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ThomasKierski · 2024-10-25T20:27:31Z

Using transforms from MONAI and MONAILabel can result in metadata containing torch.tensors and torch.Sizes. This change fixes a traceback in the restored transform resulting from an incompatibility between torch datatypes and numpy.any().

Signed-off-by: Thomas Kierski [email protected]

Using transforms from MONAI and MONAILabel can result in metadata containing torch.tensors and torch.Sizes. This change fixes a traceback in the restored transform resulting from an incompatibility between torch datatypes and numpy.any(). Signed-off-by: Thomas Kierski <[email protected]>

ThomasKierski · 2024-10-25T20:38:06Z

A snippet to reproduce the transform pipeline that resulted in this traceback is below:

    pre_transforms = Compose([
        LoadImaged(keys=("image", "label"), reader="ITKReader"),
        EnsureChannelFirstd(keys=("image", "label")),
        NormalizeLabelsInDatasetd(keys="label", label_names=label_names),
        Orientationd(keys=["image", "label"], axcodes="RAS"),
        ScaleIntensityRanged(keys=("image"), a_min=-1000, a_max=3500, b_min=0.0, b_max=1.0, clip=True),
        Resized(keys=("image", "label"), spatial_size=3*[128], mode=("area", "nearest")),
    ])

    post_transforms = Compose([
        Activationsd(keys=("pred"), softmax=True),
        AsDiscreted(
            keys=("pred", "label"),
            argmax=(True, False),
            to_onehot=num_labels,
        ),
        SplitPredsLabeld(keys="pred"),
    ])

    data = {"image": "/path/to/image.mha", "label":"/path/to/label.seg.nrrd"}
    data = pre_transforms(data)
    data["pred"] = model(data["image"])
    restorex = Restored(keys=["pred"], ref_image="image")
    restored_prediction = restorex(data)

The traceback in question:

TypeError Traceback (most recent call last)
Cell In[10], line 81
79 data = monai.data.decollate_batch(data)
80 for n in range(len(data)):
---> 81 data[n] = restorex(data[n])
82 data = monai.data.list_data_collate(data)
83 # write_sample_to_disk(data, os.path.join(outpath,os.path.basename(data["label"].meta["filename_or_obj"][0])))

File /usr/local/lib/python3.10/dist-packages/monailabel/transform/post.py:132, in Restored.call(self, data)
129 spatial_size = spatial_shape[-len(current_size) :]
131 # Undo Spacing
--> 132 if np.any(np.not_equal(current_size, spatial_size)):
133 resizer = Resize(spatial_size=spatial_size, mode=self.mode[idx])
134 result = resizer(result, mode=self.mode[idx], align_corners=self.align_corners[idx])

File <array_function internals>:200, in any(*args, **kwargs)

File /usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py:2423, in any(a, axis, out, keepdims, where)
2333 @array_function_dispatch(_any_dispatcher)
2334 def any(a, axis=None, out=None, keepdims=np._NoValue, *, where=np._NoValue):
2335 """
2336 Test whether any array element along a given axis evaluates to True.
2337
(...)
2421
2422 """
-> 2423 return _wrapreduction(a, np.logical_or, 'any', axis, None, out,
2424 keepdims=keepdims, where=where)

File /usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py:84, in _wrapreduction(obj, ufunc, method, axis, dtype, out, **kwargs)
82 return reduction(axis=axis, dtype=dtype, out=out, **passkwargs)
83 else:
---> 84 return reduction(axis=axis, out=out, **passkwargs)
86 return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

TypeError: any() received an invalid combination of arguments - got (out=NoneType, axis=NoneType, ), but expected one of:

()
(tuple of ints dim = None, bool keepdim = False)
didn't match because some of the keywords were incorrect: out, axis
(int dim, bool keepdim = False)
didn't match because some of the keywords were incorrect: out, axis
(name dim, bool keepdim = False)
didn't match because some of the keywords were incorrect: out, axis

Using transforms from MONAI and MONAILabel can result in metadata containing torch.tensors and torch.Sizes. This change fixes a traceback in the restored transform resulting from an incompatibility between torch datatypes and numpy.any(). Signed-off-by: Thomas Kierski <[email protected]> Signed-off-by: YunLiu <[email protected]>

* fix ignite-info issue Signed-off-by: YunLiu <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: YunLiu <[email protected]> * update monai version Signed-off-by: YunLiu <[email protected]> * revert version change Signed-off-by: YunLiu <[email protected]> * temp fix Signed-off-by: YunLiu <[email protected]> * minor fix Signed-off-by: YunLiu <[email protected]> * minor fix Signed-off-by: YunLiu <[email protected]> * update to 3.9 and drop 3.8 Signed-off-by: YunLiu <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#1716) updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2) - [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2) - [github.com/PyCQA/flake8: 7.0.0 → 7.1.0](PyCQA/flake8@7.0.0...7.1.0) - [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.1](pre-commit/mirrors-mypy@v1.9.0...v1.10.1) - [github.com/asottile/pyupgrade: v3.15.2 → v3.16.0](asottile/pyupgrade@v3.15.2...v3.16.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: YunLiu <[email protected]> * Bump urllib3 from 2.2.1 to 2.2.2 (#1753) Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.1 to 2.2.2. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@2.2.1...2.2.2) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: YunLiu <[email protected]> * Bump requests from 2.31.0 to 2.32.2 (#1754) Bumps [requests](https://github.com/psf/requests) from 2.31.0 to 2.32.2. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.31.0...v2.32.2) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: YunLiu <[email protected]> * ENH: Allow newer version of dependencies (#1748) Pinning basic packages such as "requests" to a specific patch level release such "2.31.0" is too strict. New releases and especially new patch releases allow to use latest security updates of various packages. Signed-off-by: James Butler <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]> Signed-off-by: YunLiu <[email protected]> * Release 0.8.4 checks and updates (#1757) * Release 0.8.4 checks and updates Signed-off-by: tangy5 <[email protected]> * Trigger monai container update Signed-off-by: tangy5 <[email protected]> * Drop python 3.8 Signed-off-by: tangy5 <[email protected]> * Drop python 3.8 Signed-off-by: tangy5 <[email protected]> --------- Signed-off-by: tangy5 <[email protected]> Co-authored-by: tangy5 <[email protected]> Signed-off-by: YunLiu <[email protected]> * Add MITK as supported platform (#1759) Signed-off-by: Ashis Ravindran <[email protected]> Signed-off-by: YunLiu <[email protected]> * Add MITK to installation docs (#1761) * Add MITK as supported platform Signed-off-by: Ashis Ravindran <[email protected]> * Update link to MONAI Label repo Signed-off-by: Ashis Ravindran <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Ashis Ravindran <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: YunLiu <[email protected]> * fix(mode): no need to initialize toolbar service (#1763) Signed-off-by: YunLiu <[email protected]> * BUG: Fix traceback in restored transform (#1766) Using transforms from MONAI and MONAILabel can result in metadata containing torch.tensors and torch.Sizes. This change fixes a traceback in the restored transform resulting from an incompatibility between torch datatypes and numpy.any(). Signed-off-by: Thomas Kierski <[email protected]> Signed-off-by: YunLiu <[email protected]> * Revert "update to 3.9 and drop 3.8" This reverts commit 8ced475. Signed-off-by: YunLiu <[email protected]> * revert Signed-off-by: YunLiu <[email protected]> * revert Signed-off-by: YunLiu <[email protected]> * revert Signed-off-by: YunLiu <[email protected]> --------- Signed-off-by: YunLiu <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: James Butler <[email protected]> Signed-off-by: tangy5 <[email protected]> Signed-off-by: Ashis Ravindran <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: SACHIDANAND ALLE <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: James Butler <[email protected]> Co-authored-by: tangy5 <[email protected]> Co-authored-by: tangy5 <[email protected]> Co-authored-by: Ashis Ravindran <[email protected]> Co-authored-by: Alireza <[email protected]> Co-authored-by: Thomas Kierski <[email protected]>

SachidanandAlle approved these changes Oct 26, 2024

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SachidanandAlle enabled auto-merge (squash) October 26, 2024 08:38

SachidanandAlle merged commit e8e1440 into Project-MONAI:main Oct 26, 2024

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BUG: Fix traceback in restored transform#1766

BUG: Fix traceback in restored transform#1766
SachidanandAlle merged 1 commit into
Project-MONAI:mainfrom
ThomasKierski:tk/fix-restored-xform

ThomasKierski commented Oct 25, 2024

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ThomasKierski commented Oct 25, 2024

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ThomasKierski commented Oct 25, 2024

The traceback in question:

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