├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── code_enhancement.md │ ├── config.yml │ ├── example.md │ └── feature_request.md ├── codecov.yml ├── dependabot.yml └── workflows │ ├── codespell.yml │ ├── link-check.yml │ ├── pytest.yml │ ├── ruff.yml │ ├── run-examples.yml │ ├── test_example.yml │ ├── test_optional_dependencies.yml │ └── test_pages.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── Makefile ├── docs ├── Makefile ├── README.md ├── _static │ └── example_bmode.png ├── conf.py ├── development │ └── development_environment.rst ├── examples_guide.rst ├── get_started │ ├── contrib.rst │ ├── first_simulation.rst │ ├── grid_overview.rst │ ├── legacy_licenses │ │ ├── gpl-3.0.rst │ │ └── mit.rst │ ├── license.rst │ ├── medium_overview.rst │ ├── sensor_overview.rst │ └── source_overview.rst ├── index.rst ├── kwave.data.rst ├── kwave.enums.rst ├── kwave.executor.rst ├── kwave.kWaveSimulation.rst ├── kwave.kWaveSimulation_helper.create_absorption_variables.rst ├── kwave.kWaveSimulation_helper.display_simulation_params.rst ├── kwave.kWaveSimulation_helper.expand_grid_matrices.rst ├── kwave.kWaveSimulation_helper.retract_transducer_grid_size.rst ├── kwave.kWaveSimulation_helper.rst ├── kwave.kWaveSimulation_helper.save_to_disk_func.rst ├── kwave.kWaveSimulation_helper.scale_source_terms_func.rst ├── kwave.kWaveSimulation_helper.set_sound_speed_ref.rst ├── kwave.kgrid.rst ├── kwave.kmedium.rst ├── kwave.ksensor.rst ├── kwave.ksource.rst ├── kwave.kspaceFirstOrder.rst ├── kwave.kspaceFirstOrder2D.rst ├── kwave.kspaceFirstOrder3D.rst ├── kwave.kspaceFirstOrderAS.rst ├── kwave.ktransducer.rst ├── kwave.options.rst ├── kwave.reconstruction.beamform.rst ├── kwave.reconstruction.converter.rst ├── kwave.reconstruction.rst ├── kwave.reconstruction.shifted_transform.rst ├── kwave.reconstruction.tools.rst ├── kwave.recorder.rst ├── kwave.rst ├── kwave.utils.checks.rst ├── kwave.utils.colormap.rst ├── kwave.utils.conversion.rst ├── kwave.utils.data.rst ├── kwave.utils.dotdictionary.rst ├── kwave.utils.filters.rst ├── kwave.utils.interp.rst ├── kwave.utils.io.rst ├── kwave.utils.mapgen.rst ├── kwave.utils.math.rst ├── kwave.utils.matrix.rst ├── kwave.utils.pml.rst ├── kwave.utils.rst ├── kwave.utils.signals.rst ├── kwave.utils.tictoc.rst ├── make.bat └── reconstruction │ ├── index.rst │ └── time_reversal.rst ├── examples ├── README.md ├── at_array_as_sensor │ ├── README.md │ ├── at_array_as_sensor.ipynb │ └── at_array_as_sensor.py ├── at_array_as_source │ ├── README.md │ ├── at_array_as_source.ipynb │ └── at_array_as_source.py ├── at_circular_piston_3D │ ├── README.md │ ├── at_circular_piston_3D.ipynb │ └── at_circular_piston_3D.py ├── at_circular_piston_AS │ ├── README.md │ ├── at_circular_piston_AS.ipynb │ └── at_circular_piston_AS.py ├── at_focused_annular_array_3D │ ├── README.md │ ├── at_focused_annular_array_3D.ipynb │ └── at_focused_annular_array_3D.py ├── at_focused_bowl_3D │ ├── README.md │ ├── at_focused_bowl_3D.ipynb │ └── at_focused_bowl_3D.py ├── at_focused_bowl_AS │ ├── README.md │ ├── at_focused_bowl_AS.ipynb │ └── at_focused_bowl_AS.py ├── at_linear_array_transducer │ ├── README.md │ ├── at_linear_array_transducer.ipynb │ └── at_linear_array_transducer.py ├── checkpointing │ ├── README.md │ └── checkpoint.py ├── ivp_photoacoustic_waveforms │ ├── README.md │ ├── ivp_photoacoustic_waveforms.ipynb │ └── ivp_photoacoustic_waveforms.py ├── na_controlling_the_pml │ ├── README.md │ ├── modified_matlab_example.m │ └── na_controlling_the_pml.ipynb ├── pr_2D_FFT_line_sensor │ ├── README.md │ ├── pr_2D_FFT_line_sensor.ipynb │ └── pr_2D_FFT_line_sensor.py ├── pr_2D_TR_line_sensor │ ├── README.md │ ├── pr_2D_TR_line_sensor.ipynb │ └── pr_2D_TR_line_sensor.py ├── pr_3D_FFT_planar_sensor │ ├── README.md │ ├── pr_3D_FFT_planar_sensor.ipynb │ └── pr_3D_FFT_planar_sensor.py ├── pr_3D_TR_planar_sensor │ ├── README.md │ ├── pr_3D_TR_planar_sensor.ipynb │ └── pr_3D_TR_planar_sensor.py ├── sd_directivity_modelling_2D │ ├── README.md │ ├── sd_directivity_modelling_2D.ipynb │ └── sd_directivity_modelling_2D.py ├── sd_focussed_detector_2D │ ├── README.md │ ├── sd_focussed_detector_2D.ipynb │ └── sd_focussed_detector_2D.py ├── sd_focussed_detector_3D │ ├── README.md │ ├── sd_focussed_detector_3D.ipynb │ └── sd_focussed_detector_3D.py ├── us_beam_patterns │ ├── README.md │ ├── us_beam_patterns.ipynb │ └── us_beam_patterns.py ├── us_bmode_linear_transducer │ ├── README.md │ ├── example_utils.py │ ├── us_bmode_linear_transducer.ipynb │ └── us_bmode_linear_transducer.py ├── us_bmode_phased_array │ ├── README.md │ ├── us_bmode_phased_array.ipynb │ └── us_bmode_phased_array.py └── us_defining_transducer │ ├── README.md │ ├── us_defining_transducer.ipynb │ └── us_defining_transducer.py ├── kwave ├── __init__.py ├── data.py ├── enums.py ├── executor.py ├── kWaveSimulation.py ├── kWaveSimulation_helper │ ├── __init__.py │ ├── create_absorption_variables.py │ ├── display_simulation_params.py │ ├── expand_grid_matrices.py │ ├── retract_transducer_grid_size.py │ ├── save_to_disk_func.py │ ├── scale_source_terms_func.py │ └── set_sound_speed_ref.py ├── kgrid.py ├── kmedium.py ├── ksensor.py ├── ksource.py ├── kspaceFirstOrder2D.py ├── kspaceFirstOrder3D.py ├── kspaceFirstOrderAS.py ├── kspaceLineRecon.py ├── kspacePlaneRecon.py ├── ktransducer.py ├── options │ ├── __init__.py │ ├── simulation_execution_options.py │ └── simulation_options.py ├── reconstruction │ ├── __init__.py │ ├── beamform.py │ ├── time_reversal.py │ └── tools.py ├── recorder.py └── utils │ ├── __init__.py │ ├── angular_spectrum.py │ ├── angular_spectrum_cw.py │ ├── atten_comp.py │ ├── checks.py │ ├── colormap.py │ ├── conversion.py │ ├── data.py │ ├── dotdictionary.py │ ├── filters.py │ ├── interp.py │ ├── io.py │ ├── kwave_array.py │ ├── mapgen.py │ ├── math.py │ ├── matlab.py │ ├── matrix.py │ ├── plot.py │ ├── pml.py │ ├── sharpness_filters.py │ ├── signals.py │ ├── tictoc.py │ └── typing.py ├── make_docs.sh ├── pyproject.toml ├── pytest.ini ├── run_examples.py ├── run_tests.sh ├── tests ├── EXAMPLE_source_one.png ├── EXAMPLE_source_two.bmp ├── __init__.py ├── diff_utils.py ├── h5_summary.py ├── matlab_test_data_collectors │ ├── matlab_collectors │ │ ├── +private_kwave_functions │ │ │ └── tolStar.m │ │ ├── +utils │ │ │ ├── TestRecorder.m │ │ │ └── rand_vector_in_range.m │ │ ├── collect_FocusAnnulusONeil.m │ │ ├── collect_FocusBowlONeil.m │ │ ├── collect_angularSpectrum.m │ │ ├── collect_angularSpectrumCW.m │ │ ├── collect_at_linear_array_transducer.m │ │ ├── collect_attenComp.m │ │ ├── collect_brenner.m │ │ ├── collect_cart2grid.m │ │ ├── collect_checkStability.m │ │ ├── collect_computeLinearTransform.m │ │ ├── collect_createCWSignals.m │ │ ├── collect_expandMatrix.m │ │ ├── collect_fourierShift.m │ │ ├── collect_gaussian.m │ │ ├── collect_gaussianFilter.m │ │ ├── collect_getAffineMatrix.m │ │ ├── collect_getColorMap.m │ │ ├── collect_getWin.m │ │ ├── collect_get_delta_BLI.m │ │ ├── collect_gradientSpect.m │ │ ├── collect_hounsfield2density.m │ │ ├── collect_interpCartData.m │ │ ├── collect_kWaveArray.m │ │ ├── collect_kWaveGrid.m │ │ ├── collect_makeArc.m │ │ ├── collect_makeBall.m │ │ ├── collect_makeBowl.m │ │ ├── collect_makeCartArc.m │ │ ├── collect_makeCartBowl.m │ │ ├── collect_makeCartCircle.m │ │ ├── collect_makeCartDisc.m │ │ ├── collect_makeCartRect.m │ │ ├── collect_makeCartSphere.m │ │ ├── collect_makeCartSphericalSegment.m │ │ ├── collect_makeCircle.m │ │ ├── collect_makeDisc.m │ │ ├── collect_makeLine.m │ │ ├── collect_makeMultiArc.m │ │ ├── collect_makeMultiBowl.m │ │ ├── collect_makeSphere.m │ │ ├── collect_makeSphericalSection.m │ │ ├── collect_maxND.m │ │ ├── collect_minND.m │ │ ├── collect_normvar.m │ │ ├── collect_reorderBinarySensorData.m │ │ ├── collect_reorderSensorData.m │ │ ├── collect_resize.m │ │ ├── collect_revolve2D.m │ │ ├── collect_rotation_matrices.m │ │ ├── collect_scaleSI.m │ │ ├── collect_scaleTime.m │ │ ├── collect_scanConversion.m │ │ ├── collect_smooth.m │ │ ├── collect_tenenbaum.m │ │ ├── collect_tolStar.m │ │ ├── collect_toneBurst.m │ │ ├── collect_trimCartPoints.m │ │ ├── collect_unmaskSensorData.m │ │ ├── collect_writeAttributes.m │ │ ├── collect_writeFlags.m │ │ ├── collect_writeGrid.m │ │ └── collect_writeMatrix.m │ ├── python_testers │ │ ├── __init__.py │ │ ├── angularSpectrumCW_test.py │ │ ├── angularSpectrum_test.py │ │ ├── attenComp_test.py │ │ ├── cart2grid_test.py │ │ ├── computeLinearTransform_test.py │ │ ├── create_cw_signals_test.py │ │ ├── expandMatrix_test.py │ │ ├── focusBowlONeil_test.py │ │ ├── focusedAnnulusONeil_test.py │ │ ├── fourierShift_test.py │ │ ├── gaussianFilter_test.py │ │ ├── gaussian_test.py │ │ ├── getAffineMatrix_test.py │ │ ├── getColorMap_test.py │ │ ├── getDeltaBLI_test.py │ │ ├── getWin_test.py │ │ ├── h5io_test.py │ │ ├── hounsfield2density.py │ │ ├── kWaveArray_test.py │ │ ├── kWaveGrid_test.py │ │ ├── makeArc_test.py │ │ ├── makeBall_test.py │ │ ├── makeBowl_test.py │ │ ├── makeCartArc_test.py │ │ ├── makeCartBowl_test.py │ │ ├── makeCartCircle_test.py │ │ ├── makeCartRect_test.py │ │ ├── makeCartSphere_test.py │ │ ├── makeCartSphericalSegment_test.py │ │ ├── makeCircle_test.py │ │ ├── makeDisc_test.py │ │ ├── makeLine_test.py │ │ ├── makeMultiArc_test.py │ │ ├── makeMultiBowl_test.py │ │ ├── makeSphere_test.py │ │ ├── makeSphericalSection_test.py │ │ ├── maxND_test.py │ │ ├── minND_test.py │ │ ├── phase_shift_interpolate_test.py │ │ ├── reorderBinarySensorData_test.py │ │ ├── reorderSensorData_test.py │ │ ├── revolve2D_test.py │ │ ├── rotation_matrices_test.py │ │ ├── scaleSI_test.py │ │ ├── scaleTime_test.py │ │ ├── scanConversion_test.py │ │ ├── sharpness_test.py │ │ ├── smooth_test.py │ │ ├── test_check_stability.py │ │ ├── test_interpcartdata.py │ │ ├── test_linear_array_transducer.py │ │ ├── test_make_cart_disc.py │ │ ├── test_resize.py │ │ ├── tolStart_test.py │ │ ├── toneBurst_test.py │ │ ├── trimCartPoints_test.py │ │ ├── unmaskSensorData_test.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── check_equality.py │ │ │ └── record_reader.py │ └── run_all_collectors.m ├── reference_outputs │ ├── out_cpp_io_in_parts.json │ ├── out_cpp_running_simulations.json │ ├── out_ivp_3D_simulation.json │ ├── out_ivp_axisymmetric_simulation.json │ ├── out_ivp_binary_sensor_mask.json │ ├── out_ivp_comparison_modelling_functions │ │ ├── input_1.json │ │ └── input_2.json │ ├── out_ivp_heterogeneous_medium.json │ ├── out_ivp_homogeneous_medium.json │ ├── out_ivp_loading_external_image.json │ ├── out_ivp_opposing_corners_sensor_mask.json │ ├── out_ivp_photoacoustic_waveforms │ │ ├── input_1.json │ │ └── input_2.json │ ├── out_ivp_sensor_frequency_response │ │ ├── input_1.json │ │ └── input_2.json │ ├── out_na_controlling_the_PML │ │ ├── input_1.json │ │ ├── input_2.json │ │ ├── input_3.json │ │ └── input_4.json │ ├── out_na_optimising_performance │ │ ├── input_1.json │ │ ├── input_2.json │ │ └── input_3.json │ ├── out_pr_2D_FFT_line_sensor.json │ ├── out_pr_2D_TR_circular_sensor.json │ ├── out_pr_2D_TR_directional_sensors │ │ ├── input_1.json │ │ └── input_2.json │ ├── out_pr_2D_TR_line_sensor.json │ ├── out_pr_3D_FFT_planar_sensor.json │ ├── out_sd_directional_array_elements.json │ ├── out_sd_directivity_modelling_2D │ │ ├── input_1.json │ │ ├── input_10.json │ │ ├── input_11.json │ │ ├── input_2.json │ │ ├── input_3.json │ │ ├── input_4.json │ │ ├── input_5.json │ │ ├── input_6.json │ │ ├── input_7.json │ │ ├── input_8.json │ │ └── input_9.json │ ├── out_sd_directivity_modelling_3D │ │ ├── input_1.json │ │ ├── input_10.json │ │ ├── input_11.json │ │ ├── input_2.json │ │ ├── input_3.json │ │ ├── input_4.json │ │ ├── input_5.json │ │ ├── input_6.json │ │ ├── input_7.json │ │ ├── input_8.json │ │ └── input_9.json │ ├── out_sd_focussed_detector_2D.json │ ├── out_sd_sensor_directivity_2D.json │ ├── out_tvsp_3D_simulation.json │ ├── out_tvsp_doppler_effect.json │ ├── out_tvsp_homogeneous_medium_dipole.json │ ├── out_tvsp_homogeneous_medium_monopole.json │ ├── out_us_beam_patterns.json │ ├── out_us_bmode_linear_transducer │ │ ├── input_1.json │ │ ├── input_10.json │ │ ├── input_11.json │ │ ├── input_12.json │ │ ├── input_13.json │ │ ├── input_14.json │ │ ├── input_15.json │ │ ├── input_16.json │ │ ├── input_17.json │ │ ├── input_18.json │ │ ├── input_19.json │ │ ├── input_2.json │ │ ├── input_20.json │ │ ├── input_21.json │ │ ├── input_22.json │ │ ├── input_23.json │ │ ├── input_24.json │ │ ├── input_25.json │ │ ├── input_26.json │ │ ├── input_27.json │ │ ├── input_28.json │ │ ├── input_29.json │ │ ├── input_3.json │ │ ├── input_30.json │ │ ├── input_31.json │ │ ├── input_32.json │ │ ├── input_33.json │ │ ├── input_34.json │ │ ├── input_35.json │ │ ├── input_36.json │ │ ├── input_37.json │ │ ├── input_38.json │ │ ├── input_39.json │ │ ├── input_4.json │ │ ├── input_40.json │ │ ├── input_41.json │ │ ├── input_42.json │ │ ├── input_43.json │ │ ├── input_44.json │ │ ├── input_45.json │ │ ├── input_46.json │ │ ├── input_47.json │ │ ├── input_48.json │ │ ├── input_49.json │ │ ├── input_5.json │ │ ├── input_50.json │ │ ├── input_51.json │ │ ├── input_52.json │ │ ├── input_53.json │ │ ├── input_54.json │ │ ├── input_55.json │ │ ├── input_56.json │ │ ├── input_57.json │ │ ├── input_58.json │ │ ├── input_59.json │ │ ├── input_6.json │ │ ├── input_60.json │ │ ├── input_61.json │ │ ├── input_62.json │ │ ├── input_63.json │ │ ├── input_64.json │ │ ├── input_65.json │ │ ├── input_66.json │ │ ├── input_67.json │ │ ├── input_68.json │ │ ├── input_69.json │ │ ├── input_7.json │ │ ├── input_70.json │ │ ├── input_71.json │ │ ├── input_72.json │ │ ├── input_73.json │ │ ├── input_74.json │ │ ├── input_75.json │ │ ├── input_76.json │ │ ├── input_77.json │ │ ├── input_78.json │ │ ├── input_79.json │ │ ├── input_8.json │ │ ├── input_80.json │ │ ├── input_81.json │ │ ├── input_82.json │ │ ├── input_83.json │ │ ├── input_84.json │ │ ├── input_85.json │ │ ├── input_86.json │ │ ├── input_87.json │ │ ├── input_88.json │ │ ├── input_89.json │ │ ├── input_9.json │ │ ├── input_90.json │ │ ├── input_91.json │ │ ├── input_92.json │ │ ├── input_93.json │ │ ├── input_94.json │ │ ├── input_95.json │ │ └── input_96.json │ ├── out_us_bmode_phased_array │ │ ├── input_1.json │ │ ├── input_10.json │ │ ├── input_11.json │ │ ├── input_12.json │ │ ├── input_13.json │ │ ├── input_14.json │ │ ├── input_15.json │ │ ├── input_16.json │ │ ├── input_17.json │ │ ├── input_18.json │ │ ├── input_19.json │ │ ├── input_2.json │ │ ├── input_20.json │ │ ├── input_21.json │ │ ├── input_22.json │ │ ├── input_23.json │ │ ├── input_24.json │ │ ├── input_25.json │ │ ├── input_26.json │ │ ├── input_27.json │ │ ├── input_28.json │ │ ├── input_29.json │ │ ├── input_3.json │ │ ├── input_30.json │ │ ├── input_31.json │ │ ├── input_32.json │ │ ├── input_33.json │ │ ├── input_4.json │ │ ├── input_5.json │ │ ├── input_6.json │ │ ├── input_7.json │ │ ├── input_8.json │ │ └── input_9.json │ ├── out_us_defining_transducer.json │ └── out_us_transducer_as_sensor.json ├── setup_test.py ├── test__init__.py ├── test_checks.py ├── test_cpp_io_in_parts.py ├── test_cpp_running_simulations.py ├── test_create_pixel_dim.py ├── test_display_simulation_params.py ├── test_element.py ├── test_executor.py ├── test_filterutils.py ├── test_ivp_3D_simulation.py ├── test_ivp_axisymmetric_karray_simulation.py ├── test_ivp_axisymmetric_simulation.py ├── test_ivp_binary_sensor_mask.py ├── test_ivp_comparison_modelling_functions.py ├── test_ivp_heterogeneous_medium.py ├── test_ivp_homogeneous_medium.py ├── test_ivp_loading_external_image.py ├── test_ivp_opposing_corners_sensor_mask.py ├── test_ivp_photoacoustic_waveforms.py ├── test_ivp_sensor_frequency_response.py ├── test_ksource.py ├── test_kutils.py ├── test_math.py ├── test_misc.py ├── test_na_controlling_the_PML.py ├── test_na_optimising_performance.py ├── test_pmlutils.py ├── test_pr_2D_FFT_line_sensor.py ├── test_pr_2D_TR_circular_sensor.py ├── test_pr_2D_TR_directional_sensors.py ├── test_pr_2D_TR_line_sensor.py ├── test_pr_3D_FFT_planar_sensor.py ├── test_reconstruction.py ├── test_sd_directional_array_elements.py ├── test_sd_directivity_modelling_2D.py ├── test_sd_directivity_modelling_3D.py ├── test_sd_focussed_detector_2D.py ├── test_sd_sensor_directivity_2D.py ├── test_sharpness_filters.py ├── test_simulation.py ├── test_simulation_execution_options.py ├── test_time_reversal.py ├── test_tvsp_3D_simulation.py ├── test_tvsp_doppler_effect.py ├── test_tvsp_homogeneous_medium_dipole.py ├── test_tvsp_homogeneous_medium_monopole.py ├── test_us_beam_patterns.py ├── test_us_bmode_linear_transducer.py ├── test_us_bmode_phased_array.py ├── test_us_defining_transducer.py ├── test_us_transducer_as_sensor.py ├── test_utils.py └── test_water.py └── uv.lock /.github/CONTRIBUTING.md: 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