ClassiPyR/_pkgdown.yml at main · EuropeanIFCBGroup/ClassiPyR · GitHub

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url: https://europeanifcbgroup.github.io/ClassiPyR/
template:
  bootstrap: 5
  bootswatch: flatly
  light-switch: yes
  bslib:
    primary: '#1A3A5C'
    link-color: '#3D8EC9'
home:
  title: ClassiPyR
  description: A Shiny application for manual image classification and validation
    of IFCB plankton images
navbar:
  structure:
    left:
    - intro
    - articles
    - reference
    - news
    right:
    - search
    - github
    - lightswitch
  components:
    articles:
      text: Articles
      menu:
      - text: Getting Started
        href: articles/getting-started.html
      - text: User Guide
        href: articles/user-guide.html
      - text: Class List Management
        href: articles/class-management.html
      - text: '---'
      - text: FAQ & Troubleshooting
        href: articles/faq.html
reference:
- title: Running the App
  desc: Functions for launching ClassiPyR
  contents:
  - run_app
  - init_python_env
  - get_config_dir
  - get_settings_path
  - update_settings_file
- title: Sample Loading
  desc: Functions for loading classifications and samples from ROI/PNG sources
  contents:
  - load_class_list
  - load_from_classifier_mat
  - load_from_csv
  - load_from_h5
  - load_from_mat
  - load_from_db
  - create_new_classifications
  - filter_to_extracted
  - scan_png_class_folder
- title: Sample Saving
  desc: Functions for saving annotations and exporting images
  contents:
  - save_sample_annotations
  - save_validation_statistics
  - copy_images_to_class_folders
- title: Database Backend
  desc: SQLite database functions for annotation storage
  contents:
  - get_default_db_dir
  - get_db_path
  - save_annotations_db
  - delete_annotations_db
  - load_annotations_db
  - list_annotated_samples_db
  - list_annotation_metadata_db
  - update_annotator
  - import_mat_to_db
  - import_all_mat_to_db
  - export_db_to_mat
  - export_all_db_to_mat
  - export_db_to_png
  - export_all_db_to_png
  - export_all_db_to_zip
  - import_png_folder_to_db
  - fill_unclassified_db
  - import_png_folder_with_unclassified
  - list_classes_db
  - save_class_taxonomy_db
  - load_class_taxonomy_db
  - save_global_class_list_db
  - load_global_class_list_db
  - load_class_annotations_db
  - save_class_review_changes_db
- title: WoRMS Taxonomy
  desc: Functions for matching class names to WoRMS AphiaID values
  contents:
  - sanitize_worms_query
  - build_worms_match_rows
- title: File Index Cache
  desc: Functions for managing the file index cache for faster startup
  contents:
  - get_file_index_path
  - load_file_index
  - save_file_index
  - rescan_file_index
- title: Dashboard
  desc: Functions for working with remote IFCB Dashboard instances
  contents:
  - parse_dashboard_url
  - list_dashboard_bins
  - download_dashboard_images
  - download_dashboard_images_bulk
  - download_dashboard_image_single
  - download_dashboard_images_individual
  - download_dashboard_adc
  - download_dashboard_autoclass
  - resolve_sample_dataset
  - get_dashboard_cache_dir
- title: Utilities
  desc: Helper functions for IFCB data processing
  contents:
  - get_sample_paths
  - read_roi_dimensions
  - is_valid_sample_name
  - sanitize_string
  - create_empty_changes_log
authors:
  Anders Torstensson:
    href: https://github.com/anderstorstensson
footer:
  structure:
    left: developed_by
    right: built_with