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Minor updates to LM datasets #483

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merged 1 commit into from
Feb 9, 2025
Merged

Minor updates to LM datasets #483

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2 changes: 2 additions & 0 deletions torch_em/data/datasets/light_microscopy/arvidsson.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,8 @@ def get_arvidsson_data(
if os.path.exists(data_dir):
return data_dir

os.makedirs(path, exist_ok=True)

zip_path = os.path.join(path, f"{dname}.zip")
util.download_source(path=zip_path, url=URLS[split], download=download, checksum=CHECKSUMS[split])
util.unzip(zip_path=os.path.join(path, f"{dname}.zip"), dst=path)
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6 changes: 3 additions & 3 deletions torch_em/data/datasets/light_microscopy/bitdepth_nucseg.py
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Expand Up @@ -67,7 +67,7 @@ def get_bitdepth_nucseg_data(path: Union[os.PathLike, str], download: bool = Fal

def get_bitdepth_nucseg_paths(
path: Union[os.PathLike, str],
magnification: Optional[Literal['20x', '40x_air', '40x_oil' '63x_oil']] = None,
magnification: Optional[Literal['20x', '40x_air', '40x_oil', '63x_oil']] = None,
download: bool = False
) -> Tuple[List[str], List[str]]:
"""Get paths to the BitDepth NucSeg data.
Expand Down Expand Up @@ -101,7 +101,7 @@ def get_bitdepth_nucseg_paths(
def get_bitdepth_nucseg_dataset(
path: Union[os.PathLike, str],
patch_shape: Tuple[int, int],
magnification: Optional[Literal['20x', '40x_air', '40x_oil' '63x_oil']] = None,
magnification: Optional[Literal['20x', '40x_air', '40x_oil', '63x_oil']] = None,
download: bool = False,
**kwargs
) -> Dataset:
Expand Down Expand Up @@ -134,7 +134,7 @@ def get_bitdepth_nucseg_loader(
path: Union[os.PathLike, str],
batch_size: int,
patch_shape: Tuple[int, int],
magnification: Optional[Literal['20x', '40x_air', '40x_oil' '63x_oil']] = None,
magnification: Optional[Literal['20x', '40x_air', '40x_oil', '63x_oil']] = None,
download: bool = False,
**kwargs
) -> DataLoader:
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6 changes: 3 additions & 3 deletions torch_em/data/datasets/light_microscopy/brifiseg.py
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Expand Up @@ -63,10 +63,10 @@ def get_brifiseg_data(path: Union[os.PathLike, str], download: bool = False) ->
if os.path.exists(data_dir):
return data_dir

tar_path = os.path.join(path, "1channel.tar")
if not os.path.exists(tar_path) and not download:
raise ValueError("The tar file is not found and download is set to 'False'.")
os.makedirs(path, exist_ok=True)

tar_path = os.path.join(path, "1channel.tar")
util.download_source(path=tar_path, url=URL, checksum=CHECKSUM, download=download)
util.unzip_tarfile(tar_path=tar_path, dst=path)

for zip_path in glob(os.path.join(os.path.join(path, "1channel"), "*.zip")):
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