magmap package

Subpackages

• magmap.atlas package
  • Submodules
    • magmap.atlas.atlas_refiner module
      • aggr_smoothing_metrics()
      • check_mirrorred()
      • crop_to_orig()
      • extend_edge()
      • find_labels_lost()
      • find_symmetric_axis()
      • import_atlas()
      • label_smoothing_metric()
      • make_labels_fg()
      • match_atlas_labels()
      • measure_atlas_refinement()
      • measure_overlap()
      • measure_overlap_combined_labels()
      • measure_overlap_labels()
      • mirror_planes()
      • smooth_labels()
      • transpose_img()
      • truncate_labels()
    • magmap.atlas.edge_seg module
      • edge_aware_segmentation()
      • edge_distances()
      • erode_labels()
      • make_edge_images()
      • make_sub_segmented_labels()
      • merge_atlas_segmentations()
    • magmap.atlas.labels_meta module
      • LabelsMeta
    • magmap.atlas.ontology module
      • LabelColumns
      • LabelsRef
      • convert_itksnap_to_df()
      • get_children_from_id()
      • get_children_from_id_df()
      • get_label()
      • get_label_at_level()
      • get_label_ids_from_position()
      • get_label_item()
      • get_label_name()
      • get_label_side()
      • get_region_middle()
      • labels_to_parent()
      • make_labels_level()
      • rel_to_abs_ages()
      • replace_labels()
      • scale_coords()
    • magmap.atlas.reg_tasks module
      • build_labels_diff_images()
    • magmap.atlas.register module
      • RegImgs
      • curate_img()
      • get_scaled_regionprops()
      • main()
      • make_label_ids_set()
      • overlay_registered_imgs()
      • register()
      • register_duo()
      • register_group()
      • register_repeat()
      • register_rev()
      • volumes_by_id()
      • volumes_by_id_compare()
    • magmap.atlas.transformer module
      • Downsampler
      • get_transposed_image_path()
      • make_modifier_plane()
      • make_modifier_resized()
      • make_modifier_scale()
      • preprocess_img()
      • rotate_img()
      • transpose_img()
• magmap.brain_globe package
  • Submodules
    • magmap.brain_globe.bg_controller module
      • AccessAtlasThread
      • BrainGlobeCtrl
      • SetupAtlasesThread
    • magmap.brain_globe.bg_model module
      • BrainGlobeMM
• magmap.cloud package
  • Submodules
    • magmap.cloud.aws module
    • magmap.cloud.notify module
      • main()
      • post()
• magmap.cv package
  • Submodules
    • magmap.cv.chunking module
      • SharedArr
      • SharedArrsContainer
      • get_mp_pool()
      • get_split_stack_total_shape()
      • init_shared_container()
      • is_fork()
      • merge_blobs()
      • merge_split_stack()
      • merge_split_stack2()
      • set_mp_start_method()
      • stack_splitter()
    • magmap.cv.classifier module
      • ClassifyImage
      • classify_blobs()
      • classify_patches()
      • extract_patches()
      • setup_classification_roi()
    • magmap.cv.colocalizer module
      • BlobMatch
      • StackColocalizer
      • colocalize_blobs()
      • colocalize_blobs_match()
      • insert_matches()
      • select_matches()
    • magmap.cv.cv_nd module
      • affine_nd()
      • angle_indices()
      • borders_distance()
      • build_heat_map()
      • calc_compactness()
      • calc_isotropic_factor()
      • carve()
      • compactness_3d()
      • compactness_count()
      • crop_to_labels()
      • exterior_nd()
      • extract_region()
      • filter_adaptive_size()
      • get_bbox_region()
      • get_label_bbox()
      • get_label_props()
      • get_selem()
      • get_thresholded_regionprops()
      • in_paint()
      • interpolate_contours()
      • interpolate_label_between_planes()
      • laplacian_of_gaussian_img()
      • make_isotropic()
      • meas_region()
      • perimeter_nd()
      • radial_dist()
      • radial_dist_diff()
      • remove_bg_from_dil_fg()
      • rescale_resize()
      • rotate90()
      • rotate_nd()
      • signed_distance_transform()
      • surface_area_3d()
      • zero_crossing()
    • magmap.cv.detector module
      • Blobs
      • calc_overlap()
      • calc_scaling_factor()
      • detect_blobs()
      • get_blobs_in_roi()
      • get_blobs_interior()
      • meas_pruning_ratio()
      • remove_close_blobs()
      • remove_close_blobs_within_array()
      • remove_close_blobs_within_sorted_array()
      • remove_duplicate_blobs()
      • show_blob_surroundings()
      • sort_blobs()
    • magmap.cv.segmenter module
      • LabelToMarkerErosion
      • SubSegmenter
      • labels_to_markers_blob()
      • labels_to_markers_erosion()
      • mask_atlas()
      • segment_from_labels()
      • segment_rw()
      • segment_ws()
      • sub_segment_labels()
      • watershed_distance()
    • magmap.cv.stack_detect module
      • Blocks
      • StackDetector
      • StackPruner
      • StackTimes
      • detect_blobs_blocks()
      • detect_blobs_stack()
      • setup_blocks()
    • magmap.cv.verifier module
      • find_closest_blobs_cdist()
      • match_blobs_roi()
      • meas_detection_accuracy()
      • setup_match_blobs_roi()
      • verify_rois()
      • verify_stack()
• magmap.gui package
  • Submodules
    • magmap.gui.atlas_editor module
      • AtlasEditor
      • InterpolatePlanes
    • magmap.gui.atlas_threads module
      • AnnotateLabels
      • RemapLevelThread
    • magmap.gui.event_handlers module
      • FileOpenHandler
    • magmap.gui.image_viewer module
      • Blitter
    • magmap.gui.import_threads module
    • magmap.gui.pixel_display module
      • PixelDisplay
    • magmap.gui.plot_editor module
      • PlotAxImg
      • PlotEditor
    • magmap.gui.roi_editor module
      • DraggableCircle
      • ROIEditor
    • magmap.gui.verifier_editor module
      • VerifierEditor
    • magmap.gui.vis_3d module
      • Vis3D
    • magmap.gui.vis_handler module
      • StaleFlags
      • ViewerTabs
      • VisHandler
    • magmap.gui.visualizer module
• magmap.io package
  • Submodules
    • magmap.io.cli module
      • args_to_dict()
      • args_with_dict()
      • main()
      • process_cli_args()
      • process_file()
      • process_proc_tasks()
      • process_tasks()
      • setup_atlas_profiles()
      • setup_dbs()
      • setup_grid_search_profiles()
      • setup_image()
      • setup_labels()
      • setup_roi_profiles()
      • shutdown()
      • update_profiles()
    • magmap.io.df_io module
      • add_cols_df()
      • append_cols()
      • coefvar_df()
      • combine_cols()
      • cond_to_cols_df()
      • data_frames_to_csv()
      • df_add()
      • df_div()
      • df_subtract()
      • dict_to_data_frame()
      • exps_by_regions()
      • filter_dfs_on_vals()
      • func_to_paired_cols()
      • join_dfs()
      • main()
      • melt_cols()
      • merge_csvs()
      • merge_excels()
      • normalize_df()
      • pivot_with_conditions()
      • print_data_frame()
      • replace_vals()
      • weight_mean()
      • weight_std()
      • zscore_df()
    • magmap.io.export_regions module
      • export_common_labels()
      • export_region_ids()
      • export_region_network()
      • make_density_image()
      • make_density_images_mp()
      • make_labels_level_img()
      • map_metric_to_labels_img()
    • magmap.io.export_rois module
      • blobs_to_csv()
      • export_rois()
      • load_roi_files()
      • make_roi_paths()
    • magmap.io.export_stack module
      • StackPlaneIO
      • animate_imgs()
      • export_planes()
      • reg_planes_to_img()
      • setup_stack()
      • stack_to_img()
    • magmap.io.importer module
      • CHANNEL_SEPARATOR
      • DEFAULT_IMG_STACK_NAME
      • assign_metadata()
      • calc_intensity_bounds()
      • calc_scaling()
      • deconstruct_img_name()
      • filename_to_base()
      • find_sizes()
      • import_multiplane_images()
      • import_planes_to_stack()
      • is_javabridge_loaded()
      • load_metadata()
      • make_filenames()
      • parse_deconstructed_name()
      • parse_ome()
      • parse_ome_raw()
      • read_file()
      • roi_to_image5d()
      • save_image_info()
      • save_np_image()
      • setup_import_dir()
      • setup_import_metadata()
      • setup_import_multipage()
      • start_jvm()
      • stop_jvm()
    • magmap.io.libmag module
      • add_missing_keys()
      • backup_file()
      • combine_arrs()
      • combine_paths()
      • compact_float()
      • convert_bin_magnitude()
      • convert_indices_to_int()
      • coords_for_indexing()
      • copy_backup()
      • create_symlink()
      • crop_mid_str()
      • dtype_within_range()
      • enum_dict_aslist()
      • enum_names_aslist()
      • flatten()
      • format_bytes()
      • format_num()
      • get_dict_keys_from_val()
      • get_dtype_info()
      • get_enum()
      • get_filename_without_ext()
      • get_git_commit()
      • get_if_within()
      • get_int()
      • get_version()
      • insert_before_ext()
      • is_binary()
      • is_int()
      • is_nan()
      • is_number()
      • is_seq()
      • last_lines()
      • log_once()
      • make_acronym()
      • make_out_path()
      • match_ext()
      • normalize()
      • npstr_to_array()
      • pad_seq()
      • print_compact()
      • printcb()
      • printv()
      • remove_file()
      • replace_seq()
      • roll_elements()
      • scale_slice()
      • series_as_str()
      • show_full_arrays()
      • splice_before()
      • splitext()
      • str_to_disp()
      • swap_elements()
      • to_seq()
      • transpose_1d()
      • transpose_1d_rev()
      • truncate_decimal_digit()
      • warn()
    • magmap.io.load_env module
      • ARGS_MAGMAP
      • ENV_NAME
      • VENV_DIR
      • is_conda_activated()
      • is_venv_activated()
      • launch_magmap()
      • launch_subprocess()
      • log_uncaught_exception()
      • main()
    • magmap.io.naming module
      • get_roi_path()
      • make_subimage_name()
    • magmap.io.np_io module
      • Image5d
      • find_scaling()
      • get_num_channels()
      • img_to_blobs_path()
      • read_np_archive()
      • read_tif()
      • setup_images()
      • write_raw_file()
      • write_tif()
    • magmap.io.packaging module
      • get_pkg_egg()
      • get_pkg_path()
    • magmap.io.sitk_io module
      • EXTS_3D
      • convert_img()
      • find_atlas_labels()
      • itk_to_sitk_img()
      • load_numpy_to_sitk()
      • load_registered_img()
      • load_registered_imgs()
      • match_world_info()
      • merge_images()
      • read_img()
      • read_sitk()
      • read_sitk_files()
      • reg_out_path()
      • replace_sitk_with_numpy()
      • sitk_to_itk_img()
      • write_img()
      • write_pts()
      • write_reg_images()
      • write_registered_image()
    • magmap.io.sqlite module
      • ClrDB
      • clean_up_blobs()
      • delete_blobs()
      • get_exp_name()
      • get_roi_offset()
      • get_roi_size()
      • insert_about()
      • insert_blobs()
      • insert_experiment()
      • insert_roi()
      • load_truth_db()
      • main()
      • match_elements()
      • merge_truth_dbs()
      • select_about()
      • select_blobs_confirmed()
      • select_or_insert_roi()
      • select_roi()
      • select_rois()
      • update_rois()
      • upgrade_db()
      • verification_stats()
    • magmap.io.subproc_io module
      • compress_file()
      • decompress_file()
      • test_compression()
    • magmap.io.yaml_io module
      • load_yaml()
      • save_yaml()
• magmap.plot package
  • Submodules
    • magmap.plot.colormaps module
      • DiscreteColormap
      • DiscreteModes
      • discrete_colormap()
      • get_borders_colormap()
      • get_cmap()
      • get_labels_discrete_colormap()
      • make_binary_cmap()
      • make_dark_linear_cmap()
      • setup_cmaps()
      • setup_colormaps()
      • setup_labels_cmap()
    • magmap.plot.plot_2d module
      • decorate_plot()
      • main()
      • plot_bars()
      • plot_catplot()
      • plot_histogram()
      • plot_image()
      • plot_lines()
      • plot_overlays()
      • plot_overlays_reg()
      • plot_probability()
      • plot_roc()
      • plot_scatter()
      • plot_swarm()
      • post_plot()
      • setup_style()
    • magmap.plot.plot_3d module
      • build_ground_truth()
      • deconvolve()
      • denoise_roi()
      • get_isotropic_vis()
      • pad_img()
      • prepare_roi()
      • prepare_subimg()
      • remap_intensity()
      • replace_vol()
      • roi_center_to_offset()
      • saturate_roi()
      • setup_channels()
      • show_surface_labels()
      • threshold()
    • magmap.plot.plot_support module
      • ImageOverlayer
      • ImageSyncMixin
      • add_scale_bar()
      • add_vspans()
      • alpha_blend_intersection()
      • extract_planes()
      • fit_frame_to_image()
      • get_aspect_ratio()
      • get_downsample_max_sizes()
      • get_plane_axis()
      • hide_axes()
      • max_plane()
      • save_fig()
      • scale_axes()
      • scale_xticks()
      • scroll_plane()
      • set_overview_title()
      • set_scinot()
      • setup_fig()
      • setup_images_for_plane()
      • setup_vspans()
      • show()
      • transpose_images()
• magmap.settings package
  • Submodules
    • magmap.settings.atlas_prof module
      • AtlasProfile
      • RegParamMap
    • magmap.settings.config module
      • ABAKeys
      • APP_NAME
      • AtlasLabels
      • AtlasMetrics
      • ClassifierData
      • Cmaps
      • DEFAULT_SAVEFIG
      • DFTasks
      • DNS_REVERSE
      • DataClass
      • DataClassProtocol
      • DocsURLs
      • FORMATS_3D
      • HemSides
      • ICON_PATH
      • ItkSnapLabels
      • LoadData
      • LoadIO
      • MetaKeys
      • MetricGroups
      • PLANE
      • POS_THRESH
      • PREFS_PATH
      • Plot2DTypes
      • PlotLabels
      • PreProcessKeys
      • ProcessTypes
      • RegNames
      • RegSuffixes
      • RegisterTypes
      • STR_FN
      • SUFFIX_BLOBS
      • SUFFIX_BLOB_CLUSTERS
      • SUFFIX_IMAGE5D
      • SUFFIX_META
      • SUFFIX_SUBIMG
      • SmoothingMetrics
      • SmoothingModes
      • Themes
      • Transforms
      • TruthDB
      • TruthDBModes
      • URI_SCHEME
      • Verbosity
      • app_dir
      • blobs
      • channel
      • classifier
      • cmap_labels
      • filenames
      • format_import_err()
      • get_roi_profile()
      • grid_search_profile
      • image5d_io
      • img5d
      • labels_img
      • labels_img_orig
      • labels_img_sitk
      • labels_level
      • labels_metadata
      • labels_ref
      • labels_scaling
      • load_labels
      • log_path
      • logger
      • magnification
      • matplotlib_style
      • meta_dict
      • metadata_paths
      • metadatas
      • plot_labels
      • prefix
      • prefix_out
      • prefixes
      • prefixes_out
      • prefs
      • proc_type
      • rc_params
      • reg_suffixes
      • rgb
      • savefig
      • series
      • series_list
      • show
      • suffix
      • truth_db_mode
      • unit_factor
      • user_app_dirs
      • verbose
      • verbosity
      • zoom
    • magmap.settings.grid_search_prof module
      • GridSearchProfile
      • make_hyperparm_arr()
    • magmap.settings.logs module
      • LogWriter
      • add_file_handler()
      • setup_logger()
      • update_log_level()
    • magmap.settings.prefs_prof module
      • PrefsProfile
    • magmap.settings.profiles module
      • RegKeys
      • SettingsDict
    • magmap.settings.roi_prof module
      • ROIProfile
• magmap.stats package
  • Submodules
    • magmap.stats.atlas_stats module
      • calc_sens_ppv()
      • meas_dice()
      • meas_improvement()
      • meas_landmark_dist()
      • meas_plot_coefvar()
      • meas_plot_zscores()
      • plot_clusters_by_label()
      • plot_intensity_nuclei()
      • plot_region_development()
      • plot_unlabeled_hemisphere()
      • smoothing_peak()
    • magmap.stats.clustering module
      • ClusterByLabel
      • cluster_blobs()
      • cluster_dbscan_metrics()
      • knn_dist()
      • plot_knns()
    • magmap.stats.mlearn module
      • GridSearchStats
      • grid_search()
      • parse_grid_stats()
    • magmap.stats.vols module
      • LabelMetrics
      • LabelToEdge
      • MeasureLabel
      • MeasureLabelOverlap
      • MetricCombos
      • get_metric_weight_col()
      • get_single_label()
      • labels_distance()
      • map_meas_to_labels()
      • measure_labels_metrics()
      • measure_labels_overlap()
• magmap.tests package
  • Submodules
    • magmap.tests.test_chunking module
      • TestChunking
    • magmap.tests.test_classifier module
      • TestClassifier
    • magmap.tests.test_cv_nd module
      • TestCvNd
    • magmap.tests.test_detector module
      • TestDetector
    • magmap.tests.test_img_equality module
      • TestImgEquality
    • magmap.tests.test_libmag module
      • TestLibmag
    • magmap.tests.test_np_io module
      • TestLibmag
    • magmap.tests.test_visualizer module
    • magmap.tests.unit_testing module
      • TestImageStackProcessing