Datasets:
# 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. | |
""" | |
This dataset contains example data for running through the multiplexed imaging data pipeline in | |
Ark Analysis: https://github.com/angelolab/ark-analysis | |
""" | |
import datasets | |
import pathlib | |
# Find for instance the citation on arxiv or on the dataset repo/website | |
_CITATION = """\ | |
@InProceedings{huggingface:dataset, | |
title = {Ark Analysis Example Dataset}, | |
author={Angelo Lab}, | |
year={2022} | |
} | |
""" | |
# TODO: Add description of the dataset here | |
# You can copy an official description | |
_DESCRIPTION = """\ | |
This dataset contains 11 Field of Views (FOVs), each with 22 channels. | |
""" | |
_HOMEPAGE = "https://github.com/angelolab/ark-analysis" | |
_LICENSE = "https://github.com/angelolab/ark-analysis/blob/main/LICENSE" | |
# 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) | |
# _URL_REPO = "https://huggingface.co/datasets/angelolab/ark_example" | |
_URL_DATA = { | |
"image_data": "./data/image_data.zip", | |
"cell_table": "./data/segmentation/cell_table.zip", | |
"deepcell_output": "./data/segmentation/deepcell_output.zip", | |
} | |
_URL_DATASET_CONFIGS = { | |
"nb1": {"image_data": _URL_DATA["image_data"]}, | |
"nb2": { | |
"image_data": _URL_DATA["image_data"], | |
"cell_table": _URL_DATA["cell_table"], | |
"deepcell_output": _URL_DATA["deepcell_output"], | |
}, | |
} | |
""" | |
Dataset Fov renaming: | |
TMA2_R8C3 -> fov0 | |
TMA6_R4C5 -> fov1 | |
TMA7_R5C4 -> fov2 | |
TMA10_R7C3 -> fov3 | |
TMA11_R9C6 -> fov4 | |
TMA13_R8C5 -> fov5 | |
TMA17_R9C2 -> fov6 | |
TMA18_R9C2 -> fov7 | |
TMA21_R2C5 -> fov8 | |
TMA21_R12C6 -> fov9 | |
TMA24_R9C1 -> fov10 | |
""" | |
# Note: Name of the dataset usually match the script name with CamelCase instead of snake_case | |
class ArkExample(datasets.GeneratorBasedBuilder): | |
"""The Dataset consists of 11 FOVs""" | |
VERSION = datasets.Version("0.0.2") | |
# 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', 'nb1') | |
# data = datasets.load_dataset('my_dataset', 'nb2') | |
BUILDER_CONFIGS = [ | |
datasets.BuilderConfig( | |
name="nb1", | |
version=VERSION, | |
description="This dataset contains only the 12 FOVs, and their 22 channels.", | |
), | |
datasets.BuilderConfig( | |
name="nb2", | |
version=VERSION, | |
description="This dataset is a superset of the nb1 and contains data from notebook 1 in order to start with notebook 2. \ | |
Therefore you can start at any notebook with this dataset.", | |
), | |
] | |
def _info(self): | |
# This is the name of the configuration selected in BUILDER_CONFIGS above | |
if self.config.name in ["nb1", "nb2", "nb3", "nb4"]: | |
features = datasets.Features( | |
{f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()} | |
) | |
else: | |
ValueError("dataset name is incorrect.") | |
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 | |
features=features, # Here we define them above because they are different between the two configurations | |
# If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and | |
# specify them. They'll be used if as_supervised=True in builder.as_dataset. | |
# supervised_keys=("sentence", "label"), | |
# 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 = _URL_DATASET_CONFIGS[self.config.name] | |
data_dirs = {} | |
for data_name, url in urls.items(): | |
dl_path = pathlib.Path(dl_manager.download_and_extract(url)) | |
data_dirs[data_name] = dl_path | |
return [ | |
datasets.SplitGenerator( | |
name=self.config.name, | |
# These kwargs will be passed to _generate_examples | |
gen_kwargs={"dataset_paths": data_dirs}, | |
), | |
] | |
# method parameters are unpacked from `gen_kwargs` as given in `_split_generators` | |
def _generate_examples(self, dataset_paths): | |
yield self.config.name, dataset_paths | |