_NAME
      • Tags.TOTAL_TIME
      • Tags.TUKEY_BANDPASS_FILTER
      • Tags.TUKEY_WINDOW_ALPHA
      • Tags.UNITS_ARBITRARY
      • Tags.UNITS_PRESSURE
      • Tags.UPSAMPLED_DATA
      • Tags.US_GEL
      • Tags.VESSEL_STRUCTURE
      • Tags.VOLUME_CREATION_MODEL_SETTINGS
      • Tags.VOLUME_CREATOR
      • Tags.VOLUME_CREATOR_SEGMENTATION_BASED
      • Tags.VOLUME_CREATOR_VERSATILE
      • Tags.VOLUME_FRACTION
      • Tags.VOLUME_NAME
      • Tags.WAVELENGTH
      • Tags.WAVELENGTHS
    • TissueProperties
      • TissueProperties.normalized_merge()
      • TissueProperties.weighted_merge()
  • visualisation
    • get_segmentation_colormap()
    • visualise_data()
    • visualise_device()
SIMPA
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