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InsightSoftwareConsortium / ITK

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
https://itk.org
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Can't process LUNA16 data with .mhd format #3701

Open USTC-yzy1996 opened 2 years ago

USTC-yzy1996 commented 2 years ago

Hi, I met an error in "https://github.com/Project-MONAI/tutorials/tree/main/detection". I went with README.md and met an error when running code: python3 luna16_prepare_env_files.py python3 luna16_prepare_images.py -c ./config/config_train_luna1616g.json The error shows that the MONAI reader can not process files with .mhd format. Please check out this bug. Thanks a lot! ^^

github-actions[bot] commented 2 years ago

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dzenanz commented 2 years ago

Do you mind providing the text of the error message? An attempt to reproduce this error entails downloading this dataset.

USTC-yzy1996 commented 2 years ago

Sure, the error messages are as follows: MONAI version: 1.0.0 Numpy version: 1.17.2+intel.0 Pytorch version: 1.7.0 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False MONAI rev id: 170093375ce29267e45681fcec09dfa856e1d7e7 MONAI file: /home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/init.py

Optional dependencies: Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION. Nibabel version: 3.1.1 scikit-image version: 0.15.0 Pillow version: 6.2.0 Tensorboard version: 1.14.0 gdown version: NOT INSTALLED or UNKNOWN VERSION. TorchVision version: NOT INSTALLED or UNKNOWN VERSION. tqdm version: 4.36.1 lmdb version: NOT INSTALLED or UNKNOWN VERSION. psutil version: 5.6.3 pandas version: 0.25.1 einops version: 0.3.0 transformers version: NOT INSTALLED or UNKNOWN VERSION. mlflow version: NOT INSTALLED or UNKNOWN VERSION. pynrrd version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit: https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py:192: UserWarning: required package for reader itkreader is not installed, or the version doesn't match requirement. f"required package for reader {_r} is not installed, or the version doesn't match requirement."

534 2022-10-22 14:57:53,095 - NibabelReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).

2022-10-22 14:57:53,095 - PILReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).

2022-10-22 14:57:53,095 - NumpyReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).

2022-10-22 14:57:53,096 - PydicomReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).

Traceback (most recent call last): 2022-10-22 14:57:53,098 - NibabelReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).

File "luna16_prepare_images.py", line 127, in 2022-10-22 14:57:53,098 - PILReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).

2022-10-22 14:57:53,098 - NumpyReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).

2022-10-22 14:57:53,098 - PydicomReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).

main()

File "luna16_prepare_images.py", line 115, in main 2022-10-22 14:57:53,099 - NibabelReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).

for batch_data in process_loader:

File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 435, in next 2022-10-22 14:57:53,099 - PILReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).

data = self._next_data()

File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 1085, in _next_data 2022-10-22 14:57:53,099 - NumpyReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).

2022-10-22 14:57:53,099 - PydicomReader: unable to load ('/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).

return self._process_data(data)

File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 1111, in _process_data data.reraise() File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/_utils.py", line 428, in reraise raise self.exc_type(msg) RuntimeError: Caught RuntimeError in DataLoader worker process 0. Original Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 91, in apply_transform return _apply_transform(transform, data, unpack_items) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 55, in _apply_transform return transform(parameters) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/dictionary.py", line 154, in call data = self._loader(d[key], reader) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py", line 259, in call f"{self.class.name} cannot find a suitable reader for file: {filename}.\n" RuntimeError: LoadImage cannot find a suitable reader for file: /ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd. Please install the reader libraries, see also the installation instructions: https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies. The current registered: [<monai.data.image_reader.PydicomReader object at 0x7f5aa3578a50>, <monai.data.image_reader.NumpyReader object at 0x7f5aa3578f50>, <monai.data.image_reader.PILReader object at 0x7f5aa3578e50>, <monai.data.image_reader.NibabelReader object at 0x7f5aa3578f10>]. Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py", line 243, in call img = reader.read(filename) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/imagereader.py", line 912, in read img = nib.load(name, **kwargs) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/nibabel/loadsave.py", line 56, in load filename) nibabel.filebasedimages.ImageFileError: Cannot work out file type of "/ssdm2/yuyu/LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd"

Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py", line 243, in call img = reader.read(filename) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/imagereader.py", line 1167, in read img = PILImage.open(name, **kwargs) TypeError: open() got an unexpected keyword argument 'affine_lps_to_ras'

Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py", line 243, in call img = reader.read(filename) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/image_reader.py", line 1074, in read img = np.load(name, allowpickle=True, **kwargs) TypeError: load() got an unexpected keyword argument 'affine_lps_to_ras'

Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/io/array.py", line 243, in call img = reader.read(filename) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/imagereader.py", line 481, in read ds = pydicom.dcmread(fp=name, **kwargs) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/pydicom/filereader.py", line 870, in dcmread force=force, specific_tags=specific_tags) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/pydicom/filereader.py", line 667, in read_partial preamble = read_preamble(fileobj, force) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/pydicom/filereader.py", line 620, in read_preamble raise InvalidDicomError("File is missing DICOM File Meta Information " pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 91, in apply_transform return _apply_transform(transform, data, unpack_items) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 55, in _applytransform return transform(parameters) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/compose.py", line 173, in call input = apply_transform(transform, input, self.map_items, self.unpack_items, self.log_stats) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 118, in apply_transform raise RuntimeError(f"applying transform {transform}") from e RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7f5ad4ef1e50>

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 198, in _worker_loop data = fetcher.fetch(index) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/dataset.py", line 105, in getitem return self._transform(index) File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/data/dataset.py", line 91, in _transform return apply_transform(self.transform, data_i) if self.transform is not None else data_i File "/home/ys3/anaconda3/envs/deepsvdd/lib/python3.7/site-packages/monai/transforms/transform.py", line 118, in apply_transform raise RuntimeError(f"applying transform {transform}") from e RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7f5aa3511f90>

dzenanz commented 2 years ago

It looks like you don't have ITK installed. Try pip install itk.