├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── build-sdist-publish.yml │ ├── build.yml │ └── draft-pdf.yml ├── .gitignore ├── FastGeodis ├── __init__.py ├── _version.py ├── common.h ├── fastgeodis.cpp ├── fastgeodis.h ├── fastgeodis_cpu.cpp ├── fastgeodis_cuda.cu ├── geodis_fastmarch.cpp ├── geodis_pixelqueue.cpp └── geodis_toivanen.cpp ├── LICENSE ├── MANIFEST.in ├── README.md ├── data ├── ISIC_546.jpg ├── brain.png ├── brain_seg.png ├── brain_seg_noisy.png ├── img2d.png └── img3d.nii.gz ├── dependency └── fmm │ ├── .github │ └── workflows │ │ ├── cmake.yml │ │ └── cpplint.yml │ ├── .gitignore │ ├── CMakeLists.txt │ ├── CPPLINT.cfg │ ├── README.md │ ├── bindings │ └── python │ │ ├── CMakeLists.txt │ │ └── py-fast-marching-method.cpp │ ├── examples │ ├── cpp │ │ ├── CMakeLists.txt │ │ └── minimal_example.cpp │ └── python │ │ └── py-fast-marching-minimal-example.py │ ├── img │ ├── fmm_readme.pdf │ ├── fmm_readme_concept.png │ ├── fmm_readme_dilation_bands.png │ ├── fmm_readme_eikonal_solvers.png │ ├── fmm_readme_input_values.png │ ├── fmm_readme_inside_outside.png │ └── fmm_readme_point_source_error.png │ ├── include │ └── thinks │ │ └── fast_marching_method │ │ └── fast_marching_method.hpp │ └── tests │ ├── CMakeLists.txt │ ├── eikonal_solvers_test.cpp │ ├── main.cpp │ ├── py-bindings-test.py │ ├── signed_arrival_time_test.cpp │ └── util.hpp ├── docs ├── .nojekyll ├── Makefile ├── make.bat ├── requirements-doc.txt └── source │ ├── acknowledgement.rst │ ├── api_docs.rst │ ├── citing.rst │ ├── conf.py │ ├── contributing.rst │ ├── experiment2d.csv │ ├── experiment3d.csv │ ├── getting_started.rst │ ├── index.rst │ ├── license.rst │ ├── methodology.rst │ ├── refs.bib │ └── usage_examples.rst ├── figures ├── 3d_axial.png ├── 3d_coronal.png ├── FastGeodis2D.png ├── FastGeodis3D.png ├── animation_pass2d.gif ├── experiment_2d.json ├── experiment_2d.png ├── experiment_2d_toivanen.png ├── experiment_3d.json ├── experiment_3d.png ├── experiment_3d_toivanen.png ├── fast_marching_compare_2d.png ├── fast_marching_compare_2d_jointhist.png ├── fast_marching_compare_3d.png ├── fast_marching_compare_3d_jointhist.png └── rasterscan_toivanen.png ├── paper ├── FastGeodis.png ├── paper.bib └── paper.md ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt ├── samples ├── demo2d.ipynb ├── demo2d.py ├── demo2d_signed.ipynb ├── demo2d_signed.py ├── demo3d.ipynb ├── demo3d.py ├── demo3d_signed.ipynb ├── demo3d_signed.py ├── demoGSF2d_SmoothingSegExample.ipynb ├── simpledemo2d.ipynb ├── simpledemo2d.py ├── simpledemo2d_profile.py ├── simpledemo2d_signed.ipynb ├── simpledemo2d_signed.py ├── simpledemo3d.ipynb ├── simpledemo3d.py ├── simpledemo3d_profile.py ├── simpledemo3d_signed.ipynb ├── simpledemo3d_signed.py ├── test_speed_benchmark_geodistk.py └── test_speed_benchmark_toivanen.py ├── setup.py └── tests ├── __init__.py ├── test_fastgeodis.py ├── test_fastmarch.py ├── test_pixelqueue.py ├── 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