├── .gitignore ├── CITATION.cff ├── GUIfunctions ├── AcquisitionGUI.mlapp ├── GeometryGUI.mlapp ├── MediumGUI.mlapp ├── MicrobubblesGUI.mlapp ├── SimulationParametersGUI.mlapp ├── TransducerGUI.mlapp ├── TransmitGUI.mlapp ├── assign_liquid_properties.m ├── assign_medium_properties.m ├── compare_structs.m ├── compute_delays.m ├── compute_gaussian_distribution.m ├── compute_polydisperse_distribution.m ├── compute_simulation_domain.m ├── compute_sound_speed_extrema.m ├── compute_surface_tension.m ├── estimate_impulse_response.m ├── estimate_memory.m ├── fit_SigmaR_evaluated.mat ├── get_documentation_urls.m ├── get_gas_properties.m ├── get_pressure_signal.m ├── get_transducer_properties.m ├── get_voltage_signal.m ├── load_from_file.m ├── reset_acquisition.m ├── reset_geometry.m ├── reset_medium.m ├── reset_microbubble.m ├── reset_simulation_parameters.m ├── reset_transducer.m ├── reset_transmit.m ├── run_local.m ├── run_local_setup.m ├── show_microbubble_positions.m ├── sparsify.m ├── stlread_gui.m ├── tissue_properties.mat ├── update_simulation_parameters.m └── write_to_file.m ├── LICENSE ├── MainGUI.mlapp ├── PATHS.mat ├── README.md ├── acoustic-module ├── calc_scatter_attenuated.m ├── check_ground_truth_data.m ├── compute_RF.m ├── compute_RF_data.m ├── compute_bubble_mass_source.m ├── compute_self_sense_pressure.m ├── compute_travel_times.m ├── define_grid.m ├── define_medium.m ├── define_sensor_MB.m ├── define_sensor_MB_all.m ├── define_sensor_transducer.m ├── define_source_transducer.m ├── estim_time_mem.m ├── evaluate_delta_function.m ├── extract_sensor_data.m ├── full_simulator.m ├── get_transducer_integration_delays.m ├── get_transducer_integration_points.m ├── hybrid_simulator.m ├── input_handling.m ├── load_microbubbles.m ├── main_RF.m ├── main_pressure_field.m ├── optimize_grid_size.m ├── preprocess_transmit.m ├── resample_signal.m ├── run_simulation.m ├── run_simulation_homogeneous.m ├── sim_setup.m ├── sim_startup.m ├── sinc_interpolation.m ├── update_sensor.m ├── update_source.m └── voxelize_media_points.m ├── delay-and-sum ├── DAS_reconstruction.m ├── compute_das_matrix.m ├── load_RF_data.m └── write_video.m ├── documentation ├── AcquisitionGUI.md ├── AcquisitionGUI.png ├── GeometryGUI.md ├── GeometryGUI.png ├── MainGUI.png ├── MediumGUI.md ├── MediumGUI.png ├── MicrobubblesGUI.md ├── MicrobubblesGUI.png ├── NewGeometry.md ├── SimulationParametersGUI.md ├── SimulationParametersGUI.png ├── TransducerGUI.md ├── TransducerGUI.png ├── TransmitGUI.md └── TransmitGUI.png ├── example_custom_data ├── custom_apodization.mat ├── custom_delays.mat ├── custom_microbubble_distribution.mat ├── custom_pressure_signal.mat ├── custom_receive_impulse_response.mat ├── custom_transducer.mat ├── custom_transmit_impulse_response.mat ├── custom_voltage_signal.mat ├── fit_SigmaR_evaluated_30PA.mat ├── fit_SigmaR_evaluated_50PA.mat ├── measured_receive_impulse_response.mat └── measured_transmit_impulse_response.mat ├── example_scripts ├── example_batched.m ├── example_medium.m ├── example_new_ground_truth.m ├── example_pressure_field.m ├── example_reconstruction.m └── example_simple.m ├── geometry_data ├── .gitignore ├── mouse_brain │ ├── GeometryProperties.mat │ └── mouse_brain.png ├── renal_tree │ ├── GeometryProperties.mat │ └── renal_tree.png ├── vtkToolbox │ ├── LICENSE │ └── README.md └── vtu2matlab.m ├── mesh-voxelisation ├── Mesh_voxelisation │ ├── COMPUTE_mesh_normals.m │ ├── CONVERT_meshformat.m │ ├── README.txt │ ├── READ_stl.m │ ├── STLvoxelisation.png │ ├── VOXELISE.m │ ├── VOXELISE_example.m │ └── sample.stl └── license.txt ├── microbubble-simulator ├── README.md ├── VariablesList.m ├── calcBubbleResponse.m ├── calc_scatter.m ├── functions │ ├── ReceiveTransferFunctionFit.mat │ ├── TransmitTransferFunctionFit.mat │ ├── TwoWayTransferFunctionFit.mat │ ├── calcBubbleResponseLinear.m │ ├── calc_surface_tension.m │ ├── calc_thermal_damp.m │ ├── compress_bubble.m │ ├── find_A_m0.m │ ├── find_domain_boundaries.m │ ├── fit_SigmaR_04-08-2017.mat │ ├── fit_SigmaR_evaluated.mat │ ├── fit_SigmaR_evaluated_30PA.mat │ ├── fit_SigmaR_evaluated_50PA.mat │ ├── getEqParam.m │ ├── getMaterialProperties.m │ ├── getPulse.m │ ├── getPulseHann.m │ ├── getPulseRect.m │ ├── getPulseTukey.m │ ├── getShellProperties.m │ ├── makeSegersArray.m │ ├── odeOutputFcn.m │ ├── plot_results.m │ └── simple_RP.m └── main.m ├── path_setup.m ├── streamline-module ├── backpropagation.m ├── filter_points.m ├── generate_streamlines.m ├── get_probability_density.m └── private │ ├── draw_random_radii.m │ ├── draw_start_position.m │ ├── exitVesselFcn.m │ ├── filter_points_proximity.m │ ├── get_step_size.m │ ├── get_velocity.m │ ├── get_vtu_indices.m │ ├── load_vessel_data.m │ ├── points_to_distribution.m │ ├── randi_weighted.m │ └── smooth_distribution.m └── time-estimation ├── ExecutionTime.m ├── README.md ├── beta_coeff.mat ├── cpu_performance.txt ├── gpu_performance.txt ├── kWave_curve.csv └── time_calibration.m /.gitignore: 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