# 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