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
    • StackPlaneIO.build_stack()
    • StackPlaneIO.convert_imgs()
    • StackPlaneIO.imgs
    • StackPlaneIO.import_img()
    • StackPlaneIO.interp_order
    • StackPlaneIO.process_plane()
    • StackPlaneIO.set_data()
  • 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
    • Image5d.rgb
  • 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
    • ClrDB.blobs_truth
    • ClrDB.conn
    • ClrDB.cur
    • ClrDB.get_rois()
    • ClrDB.insert_blob_matches()
    • ClrDB.load_db()
    • ClrDB.load_truth_blobs()
    • ClrDB.select_blob()
    • ClrDB.select_blob_by_id()
    • ClrDB.select_blob_matches()
    • ClrDB.select_blob_matches_by_blob_id()
    • ClrDB.select_blobs_by_position()
    • ClrDB.select_blobs_by_roi()
    • ClrDB.select_experiment()
    • ClrDB.select_or_insert_experiment()
    • ClrDB.start_db()
  • 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()