clabtoolkit Logo
  • bidstools module
    • str2entity()
    • entity2str()
    • delete_entity()
    • replace_entity_value()
    • replace_entity_key()
    • insert_entity()
    • recursively_replace_entity_value()
    • recursively_replace_entity_key()
    • recursively_delete_entity()
    • recursively_insert_entity()
    • get_all_entities()
    • entities4table()
    • entities_to_table()
    • get_subjects()
    • copy_bids_folder()
    • get_bids_database_table()
    • get_derivatives_folders()
    • is_bids_filename()
    • get_individual_files_and_folders()
    • generate_bids_tree()
    • generate_bids_tree_with_stats()
    • validate_bids_structure()
    • load_bids_json()
    • Key Features
    • Common Usage Examples
  • colorstools module
    • bcolors
      • bcolors.HEADER
      • bcolors.OKBLUE
      • bcolors.OKGREEN
      • bcolors.OKYELLOW
      • bcolors.OKRED
      • bcolors.OKMAGENTA
      • bcolors.PURPLE
      • bcolors.OKCYAN
      • bcolors.DARKCYAN
      • bcolors.ORANGE
      • bcolors.OKWHITE
      • bcolors.DARKWHITE
      • bcolors.OKBLACK
      • bcolors.OKGRAY
      • bcolors.OKPURPLE
      • bcolors.WARNING
      • bcolors.FAIL
      • bcolors.ENDC
      • bcolors.BOLD
      • bcolors.ITALIC
      • bcolors.UNDERLINE
      • bcolors.DIM
      • bcolors.NORMAL
      • bcolors.RESET_ALL
    • is_color_like()
    • detect_rgb_range()
    • is_valid_rgb_255()
    • is_valid_rgb_01()
    • normalize_rgb()
    • rgb2hex()
    • multi_rgb2hex()
    • is_valid_hex_color()
    • hex2rgb()
    • multi_hex2rgb()
    • invert_colors()
    • harmonize_colors()
    • readjust_colors()
    • create_random_colors()
    • get_colormaps_names()
    • create_lut_dictionary()
    • create_distinguishable_colors()
    • get_predefined_distinguishable_colors()
    • colortable_visualization()
    • get_colors_from_colortable()
    • values2colors()
    • colors_to_table()
    • visualize_colors()
    • ColorTableLoader
      • ColorTableLoader.__init__()
        • ColorTableLoader.name
        • ColorTableLoader.color
        • ColorTableLoader.opacity
        • ColorTableLoader.headerlines
      • ColorTableLoader.load_colortable()
      • ColorTableLoader.read_luttable()
      • ColorTableLoader.read_tsvtable()
      • ColorTableLoader.write_luttable()
      • ColorTableLoader.write_tsvtable()
      • ColorTableLoader.export()
      • ColorTableLoader.export_to_fslctab()
      • ColorTableLoader.export_to_nilearnctab()
      • ColorTableLoader.export_to_lutctab()
      • ColorTableLoader.export_to_tsvctab()
    • Key Features
    • Main Classes
      • ColorTableLoader
      • bcolors
    • Main Functions
      • Format Conversion
      • Validation
      • Palette Generation
      • Colour Tables
      • Visualization
    • Common Usage Examples
  • connectivitytools module
    • Connectome
      • Connectome.__init__()
      • Connectome.from_h5()
      • Connectome.load_h5()
      • Connectome.save_h5()
      • Connectome.get_region_names()
      • Connectome.get_region_colors()
      • Connectome.get_region_coordinates()
      • Connectome.set_region_coordinates()
      • Connectome.set_region_colors()
      • Connectome.set_region_names()
      • Connectome.get_default_region_colors()
      • Connectome.get_default_region_names()
      • Connectome.get_density()
      • Connectome.get_connectivity_stats()
      • Connectome.threshold()
      • Connectome.get_subnetwork()
      • Connectome.copy()
      • Connectome.plot_matrix()
      • Connectome.plot_circular_graph()
      • Connectome.generate_connectome()
      • Connectome.visualize_3d()
      • Connectome.save_visualization()
      • Connectome.get_info()
    • Key Features
    • Main Functions
    • Common Usage Examples
  • dicomtools module
    • progress_indicator()
    • org_conv_dicoms()
    • organize_dicom_files()
    • org_dicom_folder()
    • copy_dicom_file()
    • create_session_series_names()
    • uncompress_dicom_session()
    • compress_dicom_session()
    • get_dicom_info()
    • Key Features
    • Main Functions
      • DICOM Organization
    • Common Usage Examples
  • dwitools module
    • delete_dwi_volumes()
    • get_b0s()
    • maps_from_tensor_eigenvalues()
    • DiffusionScheme
      • DiffusionScheme.__init__()
      • DiffusionScheme.from_bvec_bval_files()
      • DiffusionScheme.from_bvec_bval_arrays()
      • DiffusionScheme.from_bmatrix_file()
      • DiffusionScheme.from_bmatrix_array()
      • DiffusionScheme.plot()
    • Key Features
    • Main Classes
      • DiffusionScheme
    • Main Functions
      • Volume Management
      • Tensor Maps
    • Common Usage Examples
  • freesurfertools module
    • AnnotParcellation
      • AnnotParcellation.__init__()
      • AnnotParcellation.load_from_file()
      • AnnotParcellation.get_info()
      • AnnotParcellation.is_loaded()
      • AnnotParcellation.create_from_data()
      • AnnotParcellation.save_annotation()
      • AnnotParcellation.get_info_from_name()
      • AnnotParcellation.get_info_from_id()
      • AnnotParcellation.get_regions_info()
      • AnnotParcellation.correct_vertexwise_parcellation()
      • AnnotParcellation.fill_parcellation()
      • AnnotParcellation.export_to_tsv()
      • AnnotParcellation.map_values()
      • AnnotParcellation.gii2annot()
      • AnnotParcellation.annot2gii()
      • AnnotParcellation.gcs2annot()
      • AnnotParcellation.annot2gcs()
      • AnnotParcellation.group_into_lobes()
    • FreeSurferSubject
      • FreeSurferSubject.__init__()
        • FreeSurferSubject.subj_id
        • FreeSurferSubject.subjs_dir
        • FreeSurferSubject.fs_files
      • FreeSurferSubject.get_hemi_dicts()
      • FreeSurferSubject.get_proc_status()
      • FreeSurferSubject.get_cras()
      • FreeSurferSubject.launch_freesurfer()
      • FreeSurferSubject.create_stats_table()
      • FreeSurferSubject.volume_morpho()
      • FreeSurferSubject.surface_hemi_morpho()
      • FreeSurferSubject.set_freesurfer_directory()
      • FreeSurferSubject.annot2ind()
      • FreeSurferSubject.gcs2ind()
      • FreeSurferSubject.surf2vol()
      • FreeSurferSubject.conform2native()
      • FreeSurferSubject.get_surface()
      • FreeSurferSubject.get_vertexwise_map()
      • FreeSurferSubject.get_annotation()
    • create_individual_freesurfer_table()
    • process_subject()
    • create_freesurfer_table()
    • create_fsaverage_links()
    • remove_fsaverage_links()
    • region_to_vertexwise()
    • create_vertex_colors()
    • colors2colortable()
    • resolve_colortable_duplicates()
    • find_unique_color()
    • verify_packed_rgb_values()
    • detect_hemi()
    • parse_freesurfer_lta()
    • get_cras_coordinates()
    • load_lobes_json()
    • get_version()
    • Key Features
    • Main Classes
      • AnnotParcellation
      • FreeSurferSubject
    • Main Functions
      • Table Generation
      • Transforms and Coordinates
      • Colours and Labels
      • Utilities
    • Common Usage Examples
  • imagetools module
    • MorphologicalOperations
      • MorphologicalOperations.__init__()
      • MorphologicalOperations.create_structuring_element()
      • MorphologicalOperations.erode()
      • MorphologicalOperations.dilate()
      • MorphologicalOperations.dilate_mm()
      • MorphologicalOperations.opening()
      • MorphologicalOperations.closing()
      • MorphologicalOperations.fill_holes()
      • MorphologicalOperations.remove_small_objects()
      • MorphologicalOperations.gradient()
      • MorphologicalOperations.tophat()
      • MorphologicalOperations.blackhat()
    • quick_morphology()
    • get_voxel_size()
    • get_voxel_volume()
    • get_center()
    • get_rotation_matrix()
    • get_vox_neighbors()
    • crop_image_from_mask()
    • cropped_to_native()
    • apply_multi_transf()
    • vox2mm()
    • mm2vox()
    • merge_to_4d()
    • create_spams()
    • spams2maxprob()
    • simulate_image()
    • delete_volumes_from_4D_images()
    • extract_mesh_from_volume()
    • extract_centroid_from_volume()
    • create_spams_from_volume()
    • spams2maxprob_from_volume()
    • compute_statistics_at_nonzero_voxels()
    • interpolate()
    • region_growing()
    • simulate_array()
    • delete_volumes_from_4D_array()
    • dilate_mm()
    • Key Features
    • Main Classes
      • MorphologicalOperations
    • Main Functions
      • Morphology
      • Affine Utilities
      • Image Manipulation
      • Probabilistic Maps
      • Mesh and Statistics
      • Simulation
    • Common Usage Examples
  • misctools module
    • ExplorerDict
      • ExplorerDict.__init__()
      • ExplorerDict.get_path()
      • ExplorerDict.search()
      • ExplorerDict.structure()
      • ExplorerDict.summary()
      • ExplorerDict.to_dataframe()
      • ExplorerDict.tree()
    • update_dict()
    • Key Features
    • Main Classes
      • SmartFormatter
    • Common Usage Examples
  • morphometrytools module
    • compute_reg_val_fromannot()
    • compute_reg_area_fromsurf()
    • compute_reg_nvertices_fromsurf()
    • compute_euler_fromsurf()
    • area_from_mesh()
    • euler_from_mesh()
    • compute_reg_val_fromparcellation()
    • compute_reg_volume_fromparcellation()
    • parse_freesurfer_global_fromaseg()
    • parse_freesurfer_stats_fromaseg()
    • parse_freesurfer_cortex_stats()
    • get_stats_dictionary()
    • network_metrics_to_table()
    • stats_from_vector()
    • get_units()
    • Key Features
    • Main Functions
      • Surface-based Analysis
      • Volume-based Analysis
      • FreeSurfer Analysis
      • Utility Functions
    • Common Usage Examples
  • networktools module
    • adjacency_matrix_to_csr()
    • triangulated_mesh_to_csr()
    • edges_to_csr()
    • edges_to_components()
    • connected_components()
    • Key Features
    • Main Functions
      • Graph Conversion
    • Common Usage Examples
  • parcellationtools module
    • Parcellation
      • Parcellation.__init__()
        • Parcellation.data
        • Parcellation.affine
        • Parcellation.index
        • Parcellation.name
        • Parcellation.color
        • Parcellation.opacity
        • Parcellation.headerlines
        • Parcellation.parc_file
        • Parcellation.id
        • Parcellation.space
        • Parcellation.dim
        • Parcellation.voxel_size
        • Parcellation.dtype
      • Parcellation.get_space_id()
      • Parcellation.set_space_id()
      • Parcellation.get_parcellation_id()
      • Parcellation.get_info()
      • Parcellation.get_data()
      • Parcellation.get_affine()
      • Parcellation.get_index()
      • Parcellation.get_names()
      • Parcellation.get_colors()
      • Parcellation.set_data()
      • Parcellation.set_affine()
      • Parcellation.set_index()
      • Parcellation.set_names()
      • Parcellation.set_colors()
      • Parcellation.export_summary_to_hdf5()
      • Parcellation.prepare_for_tracking()
      • Parcellation.keep_by_name()
      • Parcellation.keep_by_code()
      • Parcellation.remove_by_code()
      • Parcellation.remove_by_name()
      • Parcellation.apply_mask()
      • Parcellation.mask_image()
      • Parcellation.compute_region_adjacency()
      • Parcellation.compute_centroids()
      • Parcellation.get_regionwise_timeseries()
      • Parcellation.surface_extraction()
      • Parcellation.adjust_values()
      • Parcellation.group_by_codes()
      • Parcellation.group_by_names()
      • Parcellation.rearrange()
      • Parcellation.harmonize()
      • Parcellation.add_parcellation()
      • Parcellation.save_parcellation()
      • Parcellation.load_colortable()
      • Parcellation.sort_index()
      • Parcellation.export_colortable()
      • Parcellation.replace_values()
      • Parcellation.parc_range()
      • Parcellation.compute_morphometry_table()
      • Parcellation.compute_volume_table()
      • Parcellation.print_properties()
      • Parcellation.compute_fc_matrix()
    • RegionTimeSeries
      • RegionTimeSeries.data
      • RegionTimeSeries.region_names
      • RegionTimeSeries.region_colors
      • RegionTimeSeries.__init__()
      • RegionTimeSeries.compute_fc_matrix()
      • RegionTimeSeries.get_info()
      • RegionTimeSeries.show_content()
    • Key Features
    • Main Classes
      • Parcellation
      • RegionTimeSeries
    • Common Usage Examples
  • pipelinetools module
    • get_ids2process()
    • create_processing_status_table()
    • process_file()
    • process_freesurfer_subject()
    • scan_derivatives()
    • build_inventory()
    • build_derivatives_inventory()
    • get_processing_status_details_json()
    • get_processing_status_details_sqlite3()
    • query_processing_status_db()
    • export_db_to_json()
    • Key Features
    • Main Functions
      • Batch Processing
    • Common Usage Examples
  • plottools module
    • get_screen_size()
    • get_current_monitor_size()
    • estimate_monitor_dpi()
    • calculate_optimal_subplots_grid()
    • calculate_subplot_layout()
    • create_proportional_subplots()
    • calculate_font_sizes()
    • get_pyvista_fonts()
    • generate_spherical_coords()
    • Key Features
    • Main Functions
      • Layout Calculation
    • Common Usage Examples
  • pointstools module
    • PointCloud
      • PointCloud.coords
      • PointCloud.name
      • PointCloud.affine
      • PointCloud.colortables
      • PointCloud.point_data
      • PointCloud.__init__()
      • PointCloud.copy()
      • PointCloud.add_point_data()
      • PointCloud.transform()
      • PointCloud.filter_by_bounds()
      • PointCloud.get_bounds()
      • PointCloud.get_centroid()
      • PointCloud.filter()
      • PointCloud.to_dataframe()
      • PointCloud.save()
      • PointCloud.load()
      • PointCloud.load_colortable()
      • PointCloud.append()
      • PointCloud.explore_pointcloud()
      • PointCloud.get_pointwise_colors()
      • PointCloud.list_maps()
      • PointCloud.plot()
    • merge_pointclouds()
    • smooth_curve_coordinates()
    • Key Features
    • Main Classes
      • PointCloud
    • Main Functions
    • Common Usage Examples
  • qcqatools module
    • get_valid_slices()
    • generate_slices()
    • recursively_generate_slices()
    • generate_image_selection_webpage()
    • create_png_webpage_from_generated_slices()
    • Key Features
    • Main Functions
      • Quality Assessment
    • Common Usage Examples
  • segmentationtools module
    • abased_parcellation()
    • tissue_seg_table()
    • Key Features
    • Main Functions
      • Atlas-based Segmentation
    • Common Usage Examples
  • surfacetools module
    • Surface
      • Surface.surf
      • Surface.mesh
      • Surface.hemi
      • Surface.colortables
      • Surface.__init__()
      • Surface.load_from_file()
      • Surface.load_from_arrays()
      • Surface.load_from_mesh()
      • Surface.is_loaded()
      • Surface.create_mesh_from_arrays()
      • Surface.get_vertices()
      • Surface.get_faces()
      • Surface.get_edges()
      • Surface.get_boundary_edges()
      • Surface.get_manifold_edges()
      • Surface.compute_normals()
      • Surface.get_normals()
      • Surface.load_annotation()
      • Surface.load_scalar_maps()
      • Surface.separate_mesh_components()
      • Surface.list_overlays()
      • Surface.set_active_overlay()
      • Surface.remove_overlay()
      • Surface.get_overlay_info()
      • Surface.get_region_vertices()
      • Surface.get_vertexwise_colors()
      • Surface.prepare_colors()
      • Surface.add_surface()
      • Surface.map_volume_to_surface()
      • Surface.save_surface()
      • Surface.export_to_obj()
      • Surface.export_to_pyvista()
      • Surface.export_to_freesurfer()
      • Surface.export_annotation()
      • Surface.plot()
    • merge_surfaces()
    • create_surface_colortable()
    • Key Features
    • Main Classes
      • Surface
    • Main Functions
    • Common Usage Examples
  • tracttools module
    • Tractogram
      • Tractogram.name
      • Tractogram.tract_file
      • Tractogram.tracts
      • Tractogram.affine
      • Tractogram.header
      • Tractogram.data_per_point
      • Tractogram.data_per_streamline
      • Tractogram.colortables
      • Tractogram.centroids
      • Tractogram.centroids_indexes
      • Tractogram.__init__()
      • Tractogram.load_tractogram_from_file()
      • Tractogram.load_tractogram_from_object()
      • Tractogram.load_colortable()
      • Tractogram.smooth_streamlines()
      • Tractogram.resample_streamlines()
      • Tractogram.explore_tractogram()
      • Tractogram.streamline_to_points()
      • Tractogram.points_to_streamline()
      • Tractogram.add_tractogram()
      • Tractogram.compute_centroids()
      • Tractogram.label_streamlines_by_clusters()
      • Tractogram.get_cluster_streamlines()
      • Tractogram.compute_streamline_lengths()
      • Tractogram.interpolate_on_tractogram()
      • Tractogram.get_pointwise_colors()
      • Tractogram.reduce_streamlines()
      • Tractogram.filter()
      • Tractogram.list_maps()
      • Tractogram.get_maps_info()
      • Tractogram.get_tractogram_info()
      • Tractogram.centroids_to_tractogram()
      • Tractogram.save_tractogram()
      • Tractogram.plot()
    • resample_streamlines()
    • interpolate_streamline_values()
    • merge_tractograms()
    • trk2tck()
    • tck2trk()
    • Key Features
    • Main Classes
      • Tractogram
    • Main Functions
      • Format Conversion
      • Streamline Utilities
    • Common Usage Examples
  • visualizationtools module
    • BrainPlotter
      • BrainPlotter.config_file
      • BrainPlotter.figure_conf
      • BrainPlotter.views_conf
      • BrainPlotter.__init__()
      • BrainPlotter.plot()
      • BrainPlotter.plot_hemispheres()
      • BrainPlotter.plot_scene()
      • BrainPlotter.list_available_view_names()
      • BrainPlotter.list_available_layouts()
      • BrainPlotter.get_layout_details()
      • BrainPlotter.get_figure_config()
      • BrainPlotter.list_available_themes()
      • BrainPlotter.update_figure_config()
      • BrainPlotter.apply_theme()
      • BrainPlotter.list_figure_config_options()
      • BrainPlotter.reset_figure_config()
      • BrainPlotter.save_config()
      • BrainPlotter.preview_theme()
    • create_carpet_plot()
    • Key Features
    • Main Classes
      • BrainPlotter
    • Main Functions
    • Common Usage Examples
clabtoolkit
  • Python Module Index

Python Module Index

c
 
c
- clabtoolkit
    clabtoolkit.bidstools
    clabtoolkit.colorstools
    clabtoolkit.connectivitytools
    clabtoolkit.dicomtools
    clabtoolkit.dwitools
    clabtoolkit.freesurfertools
    clabtoolkit.imagetools
    clabtoolkit.misctools
    clabtoolkit.morphometrytools
    clabtoolkit.networktools
    clabtoolkit.parcellationtools
    clabtoolkit.pipelinetools
    clabtoolkit.plottools
    clabtoolkit.pointstools
    clabtoolkit.qcqatools
    clabtoolkit.segmentationtools
    clabtoolkit.surfacetools
    clabtoolkit.tracttools
    clabtoolkit.visualizationtools

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