├── .gitignore ├── Full tile predictions.ipynb ├── README.md ├── Saliences.ipynb ├── Tree species classification with fastai-v2.ipynb ├── batch_job_scripts ├── create_cubes.sh ├── detect_treetops.sh ├── extract_reflectance.sh ├── hist_create_cubes.sh ├── make_tile_list.py ├── match_treetops.sh ├── pack_files.sh ├── predict_area.sh ├── predict_svm.sh └── stack_tiles.sh ├── environment.yml ├── getContoursDalponte.R ├── images └── result_map.jpeg ├── make_train_data.py ├── match_field_data.py ├── notebooks ├── Comparison methods with fixed data.ipynb ├── Comparison methods.ipynb ├── Data exploration and preprocessing.ipynb ├── Distributions.ipynb ├── Individual tree detection, segmentation and matching to field data.ipynb └── Training and validation data generation.ipynb ├── predict_fastaiv2.py ├── preprocess_shapefiles.py ├── src ├── __init__.py ├── customlayers.py ├── customnets.py ├── image_utils.py ├── multichannel.py ├── spectral_variables.py └── utils.py └── stack_tiles_gdal.py 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