simulation_modules

• acoustic_module
  • AcousticAdapterBase
    • AcousticAdapterBase.forward_model()
    • AcousticAdapterBase.load_component_settings()
    • AcousticAdapterBase.run()
  • AcousticTestAdapter
    • AcousticTestAdapter.forward_model()
  • KWaveAdapter
    • KWaveAdapter.forward_model()
    • KWaveAdapter.k_wave_acoustic_forward_model()
  • perform_k_wave_acoustic_forward_simulation()
• optical_module
  • MCXAdapter
    • MCXAdapter.forward_model()
    • MCXAdapter.generate_mcx_bin_input()
    • MCXAdapter.generate_mcx_json_input()
    • MCXAdapter.get_command()
    • MCXAdapter.get_mcx_settings()
    • MCXAdapter.post_process_volumes()
    • MCXAdapter.pre_process_volumes()
    • MCXAdapter.read_mcx_output()
    • MCXAdapter.remove_mcx_output()
    • MCXAdapter.run_mcx()
    • MCXAdapter.volumes_to_mm()
  • MCXReflectanceAdapter
    • MCXReflectanceAdapter.extract_reflectance_from_fluence()
    • MCXReflectanceAdapter.forward_model()
    • MCXReflectanceAdapter.get_command()
    • MCXReflectanceAdapter.post_process_volumes()
    • MCXReflectanceAdapter.pre_process_volumes()
    • MCXReflectanceAdapter.read_mcx_output()
    • MCXReflectanceAdapter.run_forward_model()
  • OpticalAdapterBase
    • OpticalAdapterBase.forward_model()
    • OpticalAdapterBase.load_component_settings()
    • OpticalAdapterBase.run()
    • OpticalAdapterBase.run_forward_model()
  • OpticalTestAdapter
    • OpticalTestAdapter.forward_model()
• 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()

class SimulationModuleBase(global_settings: Settings)

Bases: PipelineElementBase

Defines a simulation module that is a step in the simulation pipeline. Each simulation module can only be one of Volume Creation, Light Propagation Modeling, Acoustic Wave Propagation Modeling, Image Reconstruction.

Parameters:

global_settings (Settings) – The SIMPA settings dictionary

get_additional_flags() → List[str]

Reads the list of additional flags from the corresponding component settings Tags.ADDITIONAL_FLAGS

Returns:

List[str]: list of additional flags

abstract load_component_settings() → Settings

Returns:

Loads component settings corresponding to this simulation component