API reference

The phenopype API

As most Python packages, phenopype has a Application Programming Interface (API) with a “public” and a “private” part (see https://lwn.net/Articles/795019/). The public part is documented below and includes all Python functions, classes and methods that are available for high throughput image analysis, project management, and image import and export. The private part works in the background and includes helper functions and classes that support the public API. They are not intended to be called directly by users.

The API reference

The API reference presented here is auto-generated from the docsstrings in each Python function, class or method, using Sphinx. In Python, you can access the content of each docsstring using help(). Most IDEs have a shortcut to access the docsstring, e.g. Ctrl+i in Spyder or Ctrl+Q in PyCharm.

The Project class for comprehensive image annotation, pattern recognition and feature extraction workflows:

• Project class
  • Project
    • Project.add_files()
    • Project.add_config()
    • Project.add_model()
    • Project.add_reference_template()
    • Project.add_reference()
    • Project.check_files()
    • Project.collect_results()
    • Project.copy_tag()
    • Project.edit_config()
    • Project.export_zip()
    • Project.export_training_data()

The Pype-class for high-throughput analysis:

• Pype class
  • Pype

The Project_labelling class for minimalistic labelling workflows:

• Project_labelling class
  • Project_labelling
    • Project_labelling.add_files()
    • Project_labelling.run()
    • Project_labelling.export()

Utility functions, e.g. for loading, saving and viewing images:

• Utility functions
  • load_image()
  • print_colours()
  • resize_image()
  • save_image()
  • show_image()

All image processing functions:

• Core modules
  • Preprocessing
    • blur()
    • clip_histogram()
    • create_mask()
    • detect_mask()
    • create_reference()
    • detect_reference()
    • detect_QRcode()
    • decompose_image()
    • write_comment()
  • Segmentation
    • contour_to_mask()
    • detect_contour()
    • edit_contour()
    • mask_to_contour()
    • morphology()
    • threshold()
    • watershed()
  • Measurement
    • set_landmark()
    • set_polyline()
    • detect_skeleton()
    • compute_shape_features()
    • compute_texture_features()
  • Visualization
    • draw_comment()
    • draw_contour()
    • draw_landmark()
    • draw_mask()
    • draw_polyline()
    • draw_QRcode()
    • draw_reference()
    • select_canvas()
  • Export
    • convert_annotation()
    • export_csv()
    • load_annotation()
    • save_annotation()
    • save_ROI()
    • save_canvas()

The video tracking tools:

• Video analysis
  • Motion tracker
    • motion_tracker
      • motion_tracker.video_output()
      • motion_tracker.detection_settings()
      • motion_tracker.run_tracking()
  • Tracking methods
    • tracking_method