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BUG: Fix traceback in restored transform #1766
BUG: Fix traceback in restored transform #1766
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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 <thomas.kierski@revvity.com>
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) File /usr/local/lib/python3.10/dist-packages/monailabel/transform/post.py:132, in Restored.call(self, data) 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) File /usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py:84, in _wrapreduction(obj, ufunc, method, axis, dtype, out, **kwargs) TypeError: any() received an invalid combination of arguments - got (out=NoneType, axis=NoneType, ), but expected one of:
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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 <thomas.kierski@revvity.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
* fix ignite-info issue Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * update monai version Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * revert version change Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * temp fix Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * minor fix Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * minor fix Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * update to 3.9 and drop 3.8 Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * [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 <sachidanand.alle@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * 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 <james.butler@revvity.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * Release 0.8.4 checks and updates (#1757) * Release 0.8.4 checks and updates Signed-off-by: tangy5 <yuchengt@nvidia.com> * Trigger monai container update Signed-off-by: tangy5 <yuchengt@nvidia.com> * Drop python 3.8 Signed-off-by: tangy5 <yuchengt@nvidia.com> * Drop python 3.8 Signed-off-by: tangy5 <yuchengt@nvidia.com> --------- Signed-off-by: tangy5 <yuchengt@nvidia.com> Co-authored-by: tangy5 <yuchengt@nvidia.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * Add MITK as supported platform (#1759) Signed-off-by: Ashis Ravindran <ashis.ravindran@dkfz-heidelberg.de> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * Add MITK to installation docs (#1761) * Add MITK as supported platform Signed-off-by: Ashis Ravindran <ashis.ravindran@dkfz-heidelberg.de> * Update link to MONAI Label repo Signed-off-by: Ashis Ravindran <ashis.ravindran@dkfz-heidelberg.de> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Ashis Ravindran <ashis.ravindran@dkfz-heidelberg.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * fix(mode): no need to initialize toolbar service (#1763) Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * 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 <thomas.kierski@revvity.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * Revert "update to 3.9 and drop 3.8" This reverts commit 8ced475. Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * revert Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * revert Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> * revert Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --------- Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: James Butler <james.butler@revvity.com> Signed-off-by: tangy5 <yuchengt@nvidia.com> Signed-off-by: Ashis Ravindran <ashis.ravindran@dkfz-heidelberg.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: James Butler <jamesobutler@users.noreply.github.com> Co-authored-by: tangy5 <58751975+tangy5@users.noreply.github.com> Co-authored-by: tangy5 <yuchengt@nvidia.com> Co-authored-by: Ashis Ravindran <33703127+ASHISRAVINDRAN@users.noreply.github.com> Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Thomas Kierski <54414492+ThomasKierski@users.noreply.github.com>
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 thomas.kierski@revvity.com