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| # To use default value, set to null | |
| leafmachine: | |
| use_RGB_label_images: True | |
| do: | |
| check_for_illegal_filenames: False | |
| check_for_corrupt_images_make_vertical: False | |
| print: | |
| verbose: True | |
| optional_warnings: True | |
| logging: | |
| log_level: null | |
| # Overall Project Input Settings | |
| project: | |
| # Image to Process | |
| dir_images_local: 'D:\Dropbox\LM2_Env\VoucherVision_Datasets\2022_09_07_thru12_S3_jacortez_AllAsia' # 'D:/Dropbox/LM2_Env/VoucherVision_Datasets/Compare_Set_Easy_10imgs/imgs' #'D:\D_Desktop\Richie\Imgs' #'D:/Dropbox/LM2_Env/Image_Datasets/Acacia/Acacia_prickles_4-26-23_LANCZOS/images/short' #'D:\D_Desktop\Richie\Imgs' #'home/brlab/Dropbox/LM2_Env/Image_Datasets/Manuscript_Images' # 'D:\Dropbox\LM2_Env\Image_Datasets\SET_FieldPrism_Test\TESTING_OUTPUT\Images_Processed\REU_Field_QR-Code-Images\Cannon_Corrected\Images_Corrected' # 'F:\temp_3sppFamily' # 'D:/Dropbox/LM2_Env/Image_Datasets/GBIF_BroadSample_3SppPerFamily' # SET_Diospyros/images_short' # 'D:/Dropbox/LM2_Env/Image_Datasets/SET_Diospyros/images_short' #'D:\Dropbox\LM2_Env\Image_Datasets\GBIF_BroadSample_Herbarium' #'D:/Dropbox/LM2_Env/Image_Datasets/SET_Diospyros/images_short' # str | only for image_location:local | full path for directory containing images | |
| # dir_images_local: 'D:/Dropbox/LM2_Env/VoucherVision_Datasets/Compare_Set_Easy_10imgs/imgs' #'D:\D_Desktop\Richie\Imgs' #'D:/Dropbox/LM2_Env/Image_Datasets/Acacia/Acacia_prickles_4-26-23_LANCZOS/images/short' #'D:\D_Desktop\Richie\Imgs' #'home/brlab/Dropbox/LM2_Env/Image_Datasets/Manuscript_Images' # 'D:\Dropbox\LM2_Env\Image_Datasets\SET_FieldPrism_Test\TESTING_OUTPUT\Images_Processed\REU_Field_QR-Code-Images\Cannon_Corrected\Images_Corrected' # 'F:\temp_3sppFamily' # 'D:/Dropbox/LM2_Env/Image_Datasets/GBIF_BroadSample_3SppPerFamily' # SET_Diospyros/images_short' # 'D:/Dropbox/LM2_Env/Image_Datasets/SET_Diospyros/images_short' #'D:\Dropbox\LM2_Env\Image_Datasets\GBIF_BroadSample_Herbarium' #'D:/Dropbox/LM2_Env/Image_Datasets/SET_Diospyros/images_short' # str | only for image_location:local | full path for directory containing images | |
| image_location: 'local' | |
| continue_run_from_partial_xlsx: 'D:\Dropbox\LM2_Env\VoucherVision_Datasets\POC_chatGPT__2022_09_07_thru12_S3_jacortez_AllAsia\2022_09_07_thru12_S3_jacortez_AllAsia\Transcription\transcribed.xlsx' | |
| # continue_run_from_partial_xlsx: null | |
| # Project Output Dir | |
| dir_output: 'D:/Dropbox/LM2_Env/VoucherVision_Datasets/POC_chatGPT__2022_09_07_thru12_S3_jacortez_AllAsia' # 'D:/Dropbox/LM2_Env/Image_Datasets/TEST_LM2' # 'D:\D_Desktop\Richie\Richie_Out' | |
| run_name: 'POC_chatGPT' #'images_short_TEST' #'images_short_landmark' | |
| prefix_removal: 'MICH-V-' | |
| suffix_removal: '' | |
| catalog_numerical_only: True | |
| # Embeddings and LLM | |
| use_domain_knowledge: True | |
| embeddings_database_name: 'EmbeddingsDB_all_asia_minimal_InRegion' | |
| build_new_embeddings_database: False | |
| path_to_domain_knowledge_xlsx: 'D:\Dropbox\LeafMachine2\leafmachine2\transcription\domain_knowledge/AllAsiaMinimalasof25May2023_2__InRegion.xlsx' #'D:/Dropbox/LeafMachine2/leafmachine2/transcription/domain_knowledge/AllAsiaMinimalasof25May2023_2__TRIMMEDtiny.xlsx' | |
| batch_size: 500 #null # null = all | |
| num_workers: 1 # int |DEFAULT| 4 # More is not always better. Most hardware loses performance after 4 | |
| modules: | |
| specimen_crop: True | |
| LLM_version: 'chatGPT' # from 'chatGPT' OR 'PaLM' | |
| cropped_components: | |
| # empty list for all, add to list to IGNORE, lowercase, comma seperated | |
| # archival |FROM| | |
| # ruler, barcode, colorcard, label, map, envelope, photo, attached_item, weights | |
| # plant |FROM| | |
| # leaf_whole, leaf_partial, leaflet, seed_fruit_one, seed_fruit_many, flower_one, flower_many, bud, specimen, roots, wood | |
| do_save_cropped_annotations: True | |
| save_cropped_annotations: ['label','barcode'] # 'save_all' to save all classes | |
| save_per_image: False # creates a folder for each image, saves crops into class-names folders # TODO | |
| save_per_annotation_class: True # saves crops into class-names folders | |
| binarize_labels: False | |
| binarize_labels_skeletonize: False | |
| data: | |
| save_json_rulers: False | |
| save_json_measurements: False | |
| save_individual_csv_files_rulers: False | |
| save_individual_csv_files_measurements: False | |
| include_darwin_core_data_from_combined_file: False | |
| do_apply_conversion_factor: False ########################### | |
| overlay: | |
| save_overlay_to_pdf: True | |
| save_overlay_to_jpgs: True | |
| overlay_dpi: 300 # int |FROM| 100 to 300 | |
| overlay_background_color: 'black' # str |FROM| 'white' or 'black' | |
| show_archival_detections: True | |
| ignore_archival_detections_classes: [] | |
| show_plant_detections: True | |
| ignore_plant_detections_classes: ['leaf_whole', 'specimen'] #['leaf_whole', 'leaf_partial', 'specimen'] | |
| show_segmentations: True | |
| show_landmarks: True | |
| ignore_landmark_classes: [] | |
| line_width_archival: 2 # int | |
| line_width_plant: 6 # int | |
| line_width_seg: 12 # int # thick = 12 | |
| line_width_efd: 6 # int # thick = 3 | |
| alpha_transparency_archival: 0.3 # float between 0 and 1 | |
| alpha_transparency_plant: 0 | |
| alpha_transparency_seg_whole_leaf: 0.4 | |
| alpha_transparency_seg_partial_leaf: 0.3 | |
| # Configure Archival Component Detector | |
| archival_component_detector: | |
| # ./leafmachine2/component_detector/runs/train/detector_type/detector_version/detector_iteration/weights/detector_weights | |
| detector_type: 'Archival_Detector' | |
| detector_version: 'PREP_final' | |
| detector_iteration: 'PREP_final' | |
| detector_weights: 'best.pt' | |
| minimum_confidence_threshold: 0.5 | |
| do_save_prediction_overlay_images: True | |
| ignore_objects_for_overlay: [] # list[str] # list of objects that can be excluded from the overlay # all = null | |