core

• device_digital_twins
  • detection_geometries
    • CurvedArrayDetectionGeometry
      • CurvedArrayDetectionGeometry.check_settings_prerequisites()
      • CurvedArrayDetectionGeometry.deserialize()
      • CurvedArrayDetectionGeometry.get_detector_element_orientations()
      • CurvedArrayDetectionGeometry.get_detector_element_positions_base_mm()
      • CurvedArrayDetectionGeometry.serialize()
      • CurvedArrayDetectionGeometry.update_settings_for_use_of_model_based_volume_creator()
    • DetectionGeometryBase
      • DetectionGeometryBase.deserialize()
      • DetectionGeometryBase.get_detector_element_orientations()
      • DetectionGeometryBase.get_detector_element_positions_accounting_for_device_position_mm()
      • DetectionGeometryBase.get_detector_element_positions_accounting_for_field_of_view()
      • DetectionGeometryBase.get_detector_element_positions_base_mm()
      • DetectionGeometryBase.serialize()
    • LinearArrayDetectionGeometry
      • LinearArrayDetectionGeometry.check_settings_prerequisites()
      • LinearArrayDetectionGeometry.deserialize()
      • LinearArrayDetectionGeometry.get_detector_element_orientations()
      • LinearArrayDetectionGeometry.get_detector_element_positions_base_mm()
      • LinearArrayDetectionGeometry.serialize()
      • LinearArrayDetectionGeometry.update_settings_for_use_of_model_based_volume_creator()
    • PlanarArrayDetectionGeometry
      • PlanarArrayDetectionGeometry.check_settings_prerequisites()
      • PlanarArrayDetectionGeometry.deserialize()
      • PlanarArrayDetectionGeometry.get_detector_element_orientations()
      • PlanarArrayDetectionGeometry.get_detector_element_positions_base_mm()
      • PlanarArrayDetectionGeometry.get_field_of_view_extent_mm()
      • PlanarArrayDetectionGeometry.serialize()
      • PlanarArrayDetectionGeometry.update_settings_for_use_of_model_based_volume_creator()
  • illumination_geometries
    • DiskIlluminationGeometry
      • DiskIlluminationGeometry.deserialize()
      • DiskIlluminationGeometry.get_mcx_illuminator_definition()
      • DiskIlluminationGeometry.serialize()
    • GaussianBeamIlluminationGeometry
      • GaussianBeamIlluminationGeometry.deserialize()
      • GaussianBeamIlluminationGeometry.get_mcx_illuminator_definition()
      • GaussianBeamIlluminationGeometry.serialize()
    • IlluminationGeometryBase
      • IlluminationGeometryBase.check_settings_prerequisites()
      • IlluminationGeometryBase.deserialize()
      • IlluminationGeometryBase.get_mcx_illuminator_definition()
      • IlluminationGeometryBase.serialize()
      • IlluminationGeometryBase.update_settings_for_use_of_model_based_volume_creator()
    • MSOTAcuityIlluminationGeometry
      • MSOTAcuityIlluminationGeometry.deserialize()
      • MSOTAcuityIlluminationGeometry.get_mcx_illuminator_definition()
      • MSOTAcuityIlluminationGeometry.serialize()
    • MSOTInVisionIlluminationGeometry
      • MSOTInVisionIlluminationGeometry.deserialize()
      • MSOTInVisionIlluminationGeometry.get_mcx_illuminator_definition()
      • MSOTInVisionIlluminationGeometry.serialize()
    • PencilArrayIlluminationGeometry
      • PencilArrayIlluminationGeometry.deserialize()
      • PencilArrayIlluminationGeometry.get_mcx_illuminator_definition()
      • PencilArrayIlluminationGeometry.serialize()
    • PencilBeamIlluminationGeometry
      • PencilBeamIlluminationGeometry.deserialize()
      • PencilBeamIlluminationGeometry.get_mcx_illuminator_definition()
      • PencilBeamIlluminationGeometry.serialize()
    • RectangleIlluminationGeometry
      • RectangleIlluminationGeometry.deserialize()
      • RectangleIlluminationGeometry.get_mcx_illuminator_definition()
      • RectangleIlluminationGeometry.serialize()
    • RingIlluminationGeometry
      • RingIlluminationGeometry.deserialize()
      • RingIlluminationGeometry.get_mcx_illuminator_definition()
      • RingIlluminationGeometry.serialize()
    • SlitIlluminationGeometry
      • SlitIlluminationGeometry.deserialize()
      • SlitIlluminationGeometry.get_mcx_illuminator_definition()
      • SlitIlluminationGeometry.serialize()
  • pa_devices
    • MSOTAcuityEcho
      • MSOTAcuityEcho.deserialize()
      • MSOTAcuityEcho.serialize()
      • MSOTAcuityEcho.update_settings_for_use_of_model_based_volume_creator()
    • InVision256TF
      • InVision256TF.deserialize()
      • InVision256TF.serialize()
    • RSOMExplorerP50
      • RSOMExplorerP50.deserialize()
      • RSOMExplorerP50.serialize()
    • PhotoacousticDevice
      • PhotoacousticDevice.detection_geometry
      • PhotoacousticDevice.illumination_geometries
      • PhotoacousticDevice.add_illumination_geometry()
      • PhotoacousticDevice.check_settings_prerequisites()
      • PhotoacousticDevice.deserialize()
      • PhotoacousticDevice.get_detection_geometry()
      • PhotoacousticDevice.get_illumination_geometry()
      • PhotoacousticDevice.serialize()
      • PhotoacousticDevice.set_detection_geometry()
      • PhotoacousticDevice.update_settings_for_use_of_model_based_volume_creator()
  • 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
      • GammaNoise
      • GaussianNoise
      • PoissonNoise
      • SaltAndPepperNoise
      • UniformNoise
    • FieldOfViewCropping
      • FieldOfViewCropping.run()
    • IterativeqPAI
      • IterativeqPAI.convergence_stopping_criterion()
      • IterativeqPAI.extract_initial_data_from_hdf5()
      • IterativeqPAI.forward_model_fluence()
      • IterativeqPAI.iterative_absorption_reconstruction()
      • IterativeqPAI.log_sum_squared_error()
      • IterativeqPAI.preprocessing_for_iterative_qpai()
      • IterativeqPAI.regularization_sigma()
      • IterativeqPAI.resampling_for_iterative_qpai()
      • IterativeqPAI.run()
      • IterativeqPAI.stacking_to_3d()
      • IterativeqPAI.standard_optical_properties()
      • IterativeqPAI.update_absorption_estimate()
  • multispectral
    • LinearUnmixing
      • LinearUnmixing.build_chromophore_spectra_dict()
      • LinearUnmixing.calculate_sO2()
      • LinearUnmixing.create_absorption_matrix()
      • LinearUnmixing.create_chromophore_spectra_entry()
      • LinearUnmixing.flupai()
      • LinearUnmixing.run()
    • MultispectralProcessingAlgorithm
      • MultispectralProcessingAlgorithm.run()
  • ProcessingComponentBase
• simulation_modules
  • reconstruction_module
    • create_reconstruction_settings()
    • DelayAndSumAdapter
      • DelayAndSumAdapter.reconstruction_algorithm()
    • reconstruct_delay_and_sum_pytorch()
    • DelayMultiplyAndSumAdapter
      • DelayMultiplyAndSumAdapter.reconstruction_algorithm()
    • reconstruct_delay_multiply_and_sum_pytorch()
    • ReconstructionAdapterBase
      • ReconstructionAdapterBase.load_component_settings()
      • ReconstructionAdapterBase.reconstruction_algorithm()
      • ReconstructionAdapterBase.run()
    • ReconstructionTestAdapter
      • ReconstructionTestAdapter.reconstruction_algorithm()
    • 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
      • SignedDelayMultiplyAndSumAdapter.reconstruction_algorithm()
    • reconstruct_signed_delay_multiply_and_sum_pytorch()
    • TimeReversalAdapter
      • TimeReversalAdapter.get_acoustic_properties()
      • TimeReversalAdapter.reconstruction_algorithm()
      • TimeReversalAdapter.reorder_time_series_data()
  • volume_creation_module
    • ModelBasedAdapter
      • ModelBasedAdapter.create_simulation_volume()
    • SegmentationBasedAdapter
      • SegmentationBasedAdapter.create_simulation_volume()
    • VolumeCreationAdapterBase
      • VolumeCreationAdapterBase.create_empty_volumes()
      • VolumeCreationAdapterBase.create_simulation_volume()
      • VolumeCreationAdapterBase.load_component_settings()
      • VolumeCreationAdapterBase.run()
  • SimulationModuleBase
    • SimulationModuleBase.get_additional_flags()
    • SimulationModuleBase.load_component_settings()

class PipelineElementBase(global_settings: Settings)

Bases: object

Defines a pipeline element (either simulation or processing module) that implements a run method and can be called by running the pipeline’s simulate method.

Parameters:

global_settings (Settings) – The SIMPA settings dictionary

abstract run(digital_device_twin: DigitalDeviceTwinBase)

Executes the respective simulation module

Parameters:

digital_device_twin – The digital twin that can be used by the digital device_twin.

simulate(simulation_pipeline: list, settings: Settings, digital_device_twin: DigitalDeviceTwinBase)

This method constitutes the staring point for the simulation pipeline of the SIMPA toolkit.

Parameters:

• simulation_pipeline – a list of callable functions

• settings – settings dictionary containing the simulation instructions

• digital_device_twin – a digital device twin of an imaging device as specified by the DigitalDeviceTwinBase class.

Raises:

• TypeError – if one of the given parameters is not of the correct type

• AssertionError – if the digital device twin is not able to simulate the settings specification

Returns:

list with the save paths of the simulated data within the HDF5 file.