Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __call__() (magmap.gui.pixel_display.PixelDisplay method) __repr__() (magmap.settings.profiles.SettingsDict method) A A (magmap.settings.config.ItkSnapLabels attribute) ABA_ID (magmap.settings.config.ABAKeys attribute) ABAKeys (class in magmap.settings.config) ABS_X (magmap.cv.detector.Blobs.Cols attribute) ABS_Y (magmap.cv.detector.Blobs.Cols attribute) ABS_Z (magmap.cv.detector.Blobs.Cols attribute) AccessAtlasThread (class in magmap.brain_globe.bg_controller) ACRONYM (magmap.settings.config.ABAKeys attribute) ACTIVE (magmap.settings.profiles.RegKeys attribute) adaptive_closing (magmap.settings.config.SmoothingModes attribute) adaptive_erosion (magmap.settings.config.SmoothingModes attribute) adaptive_opening (magmap.settings.config.SmoothingModes attribute) add_artist() (magmap.gui.image_viewer.Blitter method) add_cols_df() (in module magmap.io.df_io) ADD_CSV_COLS (magmap.settings.config.DFTasks attribute) add_file_handler() (in module magmap.settings.logs) add_missing_keys() (in module magmap.io.libmag) add_profiles() (magmap.settings.profiles.SettingsDict method) add_scale_bar() (in module magmap.plot.plot_support) add_vspans() (in module magmap.plot.plot_support) additive_blend (magmap.gui.roi_editor.ROIEditor property) (magmap.plot.plot_support.ImageOverlayer attribute) (magmap.plot.plot_support.ImageSyncMixin property) affine_nd() (in module magmap.cv.cv_nd) alpha (magmap.gui.plot_editor.PlotEditor attribute) alpha_blend_intersection() (in module magmap.plot.plot_support) ALPHA_DEFAULT (magmap.gui.plot_editor.PlotEditor attribute) alpha_img3d (magmap.gui.plot_editor.PlotEditor attribute) alpha_updater() (magmap.gui.plot_editor.PlotEditor method) ALPHAS_CHL (magmap.settings.config.PlotLabels attribute) angle_indices() (in module magmap.cv.cv_nd) ANIMATED (magmap.settings.config.ProcessTypes attribute) ANNOT_COL (magmap.settings.config.PlotLabels attribute) annotate_labels() (magmap.plot.plot_support.ImageOverlayer method) AnnotateLabels (class in magmap.gui.atlas_threads) ANNOTATION (magmap.settings.config.RegSuffixes attribute) app_dir (in module magmap.settings.config) APP_NAME (in module magmap.settings.config) append_cols() (in module magmap.io.df_io) APPEND_CSVS_COLS (magmap.settings.config.DFTasks attribute) ARGS_MAGMAP (in module magmap.io.load_env) artists (magmap.gui.image_viewer.Blitter property) aspect (magmap.plot.plot_support.ImageOverlayer attribute) ATLAS (magmap.settings.config.RegSuffixes attribute) atlas_edge (magmap.cv.segmenter.SubSegmenter attribute) AtlasLabels (class in magmap.settings.config) AtlasMetrics (class in magmap.settings.config) AtlasProfile (class in magmap.settings.atlas_prof) ax (magmap.plot.plot_support.ImageOverlayer attribute) axes_exit() (magmap.plot.plot_support.ImageSyncMixin method) B B (magmap.settings.config.ItkSnapLabels attribute) BACKGROUND (magmap.settings.config.PlotLabels attribute) backup_file() (in module magmap.io.libmag) BAR_PLOT (magmap.settings.config.Plot2DTypes attribute) BAR_PLOT_VOLS_STATS (magmap.settings.config.Plot2DTypes attribute) BAR_PLOT_VOLS_STATS_EFFECTS (magmap.settings.config.Plot2DTypes attribute) BASENAME (magmap.cv.detector.Blobs.Keys attribute) bg_mm (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) BINARY (magmap.settings.config.AtlasLabels attribute) Blitter (class in magmap.gui.image_viewer) blitter (magmap.gui.plot_editor.PlotEditor attribute) blob (magmap.gui.verifier_editor.VerifierEditor.BlobView attribute) BLOB_COLORS (magmap.gui.roi_editor.DraggableCircle attribute) blob_for_db() (magmap.cv.detector.Blobs class method) BLOB_MATCHES (magmap.settings.config.LoadData attribute) BLOB_PREPROCESSING (magmap.settings.roi_prof.ROIProfile attribute) Blobs (class in magmap.cv.detector) blobs (in module magmap.settings.config) (magmap.cv.detector.Blobs property) BLOBS (magmap.cv.detector.Blobs.Keys attribute) (magmap.settings.config.LoadData attribute) Blobs.Cols (class in magmap.cv.detector) Blobs.Keys (class in magmap.cv.detector) blobs_in_channel() (magmap.cv.detector.Blobs class method) BLOBS_NP_VER (magmap.cv.detector.Blobs attribute) BLOCK_SIZES (magmap.settings.roi_prof.ROIProfile attribute) BORDERS (magmap.settings.config.RegSuffixes attribute) borders_distance() (in module magmap.cv.cv_nd) BOTH (magmap.settings.config.HemSides attribute) BOTTOM (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) BRAIN_GLOBE (magmap.settings.config.LoadIO attribute) BrainGlobeCtrl (class in magmap.brain_globe.bg_controller) BrainGlobeMM (class in magmap.brain_globe.bg_model) build_ground_truth() (in module magmap.plot.plot_3d) build_heat_map() (in module magmap.cv.cv_nd) build_pool_init() (magmap.cv.chunking.SharedArrsContainer class method) C calc_compactness() (in module magmap.cv.cv_nd) calc_isotropic_factor() (in module magmap.cv.cv_nd) calc_overlap() (in module magmap.cv.detector) calc_scaling_factor() (in module magmap.cv.detector) carve() (in module magmap.cv.cv_nd) CAT_PLOT (magmap.settings.config.Plot2DTypes attribute) change_brightness_contrast() (magmap.gui.plot_editor.PlotEditor static method) channel (in module magmap.settings.config) CHANNEL (magmap.cv.detector.Blobs.Cols attribute) (magmap.settings.config.AtlasMetrics attribute) check_file_changed() (magmap.settings.profiles.SettingsDict method) CHILDREN (magmap.settings.config.ABAKeys attribute) CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) classifier (in module magmap.settings.config) ClassifierData (class in magmap.settings.config) CLASSIFY (magmap.settings.config.ProcessTypes attribute) closing (magmap.settings.config.SmoothingModes attribute) CLUSTER_BLOBS (magmap.settings.config.RegisterTypes attribute) CMAP_BUBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_CYBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_GRBK_NAME (magmap.settings.config.Cmaps attribute) cmap_labels (in module magmap.settings.config) (magmap.gui.plot_editor.PlotEditor attribute) CMAP_MGBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_RDBK_NAME (magmap.settings.config.Cmaps attribute) CMAP_YLBK_NAME (magmap.settings.config.Cmaps attribute) Cmaps (class in magmap.settings.config) COEFVAR (magmap.settings.config.RegisterTypes attribute) coefvar_df() (in module magmap.io.df_io) COLOC_MATCH (magmap.settings.config.ProcessTypes attribute) COLOCS (magmap.cv.detector.Blobs.Keys attribute) cols (magmap.cv.detector.Blobs property) COLS (magmap.cv.detector.Blobs.Keys attribute) combine_arrs() (in module magmap.io.libmag) COMBINE_COLS (magmap.settings.config.RegisterTypes attribute) combine_cols() (in module magmap.io.df_io) combine_paths() (in module magmap.io.libmag) COMBINED (magmap.settings.config.RegNames attribute) compact_float() (in module magmap.io.libmag) COMPACTION (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS (magmap.settings.config.SmoothingMetrics attribute) compactness_3d() (in module magmap.cv.cv_nd) compactness_count() (in module magmap.cv.cv_nd) COMPACTNESS_CV (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS_ORIG (magmap.settings.config.SmoothingMetrics attribute) COMPACTNESS_SD (magmap.settings.config.SmoothingMetrics attribute) compress_file() (in module magmap.io.subproc_io) cond_to_cols_df() (in module magmap.io.df_io) CONDITION (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.PlotLabels attribute) CONFIRMED (magmap.cv.detector.Blobs.Cols attribute) connect() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) convert_bin_magnitude() (in module magmap.io.libmag) convert_img_labels() (magmap.plot.colormaps.DiscreteColormap method) convert_indices_to_int() (in module magmap.io.libmag) CONVERT_ITKSNAP_LABELS (magmap.settings.config.RegisterTypes attribute) convert_itksnap_to_df() (in module magmap.atlas.ontology) convert_shared_arr() (magmap.cv.chunking.SharedArrsContainer class method) coords_for_indexing() (in module magmap.io.libmag) copy_backup() (in module magmap.io.libmag) create_aba_reverse_lookup() (magmap.atlas.ontology.LabelsRef method) create_lookup_pd() (magmap.atlas.ontology.LabelsRef method) create_ref_lookup() (magmap.atlas.ontology.LabelsRef method) create_reverse_lookup() (magmap.atlas.ontology.LabelsRef method) create_symlink() (in module magmap.io.libmag) crop_mid_str() (in module magmap.io.libmag) crop_to_labels() (in module magmap.cv.cv_nd) CUT (magmap.gui.roi_editor.DraggableCircle attribute) D DARK (magmap.settings.config.Themes attribute) data_frames_to_csv() (in module magmap.io.df_io) DataClass (class in magmap.settings.config) DataClassProtocol (class in magmap.settings.config) DBSCAN_EPS (magmap.settings.profiles.RegKeys attribute) DBSCAN_MINPTS (magmap.settings.profiles.RegKeys attribute) decompress_file() (in module magmap.io.subproc_io) deconvolve() (in module magmap.plot.plot_3d) DECORATE_PLOT (magmap.settings.config.Plot2DTypes attribute) DEFAULT (magmap.settings.config.Themes attribute) DEFAULT_NAME (magmap.settings.profiles.SettingsDict attribute) DEFAULT_SAVEFIG (in module magmap.settings.config) DENOISE (magmap.settings.config.PreProcessKeys attribute) denoise_roi() (in module magmap.plot.plot_3d) DENSITY (magmap.settings.config.RegSuffixes attribute) DETECT (magmap.settings.config.ProcessTypes attribute) detect_blobs() (in module magmap.cv.detector) DETECT_COLOC (magmap.settings.config.ProcessTypes attribute) df_add() (in module magmap.io.df_io) df_div() (in module magmap.io.df_io) df_subtract() (in module magmap.io.df_io) DFTasks (class in magmap.settings.config) dict_to_data_frame() (in module magmap.io.df_io) disconnect() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) discrete_colormap() (in module magmap.plot.colormaps) DiscreteColormap (class in magmap.plot.colormaps) DiscreteModes (class in magmap.plot.colormaps) DISPLACEMENT (magmap.settings.config.SmoothingMetrics attribute) DIVIDE_COLS (magmap.settings.config.DFTasks attribute) DNS_REVERSE (in module magmap.settings.config) DOCS_URL (magmap.settings.config.DocsURLs attribute) DOCS_URL_SETTINGS (magmap.settings.config.DocsURLs attribute) DOCS_URL_VIEWER (magmap.settings.config.DocsURLs attribute) DocsURLs (class in magmap.settings.config) Downsampler (class in magmap.atlas.transformer) DPI (magmap.settings.config.PlotLabels attribute) DraggableCircle (class in magmap.gui.roi_editor) draw_crosslines() (magmap.gui.plot_editor.PlotEditor method) DROP_DUPS (magmap.settings.config.PlotLabels attribute) DSC_ATLAS_LABELS (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_LABELS_HEM (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_SAMPLE (magmap.settings.config.AtlasMetrics attribute) DSC_ATLAS_SAMPLE_CUR (magmap.settings.config.AtlasMetrics attribute) DSC_LABELS_ORIG_NEW_COMBINED (magmap.settings.config.AtlasMetrics attribute) DSC_LABELS_ORIG_NEW_INDIV (magmap.settings.config.AtlasMetrics attribute) DSC_SAMPLE_LABELS (magmap.settings.config.AtlasMetrics attribute) DTYPE (magmap.settings.config.MetaKeys attribute) dtype_within_range() (in module magmap.io.libmag) E EDGE_AWARE_REANNOTATION (magmap.settings.profiles.RegKeys attribute) EDIT (magmap.settings.config.TruthDBModes attribute) edit_mode (magmap.gui.plot_editor.PlotEditor property) edited (magmap.plot.plot_support.ImageSyncMixin attribute) enable_btn() (magmap.plot.plot_support.ImageSyncMixin static method) enum_dict_aslist() (in module magmap.io.libmag) enum_names_aslist() (in module magmap.io.libmag) ENV_NAME (in module magmap.io.load_env) erode_label() (magmap.cv.segmenter.LabelToMarkerErosion class method) ERR_COL (magmap.settings.config.PlotLabels attribute) ERR_COL_ABS (magmap.settings.config.PlotLabels attribute) eventFilter() (magmap.gui.event_handlers.FileOpenHandler method) EXPORT_BLOBS (magmap.settings.config.ProcessTypes attribute) EXPORT_COMMON_LABELS (magmap.settings.config.RegisterTypes attribute) EXPORT_METRICS_COMPACTNESS (magmap.settings.config.RegisterTypes attribute) EXPORT_PLANES (magmap.settings.config.ProcessTypes attribute) EXPORT_PLANES_CHANNELS (magmap.settings.config.ProcessTypes attribute) EXPORT_RAW (magmap.settings.config.ProcessTypes attribute) EXPORT_REGIONS (magmap.settings.config.RegisterTypes attribute) EXPORT_ROIS (magmap.settings.config.ProcessTypes attribute) EXPORT_TIF (magmap.settings.config.ProcessTypes attribute) EXPS_BY_REGION (magmap.settings.config.DFTasks attribute) exps_by_regions() (in module magmap.io.df_io) exterior_nd() (in module magmap.cv.cv_nd) EXTRACT (magmap.settings.config.ProcessTypes attribute) EXTRACT_FROM_CSV (magmap.settings.config.DFTasks attribute) extract_planes() (in module magmap.plot.plot_support) extract_region() (in module magmap.cv.cv_nd) F FDR (magmap.stats.mlearn.GridSearchStats attribute) fig (magmap.gui.image_viewer.Blitter attribute) (magmap.plot.plot_support.ImageSyncMixin attribute) fig_save_dir (magmap.settings.prefs_prof.PrefsProfile attribute) filenames (in module magmap.settings.config) FileOpenHandler (class in magmap.gui.event_handlers) filter_adaptive_size() (in module magmap.cv.cv_nd) filter_dfs_on_vals() (in module magmap.io.df_io) FILTER_SIZE (magmap.settings.config.SmoothingMetrics attribute) find_scaling() (in module magmap.io.np_io) fit_frame_to_image() (in module magmap.plot.plot_support) FIXED_MASK (magmap.settings.config.RegSuffixes attribute) flatten() (in module magmap.io.libmag) FLIP (magmap.settings.config.Transforms attribute) FLIP_HORIZ (magmap.settings.config.Transforms attribute) FLIP_VERT (magmap.settings.config.Transforms attribute) flush() (magmap.settings.logs.LogWriter method) FN (magmap.stats.mlearn.GridSearchStats attribute) fn_feedback (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_opened_atlas (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_progress (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_set_atlases_table (magmap.brain_globe.bg_controller.BrainGlobeCtrl attribute) fn_update_blob (magmap.gui.verifier_editor.VerifierEditor attribute) fn_update_coords (magmap.gui.plot_editor.PlotEditor attribute) format_blobs() (magmap.cv.detector.Blobs method) format_bytes() (in module magmap.io.libmag) format_import_err() (in module magmap.settings.config) format_num() (in module magmap.io.libmag) FORMATS_3D (in module magmap.settings.config) FP (magmap.stats.mlearn.GridSearchStats attribute) FROM_LABEL (magmap.atlas.ontology.LabelColumns attribute) FULL_ANNOTATION (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) func_to_paired_cols() (in module magmap.io.df_io) G G (magmap.settings.config.ItkSnapLabels attribute) gaussian (magmap.settings.config.SmoothingModes attribute) get_aspect_ratio() (in module magmap.plot.plot_support) get_atlas() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_avail_atlases() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_bbox_region() (in module magmap.cv.cv_nd) get_blob_abs_coords() (magmap.cv.detector.Blobs class method) get_blob_col() (magmap.cv.detector.Blobs class method) get_blob_confirmed() (magmap.cv.detector.Blobs class method) get_blob_truth() (magmap.cv.detector.Blobs class method) get_blobs_channel() (magmap.cv.detector.Blobs class method) get_blobs_in_roi() (in module magmap.cv.detector) get_blobs_interior() (in module magmap.cv.detector) get_borders_colormap() (in module magmap.plot.colormaps) get_children_from_id() (in module magmap.atlas.ontology) get_cmap() (in module magmap.plot.colormaps) get_dict_keys_from_val() (in module magmap.io.libmag) get_displayed_img() (magmap.gui.plot_editor.PlotEditor method) get_downsample_max_sizes() (in module magmap.plot.plot_support) get_dtype_info() (in module magmap.io.libmag) get_enum() (in module magmap.io.libmag) get_filename_without_ext() (in module magmap.io.libmag) get_files() (magmap.settings.atlas_prof.AtlasProfile static method) (magmap.settings.grid_search_prof.GridSearchProfile static method) (magmap.settings.profiles.SettingsDict static method) (magmap.settings.roi_prof.ROIProfile static method) get_git_commit() (in module magmap.io.libmag) get_if_within() (in module magmap.io.libmag) get_img_display_settings() (magmap.plot.plot_support.ImageSyncMixin method) get_int() (in module magmap.io.libmag) get_isotropic_vis() (in module magmap.plot.plot_3d) get_label() (in module magmap.atlas.ontology) get_label_at_level() (in module magmap.atlas.ontology) get_label_bbox() (in module magmap.cv.cv_nd) get_label_ids_from_position() (in module magmap.atlas.ontology) get_label_item() (in module magmap.atlas.ontology) get_label_name() (in module magmap.atlas.ontology) get_label_props() (in module magmap.cv.cv_nd) get_label_side() (in module magmap.atlas.ontology) get_labels_discrete_colormap() (in module magmap.plot.colormaps) get_local_atlases() (magmap.brain_globe.bg_model.BrainGlobeMM method) get_mp_pool() (in module magmap.cv.chunking) get_msg() (magmap.gui.pixel_display.PixelDisplay method) get_node() (magmap.atlas.ontology.LabelsRef method) get_num_channels() (in module magmap.io.np_io) get_pkg_egg() (in module magmap.io.packaging) get_pkg_path() (in module magmap.io.packaging) get_plane_axis() (in module magmap.plot.plot_support) get_plot_ax_img() (magmap.gui.plot_editor.PlotEditor static method) get_profile() (magmap.settings.profiles.SettingsDict method) get_ref_lookup_as_df() (magmap.atlas.ontology.LabelsRef method) get_region_middle() (in module magmap.atlas.ontology) get_roi_path() (in module magmap.io.naming) get_roi_profile() (in module magmap.settings.config) get_save_path() (magmap.gui.roi_editor.ROIEditor method) get_selem() (in module magmap.cv.cv_nd) get_split_stack_total_shape() (in module magmap.cv.chunking) get_thresholded_regionprops() (in module magmap.cv.cv_nd) get_transposed_image_path() (in module magmap.atlas.transformer) get_version() (in module magmap.io.libmag) GRID (magmap.plot.colormaps.DiscreteModes attribute) grid_search() (in module magmap.stats.mlearn) grid_search_profile (in module magmap.settings.config) GridSearchProfile (class in magmap.settings.grid_search_prof) GridSearchStats (class in magmap.stats.mlearn) GROUP (magmap.settings.config.RegisterTypes attribute) GROUP_COL (magmap.settings.config.PlotLabels attribute) H HemSides (class in magmap.settings.config) hide_axes() (in module magmap.plot.plot_support) HLINE (magmap.settings.config.PlotLabels attribute) hyperparams (magmap.settings.grid_search_prof.GridSearchProfile attribute) I ICON_PATH (in module magmap.settings.config) ID (magmap.settings.config.AtlasLabels attribute) (magmap.settings.config.ItkSnapLabels attribute) ID_COL (magmap.settings.config.PlotLabels attribute) ignore_invis (magmap.plot.plot_support.ImageOverlayer attribute) Image5d (class in magmap.io.np_io) image5d (magmap.gui.roi_editor.ROIEditor attribute) image5d_io (in module magmap.settings.config) ImageOverlayer (class in magmap.plot.plot_support) ImageOverlayer.RotTransform (class in magmap.plot.plot_support) ImageSyncMixin (class in magmap.plot.plot_support) img (magmap.atlas.transformer.Downsampler attribute) (magmap.gui.plot_editor.PlotAxImg attribute) img3d (magmap.gui.plot_editor.PlotEditor attribute) img3d_labels (magmap.gui.plot_editor.PlotEditor attribute) img5d (in module magmap.settings.config) (magmap.plot.plot_support.ImageSyncMixin attribute) IMG_ATLAS (magmap.settings.config.RegNames attribute) IMG_ATLAS_EDGE (magmap.settings.config.RegNames attribute) IMG_ATLAS_LOG (magmap.settings.config.RegNames attribute) IMG_ATLAS_MASK (magmap.settings.config.RegNames attribute) IMG_ATLAS_PRECUR (magmap.settings.config.RegNames attribute) IMG_BORDERS (magmap.settings.config.RegNames attribute) IMG_EXP (magmap.settings.config.RegNames attribute) IMG_EXP_MASK (magmap.settings.config.RegNames attribute) IMG_GROUPED (magmap.settings.config.RegNames attribute) IMG_HEAT_COLOC (magmap.settings.config.RegNames attribute) IMG_HEAT_MAP (magmap.settings.config.RegNames attribute) IMG_LABELS (magmap.settings.config.RegNames attribute) IMG_LABELS_DIFF (magmap.settings.config.RegNames attribute) IMG_LABELS_DIST (magmap.settings.config.RegNames attribute) IMG_LABELS_EDGE (magmap.settings.config.RegNames attribute) IMG_LABELS_EDGE_LEVEL (magmap.settings.config.RegNames attribute) IMG_LABELS_INTERIOR (magmap.settings.config.RegNames attribute) IMG_LABELS_LEVEL (magmap.settings.config.RegNames attribute) IMG_LABELS_MARKERS (magmap.settings.config.RegNames attribute) IMG_LABELS_PRECUR (magmap.settings.config.RegNames attribute) IMG_LABELS_SUBSEG (magmap.settings.config.RegNames attribute) IMG_LABELS_TRANS (magmap.settings.config.RegNames attribute) IMG_LABELS_TRUNC (magmap.settings.config.RegNames attribute) IMG_LABELS_TRUNC_PRECUR (magmap.settings.config.RegNames attribute) img_to_blobs_path() (in module magmap.io.np_io) IMPORT_ATLAS (magmap.settings.config.RegisterTypes attribute) import_dir (magmap.settings.prefs_prof.PrefsProfile attribute) IMPORT_ONLY (magmap.settings.config.ProcessTypes attribute) imshow_multichannel() (magmap.plot.plot_support.ImageOverlayer method) in_paint() (in module magmap.cv.cv_nd) include (magmap.settings.config.ClassifierData attribute) init_shared_container() (in module magmap.cv.chunking) input_img (magmap.gui.plot_editor.PlotAxImg attribute) insert_before_ext() (in module magmap.io.libmag) interpolate_contours() (in module magmap.cv.cv_nd) interpolate_label_between_planes() (in module magmap.cv.cv_nd) INTERPOLATION (magmap.settings.config.Transforms attribute) is_binary() (in module magmap.io.libmag) is_conda_activated() (in module magmap.io.load_env) is_fork() (in module magmap.cv.chunking) is_identical_settings() (magmap.settings.profiles.SettingsDict static method) is_int() (in module magmap.io.libmag) is_nan() (in module magmap.io.libmag) is_number() (in module magmap.io.libmag) is_seq() (in module magmap.io.libmag) is_venv_activated() (in module magmap.io.load_env) ItkSnapLabels (class in magmap.settings.config) J join_dfs() (in module magmap.io.df_io) K KNN_N (magmap.settings.profiles.RegKeys attribute) L LABEL_LOSS (magmap.settings.config.SmoothingMetrics attribute) label_motion_thresh (magmap.gui.plot_editor.PlotEditor attribute) LabelColumns (class in magmap.atlas.ontology) labels_annots (magmap.plot.plot_support.ImageOverlayer attribute) LABELS_DIFF (magmap.settings.config.RegisterTypes attribute) LABELS_DIFF_STATS (magmap.settings.config.RegisterTypes attribute) LABELS_DIST (magmap.settings.config.RegisterTypes attribute) labels_img (in module magmap.settings.config) (magmap.cv.segmenter.LabelToMarkerErosion attribute) labels_img_np (magmap.cv.segmenter.SubSegmenter attribute) labels_img_orig (in module magmap.settings.config) labels_img_sitk (in module magmap.settings.config) labels_level (in module magmap.settings.config) (magmap.gui.plot_editor.PlotEditor attribute) labels_metadata (in module magmap.settings.config) labels_ref (in module magmap.settings.config) labels_scaling (in module magmap.settings.config) labels_to_markers_blob() (in module magmap.cv.segmenter) labels_to_markers_erosion() (in module magmap.cv.segmenter) labels_to_parent() (in module magmap.atlas.ontology) LabelsMeta (class in magmap.atlas.labels_meta) LabelsRef (class in magmap.atlas.ontology) LabelToMarkerErosion (class in magmap.cv.segmenter) laplacian_of_gaussian_img() (in module magmap.cv.cv_nd) last_lines() (in module magmap.io.libmag) LAT_UNLBL_PLANES (magmap.settings.config.AtlasMetrics attribute) LAT_UNLBL_VOL (magmap.settings.config.AtlasMetrics attribute) launch_magmap() (in module magmap.io.load_env) launch_subprocess() (in module magmap.io.load_env) LAYOUT (magmap.settings.config.PlotLabels attribute) LEFT (magmap.settings.config.HemSides attribute) LEGEND_NAMES (magmap.settings.config.PlotLabels attribute) LEVEL (magmap.settings.config.ABAKeys attribute) (magmap.settings.config.AtlasLabels attribute) (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.Verbosity attribute) LINE_PLOT (magmap.settings.config.Plot2DTypes attribute) LOAD (magmap.settings.config.ProcessTypes attribute) load() (magmap.atlas.labels_meta.LabelsMeta method) (magmap.atlas.ontology.LabelsRef method) load_blobs() (magmap.cv.detector.Blobs method) load_labels (in module magmap.settings.config) load_labels_ref() (magmap.atlas.ontology.LabelsRef method) load_yaml() (in module magmap.io.yaml_io) LoadData (class in magmap.settings.config) LoadIO (class in magmap.settings.config) log_once() (in module magmap.io.libmag) log_path (in module magmap.settings.config) LOG_PATH (magmap.settings.config.Verbosity attribute) log_uncaught_exception() (in module magmap.io.load_env) logger (in module magmap.settings.config) LogWriter (class in magmap.settings.logs) M magmap module magmap.atlas module magmap.atlas.labels_meta module magmap.atlas.ontology module magmap.atlas.transformer module magmap.brain_globe module magmap.brain_globe.bg_controller module magmap.brain_globe.bg_model module magmap.cloud module magmap.cv module magmap.cv.chunking module magmap.cv.cv_nd module magmap.cv.detector module magmap.cv.segmenter module magmap.gui module magmap.gui.atlas_threads module magmap.gui.event_handlers module magmap.gui.image_viewer module magmap.gui.pixel_display module magmap.gui.plot_editor module magmap.gui.roi_editor module magmap.gui.verifier_editor module magmap.io module magmap.io.df_io module magmap.io.libmag module magmap.io.load_env module magmap.io.naming module magmap.io.np_io module magmap.io.packaging module magmap.io.subproc_io module magmap.io.yaml_io module magmap.plot module magmap.plot.colormaps module magmap.plot.plot_3d module magmap.plot.plot_support module magmap.settings module magmap.settings.atlas_prof module magmap.settings.config module magmap.settings.grid_search_prof module magmap.settings.logs module magmap.settings.prefs_prof module magmap.settings.profiles module magmap.settings.roi_prof module magmap.stats module magmap.stats.mlearn module magmap.tests module magmap.tests.test_chunking module magmap.tests.test_cv_nd module magmap.tests.test_detector module magmap.tests.test_libmag module magnification (in module magmap.settings.config) MAGNIFICATION (magmap.settings.config.MetaKeys attribute) main() (in module magmap.io.df_io) (in module magmap.io.load_env) (in module stitch.tile_config) make_acronym() (in module magmap.io.libmag) make_binary_cmap() (in module magmap.plot.colormaps) make_cmap() (magmap.plot.colormaps.DiscreteColormap method) make_dark_linear_cmap() (in module magmap.plot.colormaps) MAKE_DENSITY_IMAGES (magmap.settings.config.RegisterTypes attribute) MAKE_EDGE_IMAGES (magmap.settings.config.RegisterTypes attribute) MAKE_EDGE_IMAGES_EXP (magmap.settings.config.RegisterTypes attribute) make_hyperparm_arr() (in module magmap.settings.grid_search_prof) make_isotropic() (in module magmap.cv.cv_nd) MAKE_LABELS_LEVEL (magmap.settings.config.RegisterTypes attribute) make_labels_level() (in module magmap.atlas.ontology) make_modifier_plane() (in module magmap.atlas.transformer) make_modifier_resized() (in module magmap.atlas.transformer) make_modifier_scale() (in module magmap.atlas.transformer) make_out_path() (in module magmap.io.libmag) make_random_blobs() (magmap.tests.test_detector.TestDetector method) make_subimage_name() (in module magmap.io.naming) MAKE_SUBSEGS (magmap.settings.config.RegisterTypes attribute) MARGIN (magmap.settings.config.PlotLabels attribute) MARKER (magmap.settings.config.PlotLabels attribute) MARKER_EROSION (magmap.settings.profiles.RegKeys attribute) MARKER_EROSION_MIN (magmap.settings.profiles.RegKeys attribute) MARKER_EROSION_USE_MIN (magmap.settings.profiles.RegKeys attribute) mask_atlas() (in module magmap.cv.segmenter) match_ext() (in module magmap.io.libmag) matplotlib_style (in module magmap.settings.config) max_plane() (in module magmap.plot.plot_support) MEAS_IMPROVEMENT (magmap.settings.config.RegisterTypes attribute) meas_pruning_ratio() (in module magmap.cv.detector) meas_region() (in module magmap.cv.cv_nd) meas_wt() (magmap.cv.segmenter.LabelToMarkerErosion class method) MELT_COLS (magmap.settings.config.RegisterTypes attribute) melt_cols() (in module magmap.io.df_io) MERGE_ATLAS_SEGS (magmap.settings.config.RegisterTypes attribute) MERGE_ATLAS_SEGS_EXP (magmap.settings.config.RegisterTypes attribute) merge_blobs() (in module magmap.cv.chunking) MERGE_CSVS (magmap.settings.config.DFTasks attribute) merge_csvs() (in module magmap.io.df_io) MERGE_CSVS_COLS (magmap.settings.config.DFTasks attribute) MERGE_EXCELS (magmap.settings.config.DFTasks attribute) merge_excels() (in module magmap.io.df_io) MERGE_IMAGES (magmap.settings.config.RegisterTypes attribute) MERGE_IMAGES_CHANNELS (magmap.settings.config.RegisterTypes attribute) merge_split_stack() (in module magmap.cv.chunking) merge_split_stack2() (in module magmap.cv.chunking) MESH (magmap.settings.config.ItkSnapLabels attribute) meta_dict (in module magmap.settings.config) metadata_paths (in module magmap.settings.config) metadatas (in module magmap.settings.config) MetaKeys (class in magmap.settings.config) MetricGroups (class in magmap.settings.config) METRICS_CLUSTER (magmap.settings.profiles.RegKeys attribute) MIDDLE (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) MODE (magmap.settings.config.TruthDB attribute) model (magmap.settings.config.ClassifierData attribute) modified_cmap() (magmap.plot.colormaps.DiscreteColormap method) modify_settings() (magmap.settings.profiles.SettingsDict method) module magmap magmap.atlas magmap.atlas.labels_meta magmap.atlas.ontology magmap.atlas.transformer magmap.brain_globe magmap.brain_globe.bg_controller magmap.brain_globe.bg_model magmap.cloud magmap.cv magmap.cv.chunking magmap.cv.cv_nd magmap.cv.detector magmap.cv.segmenter magmap.gui magmap.gui.atlas_threads magmap.gui.event_handlers magmap.gui.image_viewer magmap.gui.pixel_display magmap.gui.plot_editor magmap.gui.roi_editor magmap.gui.verifier_editor magmap.io magmap.io.df_io magmap.io.libmag magmap.io.load_env magmap.io.naming magmap.io.np_io magmap.io.packaging magmap.io.subproc_io magmap.io.yaml_io magmap.plot magmap.plot.colormaps magmap.plot.plot_3d magmap.plot.plot_support magmap.settings magmap.settings.atlas_prof magmap.settings.config magmap.settings.grid_search_prof magmap.settings.logs magmap.settings.prefs_prof magmap.settings.profiles magmap.settings.roi_prof magmap.stats magmap.stats.mlearn magmap.tests magmap.tests.test_chunking magmap.tests.test_cv_nd magmap.tests.test_detector magmap.tests.test_libmag run stitch.tile_config MOVING_MASK (magmap.settings.config.RegSuffixes attribute) multiply_blob_abs_coords() (magmap.cv.detector.Blobs class method) multiply_blob_rel_coords() (magmap.cv.detector.Blobs class method) MULTIPLY_COLS (magmap.settings.config.DFTasks attribute) N NAME (magmap.settings.config.ABAKeys attribute) (magmap.settings.config.ItkSnapLabels attribute) NAME_KEY (magmap.settings.profiles.SettingsDict attribute) NAN_COLOR (magmap.settings.config.PlotLabels attribute) nav_motion_thresh (magmap.gui.plot_editor.PlotEditor attribute) NEW_ATLAS (magmap.settings.config.RegisterTypes attribute) NO_CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) NORMALIZE (magmap.settings.config.DFTasks attribute) normalize() (in module magmap.io.libmag) normalize_df() (in module magmap.io.df_io) NP (magmap.settings.config.LoadIO attribute) npstr_to_array() (in module magmap.io.libmag) O OFFSET (magmap.settings.config.AtlasMetrics attribute) on_axes_exit() (magmap.gui.plot_editor.PlotEditor method) on_close() (magmap.plot.plot_support.ImageSyncMixin method) on_draw() (magmap.gui.image_viewer.Blitter method) on_key_press() (magmap.gui.plot_editor.PlotEditor method) on_motion() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) on_pick() (magmap.gui.roi_editor.DraggableCircle method) on_press() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) on_release() (magmap.gui.plot_editor.PlotEditor method) (magmap.gui.roi_editor.DraggableCircle method) open_atlas() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) opening (magmap.settings.config.SmoothingModes attribute) ORIG_COLORS (magmap.settings.config.AtlasLabels attribute) origin (magmap.plot.plot_support.ImageOverlayer attribute) overlay_images() (magmap.plot.plot_support.ImageOverlayer method) overlayer (magmap.gui.plot_editor.PlotEditor attribute) OVERLAYS (magmap.settings.config.RegisterTypes attribute) P pad_img() (in module magmap.plot.plot_3d) pad_seq() (in module magmap.io.libmag) PADDING (magmap.settings.config.PlotLabels attribute) PARAM (magmap.stats.mlearn.GridSearchStats attribute) PARENT (magmap.settings.config.AtlasMetrics attribute) PARENT_ID (magmap.settings.config.ABAKeys attribute) parse_grid_stats() (in module magmap.stats.mlearn) PATH (magmap.settings.config.TruthDB attribute) PATH_LABELS_META (magmap.atlas.labels_meta.LabelsMeta attribute) PATH_PREFIX (magmap.settings.atlas_prof.AtlasProfile attribute) (magmap.settings.grid_search_prof.GridSearchProfile attribute) (magmap.settings.roi_prof.ROIProfile attribute) PATH_PROFILES (magmap.settings.profiles.SettingsDict attribute) PATH_REF (magmap.settings.config.AtlasLabels attribute) perimeter_nd() (in module magmap.cv.cv_nd) picked (magmap.gui.roi_editor.DraggableCircle attribute) PIVOT_CONDS (magmap.settings.config.RegisterTypes attribute) pivot_with_conditions() (in module magmap.io.df_io) PixelDisplay (class in magmap.gui.pixel_display) PLANE (in module magmap.settings.config) plane (magmap.gui.plot_editor.PlotEditor attribute) Plot2DTypes (class in magmap.settings.config) plot_2d_stack() (magmap.gui.roi_editor.ROIEditor method) plot_ax_imgs (magmap.gui.plot_editor.PlotEditor property) PLOT_CLUSTER_BLOBS (magmap.settings.config.RegisterTypes attribute) plot_ed (magmap.gui.verifier_editor.VerifierEditor.BlobView attribute) plot_eds (magmap.plot.plot_support.ImageSyncMixin attribute) PLOT_INTENS_NUC (magmap.settings.config.RegisterTypes attribute) PLOT_KNNS (magmap.settings.config.RegisterTypes attribute) plot_labels (in module magmap.settings.config) PLOT_LATERAL_UNLABELED (magmap.settings.config.RegisterTypes attribute) PLOT_REGION_DEV (magmap.settings.config.RegisterTypes attribute) plot_roi() (magmap.gui.roi_editor.ROIEditor method) PLOT_SMOOTHING_METRICS (magmap.settings.config.RegisterTypes attribute) PlotAxImg (class in magmap.gui.plot_editor) PlotEditor (class in magmap.gui.plot_editor) PlotLabels (class in magmap.settings.config) POINT_CLOUD (magmap.settings.config.MetricGroups attribute) POS (magmap.stats.mlearn.GridSearchStats attribute) POS_THRESH (in module magmap.settings.config) PPV (magmap.stats.mlearn.GridSearchStats attribute) prefix (in module magmap.settings.config) prefix_out (in module magmap.settings.config) prefixes (in module magmap.settings.config) prefixes_out (in module magmap.settings.config) prefs (in module magmap.settings.config) PREFS_PATH (in module magmap.settings.config) PrefsProfile (class in magmap.settings.prefs_prof) prepare_roi() (in module magmap.plot.plot_3d) prepare_subimg() (in module magmap.plot.plot_3d) PREPROCESS (magmap.settings.config.ProcessTypes attribute) preprocess_img() (in module magmap.atlas.transformer) PreProcessKeys (class in magmap.settings.config) print_compact() (in module magmap.io.libmag) print_data_frame() (in module magmap.io.df_io) printcb() (in module magmap.io.libmag) printv() (in module magmap.io.libmag) proc_type (in module magmap.settings.config) ProcessTypes (class in magmap.settings.config) profiles (magmap.settings.grid_search_prof.GridSearchProfile attribute) (magmap.settings.roi_prof.ROIProfile attribute) progress (magmap.brain_globe.bg_controller.AccessAtlasThread attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) R R (magmap.settings.config.ItkSnapLabels attribute) radial_dist() (in module magmap.cv.cv_nd) radial_dist_diff() (in module magmap.cv.cv_nd) RADIUS (magmap.cv.detector.Blobs.Cols attribute) RANDOMN (magmap.plot.colormaps.DiscreteModes attribute) rc_params (in module magmap.settings.config) read_np_archive() (in module magmap.io.np_io) read_tif() (in module magmap.io.np_io) refresh_img3d_labels() (magmap.gui.plot_editor.PlotEditor method) refresh_profile() (magmap.settings.profiles.SettingsDict method) reg_suffixes (in module magmap.settings.config) REGION (magmap.settings.config.AtlasMetrics attribute) REGION_ABBR (magmap.settings.config.AtlasMetrics attribute) REGION_NAME (magmap.settings.config.AtlasMetrics attribute) REGISTER_REV (magmap.settings.config.RegisterTypes attribute) RegisterTypes (class in magmap.settings.config) RegKeys (class in magmap.settings.profiles) RegNames (class in magmap.settings.config) RegParamMap (class in magmap.settings.atlas_prof) RegSuffixes (class in magmap.settings.config) rel_to_abs_ages() (in module magmap.atlas.ontology) REMAP (magmap.settings.config.PreProcessKeys attribute) remap_intensity() (in module magmap.plot.plot_3d) RemapLevelThread (class in magmap.gui.atlas_threads) remove_abs_blob_coords() (magmap.cv.detector.Blobs class method) remove_atlas() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) remove_bg_from_dil_fg() (in module magmap.cv.cv_nd) remove_close_blobs() (in module magmap.cv.detector) remove_close_blobs_within_array() (in module magmap.cv.detector) remove_close_blobs_within_sorted_array() (in module magmap.cv.detector) remove_duplicate_blobs() (in module magmap.cv.detector) remove_file() (in module magmap.io.libmag) remove_labels() (magmap.plot.plot_support.ImageOverlayer method) remove_local_atlas() (magmap.brain_globe.bg_model.BrainGlobeMM method) remove_self() (magmap.gui.roi_editor.DraggableCircle method) REPEAT_CIRCLES (magmap.gui.roi_editor.ROIEditor.CircleStyles attribute) replace_labels() (in module magmap.atlas.ontology) replace_rel_with_abs_blob_coords() (magmap.cv.detector.Blobs class method) replace_seq() (in module magmap.io.libmag) REPLACE_VALS (magmap.settings.config.DFTasks attribute) replace_vals() (in module magmap.io.df_io) replace_vol() (in module magmap.plot.plot_3d) RESCALE (magmap.settings.config.Transforms attribute) rescale_resize() (in module magmap.cv.cv_nd) rescale_sub_roi() (magmap.atlas.transformer.Downsampler class method) RESOLUTIONS (magmap.cv.detector.Blobs.Keys attribute) (magmap.settings.config.MetaKeys attribute) rgb (in module magmap.settings.config) (magmap.gui.plot_editor.PlotAxImg attribute) (magmap.io.np_io.Image5d attribute) (magmap.plot.plot_support.ImageOverlayer attribute) RIGHT (magmap.settings.config.HemSides attribute) ROC_CURVE (magmap.settings.config.Plot2DTypes attribute) roi_center_to_offset() (in module magmap.plot.plot_3d) roi_circles (magmap.settings.prefs_prof.PrefsProfile attribute) ROI_COLS (magmap.gui.roi_editor.ROIEditor attribute) ROI_OFFSET (magmap.cv.detector.Blobs.Keys attribute) roi_plane (magmap.settings.prefs_prof.PrefsProfile attribute) ROI_SIZE (magmap.cv.detector.Blobs.Keys attribute) roi_styles (magmap.settings.prefs_prof.PrefsProfile attribute) ROIEditor (class in magmap.gui.roi_editor) ROIEditor.CircleStyles (class in magmap.gui.roi_editor) ROIEditor.ZLevels (class in magmap.gui.roi_editor) ROIProfile (class in magmap.settings.roi_prof) roll_elements() (in module magmap.io.libmag) ROTATE (magmap.settings.config.PreProcessKeys attribute) (magmap.settings.config.Transforms attribute) rotate90() (in module magmap.cv.cv_nd) ROTATE_DEG (magmap.settings.config.Transforms attribute) rotate_img() (in module magmap.atlas.transformer) rotate_nd() (in module magmap.cv.cv_nd) ROTATION (magmap.settings.config.PlotLabels attribute) run module run() (magmap.brain_globe.bg_controller.AccessAtlasThread method) (magmap.brain_globe.bg_controller.SetupAtlasesThread method) (magmap.gui.atlas_threads.AnnotateLabels method) (magmap.gui.atlas_threads.RemapLevelThread method) S SA_VOL (magmap.settings.config.SmoothingMetrics attribute) SA_VOL_FRAC (magmap.settings.config.SmoothingMetrics attribute) SA_VOL_ORIG (magmap.settings.config.SmoothingMetrics attribute) SAMPLE (magmap.settings.config.AtlasMetrics attribute) SATURATE (magmap.settings.config.PreProcessKeys attribute) saturate_roi() (in module magmap.plot.plot_3d) save() (magmap.atlas.labels_meta.LabelsMeta method) save_archive() (magmap.cv.detector.Blobs method) save_fig() (in module magmap.plot.plot_support) (magmap.plot.plot_support.ImageSyncMixin method) save_path (magmap.atlas.labels_meta.LabelsMeta property) save_settings() (magmap.settings.profiles.SettingsDict method) SAVE_STEPS (magmap.settings.profiles.RegKeys attribute) save_yaml() (in module magmap.io.yaml_io) savefig (in module magmap.settings.config) scale_axes() (in module magmap.plot.plot_support) SCALE_BAR (magmap.settings.config.PlotLabels attribute) scale_coords() (in module magmap.atlas.ontology) scale_slice() (in module magmap.io.libmag) scale_xticks() (in module magmap.plot.plot_support) SCATTER_PLOT (magmap.settings.config.Plot2DTypes attribute) scroll_overview() (magmap.gui.plot_editor.PlotEditor method) scroll_plane() (in module magmap.plot.plot_support) segment_from_labels() (in module magmap.cv.segmenter) segment_rw() (in module magmap.cv.segmenter) segment_ws() (in module magmap.cv.segmenter) SENS (magmap.stats.mlearn.GridSearchStats attribute) series (in module magmap.settings.config) series_as_str() (in module magmap.io.libmag) series_list (in module magmap.settings.config) set_blob_abs_coords() (magmap.cv.detector.Blobs class method) set_blob_channel() (magmap.cv.detector.Blobs class method) set_blob_col() (magmap.cv.detector.Blobs class method) set_blob_confirmed() (magmap.cv.detector.Blobs class method) set_blob_truth() (magmap.cv.detector.Blobs class method) set_circle_visibility() (magmap.gui.roi_editor.ROIEditor method) set_data() (magmap.atlas.transformer.Downsampler class method) set_images() (magmap.cv.segmenter.SubSegmenter class method) set_labels_img() (magmap.cv.segmenter.LabelToMarkerErosion class method) set_labels_level() (magmap.plot.plot_support.ImageSyncMixin method) set_mp_start_method() (in module magmap.cv.chunking) set_overview_title() (in module magmap.plot.plot_support) set_scinot() (in module magmap.plot.plot_support) set_show_crosslines() (magmap.plot.plot_support.ImageSyncMixin method) set_show_label() (magmap.gui.plot_editor.PlotEditor method) set_show_labels() (magmap.plot.plot_support.ImageSyncMixin method) SettingsDict (class in magmap.settings.profiles) setup_channels() (in module magmap.plot.plot_3d) setup_cmaps() (in module magmap.plot.colormaps) setup_colormaps() (in module magmap.plot.colormaps) setup_fig() (in module magmap.plot.plot_support) setup_images() (in module magmap.io.np_io) setup_images_for_plane() (in module magmap.plot.plot_support) setup_labels_cmap() (in module magmap.plot.colormaps) setup_logger() (in module magmap.settings.logs) setup_shared_arrs() (magmap.cv.chunking.SharedArrsContainer class method) setup_transform() (magmap.plot.plot_support.ImageOverlayer method) setup_vspans() (in module magmap.plot.plot_support) SetupAtlasesThread (class in magmap.brain_globe.bg_controller) SHAPE (magmap.settings.config.MetaKeys attribute) SHAPES (magmap.settings.config.MetricGroups attribute) shared_arrs (magmap.cv.chunking.SharedArrsContainer attribute) SharedArr (class in magmap.cv.chunking) SharedArrsContainer (class in magmap.cv.chunking) shift_blob_abs_coords() (magmap.cv.detector.Blobs class method) shift_blob_rel_coords() (magmap.cv.detector.Blobs class method) shift_blobs() (magmap.cv.detector.Blobs class method) show (in module magmap.settings.config) show() (in module magmap.plot.plot_support) show_blob_surroundings() (in module magmap.cv.detector) show_blobs_per_channel() (magmap.cv.detector.Blobs class method) show_colocalized_blobs() (magmap.gui.roi_editor.ROIEditor method) show_fig() (magmap.gui.verifier_editor.VerifierEditor method) show_full_arrays() (in module magmap.io.libmag) show_labels() (magmap.gui.plot_editor.PlotEditor method) show_labels_annots() (magmap.plot.plot_support.ImageSyncMixin method) show_overview() (magmap.gui.plot_editor.PlotEditor method) show_roi() (magmap.gui.plot_editor.PlotEditor method) show_subplot() (magmap.gui.roi_editor.ROIEditor method) show_surface_labels() (in module magmap.plot.plot_3d) show_views() (magmap.gui.verifier_editor.VerifierEditor method) SIDE (magmap.settings.config.AtlasMetrics attribute) signal (magmap.brain_globe.bg_controller.AccessAtlasThread attribute) (magmap.brain_globe.bg_controller.SetupAtlasesThread attribute) (magmap.gui.atlas_threads.AnnotateLabels attribute) (magmap.gui.atlas_threads.RemapLevelThread attribute) signal_prog (magmap.gui.atlas_threads.AnnotateLabels attribute) (magmap.gui.atlas_threads.RemapLevelThread attribute) signed_distance_transform() (in module magmap.cv.cv_nd) SIMILARITY_METRIC (magmap.settings.config.AtlasMetrics attribute) SINGLE (magmap.settings.config.RegisterTypes attribute) SITK (magmap.settings.config.LoadIO attribute) SIZE (magmap.settings.config.AtlasMetrics attribute) (magmap.settings.config.PlotLabels attribute) SKELETON_EROSION (magmap.settings.profiles.RegKeys attribute) SM_QUALITY (magmap.settings.config.SmoothingMetrics attribute) SMOOTHING_METRICS_AGGR (magmap.settings.config.RegisterTypes attribute) SMOOTHING_PEAKS (magmap.settings.config.RegisterTypes attribute) SmoothingMetrics (class in magmap.settings.config) SmoothingModes (class in magmap.settings.config) sort_blobs() (in module magmap.cv.detector) spectral_unmixing (magmap.settings.roi_prof.ROIProfile attribute) splice_before() (in module magmap.io.libmag) splitext() (in module magmap.io.libmag) stack_split_remerge() (magmap.tests.test_chunking.TestChunking static method) stack_splitter() (in module magmap.cv.chunking) stitch.tile_config module STR_FN (in module magmap.settings.config) str_to_disp() (in module magmap.io.libmag) sub_segment() (magmap.cv.segmenter.SubSegmenter class method) sub_segment_labels() (in module magmap.cv.segmenter) SubSegmenter (class in magmap.cv.segmenter) SUBTRACT_COLS (magmap.settings.config.DFTasks attribute) suffix (in module magmap.settings.config) SUFFIX_BLOB_CLUSTERS (in module magmap.settings.config) SUFFIX_BLOBS (in module magmap.settings.config) SUFFIX_IMAGE5D (in module magmap.settings.config) SUFFIX_META (in module magmap.settings.config) SUFFIX_SUBIMG (in module magmap.settings.config) SUM_COLS (magmap.settings.config.DFTasks attribute) surface_area_3d() (in module magmap.cv.cv_nd) swap_elements() (in module magmap.io.libmag) SWARM_PLOT (magmap.settings.config.Plot2DTypes attribute) SYMMETRIC_COLORS (magmap.settings.config.AtlasLabels attribute) T test_angle_indices() (magmap.tests.test_cv_nd.TestCvNd method) test_blob_accessors() (magmap.tests.test_detector.TestDetector method) test_combine_paths() (magmap.tests.test_libmag.TestLibmag method) test_compression() (in module magmap.io.subproc_io) test_flatten() (magmap.tests.test_libmag.TestLibmag method) test_format_bytes() (magmap.tests.test_libmag.TestLibmag method) test_get_filename_without_ext() (magmap.tests.test_libmag.TestLibmag method) test_get_int() (magmap.tests.test_libmag.TestLibmag method) test_insert_before_ext() (magmap.tests.test_libmag.TestLibmag method) test_is_int() (magmap.tests.test_libmag.TestLibmag method) test_is_number() (magmap.tests.test_libmag.TestLibmag method) test_make_abbreviation() (magmap.tests.test_libmag.TestLibmag method) test_match_ext() (magmap.tests.test_libmag.TestLibmag method) test_pad_seq() (magmap.tests.test_libmag.TestLibmag method) test_replace_seq() (magmap.tests.test_libmag.TestLibmag method) test_rescale_resize() (magmap.tests.test_cv_nd.TestCvNd method) test_series_as_str() (magmap.tests.test_libmag.TestLibmag method) test_splice_before() (magmap.tests.test_libmag.TestLibmag method) test_splitext() (magmap.tests.test_libmag.TestLibmag method) test_stack_splitter() (magmap.tests.test_chunking.TestChunking method) test_str_to_disp() (magmap.tests.test_libmag.TestLibmag method) TestChunking (class in magmap.tests.test_chunking) TestCvNd (class in magmap.tests.test_cv_nd) TestDetector (class in magmap.tests.test_detector) TestLibmag (class in magmap.tests.test_libmag) TEXT_POS (magmap.settings.config.PlotLabels attribute) Themes (class in magmap.settings.config) threshold() (in module magmap.plot.plot_3d) TIFFFILE (magmap.settings.config.LoadIO attribute) TITLE (magmap.settings.config.PlotLabels attribute) TN (magmap.stats.mlearn.GridSearchStats attribute) TO_LABEL (magmap.atlas.ontology.LabelColumns attribute) to_seq() (in module magmap.io.libmag) toggle_btn() (magmap.plot.plot_support.ImageSyncMixin static method) TOP (magmap.gui.roi_editor.ROIEditor.ZLevels attribute) TP (magmap.stats.mlearn.GridSearchStats attribute) transform (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) TRANSFORM (magmap.settings.config.ProcessTypes attribute) Transforms (class in magmap.settings.config) TRANSLATE_CHILDREN (magmap.settings.config.AtlasLabels attribute) translate_coord() (magmap.gui.plot_editor.PlotEditor method) TRANSLATE_LABELS (magmap.settings.config.AtlasLabels attribute) transpose_1d() (in module magmap.io.libmag) transpose_1d_rev() (in module magmap.io.libmag) transpose_images() (in module magmap.plot.plot_support) transpose_img() (in module magmap.atlas.transformer) truncate_decimal_digit() (in module magmap.io.libmag) TRUTH (magmap.cv.detector.Blobs.Cols attribute) truth_db_mode (in module magmap.settings.config) TruthDB (class in magmap.settings.config) TruthDBModes (class in magmap.settings.config) U unit_factor (in module magmap.settings.config) update() (magmap.gui.image_viewer.Blitter method) update_alpha_blend() (magmap.gui.plot_editor.PlotEditor method) update_atlas_table() (magmap.brain_globe.bg_controller.BrainGlobeCtrl method) update_coord() (magmap.gui.plot_editor.PlotEditor method) update_img_display() (magmap.gui.plot_editor.PlotEditor method) update_imgs_display() (magmap.gui.roi_editor.ROIEditor method) (magmap.plot.plot_support.ImageSyncMixin method) update_log_level() (in module magmap.settings.logs) update_max_intens_proj() (magmap.gui.roi_editor.ROIEditor method) (magmap.plot.plot_support.ImageSyncMixin method) update_plane_slider() (magmap.gui.plot_editor.PlotEditor method) update_plot_ax_img_display() (magmap.gui.plot_editor.PlotEditor static method) update_prog() (magmap.brain_globe.bg_controller.AccessAtlasThread method) (magmap.brain_globe.bg_controller.SetupAtlasesThread method) (magmap.gui.atlas_threads.AnnotateLabels method) (magmap.gui.atlas_threads.RemapLevelThread method) URI_SCHEME (in module magmap.settings.config) user_app_dirs (in module magmap.settings.config) V VENV_DIR (in module magmap.io.load_env) VER (magmap.cv.detector.Blobs.Keys attribute) verbose (in module magmap.settings.config) Verbosity (class in magmap.settings.config) verbosity (in module magmap.settings.config) VERIFIED (magmap.settings.config.TruthDBModes attribute) VerifierEditor (class in magmap.gui.verifier_editor) VerifierEditor.BlobView (class in magmap.gui.verifier_editor) VERIFY (magmap.settings.config.TruthDBModes attribute) VIEW (magmap.settings.config.TruthDBModes attribute) view_subimg() (magmap.gui.plot_editor.PlotEditor method) VIS (magmap.settings.config.ItkSnapLabels attribute) VOL (magmap.settings.config.SmoothingMetrics attribute) VOL_ATLAS (magmap.settings.config.AtlasMetrics attribute) VOL_COMPARE (magmap.settings.config.RegisterTypes attribute) VOL_LABELS (magmap.settings.config.AtlasMetrics attribute) VOL_ORIG (magmap.settings.config.SmoothingMetrics attribute) VOL_STATS (magmap.settings.config.RegisterTypes attribute) VSPAN_COL (magmap.settings.config.PlotLabels attribute) VSPAN_FORMAT (magmap.settings.config.PlotLabels attribute) W warn() (in module magmap.io.libmag) watershed_distance() (in module magmap.cv.segmenter) WATERSHED_MASK_FILTER (magmap.settings.profiles.RegKeys attribute) weight_mean() (in module magmap.io.df_io) weight_std() (in module magmap.io.df_io) write() (magmap.settings.logs.LogWriter method) write_raw_file() (in module magmap.io.np_io) write_tif() (in module magmap.io.np_io) WT_COL (magmap.settings.config.PlotLabels attribute) wt_dists (magmap.cv.segmenter.LabelToMarkerErosion attribute) X X (magmap.cv.detector.Blobs.Cols attribute) X_COL (magmap.settings.config.PlotLabels attribute) X_LABEL (magmap.settings.config.PlotLabels attribute) X_LIM (magmap.settings.config.PlotLabels attribute) X_SCALE (magmap.settings.config.PlotLabels attribute) X_TICK_LABELS (magmap.settings.config.PlotLabels attribute) X_UNIT (magmap.settings.config.PlotLabels attribute) xlims (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) Y Y (magmap.cv.detector.Blobs.Cols attribute) Y_COL (magmap.settings.config.PlotLabels attribute) Y_LABEL (magmap.settings.config.PlotLabels attribute) Y_LIM (magmap.settings.config.PlotLabels attribute) Y_SCALE (magmap.settings.config.PlotLabels attribute) Y_TICK_LABELS (magmap.settings.config.PlotLabels attribute) Y_UNIT (magmap.settings.config.PlotLabels attribute) ylims (magmap.plot.plot_support.ImageOverlayer.RotTransform attribute) Z Z (magmap.cv.detector.Blobs.Cols attribute) zero_crossing() (in module magmap.cv.cv_nd) zoom (in module magmap.settings.config) ZOOM (magmap.settings.config.MetaKeys attribute) ZOOM_SHIFT (magmap.settings.config.PlotLabels attribute) zscore_df() (in module magmap.io.df_io) ZSCORES (magmap.settings.config.RegisterTypes attribute)