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README.md

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## Build Data Sets
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:warning: For using your own data set, the following steps are not needed. Please check the
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[existing datasets](https://github.com/mathpluscode/ImgX-DiffSeg/blob/main/imgx_datasets/) for
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examples of using TFDS. Particularly,
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[BraTS 2021](https://github.com/mathpluscode/ImgX-DiffSeg/blob/main/imgx_datasets/brats2021_mr/brats2021_mr_dataset_builder.py)
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does not require downloading.
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:muscle: We are working on a toy example for using custom data sets without TFDS, thanks for your
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understanding.
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Use the following commands to (re)build all data sets. Check the [README](imgx_datasets/README.md)
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of imgx_datasets for details. Especially, manual downloading is required for the BraTS 2021 dataset.
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make rebuild_dataset
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```
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Or build the selected data set by running one of the following commands.
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```bash
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tfds build imgx_datasets/male_pelvic_mr
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tfds build imgx_datasets/amos_ct
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tfds build imgx_datasets/muscle_us
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tfds build imgx_datasets/brats2021_mr # requires downloading data manually
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```
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## Experiment
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### Training and Testing

imgx_datasets/brats2021_mr/brats2021_mr_dataset_builder.py

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Returns:
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dict mapping split to generators.
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"""
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# Download data from zenodo
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# Manually downloaded
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data_dir = dl_manager.manual_dir / BRATS2021_MR_TFDS_FOLD / "BraTS2021_Training_Data"
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preprocessed_dir = dl_manager.manual_dir / BRATS2021_MR_TFDS_FOLD / "preprocessed"
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preprocessed_dir.mkdir(parents=True, exist_ok=True)

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