SIMPA
Welcome to the SIMPA documentation!
The toolkit for Simulation and Image Processing for Photonics and Acoustics (SIMPA) aims to facilitate realistic image simulation for optical and acoustic imaging modalities by providing adapters to crucial modelling steps, such as volume generation; optical modelling; acoustic modelling; and image reconstruction. SIMPA provides a communication layer between various modules that implement optical and acoustic forward and inverse models. Non-experts can use the toolkit to create sensible simulations from default parameters in an end-to-end fashion. Domain experts are provided with the functionality to set up a highly customisable pipeline according to their specific use cases and tool requirements.
SIMPA examples
Package reference
- core
- io_handling
- log
- utils
- libraries
- absorption_spectra_data
- anisotropy_spectra_data
- scattering_spectra_data
- structure_library
MorphologicalTissuePropertiesOpticalTissuePropertiesStandardPropertiesMolecularCompositionMolecularCompositionGeneratorMoleculeMoleculeLibraryAbsorptionSpectrumLibraryAnisotropySpectrumLibraryScatteringSpectrumLibrarySpectraLibrarySpectrumget_simpa_internal_absorption_spectra_by_names()view_saved_spectra()TissueLibrary
- quality_assurance
calculate_gruneisen_parameter_from_temperature()calculate_oxygenation()create_spline_for_range()min_max_normalization()positive_gauss()randomize_uniform()rotation()rotation_matrix_between_vectors()rotation_x()rotation_y()rotation_z()spline_evaluator2d_voxel()EPSSegmentationClassesSegmentationClasses.AIRSegmentationClasses.BLOODSegmentationClasses.BONESegmentationClasses.COUPLING_ARTIFACTSegmentationClasses.DERMISSegmentationClasses.EPIDERMISSegmentationClasses.FATSegmentationClasses.GENERICSegmentationClasses.HEAVY_WATERSegmentationClasses.LYMPH_NODESegmentationClasses.MEDIPRENESegmentationClasses.MUSCLESegmentationClasses.SOFT_TISSUESegmentationClasses.ULTRASOUND_GELSegmentationClasses.WATER
create_deformation_settings()get_functional_from_deformation_settings()generate_dict_path()get_data_field_from_simpa_output()generate_matlab_cmd()PathManagerget_processing_device()SerializableSIMPAClassSettingsSettings.deserialize()Settings.get_acoustic_settings()Settings.get_optical_settings()Settings.get_reconstruction_settings()Settings.get_volume_creation_settings()Settings.serialize()Settings.set_acoustic_settings()Settings.set_optical_settings()Settings.set_reconstruction_settings()Settings.set_volume_creation_settings()
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_CLASS_MAPPINGTags.SENSOR_BANDWIDTH_PERCENTTags.SENSOR_CENTER_FREQUENCY_HZTags.SENSOR_CONCAVETags.SENSOR_DIRECTIVITY_PATTERNTags.SENSOR_DIRECTIVITY_SIZE_MTags.SENSOR_ELEMENT_POSITIONSTags.SENSOR_LINEARTags.SENSOR_NUM_ELEMENTSTags.SENSOR_NUM_USED_ELEMENTSTags.SENSOR_PITCH_MMTags.SENSOR_RADIUS_MMTags.SENSOR_SAMPLING_RATE_MHZTags.SETTINGSTags.SIGNAL_THRESHOLDTags.SIMPA_NAMED_ABSORPTION_SPECTRUM_COPPER_SULPHIDETags.SIMPA_NAMED_ABSORPTION_SPECTRUM_DEOXYHEMOGLOBINTags.SIMPA_NAMED_ABSORPTION_SPECTRUM_FATTags.SIMPA_NAMED_ABSORPTION_SPECTRUM_MELANINTags.SIMPA_NAMED_ABSORPTION_SPECTRUM_NICKEL_SULPHIDETags.SIMPA_NAMED_ABSORPTION_SPECTRUM_OXYHEMOGLOBINTags.SIMPA_NAMED_ABSORPTION_SPECTRUM_WATERTags.SIMPA_OUTPUT_NAMETags.SIMPA_OUTPUT_PATHTags.SIMPA_VERSIONTags.SIMULATE_DEFORMED_LAYERSTags.SIMULATIONSTags.SIMULATION_PATHTags.SIMULATION_PIPELINETags.SIMULATION_PROPERTIESTags.SPACING_MMTags.SPHERICAL_STRUCTURETags.STRUCTURESTags.STRUCTURE_BIFURCATION_LENGTH_MMTags.STRUCTURE_CURVATURE_FACTORTags.STRUCTURE_DIRECTIONTags.STRUCTURE_ECCENTRICITYTags.STRUCTURE_END_MMTags.STRUCTURE_FIRST_EDGE_MMTags.STRUCTURE_RADIUS_MMTags.STRUCTURE_RADIUS_VARIATION_FACTORTags.STRUCTURE_SECOND_EDGE_MMTags.STRUCTURE_SEGMENTATION_TYPETags.STRUCTURE_START_MMTags.STRUCTURE_THIRD_EDGE_MMTags.STRUCTURE_TYPETags.STRUCTURE_X_EXTENT_MMTags.STRUCTURE_Y_EXTENT_MMTags.STRUCTURE_Z_EXTENT_MMTags.TIME_STEPTags.TISSUE_PROPERTIES_OUPUT_NAMETags.TOTAL_TIMETags.TUKEY_BANDPASS_FILTERTags.TUKEY_WINDOW_ALPHATags.UNITS_ARBITRARYTags.UNITS_PRESSURETags.UPSAMPLED_DATATags.US_GELTags.VESSEL_STRUCTURETags.VOLUME_CREATION_MODEL_SETTINGSTags.VOLUME_CREATORTags.VOLUME_CREATOR_SEGMENTATION_BASEDTags.VOLUME_CREATOR_VERSATILETags.VOLUME_NAMETags.WAVELENGTHTags.WAVELENGTHS
TissueProperties
- libraries
- visualisation