Add Medical Segmentation Decathlon dataset (#224)

Add Medical Segmentation Decathlon dataset

scripts/datasets/medical/check_msd.py

@@ -0,0 +1,22 @@
+from torch_em.util.debug import check_loader
+from torch_em.data.datasets.medical import get_msd_loader
+
+
+MSD_ROOT = "/media/anwai/ANWAI/data/msd"
+
+
+def check_msd():
+    loader = get_msd_loader(
+        path=MSD_ROOT,
+        patch_shape=(1, 512, 512),
+        batch_size=2,
+        ndim=2,
+        download=True,
+        task_names="braintumour",
+    )
+    print(f"Length of the loader: {len(loader)}")
+    check_loader(loader, 8)
+
+
+if __name__ == "__main__":
+    check_msd()

torch_em/data/datasets/medical/__init__.py

@@ -3,6 +3,7 @@
 from .busi import get_busi_dataset, get_busi_loader
 from .camus import get_camus_dataset, get_camus_loader
 from .drive import get_drive_dataset, get_drive_loader
+from .msd import get_msd_dataset, get_msd_loader
 from .papila import get_papila_dataset, get_papila_loader
 from .plethora import get_plethora_dataset, get_plethora_loader
 from .sa_med2d import get_sa_med2d_dataset, get_sa_med2d_loader

torch_em/data/datasets/medical/msd.py

@@ -0,0 +1,148 @@
+import os
+from glob import glob
+from pathlib import Path
+from typing import Tuple, List, Union
+
+import torch_em
+
+from .. import util
+from ....data import ConcatDataset
+
+
+URL = {
+    "braintumour": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task01_BrainTumour.tar",
+    "heart": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task02_Heart.tar",
+    "liver": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task03_Liver.tar",
+    "hippocampus": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task04_Hippocampus.tar",
+    "prostate": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task05_Prostate.tar",
+    "lung": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task06_Lung.tar",
+    "pancreas": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task07_Pancreas.tar",
+    "hepaticvessel": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task08_HepaticVessel.tar",
+    "spleen": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task09_Spleen.tar",
+    "colon": "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task10_Colon.tar",
+}
+
+CHECKSUM = {
+    "braintumour": "d423911308d2ae5396d9c6bf4fad2b68cfde2dd09044269da9c0d639c22753c4",
+    "heart": "4277dc6dfe100142aa8060e895f6ff0f81c5b733703ea250bd294df8f820bcba",
+    "liver": "4007d9db1acda850d57a6ceb2b3998b7a0d43f8ad5a3f740dc38bc0cb8b7a2c5",
+    "hippocampus": "282d808a3e84e5a52f090d9dd4c0b0057b94a6bd51ad41569aef5ff303287771",
+    "prostate": "8cbbd7147691109b880ff8774eb6ab26704b1be0935482e7996a36a4ed31ec79",
+    "lung": "f782cd09da9cf7a3128475d4a53650d371db10f0427aa76e166fccfcb2654161",
+    "pancreas": "e40181a0229ca85c2588d6ebb90fa6674f84eb1e66f0f968cda088d011769732",
+    "hepaticvessel": "ee880799f12e3b6e1ef2f8645f6626c5b39de77a4f1eae6f496c25fbf306ba04",
+    "spleen": "dfeba347daae4fb08c38f4d243ab606b28b91b206ffc445ec55c35489fa65e60",
+    "colon": "a26bfd23faf2de703f5a51a262cd4e2b9774c47e7fb86f0e0a854f8446ec2325",
+}
+
+FILENAMES = {
+    "braintumour": "Task01_BrainTumour.tar",
+    "heart": "Task02_Heart.tar",
+    "liver": "Task03_Liver.tar",
+    "hippocampus": "Task04_Hippocampus.tar",
+    "prostate": "Task05_Prostate.tar",
+    "lung": "Task06_Lung.tar",
+    "pancreas": "Task07_Pancreas.tar",
+    "hepaticvessel": "Task08_HepaticVessel.tar",
+    "spleen": "Task09_Spleen.tar",
+    "colon": "Task10_Colon.tar",
+}
+
+
+def get_msd_data(path, task_name, download):
+    os.makedirs(path, exist_ok=True)
+
+    data_dir = os.path.join(path, "data", task_name)
+    if os.path.exists(data_dir):
+        return data_dir
+
+    fpath = os.path.join(path, FILENAMES[task_name])
+
+    util.download_source(path=fpath, url=URL[task_name], download=download, checksum=None)
+    util.unzip_tarfile(tar_path=fpath, dst=data_dir, remove=False)
+
+    return data_dir
+
+
+def get_msd_dataset(
+    path: str,
+    patch_shape: Tuple[int, ...],
+    ndim: int,
+    task_names: Union[str, List[str]],
+    download: bool = False,
+    **kwargs
+):
+    """Dataset for semantic segmentation in 10 medical imaging datasets.
+
+    This dataset is from the Medical Segmentation Decathlon Challenge:
+    - Antonelli et al. - https://doi.org/10.1038/s41467-022-30695-9
+    - Link - http://medicaldecathlon.com/
+
+    Please cite it if you use this dataset for a publication.
+
+    Args:
+        path: The path to prepare the dataset.
+        patch_shape: The patch shape (for 2d or 3d patches)
+        ndim: The dimensions of inputs (use `2` for getting `2d` patches, and `3` for getting 3d patches)
+        task_names: The names for the 10 different segmentation tasks (see the challenge website for further details):
+            1. tasks with 1 modality inputs are: heart, liver, hippocampus, lung, pancreas, hepaticvessel, spleen, colon
+            2. tasks with multi-modality inputs are:
+                - braintumour: with 4 modality (channel) inputs
+                - prostate: with 2 modality (channel) inputs
+        download: Downloads the dataset
+
+    Here's an example for how to pass different tasks:
+    ```python
+    # we want to get datasets for one task, eg. "heart"
+    task_names = ["heart"]
+
+    # we want to get datasets for multiple tasks
+    # NOTE 1: it's important to note that datasets with similar number of modality (channels) can be paired together.
+    # to use different datasets together, you need to use "raw_transform" to update inputs per dataset
+    # to pair as desired patch shapes per batch.
+    # Example 1: "heart", "liver", "lung" all have one modality inputs
+    task_names = ["heart", "lung", "liver"]
+
+    # Example 2: "braintumour" and "prostate" have multi-modal inputs, however the no. of modalities are not equal.
+    # hence, you can use only one at a time.
+    task_names = ["prostate"]
+    ```
+    """
+    if isinstance(task_names, str):
+        task_names = [task_names]
+
+    _datasets = []
+    for task_name in task_names:
+        data_dir = get_msd_data(path, task_name, download)
+        image_paths = glob(os.path.join(data_dir, Path(FILENAMES[task_name]).stem, "imagesTr", "*.nii.gz"))
+        label_paths = glob(os.path.join(data_dir, Path(FILENAMES[task_name]).stem, "labelsTr", "*.nii.gz"))
+
+        if task_name in ["braintumour", "prostate"]:
+            kwargs["with_channels"] = True
+
+        this_dataset = torch_em.default_segmentation_dataset(
+            raw_paths=image_paths,
+            raw_key="data",
+            label_paths=label_paths,
+            label_key="data",
+            patch_shape=patch_shape,
+            ndim=ndim,
+            **kwargs
+        )
+        _datasets.append(this_dataset)
+
+    return ConcatDataset(*_datasets)
+
+
+def get_msd_loader(
+    path, patch_shape, batch_size, ndim, task_names, download=False, **kwargs
+):
+    """Dataloader for semantic segmentation from 10 highly variable medical segmentation tasks.
+    See `get_msd_dataset` for details.
+    """
+    ds_kwargs, loader_kwargs = util.split_kwargs(
+        torch_em.default_segmentation_dataset, **kwargs
+    )
+    ds = get_msd_dataset(path, patch_shape, ndim, task_names, download, **ds_kwargs)
+    loader = torch_em.get_data_loader(ds, batch_size=batch_size, **loader_kwargs)
+    return loader

torch_em/data/datasets/util.py

@@ -196,6 +196,27 @@ def update_kwargs(kwargs, key, value, msg=None):
     return kwargs
 
 
+def unzip_tarfile(tar_path, dst, remove=True):
+    import tarfile
+
+    if tar_path.endswith(".tar.gz"):
+        access_mode = "r:gz"
+    elif tar_path.endswith(".tar"):
+        access_mode = "r:"
+    else:
+        raise ValueError(
+            "The provided file isn't a supported archive to unpack. ",
+            f"Please check the file: {tar_path}"
+        )
+
+    tar = tarfile.open(tar_path, access_mode)
+    tar.extractall(dst)
+    tar.close()
+
+    if remove:
+        os.remove(tar_path)
+
+
 def unzip(zip_path, dst, remove=True):
     with zipfile.ZipFile(zip_path, "r") as f:
         f.extractall(dst)