LM2_fast.yaml

leafmachine:
  archival_component_detector:
    detector_iteration: PREP_final
    detector_type: Archival_Detector
    detector_version: PREP_final
    detector_weights: best.pt
    do_save_prediction_overlay_images: true
    ignore_objects_for_overlay: []
    minimum_confidence_threshold: 0.7
    ruler_binary_detector: model_scripted_resnet_720_withCompression.pt
    ruler_detector: ruler_classifier_38classes_v-1.pt
  armature_component_detector:
    detector_iteration: ARM_A_1000
    detector_type: Armature_Detector
    detector_version: ARM_A_1000
    detector_weights: best.pt
    do_save_prediction_overlay_images: true
    ignore_objects_for_overlay: []
    minimum_confidence_threshold: 0.5
  cropped_components:
    binarize_labels: false
    binarize_labels_skeletonize: false
    do_save_cropped_annotations: false
    save_cropped_annotations:
    - label
    save_per_annotation_class: false
    save_per_image: false
  data:
    do_apply_conversion_factor: true
    include_darwin_core_data_from_combined_file: false
    save_individual_csv_files_landmarks: false
    save_individual_csv_files_measurements: false
    save_individual_csv_files_rulers: false
    save_individual_efd_files: false
    save_json_measurements: false
    save_json_rulers: false
  do:
    check_for_corrupt_images_make_vertical: false #true #########################################
    check_for_illegal_filenames: false #true #########################################
    run_leaf_processing: true 
  landmark_detector:
    detector_iteration: Landmarks
    detector_type: Landmark_Detector_YOLO
    detector_version: Landmarks
    detector_weights: best.pt
    do_save_QC_images: false
    do_save_final_images: false
    do_save_prediction_overlay_images: false
    do_show_QC_images: false
    do_show_final_images: false
    ignore_objects_for_overlay: []
    landmark_partial_leaves: false
    landmark_whole_leaves: true
    minimum_confidence_threshold: 0.02
    use_existing_landmark_detections: null
  landmark_detector_armature:
    detector_iteration: Landmarks_Arm_A_200
    detector_type: Landmark_Detector_YOLO
    detector_version: Landmarks_Arm_A_200
    detector_weights: last.pt
    do_save_QC_images: true
    do_save_final_images: true
    do_save_prediction_overlay_images: true
    do_show_QC_images: true
    do_show_final_images: true
    ignore_objects_for_overlay: []
    minimum_confidence_threshold: 0.06
    upscale_factor: 10
    use_existing_landmark_detections: null
  leaf_segmentation:
    calculate_elliptic_fourier_descriptors: false
    detector_version: uniform_spaced_oriented_traces_mid15_pet5_clean_640_flipidx_pt2
    elliptic_fourier_descriptor_order: 40
    find_minimum_bounding_box: true
    generate_overlay: false
    keep_only_best_one_leaf_one_petiole: true
    minimum_confidence_threshold: 0.7
    overlay_background_color: black
    overlay_dpi: 300
    overlay_line_width: 1
    save_each_segmentation_overlay_image: false
    save_full_image_masks_color: true
    save_individual_overlay_images: false
    save_keypoint_overlay: true
    save_masks_color: true
    save_oriented_images: true
    save_oriented_mask: true
    save_rgb_cropped_images: true
    save_segmentation_overlay_images_to_pdf: false
    save_simple_txt: true
    segment_partial_leaves: false
    segment_whole_leaves: true
    segmentation_model: Group3_Dataset_100000_Iter_1176PTS_512Batch_smooth_l1_LR00025_BGR
    use_efds_for_png_masks: false
  logging:
    log_level: null
  modules:
    armature: false
    specimen_crop: false
  overlay:
    alpha_transparency_archival: 0.3
    alpha_transparency_plant: 0.0
    alpha_transparency_seg_partial_leaf: 0.3
    alpha_transparency_seg_whole_leaf: 0.4
    ignore_archival_detections_classes: []
    ignore_landmark_classes: []
    ignore_plant_detections_classes:
    - leaf_whole
    line_width_archival: 12
    line_width_efd: 12
    line_width_plant: 12
    line_width_seg: 12
    overlay_background_color: black
    overlay_dpi: 300
    save_overlay_to_jpgs: true
    save_overlay_to_pdf: false
    show_archival_detections: true
    show_landmarks: true
    show_plant_detections: true
    show_segmentations: true
  plant_component_detector:
    detector_iteration: PLANT_LeafPriority
    detector_type: Plant_Detector
    detector_version: PLANT_LeafPriority
    detector_weights: LeafPriority.pt
    do_save_prediction_overlay_images: true
    ignore_objects_for_overlay: []
    minimum_confidence_threshold: 0.7
  print:
    optional_warnings: true
    verbose: true
  project:
    GBIF_mode: all
    accept_only_ideal_leaves: true
    batch_size: 200
    censor_archival_components: false
    dir_images_local: /media/nas/GBIF_Downloads/Cornales/Nyssaceae/img
    dir_images_subset: ''
    dir_output: /media/nas/GBIF_Downloads/Cornales/Nyssaceae/LM2
    hide_archival_components:
    - ruler
    - barcode
    - label
    - colorcard
    - map
    - photo
    - weights
    image_location: local
    minimum_total_reproductive_counts: 0
    n_images_per_species: 1000000
    num_workers: 12
    num_workers_ruler: 12
    num_workers_seg: 12
    overlay_background_color: black
    overlay_dpi: 300
    path_combined_csv_local: null
    path_images_csv_local: null
    path_occurrence_csv_local: null
    process_subset_of_images: false
    replacement_color: '#FFFFFF'
    run_name: Cornales_Nyssaceae
    species_list: ''
    use_CF_predictor: true
    use_existing_archival_component_detections: null
    use_existing_plant_component_detections: null
  ruler_detection:
    detect_ruler_type: true
    minimum_confidence_threshold: 0.5
    ruler_binary_detector: model_scripted_resnet_720_withCompression.pt
    ruler_detector: ruler_classifier_38classes_v-1.pt
    save_ruler_processed: false
    save_ruler_validation: false
    save_ruler_validation_summary: true