Package index • ClassiPyR

Running the App

Functions for launching ClassiPyR

run_app(): Run the ClassiPyR Shiny Application
init_python_env(): Initialize Python environment for iRfcb
get_config_dir(): Get ClassiPyR configuration directory
get_settings_path(): Get path to settings file

Sample Loading

Functions for loading classifications and samples from ROI/PNG sources

load_class_list(): Load class list from MAT or TXT file
load_from_classifier_mat(): Load classifications from MATLAB classifier output file
load_from_csv(): Load classifications from CSV file (validation mode)
load_from_h5(): Load classifications from HDF5 classifier output file
load_from_mat(): Load classifications from existing MAT annotation file
load_from_db(): Load classifications from SQLite database
create_new_classifications(): Create new classifications for annotation mode
filter_to_extracted(): Filter classifications to only include extracted images
scan_png_class_folder(): Scan a PNG folder with class subfolders

Sample Saving

Functions for saving annotations and exporting images

save_sample_annotations(): Save sample annotations
save_validation_statistics(): Save validation statistics to CSV files
copy_images_to_class_folders(): Copy images to class-organized folders

Database Backend

SQLite database functions for annotation storage

get_default_db_dir(): Get default database directory
get_db_path(): Get path to the annotations SQLite database
save_annotations_db(): Save annotations to SQLite
delete_annotations_db(): Delete annotations for a sample from the SQLite database
load_annotations_db(): Load annotations from the SQLite database
list_annotated_samples_db(): List samples with annotations in the database
list_annotation_metadata_db(): List distinct years, months, and instruments from annotations
update_annotator(): Update the annotator name for one or more samples
import_mat_to_db(): Import a .mat annotation file into the SQLite database
import_all_mat_to_db(): Bulk import .mat annotation files into the SQLite database
export_db_to_mat(): Export annotations from SQLite to a .mat file
export_all_db_to_mat(): Bulk export all annotated samples from SQLite to .mat files
export_db_to_png(): Export annotated images from SQLite to class-organized PNG folders
export_all_db_to_png(): Bulk export all annotated samples from SQLite to class-organized PNGs
export_all_db_to_zip(): Bulk export all annotated samples from SQLite to EcoTaxa-ready ZIP
import_png_folder_to_db(): Import annotations from a PNG class folder into the SQLite database
list_classes_db(): List all classes with counts in the annotations database
save_class_taxonomy_db(): Save class taxonomy mappings to SQLite
load_class_taxonomy_db(): Load class taxonomy mappings from SQLite
save_global_class_list_db(): Save annotations to the SQLite database
load_global_class_list_db(): Load global class list from SQLite
load_class_annotations_db(): Load all annotations for a specific class from the database
save_class_review_changes_db(): Save class review changes to the database

WoRMS Taxonomy

Functions for matching class names to WoRMS AphiaID values

sanitize_worms_query(): Sanitize taxon names for WoRMS matching
build_worms_match_rows(): Build WoRMS match rows for class names

File Index Cache

Functions for managing the file index cache for faster startup

get_file_index_path(): Get path to file index cache
load_file_index(): Load file index from disk cache
save_file_index(): Save file index to disk cache
rescan_file_index(): Rescan folders and rebuild the file index cache

Dashboard

Functions for working with remote IFCB Dashboard instances

parse_dashboard_url(): Parse an IFCB Dashboard URL
list_dashboard_bins(): List bins from an IFCB Dashboard
download_dashboard_images(): Download and extract PNG images from the Dashboard
download_dashboard_images_bulk(): Bulk download zip archives for multiple samples from the Dashboard
download_dashboard_image_single(): Download a single PNG image from the Dashboard
download_dashboard_images_individual(): Download individual PNG images from the Dashboard
download_dashboard_adc(): Download ADC file from the Dashboard
download_dashboard_autoclass(): Download and parse autoclass scores from the Dashboard
resolve_sample_dataset(): Resolve the dataset name for a sample from the Dashboard API
get_dashboard_cache_dir(): Get persistent cache directory for dashboard downloads

Utilities

Helper functions for IFCB data processing

get_sample_paths(): Get sample paths from sample name
read_roi_dimensions(): Read ROI dimensions from ADC file
is_valid_sample_name(): Validate IFCB sample name format
sanitize_string(): Sanitize string for safe use in HTML/file paths
create_empty_changes_log(): Create empty changes log data frame