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setup.bat
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:: Download PUMA dataset
echo "Downloading PUMA dataset..."
wget https://zenodo.org/records/14213079/files/01_training_dataset_geojson_nuclei.zip?download=1 -O data/01_training_dataset_geojson_nuclei.zip
wget https://zenodo.org/records/14213079/files/01_training_dataset_tif_ROIs.zip?download=1 -O data/01_training_dataset_tif_ROIs.zip
:: Unzip
echo "Unzipping datasets..."
tar -xf data/01_training_dataset_geojson_nuclei.zip -C data
tar -xf data/01_training_dataset_tif_ROIs.zip -C data
:: Remove zip files
echo "Cleaning up zip files..."
rm data/01_training_dataset_geojson_nuclei.zip
rm data/01_training_dataset_tif_ROIs.zip
:: Download pre-trained resnet model
echo "Downloading pre-trained ResNet model..."
wget https://download.pytorch.org/models/resnet50-0676ba61.pth -O pretrained/resnet50-0676ba61.pth
echo "Download and setup complete."