NeuroRuler package

Subpackages

• NeuroRuler.CLI package
  • Submodules
  • NeuroRuler.CLI.main module
    • main()
  • Module contents
    • cli()
• NeuroRuler.GUI package
  • Submodules
  • NeuroRuler.GUI.helpers module
    • ErrorMessageBox
      • ErrorMessageBox.__init__()
    • InformationDialog
      • InformationDialog.__init__()
    • InformationMessageBox()
    • WINDOW_TITLE_PADDING
    • mask_QImage()
    • sitk_slice_to_qimage()
    • string_to_QColor()
  • NeuroRuler.GUI.main module
    • MainWindow
      • MainWindow.__init__()
      • MainWindow.browse_files()
      • MainWindow.disable_binary_threshold_inputs()
      • MainWindow.disable_elements()
      • MainWindow.enable_binary_threshold_inputs()
      • MainWindow.enable_elements()
      • MainWindow.export_curr_slice_as_img()
      • MainWindow.export_json()
      • MainWindow.import_json()
      • MainWindow.next_img()
      • MainWindow.orient_curr_image()
      • MainWindow.previous_img()
      • MainWindow.remove_curr_img()
      • MainWindow.render_all_sliders()
      • MainWindow.render_circumference()
      • MainWindow.render_curr_slice()
      • MainWindow.render_image_num_and_path()
      • MainWindow.render_scaled_qpixmap_from_qimage()
      • MainWindow.render_smooth_slice()
      • MainWindow.render_threshold()
      • MainWindow.reset_settings()
      • MainWindow.resizeEvent()
      • MainWindow.rotate_x()
      • MainWindow.rotate_y()
      • MainWindow.rotate_z()
      • MainWindow.set_view_z()
      • MainWindow.settings_export_view_toggle()
      • MainWindow.slice_update()
      • MainWindow.test_stuff()
      • MainWindow.toggle_setting_to_false()
      • MainWindow.toggle_setting_to_true()
      • MainWindow.update_binary_filter_settings()
      • MainWindow.update_smoothing_settings()
      • MainWindow.update_view()
    • SETTINGS_VIEW_ENABLED
    • UNSCALED_QPIXMAP
    • display_dimensions()
    • display_direction()
    • display_metadata()
    • display_properties()
    • display_spacing()
    • error_message_box()
    • information_dialog()
    • main()
  • Module contents
    • gui()
• NeuroRuler.utils package
  • Submodules
  • NeuroRuler.utils.cli_settings module
    • CONDUCTANCE_PARAMETER
    • DEBUG
    • FILE
    • LOWER_BINARY_THRESHOLD
    • RAW
    • SLICE
    • SMOOTHING_ITERATIONS
    • THETA_X
    • THETA_Y
    • THETA_Z
    • THRESHOLD_FILTER
    • TIME_STEP
    • UPPER_BINARY_THRESHOLD
    • get_settings()
  • NeuroRuler.utils.constants module
    • BinaryColor
      • BinaryColor.Black
      • BinaryColor.White
    • JSON_CLI_CONFIG_PATH
    • JSON_GUI_CONFIG_PATH
    • MESSAGE_TO_SHOW_IF_UNITS_NOT_FOUND
    • NIFTI_METADATA_UNITS_KEY
    • NIFTI_METADATA_UNITS_VALUE_TO_PHYSICAL_UNITS
    • NUM_CONTOURS_IN_INVALID_SLICE
    • NUM_DIGITS_TO_ROUND_TO
    • ORIENTATION_STRINGS
    • OUTPUT_DIR
    • PRIMARY_MONITOR_DIMENSIONS
    • ROTATION_MAX
    • ROTATION_MIN
    • SUPPORTED_IMAGE_EXTENSIONS
    • SUPPORTED_IMAGE_EXTENSIONS_REGEX
    • THEMES
    • THEME_DIR
    • ThresholdFilter
      • ThresholdFilter.Binary
      • ThresholdFilter.Otsu
    • View
      • View.X
      • View.Y
      • View.Z
    • X_ORIENTATION_STR
    • Y_ORIENTATION_STR
    • Z_ORIENTATION_STR
    • degrees_to_radians()
    • deprecated()
    • get_path_stem()
  • NeuroRuler.utils.exceptions module
    • ArraysDifferentShape
      • ArraysDifferentShape.__init__()
    • ComputeCircumferenceOfInvalidSlice
      • ComputeCircumferenceOfInvalidSlice.__init__()
    • InvalidColor
      • InvalidColor.__init__()
    • InvalidJSONField
      • InvalidJSONField.__init__()
    • RotationOutOfBounds
      • RotationOutOfBounds.__init__()
  • NeuroRuler.utils.global_vars module
    • BINARY_THRESHOLD_FILTER
    • CONDUCTANCE_PARAMETER
    • CURR_IMAGE_INDEX
    • EULER_3D_TRANSFORM
    • GROUP_MAX_SPACING_DIFF
    • IMAGE_DICT
    • LOWER_BINARY_THRESHOLD
    • ORIENT_FILTER
    • OTSU_THRESHOLD_FILTER
    • READER
    • SLICE
    • SMOOTHING_FILTER
    • SMOOTHING_ITERATIONS
    • THETA_X
    • THETA_Y
    • THETA_Z
    • TIME_STEP
    • UPPER_BINARY_THRESHOLD
    • VIEW
    • X_CENTER
    • Y_CENTER
  • NeuroRuler.utils.gui_settings module
    • CONTOUR_COLOR
    • DEBUG
    • DISPLAY_ADVANCED_MENU_MESSAGES_IN_TERMINAL
    • FILE_BROWSER_START_DIR
    • GROUP_MAX_SPACING_DIFF
    • STARTUP_HEIGHT_RATIO
    • STARTUP_WIDTH_RATIO
    • THEME_NAME
  • NeuroRuler.utils.img_helpers module
    • ImageProperties
      • ImageProperties.center
      • ImageProperties.size
      • ImageProperties.spacing
    • are_properties_eq()
    • clear_globals()
    • del_curr_img()
    • get_all_paths()
    • get_center_of_rotation()
    • get_curr_binary_thresholded_slice()
    • get_curr_image()
    • get_curr_image_size()
    • get_curr_metadata()
    • get_curr_otsu_slice()
    • get_curr_path()
    • get_curr_physical_units()
    • get_curr_properties_tuple()
    • get_curr_rotated_slice()
    • get_curr_smooth_slice()
    • get_middle_dimension()
    • get_properties_from_path()
    • get_properties_from_sitk_image()
    • get_rotated_slice_hardcoded()
    • image_dict_is_empty()
    • initialize_globals()
    • next_img()
    • orient_curr_image()
    • previous_img()
    • set_curr_image()
    • update_images()
  • NeuroRuler.utils.imgproc module
    • MAX_NUM_MISMATCHED_PIXELS_FOR_BACKGROUND_COLOR_DETECTION
    • NUM_PIXELS_TO_CHECK_ON_EACH_EDGE_FOR_BACKGROUND_COLOR_DETECTION
    • background_color_of_binary_thresholded_slice()
    • contour()
    • distance_2d_with_spacing()
    • length_of_contour()
    • length_of_contour_with_spacing()
    • select_largest_component()
  • NeuroRuler.utils.parser module
    • JSON_SETTINGS
    • iterable_of_str_to_str()
    • load_json()
    • parse_bool()
    • parse_cli()
    • parse_cli_config()
    • parse_float()
    • parse_gui_cli()
    • parse_gui_config()
    • parse_int()
    • parse_main_color_from_theme_json()
    • parse_path()
    • parse_str()
  • Module contents

Module contents