├── .codespellrc ├── .gitattributes ├── .github └── workflows │ ├── build_and_test_mac.yml │ ├── build_and_test_ubuntu.yml │ ├── build_and_test_windows.yml │ ├── build_cuda11_wheels.yml │ ├── build_cuda12_wheels.yml │ ├── build_wheels.yml │ ├── publish_cuda11_pypi.yml │ ├── publish_cuda12_pypi.yml │ ├── publish_docker.yml │ └── publish_pypi.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── ci-utils ├── build_conda.sh ├── docker_copy_3rd_party_libs.sh ├── envs │ ├── conda_cpp.txt │ ├── conda_gpu.txt │ ├── conda_linux_compiler.txt │ ├── conda_linux_gpu.txt │ └── conda_py.txt ├── install_cuda_windows.ps1 ├── install_cuda_yum.sh ├── install_prereq_linux.sh ├── install_prereq_win.bat └── install_win_nyxus.bat ├── cmake-modules ├── FindBLOSC.cmake ├── FindFastLoader.cmake └── FindHedgehog.cmake ├── codespellignore.txt ├── docs ├── Makefile ├── make.bat └── source │ ├── Math.rst │ ├── Math │ ├── bw_mask.png │ ├── chord.jpg │ ├── contour_tracing_moore_algorithm_1.jpg │ ├── contour_tracing_moore_algorithm_2.jpg │ ├── contour_tracing_moore_algorithm_3.jpg │ ├── erosion.jpg │ ├── erosion2vanish.png │ ├── f_2dmoments.rst │ ├── f_erosion.rst │ ├── f_fractal_dimension.rst │ ├── f_gabor.rst │ ├── f_glcm.rst │ ├── f_gldm.rst │ ├── f_gldzm.rst │ ├── f_glrlm.rst │ ├── f_glszm.rst │ ├── f_image_quality.rst │ ├── f_morphology.rst │ ├── f_ngldm.rst │ ├── f_ngtdm.rst │ ├── f_pixel_intensity.rst │ ├── f_zernike.rst │ ├── feret3.jpg │ ├── gabor_gamma.png │ ├── martin.jpg │ ├── nassenstein.jpg │ ├── structuring_element.jpg │ ├── structuring_element_2.jpg │ └── translation.jpg │ ├── Reference.rst │ ├── References │ └── Classes.rst │ ├── cmdline_and_examples.rst │ ├── conf.py │ ├── devguide.rst │ ├── featurelist.rst │ ├── imagequality.rst │ ├── img │ ├── child_int.png │ ├── child_seg.png │ ├── parent_int.png │ └── parent_seg.png │ ├── index.rst │ ├── nyxus_workflow.jpg │ └── supported_formats.rst ├── environment.yml ├── plugin.json ├── pytest.ini ├── setup.cfg ├── setup.py ├── src └── nyx │ ├── 3rdparty │ ├── dsyevj3.cpp │ ├── dsyevj3.h │ └── quickhull.hpp │ ├── abs_tile_loader.h │ ├── arrow_helpers.cpp │ ├── arrow_output_stream.cpp │ ├── arrow_output_stream.h │ ├── cache.cpp │ ├── cache.h │ ├── cli_anisotropy_options.cpp │ ├── cli_anisotropy_options.h │ ├── cli_fpimage_options.cpp │ ├── cli_fpimage_options.h │ ├── cli_gabor_options.cpp │ ├── cli_gabor_options.h │ ├── cli_glcm_options.cpp │ ├── cli_glcm_options.h │ ├── cli_gpu_options.cpp │ ├── cli_gpu_options.h │ ├── cli_nested_roi_options.cpp │ ├── cli_nested_roi_options.h │ ├── cli_option_constants.h │ ├── cli_result_options.h │ ├── common_stats.cpp │ ├── dataset.cpp │ ├── dataset.h │ ├── dirs_and_files.cpp │ ├── dirs_and_files.h │ ├── env_features.cpp │ ├── environment.cpp │ ├── environment.h │ ├── environment_basic.cpp │ ├── environment_basic.h │ ├── feature_method.cpp │ ├── feature_method.h │ ├── feature_mgr.cpp │ ├── feature_mgr.h │ ├── feature_mgr_init.cpp │ ├── feature_settings.h │ ├── features │ ├── 2d_geomoments.cpp │ ├── 2d_geomoments.h │ ├── 2d_geomoments_basic.cpp │ ├── 2d_geomoments_basic_nt.cpp │ ├── 3d_glcm.cpp │ ├── 3d_glcm.h │ ├── 3d_glcm_nontriv.cpp │ ├── 3d_gldm.cpp │ ├── 3d_gldm.h │ ├── 3d_gldzm.cpp │ ├── 3d_gldzm.h │ ├── 3d_glrlm.cpp │ ├── 3d_glrlm.h │ ├── 3d_glrlm_nontriv.cpp │ ├── 3d_glszm.cpp │ ├── 3d_glszm.h │ ├── 3d_intensity.cpp │ ├── 3d_intensity.h │ ├── 3d_ngldm.cpp │ ├── 3d_ngldm.h │ ├── 3d_ngtdm.cpp │ ├── 3d_ngtdm.h │ ├── 3d_surface.cpp │ ├── 3d_surface.h │ ├── aabb.h │ ├── basic_morphology.cpp │ ├── basic_morphology.h │ ├── caliper.h │ ├── caliper_feret.cpp │ ├── caliper_martin.cpp │ ├── caliper_nassenstein.cpp │ ├── chords.cpp │ ├── chords.h │ ├── chords_nontriv.cpp │ ├── circle.cpp │ ├── circle.h │ ├── contour.cpp │ ├── contour.h │ ├── convex_hull.h │ ├── convex_hull_nontriv.cpp │ ├── ellipse_fitting.cpp │ ├── ellipse_fitting.h │ ├── erosion.cpp │ ├── erosion.h │ ├── euler_number.cpp │ ├── euler_number.h │ ├── extrema.cpp │ ├── extrema.h │ ├── focus_score.cpp │ ├── focus_score.h │ ├── fractal_dim.cpp │ ├── fractal_dim.h │ ├── gabor.cpp │ ├── gabor.h │ ├── gabor_nontriv.cpp │ ├── geo_len_thickness.cpp │ ├── geodetic_len_thickness.h │ ├── glcm.cpp │ ├── glcm.h │ ├── glcm_nontriv.cpp │ ├── gldm.cpp │ ├── gldm.h │ ├── gldzm.cpp │ ├── gldzm.h │ ├── glrlm.cpp │ ├── glrlm.h │ ├── glszm.cpp │ ├── glszm.h │ ├── hexagonality_polygonality.cpp │ ├── hexagonality_polygonality.h │ ├── histogram.h │ ├── image_cube.h │ ├── image_matrix.cpp │ ├── image_matrix.h │ ├── image_matrix_nontriv.cpp │ ├── image_matrix_nontriv.h │ ├── intensity.cpp │ ├── intensity.h │ ├── moments.h │ ├── neighbors.cpp │ ├── neighbors.h │ ├── ngldm.cpp │ ├── ngldm.h │ ├── ngtdm.cpp │ ├── ngtdm.h │ ├── pixel.cpp │ ├── pixel.h │ ├── power_spectrum.cpp │ ├── power_spectrum.h │ ├── radial_distribution.cpp │ ├── radial_distribution.h │ ├── roi_radius.cpp │ ├── roi_radius.h │ ├── rotation.cpp │ ├── rotation.h │ ├── saturation.cpp │ ├── saturation.h │ ├── sharpness.cpp │ ├── sharpness.h │ ├── specfunc.cpp │ ├── specfunc.h │ ├── texture_feature.cpp │ ├── texture_feature.h │ ├── zernike.cpp │ ├── zernike.h │ └── zernike_nontriv.cpp │ ├── features_calc_workflow.cpp │ ├── featureset.cpp │ ├── featureset.h │ ├── globals.cpp │ ├── globals.h │ ├── gpu │ ├── cache.cu │ ├── erosion.cu │ ├── find_cuda_gpu.c │ ├── gabor.cu │ ├── gabor.cuh │ ├── geomoments.cuh │ ├── geomoments_central.cu │ ├── geomoments_hu.cu │ ├── geomoments_main.cu │ ├── geomoments_norm.cu │ ├── geomoments_origin.cu │ ├── geomoments_raw.cu │ ├── geomoments_weighting.cu │ ├── glszm.cu │ ├── glszm.cuh │ ├── gpu.h │ ├── gpu_helpers.cu │ ├── gpucache.cu │ ├── helper_cuda.h │ ├── helper_string.h │ ├── image_moments2.cu │ └── reducers.cu │ ├── gpucache.cpp │ ├── grayscale_tiff.h │ ├── helpers │ ├── BS_thread_pool.hpp │ ├── diag.cpp │ ├── fft.h │ ├── fsystem.h │ ├── helpers.cpp │ ├── helpers.h │ ├── lstsq.h │ ├── system_resource.h │ ├── timing.cpp │ └── timing.h │ ├── image_loader.cpp │ ├── image_loader.h │ ├── image_loader1x.cpp │ ├── image_loader1x.h │ ├── io │ └── nifti │ │ ├── laynii_lib.cpp │ │ ├── laynii_lib.h │ │ ├── nifti1.h │ │ ├── nifti2.h │ │ ├── nifti2_io.cpp │ │ ├── nifti2_io.h │ │ ├── znzlib.cpp │ │ └── znzlib.h │ ├── main_nyxus.cpp │ ├── nested_feature_aggregation.h │ ├── nested_roi.cpp │ ├── nested_roi.h │ ├── nyxus_dicom_loader.h │ ├── omezarr.h │ ├── output_2_apache.cpp │ ├── output_2_buffer.cpp │ ├── output_2_csv.cpp │ ├── output_types.h │ ├── output_writers.cpp │ ├── output_writers.h │ ├── parallel.h │ ├── phase1.cpp │ ├── phase2_25d.cpp │ ├── phase2_2d.cpp │ ├── phase2_3d.cpp │ ├── phase3.cpp │ ├── pixel_feed.cpp │ ├── python │ ├── nested_roi_py.cpp │ ├── new_bindings_py.cpp │ ├── nyxus │ │ ├── __init__.py │ │ ├── _version.py │ │ ├── functions.py │ │ └── nyxus.py │ └── table_caster.h │ ├── raw_dicom.h │ ├── raw_format.h │ ├── raw_image_loader.cpp │ ├── raw_image_loader.h │ ├── raw_nifti.cpp │ ├── raw_nifti.h │ ├── raw_omezarr.h │ ├── raw_tiff.h │ ├── reduce_trivial_rois.cpp │ ├── results_cache.h │ ├── roi_blacklist.cpp │ ├── roi_blacklist.h │ ├── roi_cache.cpp │ ├── roi_cache.h │ ├── roi_cache_basic.cpp │ ├── roi_cache_basic.h │ ├── save_option.h │ ├── slideprops.cpp │ ├── slideprops.h │ ├── strpat.cpp │ ├── strpat.h │ ├── version.h │ ├── workflow_2d_segmented.cpp │ ├── workflow_2d_whole.cpp │ ├── workflow_3d_segmented.cpp │ ├── workflow_3d_whole.cpp │ └── workflow_pythonapi.cpp ├── tests ├── CMakeLists.txt ├── CMakeLists.txt.gtest ├── data │ └── nifti │ │ ├── compat_int │ │ └── compat_int_mri.nii │ │ ├── compat_seg │ │ └── compat_seg_liver.nii │ │ ├── mask │ │ └── mask.nii.gz │ │ ├── phantoms │ │ ├── 2torus.nii │ │ ├── ut_inten.nii │ │ └── ut_mask57.nii │ │ └── signal │ │ ├── signal1.nii │ │ └── signal2.nii.gz ├── python │ ├── data │ │ ├── int │ │ │ ├── p0_y1_r1_c0.ome.tif │ │ │ └── p0_y1_r1_c1.ome.tif │ │ └── seg │ │ │ ├── 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