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Add function in datasets to get input paths #367

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merged 3 commits into from
Oct 9, 2024
Merged

Add function in datasets to get input paths #367

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b6829d4
Add function in datasets to get input paths
anwai98 Oct 9, 2024
ba6100a
Add _paths functionality to all microscopy datasets
anwai98 Oct 9, 2024
bee8d76
Make download optional for livecell functions
anwai98 Oct 9, 2024
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4 changes: 2 additions & 2 deletions torch_em/data/datasets/light_microscopy/deepbacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def get_deepbacs_data(path: Union[os.PathLike, str], bac_type: str, download: bo
return data_folder


def _get_paths(path, bac_type, split):
def _get_deepbacs_paths(path, bac_type, split):
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# the bacteria types other than mixed are a bit more complicated so we don't have the dataloaders for them yet
# mixed is the combination of all other types
if split == "train":
Expand Down Expand Up @@ -139,7 +139,7 @@ def get_deepbacs_dataset(
"""
assert split in ("train", "val", "test")
get_deepbacs_data(path, bac_type, download)
image_folder, label_folder = _get_paths(path, bac_type, split)
image_folder, label_folder = _get_deepbacs_paths(path, bac_type, split)
dataset = torch_em.default_segmentation_dataset(
image_folder, "*.tif", label_folder, "*.tif", patch_shape=patch_shape, **kwargs
)
Expand Down
7 changes: 6 additions & 1 deletion torch_em/data/datasets/light_microscopy/livecell.py
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Expand Up @@ -156,6 +156,11 @@ def _download_livecell_annotations(path, split, download, cell_types, label_path
return _create_segmentations_from_annotations(annotation_file, image_folder, seg_folder, cell_types)


def _get_livecell_paths(path, split, download=False, cell_types=None, label_path=None):
image_paths, seg_paths = _download_livecell_annotations(path, split, download, cell_types, label_path)
return image_paths, seg_paths


def get_livecell_data(
path: Union[os.PathLike, str],
split: str,
Expand All @@ -177,7 +182,7 @@ def get_livecell_data(
The paths to the label data.
"""
_download_livecell_images(path, download)
image_paths, seg_paths = _download_livecell_annotations(path, split, download, cell_types, label_path)
image_paths, seg_paths = _get_livecell_paths(path, split, download, cell_types, label_path)
return image_paths, seg_paths


Expand Down
9 changes: 7 additions & 2 deletions torch_em/data/datasets/light_microscopy/plantseg.py
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Expand Up @@ -138,6 +138,12 @@ def get_plantseg_data(path: Union[os.PathLike, str], download: bool, name: str,
return out_path


def _get_plantseg_paths(data_path):
file_paths = glob(os.path.join(data_path, "*.h5"))
file_paths.sort()
return file_paths


def get_plantseg_dataset(
path: Union[os.PathLike, str],
name: str,
Expand Down Expand Up @@ -168,8 +174,7 @@ def get_plantseg_dataset(
assert len(patch_shape) == 3
data_path = get_plantseg_data(path, download, name, split)

file_paths = glob(os.path.join(data_path, "*.h5"))
file_paths.sort()
file_paths = _get_plantseg_paths(data_path)

kwargs, _ = util.add_instance_label_transform(
kwargs, add_binary_target=binary, binary=binary, boundaries=boundaries,
Expand Down