ark_example.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.

"""
This dataset contains example data for running through the multiplexed imaging data pipeline in
Ark Analysis: https://github.com/angelolab/ark-analysis
"""

import json
import os

import datasets
import pathlib
import glob
import tifffile
import xarray as xr
import numpy as np

# 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"

# 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)
_URL_REPO = "https://huggingface.co/datasets/angelolab/ark_example/resolve/main"


_URLS = {"base_dataset": f"{_URL_REPO}/data/input_data.zip"}

"""
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
"""

# TODO: 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("0.0.1")

    # 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', 'base_dataset')
    # data = datasets.load_dataset('my_dataset', 'dev_dataset')
    BUILDER_CONFIGS = [
        datasets.BuilderConfig(
            name="base_dataset",
            version=VERSION,
            description="This dataset contains only the 12 FOVs.",
        ),
        datasets.BuilderConfig(
            name="dev_dataset",
            version=VERSION,
            description="This dataset is a superset of the base_dataset, and contains intermediate data for all notebooks. \
                Therefore you can start at any notebook with this dataset.",
        ),
    ]

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

    def _info(self):
        # This is the name of the configuration selected in BUILDER_CONFIGS above
        if self.config.name == "base_dataset":
            features = datasets.Features(
                {
                    "Channel Data": datasets.Sequence(datasets.Image()),
                    "Channel Names": datasets.Sequence(datasets.Value("string")),
                    "Data Path": datasets.Value("string"),
                }
            )
        else:  # This is an example to show how to have different features for "first_domain" and "second_domain"
            features = datasets.Features(
                {
                    "sentence": datasets.Value("string"),
                    "option2": datasets.Value("string"),
                    "second_domain_answer": datasets.Value("string")
                    # These are the features of your dataset like images, labels ...
                }
            )
        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 = _URLS[self.config.name]
        data_dir = dl_manager.download_and_extract(urls)

        return [
            datasets.SplitGenerator(
                name="base_dataset",
                # These kwargs will be passed to _generate_examples
                gen_kwargs={"filepath": pathlib.Path(data_dir)},
            ),
        ]

    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    def _generate_examples(self, filepath: pathlib.Path):

        # Get all TMA paths
        file_paths = list(pathlib.Path(filepath / "input_data").glob("*"))

        # Loop over all the TMAs
        for fp in file_paths:

            # Get the TMA FOV Name
            fov_name = fp.stem

            # Get all channels per TMA FOV
            channel_paths = fp.glob("*.tiff")

            chan_data = []
            chan_names = []
            for chan in channel_paths:
                chan_name = chan.stem
                chan_image: np.ndarray = tifffile.imread(chan)

                chan_data.append(chan_image)
                chan_names.append(chan_name)

            if self.config.name == "base_dataset":
                yield fov_name, {
                    "Channel Data": chan_data,
                    "Channel Names": chan_names,
                    "Data Path": filepath.as_posix(),
                }