3d-brain-mri.py

# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# TODO: Address all TODOs and remove all explanatory comments
"""TODO: Add a description here."""


import csv
import json
import os

import datasets


# TODO: Add BibTeX citation
# Find for instance the citation on arxiv or on the dataset repo/website
_CITATION = """\
@InProceedings{huggingface:dataset,
title = {The University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) (Version 4) [Dataset]},
author={Calabrese, E., Villanueva-Meyer, J., Rudie, J., Rauschecker, A., Baid, U., Bakas, S., Cha, S., Mongan, J., & Hess, C},
year={2022}
}
"""


# TODO: Add description of the dataset here
# You can copy an official description
_DESCRIPTION = """\
This dataset is based on the UCSF-PDGM: The University of California San Francisco Preoperative Diffuse Glioma MRI research dataset.
"""

# TODO: Add a link to an official homepage for the dataset here
_HOMEPAGE = "https://www.cancerimagingarchive.net/collection/ucsf-pdgm/"

# TODO: Add the licence for the dataset here if you can find it
_LICENSE = "CC BY 4.0"

# TODO: Add link to the official dataset URLs here
# The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
_URLS = {
    "data": "https://huggingface.co/datasets/determined-ai/3d-brain-mri/resolve/main/dataset-3d-brain.zip"
}


# TODO: Name of the dataset usually matches the script name with CamelCase instead of snake_case
class BrainMRI(datasets.GeneratorBasedBuilder):
    """TODO: Short description of my dataset."""

    VERSION = datasets.Version("1.0.0")

    # This is an example of a dataset with multiple configurations.
    # If you don't want/need to define several sub-sets in your dataset,
    # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.

    # If you need to make complex sub-parts in the datasets with configurable options
    # You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig
    # BUILDER_CONFIG_CLASS = MyBuilderConfig

    # You will be able to load one or the other configurations in the following list with
    # data = datasets.load_dataset('my_dataset', 'first_domain')
    # data = datasets.load_dataset('my_dataset', 'second_domain')
    BUILDER_CONFIGS = [
        datasets.BuilderConfig(name="data", version=VERSION, description="This is the data")
    ]

    DEFAULT_CONFIG_NAME = "data"  # It's not mandatory to have a default configuration. Just use one if it make sense.

    def _info(self):
        # TODO: This method specifies the datasets.DatasetInfo object which contains informations and typings for the dataset
        return datasets.DatasetInfo(
            # This is the description that will appear on the datasets page.
            description=_DESCRIPTION,
            # This defines the different columns of the dataset and their types
            # Homepage of the dataset for documentation
            homepage=_HOMEPAGE,
            # License for the dataset if available
            license=_LICENSE,
            # Citation for the dataset
            citation=_CITATION,
        )

    def _split_generators(self, dl_manager):
        # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
        # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name

        # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS
        # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
        # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
        urls = _URLS[self.config.name]
        data_dir = dl_manager.download_and_extract(urls)
        return []

    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    def _generate_examples(self, filepath, split):
        # TODO: This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
        # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
        pass