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Fix unused arg in SlidingPatchWSIDataset (Project-MONAI#6047)
### Description This PR removes `map_level` from `SlidingPatchWSIDataset`, which seems to be left from the previous changes and has not used anywhere. Also it updates the outdated docstring. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] In-line docstrings updated. --------- Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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monai/data/wsi_datasets.py

Lines changed: 14 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -36,8 +36,8 @@ class PatchWSIDataset(Dataset):
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Args:
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data: the list of input samples including image, location, and label (see the note below for more details).
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size: the size of patch to be extracted from the whole slide image.
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level: the level at which the patches to be extracted (default to 0).
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patch_size: the size of patch to be extracted from the whole slide image.
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patch_level: the level at which the patches to be extracted (default to 0).
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transform: transforms to be executed on input data.
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include_label: whether to load and include labels in the output
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center_location: whether the input location information is the position of the center of the patch
@@ -171,26 +171,29 @@ def _transform(self, index: int):
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class SlidingPatchWSIDataset(Randomizable, PatchWSIDataset):
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"""
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This dataset extracts patches from whole slide images (without loading the whole image)
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This dataset extracts patches in sliding-window manner from whole slide images (without loading the whole image).
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It also reads labels for each patch and provides each patch with its associated class labels.
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Args:
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data: the list of input samples including image, location, and label (see the note below for more details).
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size: the size of patch to be extracted from the whole slide image.
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level: the level at which the patches to be extracted (default to 0).
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patch_size: the size of patch to be extracted from the whole slide image.
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patch_level: the level at which the patches to be extracted (default to 0).
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mask_level: the resolution level at which the mask/map is created (for `ProbMapProducer` for instance).
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overlap: the amount of overlap of neighboring patches in each dimension (a value between 0.0 and 1.0).
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If only one float number is given, it will be applied to all dimensions. Defaults to 0.0.
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offset: the offset of image to extract patches (the starting position of the upper left patch).
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offset_limits: if offset is set to "random", a tuple of integers defining the lower and upper limit of the
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random offset for all dimensions, or a tuple of tuples that defines the limits for each dimension.
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overlap: the amount of overlap of neighboring patches in each dimension (a value between 0.0 and 1.0).
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If only one float number is given, it will be applied to all dimensions. Defaults to 0.0.
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transform: transforms to be executed on input data.
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include_label: whether to load and include labels in the output
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center_location: whether the input location information is the position of the center of the patch
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additional_meta_keys: the list of keys for items to be copied to the output metadata from the input data
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reader: the module to be used for loading whole slide imaging. Defaults to cuCIM. If `reader` is
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- a string, it defines the backend of `monai.data.WSIReader`.
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- a class (inherited from `BaseWSIReader`), it is initialized and set as wsi_reader,
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- an instance of a class inherited from `BaseWSIReader`, it is set as the wsi_reader.
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map_level: the resolution level at which the output map is created.
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seed: random seed to randomly generate offsets. Defaults to 0.
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kwargs: additional arguments to pass to `WSIReader` or provided whole slide reader class
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@@ -204,6 +207,7 @@ class SlidingPatchWSIDataset(Randomizable, PatchWSIDataset):
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{"image": "path/to/image2.tiff", "patch_size": [20, 20], "patch_level": 2}
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]
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Unlike `MaskedPatchWSIDataset`, this dataset does not filter any patches.
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"""
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def __init__(
@@ -220,7 +224,6 @@ def __init__(
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center_location: bool = False,
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additional_meta_keys: Sequence[str] = (ProbMapKeys.LOCATION, ProbMapKeys.SIZE, ProbMapKeys.COUNT),
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reader="cuCIM",
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map_level: int = 0,
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seed: int = 0,
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**kwargs,
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):
@@ -322,8 +325,8 @@ class MaskedPatchWSIDataset(PatchWSIDataset):
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Args:
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data: the list of input samples including image, location, and label (see the note below for more details).
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size: the size of patch to be extracted from the whole slide image.
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level: the level at which the patches to be extracted (default to 0).
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patch_size: the size of patch to be extracted from the whole slide image.
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patch_level: the level at which the patches to be extracted (default to 0).
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mask_level: the resolution level at which the mask is created.
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transform: transforms to be executed on input data.
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include_label: whether to load and include labels in the output

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