Commit
•
b429893
1
Parent(s):
bc53ced
Download data from Hub (#5)
Browse files- Move data to data dir (dec3021e71af4c43fed5f3b09e815f21b293ad99)
- Update script to download data from the Hub (db9ed1017f7752a08dbce2c5d01ad4982b63be11)
- Fix style (39fc043dd7eec650f180a7bec89278ab0273d146)
Co-authored-by: Albert Villanova <[email protected]>
This view is limited to 50 files because it contains too many changes.
See raw diff
- AeroPath.py +29 -123
- {1 → data/1}/1_CT_HR.nii.gz +0 -0
- {1 → data/1}/1_CT_HR_label_airways.nii.gz +0 -0
- {1 → data/1}/1_CT_HR_label_lungs.nii.gz +0 -0
- {10 → data/10}/10_CT_HR.nii.gz +0 -0
- {10 → data/10}/10_CT_HR_label_airways.nii.gz +0 -0
- {10 → data/10}/10_CT_HR_label_lungs.nii.gz +0 -0
- {11 → data/11}/11_CT_HR.nii.gz +0 -0
- {11 → data/11}/11_CT_HR_label_airways.nii.gz +0 -0
- {11 → data/11}/11_CT_HR_label_lungs.nii.gz +0 -0
- {12 → data/12}/12_CT_HR.nii.gz +0 -0
- {12 → data/12}/12_CT_HR_label_airways.nii.gz +0 -0
- {12 → data/12}/12_CT_HR_label_lungs.nii.gz +0 -0
- {13 → data/13}/13_CT_HR.nii.gz +0 -0
- {13 → data/13}/13_CT_HR_label_airways.nii.gz +0 -0
- {13 → data/13}/13_CT_HR_label_lungs.nii.gz +0 -0
- {14 → data/14}/14_CT_HR.nii.gz +0 -0
- {14 → data/14}/14_CT_HR_label_airways.nii.gz +0 -0
- {14 → data/14}/14_CT_HR_label_lungs.nii.gz +0 -0
- {15 → data/15}/15_CT_HR.nii.gz +0 -0
- {15 → data/15}/15_CT_HR_label_airways.nii.gz +0 -0
- {15 → data/15}/15_CT_HR_label_lungs.nii.gz +0 -0
- {16 → data/16}/16_CT_HR.nii.gz +0 -0
- {16 → data/16}/16_CT_HR_label_airways.nii.gz +0 -0
- {16 → data/16}/16_CT_HR_label_lungs.nii.gz +0 -0
- {17 → data/17}/17_CT_HR.nii.gz +0 -0
- {17 → data/17}/17_CT_HR_label_airways.nii.gz +0 -0
- {17 → data/17}/17_CT_HR_label_lungs.nii.gz +0 -0
- {18 → data/18}/18_CT_HR.nii.gz +0 -0
- {18 → data/18}/18_CT_HR_label_airways.nii.gz +0 -0
- {18 → data/18}/18_CT_HR_label_lungs.nii.gz +0 -0
- {19 → data/19}/19_CT_HR.nii.gz +0 -0
- {19 → data/19}/19_CT_HR_label_airways.nii.gz +0 -0
- {19 → data/19}/19_CT_HR_label_lungs.nii.gz +0 -0
- {2 → data/2}/2_CT_HR.nii.gz +0 -0
- {2 → data/2}/2_CT_HR_label_airways.nii.gz +0 -0
- {2 → data/2}/2_CT_HR_label_lungs.nii.gz +0 -0
- {20 → data/20}/20_CT_HR.nii.gz +0 -0
- {20 → data/20}/20_CT_HR_label_airways.nii.gz +0 -0
- {20 → data/20}/20_CT_HR_label_lungs.nii.gz +0 -0
- {21 → data/21}/21_CT_HR.nii.gz +0 -0
- {21 → data/21}/21_CT_HR_label_airways.nii.gz +0 -0
- {21 → data/21}/21_CT_HR_label_lungs.nii.gz +0 -0
- {22 → data/22}/22_CT_HR.nii.gz +0 -0
- {22 → data/22}/22_CT_HR_label_airways.nii.gz +0 -0
- {22 → data/22}/22_CT_HR_label_lungs.nii.gz +0 -0
- {23 → data/23}/23_CT_HR.nii.gz +0 -0
- {23 → data/23}/23_CT_HR_label_airways.nii.gz +0 -0
- {23 → data/23}/23_CT_HR_label_lungs.nii.gz +0 -0
- {24 → data/24}/24_CT_HR.nii.gz +0 -0
AeroPath.py
CHANGED
@@ -1,29 +1,16 @@
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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# TODO: Address all TODOs and remove all explanatory comments
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"""TODO: Add a description here."""
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import csv
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import json
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import os
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import datasets
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# TODO: Add BibTeX citation
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# Find for instance the citation on arxiv or on the dataset repo/website
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_CITATION = """\
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@misc{støverud2023aeropath,
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title={AeroPath: An airway segmentation benchmark dataset with challenging pathology},
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}
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"""
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"""
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# TODO: Add the licence for the dataset here if you can find it
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_LICENSE = "MIT"
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# TODO: Add link to the official dataset URLs here
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# The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
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# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
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_URLS = {
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#"first_domain": "https://huggingface.co/great-new-dataset-first_domain.zip",
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#"second_domain": "https://huggingface.co/great-new-dataset-second_domain.zip",
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"zenodo": "https://zenodo.org/records/10069289/files/AeroPath.zip?download=1"
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}
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# TODO: Name of the dataset usually matches the script name with CamelCase instead of snake_case
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class AeroPath(datasets.GeneratorBasedBuilder):
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"""An airway segmentation benchmark dataset with challenging pathology."""
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VERSION = datasets.Version("1.0.0")
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# This is an example of a dataset with multiple configurations.
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# If you don't want/need to define several sub-sets in your dataset,
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# just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
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# If you need to make complex sub-parts in the datasets with configurable options
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# You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig
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# BUILDER_CONFIG_CLASS = MyBuilderConfig
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# You will be able to load one or the other configurations in the following list with
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# data = datasets.load_dataset('my_dataset', 'first_domain')
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# data = datasets.load_dataset('my_dataset', 'second_domain')
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BUILDER_CONFIGS = [
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#datasets.BuilderConfig(name="first_domain", version=VERSION, description="This part of my dataset covers a first domain"),
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#datasets.BuilderConfig(name="second_domain", version=VERSION, description="This part of my dataset covers a second domain"),
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datasets.BuilderConfig(name="zenodo", version=VERSION, description="This includes all 27 CTs stored as a single zip on Zenodo"),
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]
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DEFAULT_CONFIG_NAME = "zenodo" # It's not mandatory to have a default configuration. Just use one if it make sense.
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self.DATA_DIR = None
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def get_patient(self, patient_id):
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if (patient_id < 1) or (patiend_id > 27):
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raise ValueError("patient_id should be an integer in range [1, 27].")
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def _info(self):
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# These are the features of your dataset like images, labels ...
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}
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)
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else:
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raise ValueError("Only 'zenodo' is supported.")# This is an example to show how to have different features for "first_domain" and "second_domain"
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return datasets.DatasetInfo(
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# This is the description that will appear on the datasets page.
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description=_DESCRIPTION,
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features=features, # Here we define them above because they are different between the two configurations
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# If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and
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# specify them. They'll be used if as_supervised=True in builder.as_dataset.
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# supervised_keys=("sentence", "label"),
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# Homepage of the dataset for documentation
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homepage=_HOMEPAGE,
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# License for the dataset if available
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license=_LICENSE,
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# Citation for the dataset
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citation=_CITATION,
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)
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def get_data_dir(self):
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return self.DATA_DIR
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def _split_generators(self, dl_manager):
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# If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name
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# dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS
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# 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.
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# By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
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urls = _URLS[self.config.name]
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self.DATA_DIR = dl_manager.download_and_extract(urls)
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# append AeroPath
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self.DATA_DIR = os.path.join(self.DATA_DIR, "AeroPath")
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print("data is downloaded to:", self.DATA_DIR)
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return [
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datasets.SplitGenerator(
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name=datasets.Split.TEST,
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# These kwargs will be passed to _generate_examples
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gen_kwargs={
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"
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},
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),
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]
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# The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
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for patient_id in os.listdir(self.DATA_DIR):
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curr_path = os.path.join(self.DATA_DIR, patient_id)
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if patient_id in ["README.md", "license.md"]:
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continue
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yield patient_id, {
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"ct": os.path.join(curr_path, patient_id + "_CT_HR.nii.gz"),
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"airways": os.path.join(curr_path, patient_id + "_CT_HR_label_airways.nii.gz"),
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"lungs": os.path.join(curr_path, patient_id + "_CT_HR_label_lungs.nii.gz"),
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}
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"""AeroPath: An airway segmentation benchmark dataset with challenging pathology."""
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import datasets
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_DESCRIPTION = """\
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AeroPath: An airway segmentation benchmark dataset with challenging pathology.
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"""
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_HOMEPAGE = "https://github.com/raidionics/AeroPath"
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_LICENSE = "MIT"
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_CITATION = """\
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@misc{støverud2023aeropath,
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title={AeroPath: An airway segmentation benchmark dataset with challenging pathology},
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}
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"""
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_URLS = [
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{
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"ct": f"data/{i}/{i}_CT_HR.nii.gz",
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"airways": f"data/{i}/{i}_CT_HR_label_airways.nii.gz",
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"lungs": f"data/{i}/{i}_CT_HR_label_lungs.nii.gz",
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}
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for i in range(1, 28)
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]
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class AeroPath(datasets.GeneratorBasedBuilder):
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"""An airway segmentation benchmark dataset with challenging pathology."""
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VERSION = datasets.Version("1.0.0")
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def _info(self):
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features = datasets.Features(
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{
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"ct": datasets.Value("string"),
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"airways": datasets.Value("string"),
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"lungs": datasets.Value("string"),
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}
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)
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return datasets.DatasetInfo(
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description=_DESCRIPTION,
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features=features,
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homepage=_HOMEPAGE,
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license=_LICENSE,
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citation=_CITATION,
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)
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def _split_generators(self, dl_manager):
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data_dirs = dl_manager.download(_URLS)
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return [
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datasets.SplitGenerator(
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name=datasets.Split.TEST,
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# These kwargs will be passed to _generate_examples
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gen_kwargs={
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"data_dirs": data_dirs,
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},
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),
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]
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def _generate_examples(self, data_dirs):
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for key, patient in enumerate(data_dirs):
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yield key, patient
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{1 → data/1}/1_CT_HR.nii.gz
RENAMED
File without changes
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{1 → data/1}/1_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{1 → data/1}/1_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{10 → data/10}/10_CT_HR.nii.gz
RENAMED
File without changes
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{10 → data/10}/10_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{10 → data/10}/10_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{11 → data/11}/11_CT_HR.nii.gz
RENAMED
File without changes
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{11 → data/11}/11_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{11 → data/11}/11_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{12 → data/12}/12_CT_HR.nii.gz
RENAMED
File without changes
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{12 → data/12}/12_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{12 → data/12}/12_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{13 → data/13}/13_CT_HR.nii.gz
RENAMED
File without changes
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{13 → data/13}/13_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{13 → data/13}/13_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{14 → data/14}/14_CT_HR.nii.gz
RENAMED
File without changes
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{14 → data/14}/14_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{14 → data/14}/14_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{15 → data/15}/15_CT_HR.nii.gz
RENAMED
File without changes
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{15 → data/15}/15_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{15 → data/15}/15_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{16 → data/16}/16_CT_HR.nii.gz
RENAMED
File without changes
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{16 → data/16}/16_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{16 → data/16}/16_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{17 → data/17}/17_CT_HR.nii.gz
RENAMED
File without changes
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{17 → data/17}/17_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{17 → data/17}/17_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{18 → data/18}/18_CT_HR.nii.gz
RENAMED
File without changes
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{18 → data/18}/18_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{18 → data/18}/18_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{19 → data/19}/19_CT_HR.nii.gz
RENAMED
File without changes
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{19 → data/19}/19_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{19 → data/19}/19_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{2 → data/2}/2_CT_HR.nii.gz
RENAMED
File without changes
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{2 → data/2}/2_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{2 → data/2}/2_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{20 → data/20}/20_CT_HR.nii.gz
RENAMED
File without changes
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{20 → data/20}/20_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{20 → data/20}/20_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{21 → data/21}/21_CT_HR.nii.gz
RENAMED
File without changes
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{21 → data/21}/21_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{21 → data/21}/21_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{22 → data/22}/22_CT_HR.nii.gz
RENAMED
File without changes
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{22 → data/22}/22_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{22 → data/22}/22_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{23 → data/23}/23_CT_HR.nii.gz
RENAMED
File without changes
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{23 → data/23}/23_CT_HR_label_airways.nii.gz
RENAMED
File without changes
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{23 → data/23}/23_CT_HR_label_lungs.nii.gz
RENAMED
File without changes
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{24 → data/24}/24_CT_HR.nii.gz
RENAMED
File without changes
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