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Update ISBI dataset download #210

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Feb 5, 2024
Merged

Update ISBI dataset download #210

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14 changes: 10 additions & 4 deletions torch_em/data/datasets/isbi2012.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
import os

import torch_em
from . import util

Expand All @@ -14,10 +16,14 @@ def get_isbi_dataset(
This dataset is from the publication https://doi.org/10.3389/fnana.2015.00142.
Please cite it if you use this dataset for a publication.
"""
if not path.endswith(".h5"):
raise ValueError("Isbi path must be a hdf5 file.")
if path.endswith(".h5"):
volume_path = path
else:
os.makedirs(path, exist_ok=True)
volume_path = os.path.join(path, "isbi.h5")

assert len(patch_shape) == 3
util.download_source(path, ISBI_URL, download, CHECKSUM)
util.download_source(volume_path, ISBI_URL, download, CHECKSUM)
ndim = 2 if patch_shape[0] == 1 else 3
kwargs = util.update_kwargs(kwargs, "ndim", ndim)

Expand All @@ -28,7 +34,7 @@ def get_isbi_dataset(
raw_key = "raw"
label_key = "labels/membranes" if use_original_labels else "labels/gt_segmentation"

return torch_em.default_segmentation_dataset(path, raw_key, path, label_key, patch_shape, **kwargs)
return torch_em.default_segmentation_dataset(volume_path, raw_key, volume_path, label_key, patch_shape, **kwargs)


def get_isbi_loader(
Expand Down