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test_tciadataset #6945

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wyli opened this issue Sep 5, 2023 · 0 comments · Fixed by #6946
Closed

test_tciadataset #6945

wyli opened this issue Sep 5, 2023 · 0 comments · Fixed by #6946

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@wyli
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wyli commented Sep 5, 2023 

[2023-09-05T13:22:13.399Z] ======================================================================
[2023-09-05T13:22:13.399Z] ERROR: test_values (tests.test_tciadataset.TestTciaDataset)
[2023-09-05T13:22:13.399Z] ----------------------------------------------------------------------
[2023-09-05T13:22:13.399Z] Traceback (most recent call last):
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 141, in apply_transform
[2023-09-05T13:22:13.399Z]     return _apply_transform(transform, data, unpack_items, lazy, overrides, log_stats)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 98, in _apply_transform
[2023-09-05T13:22:13.399Z]     return transform(data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(data)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/io/dictionary.py", line 164, in __call__
[2023-09-05T13:22:13.399Z]     data = self._loader(d[key], reader)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/io/array.py", line 290, in __call__
[2023-09-05T13:22:13.399Z]     img_array, meta_data = reader.get_data(img)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/data/image_reader.py", line 599, in get_data
[2023-09-05T13:22:13.399Z]     affine = self._get_affine(metadata, self.affine_lps_to_ras)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/data/image_reader.py", line 666, in _get_affine
[2023-09-05T13:22:13.399Z]     spacing = metadata["00280030"]["Value"]
[2023-09-05T13:22:13.399Z] KeyError: '00280030'
[2023-09-05T13:22:13.399Z] 
[2023-09-05T13:22:13.399Z] The above exception was the direct cause of the following exception:
[2023-09-05T13:22:13.399Z] 
[2023-09-05T13:22:13.399Z] Traceback (most recent call last):
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 141, in apply_transform
[2023-09-05T13:22:13.399Z]     return _apply_transform(transform, data, unpack_items, lazy, overrides, log_stats)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 98, in _apply_transform
[2023-09-05T13:22:13.399Z]     return transform(data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(data)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/compose.py", line 335, in __call__
[2023-09-05T13:22:13.399Z]     result = execute_compose(
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/compose.py", line 111, in execute_compose
[2023-09-05T13:22:13.399Z]     data = apply_transform(
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 171, in apply_transform
[2023-09-05T13:22:13.399Z]     raise RuntimeError(f"applying transform {transform}") from e
[2023-09-05T13:22:13.399Z] RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7f449a92b5e0>
[2023-09-05T13:22:13.399Z] 
[2023-09-05T13:22:13.399Z] The above exception was the direct cause of the following exception:
[2023-09-05T13:22:13.399Z] 
[2023-09-05T13:22:13.399Z] Traceback (most recent call last):
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/tests/test_tciadataset.py", line 61, in test_values
[2023-09-05T13:22:13.399Z]     _test_dataset(data)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/tests/test_tciadataset.py", line 43, in _test_dataset
[2023-09-05T13:22:13.399Z]     self.assertTrue("image" in dataset[0])
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/data/dataset.py", line 112, in __getitem__
[2023-09-05T13:22:13.399Z]     return self._transform(index)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/data/dataset.py", line 910, in _transform
[2023-09-05T13:22:13.399Z]     return super()._transform(index)
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/data/dataset.py", line 98, in _transform
[2023-09-05T13:22:13.399Z]     return apply_transform(self.transform, data_i) if self.transform is not None else data_i
[2023-09-05T13:22:13.399Z]   File "/home/jenkins/agent/workspace/MONAI-postmerge/monai_github/monai/transforms/transform.py", line 171, in apply_transform
[2023-09-05T13:22:13.399Z]     raise RuntimeError(f"applying transform {transform}") from e
[2023-09-05T13:22:13.399Z] RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7f449a90de20>
[2023-09-05T13:22:13.399Z] 
[2023-09-05T13:22:13.399Z] ----------------------------------------------------------------------
KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Sep 5, 2023
@KumoLiu
fix Project-MONAI#6945
1ed4f94 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Sep 5, 2023
Merged
7 tasks
@wyli wyli closed this as completed in #6946 Sep 5, 2023
wyli pushed a commit that referenced this issue Sep 5, 2023
@KumoLiu
Fix KeyError in PydicomReader (#6946)
c4ed1f8 
Fixes #6945 .

### Description
Try get "00280030" (PixelSpacing) first.

### 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).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: KumoLiu <[email protected]>
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Fix KeyError in PydicomReader KumoLiu/MONAI
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@wyli