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import datasets |
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import numpy as np |
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import pandas as pd |
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from pathlib import Path |
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import os |
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_CITATION = """\ |
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Alves, N., & Boulogne, L. (2023). Kidney CT Abnormality [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8043408 |
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""" |
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_DESCRIPTION = """\ |
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This dataset in total is comprised of 986 .mha (medical high-resolution image) files. Each of these files contains multiple layers of CT scans of the kidney. |
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The dataset has been speparated into train and test set by initial processing. |
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""" |
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_HOMEPAGE = "https://zenodo.org/records/8043408" |
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_LICENSE = "CC BY-NC-SA 4.0" |
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_URL = "https://huggingface.co/datasets/Euniceyeee/kidney-ct-abnormality" |
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_URLS = { |
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'train': "https://huggingface.co/datasets/Euniceyeee/kidney-ct-abnormality/resolve/main/train.zip", |
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'test': "https://huggingface.co/datasets/Euniceyeee/kidney-ct-abnormality/resolve/main/test.zip" |
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} |
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_METADATA_URL = { |
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"metadata": "https://huggingface.co/datasets/Euniceyeee/kidney-ct-abnormality/resolve/main/dataset.csv" |
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} |
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LABELS = [ |
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'Normal', |
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'Abnormal' |
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] |
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class KidneyCTAbnormality(datasets.GeneratorBasedBuilder): |
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"""Collection of brain xray images for fine-grain classification.""" |
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_URLS = _URLS |
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VERSION = datasets.Version("1.0.0") |
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def _info(self): |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=datasets.Features( |
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{ |
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"image": datasets.Image(), |
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"label": datasets.ClassLabel(num_classes=2, names=LABELS), |
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} |
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), |
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supervised_keys=("image", "label"), |
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homepage=_HOMEPAGE, |
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citation=_CITATION, |
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license=_LICENSE |
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) |
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def _split_generators(self, dl_manager): |
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metadata_url = dl_manager.download(_METADATA_URL) |
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df_metadata = pd.read_csv(metadata_url['metadata']) |
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files_metadata = {} |
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for _, row in df_metadata.iterrows(): |
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split_value = row['split'] |
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files_metadata.setdefault(split_value, []) |
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files_metadata[split_value].append(row.to_dict()) |
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img_url = self._URLS |
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data_dir = dl_manager.download_and_extract(img_url) |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, |
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gen_kwargs={ |
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"filepath": data_dir['train'], |
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"meta": files_metadata["train"] |
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}, |
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), |
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datasets.SplitGenerator( |
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name=datasets.Split.TEST, |
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gen_kwargs={ |
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"filepath": data_dir['train'], |
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"meta": files_metadata["test"] |
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}, |
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), |
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] |
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def _generate_examples(self, download_path, metadata): |
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"""Generate images and labels for splits.""" |
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for i, meta in enumerate(metadata): |
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img_path = os.path.join( |
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download_path, |
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meta["split"], |
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meta["abnormality"], |
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meta["file_name"], |
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) |
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yield i, { |
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"image": img_path, |
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"label": meta["abnormality"], |
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} |