Detection tutorial does not read original Luna files #1102
Description
I am trying to run detection tutorial (https://github.com/Project-MONAI/tutorials/tree/main/detection) using original LUNA16 files in mhd+raw format
Environment is as follows:
- Linux
- Python 3.10.8
- cuda/11.6.0
- GPU model: NVIDIA Tesla V100
MONAI version: 1.0.1
Numpy version: 1.23.5
Pytorch version: 1.13.0
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 8271a193229fe4437026185e218d5b06f7c8ce69
Optional dependencies:
Pytorch Ignite version: 0.4.10
Nibabel version: 4.0.2
scikit-image version: 0.19.3
Pillow version: 9.3.0
Tensorboard version: 2.11.0
gdown version: 4.6.0
TorchVision version: 0.14.0
tqdm version: 4.64.1
lmdb version: 1.4.0
psutil version: 5.9.4
pandas version: 1.5.2
einops version: 0.6.0
transformers version: 4.21.3
mlflow version: 2.0.1
pynrrd version: 1.0.0
According to the tutorial, I should run:
python3 luna16_prepare_env_files.py
python3 luna16_prepare_images.py -c ./config/config_train_luna16_16g.jsonn
Script luna16_prepare_env_files.py runts correctly. When I run luna16_prepare_images.py I got an error when trying to read mhd+raw files. The mhd+raw files are correct (I can read them in external software). The error output is attached below.
What additional requirements should be installed to correctly read mhd+raw files?
The next issue is that at google drive at https://drive.google.com/drive/folders/1JozrufA1VIZWJIc5A1EMV3J4CNCYovKK you have shared resampled nifti files. But there are only about 600 files at google drive while in LUNA16 there are more than 880 files.
UserWarning: required package for reader itkreader is not installed, or the version doesn't match requirement.
warnings.warn(
2022-12-12 14:07:16,152 - NibabelReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).
2022-12-12 14:07:16,153 - PILReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).
2022-12-12 14:07:16,153 - NumpyReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).
2022-12-12 14:07:16,157 - NrrdReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).
2022-12-12 14:07:16,160 - PydicomReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143.mhd',).
Traceback (most recent call last):
File "/net/ascratch/people/plgztabor/MONAI/luna16_prepare_images.py", line 122, in
main()
File "/net/ascratch/people/plgztabor/MONAI/luna16_prepare_images.py", line 110, in main
for batch_data in process_loader:
2022-12-12 14:07:16,167 - NrrdReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 628, in next
data = self._next_data()
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 1333, in _next_data
2022-12-12 14:07:16,167 - PydicomReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.287966244644280690737019247886.mhd',).
return self._process_data(data)
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 1359, in _process_data
data.reraise()
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/torch/_utils.py", line 543, in reraise
2022-12-12 14:07:16,169 - NibabelReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).
2022-12-12 14:07:16,169 - PILReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).
2022-12-12 14:07:16,169 - NumpyReader: unable to load ('/net/ascratch/people/plgztabor/MONAI/DATA/1.3.6.1.4.1.14519.5.2.1.6279.6001.768276876111112560631432843476.mhd',).
raise exception
RuntimeError: Caught RuntimeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/monai/transforms/transform.py", line 91, in apply_transform
return _apply_transform(transform, data, unpack_items)
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/monai/transforms/transform.py", line 55, in _apply_transform
return transform(parameters)
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/monai/transforms/io/dictionary.py", line 154, in call
data = self._loader(d[key], reader)
File "/net/software/testing/software/monai/1.0.1/lib/python3.10/site-packages/monai/transforms/io/array.py", line 258, in call
raise RuntimeError(
RuntimeError: LoadImage cannot find a suitable reader for file: /net/ascratch/people/plgztabor/MONAI/DATA/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 0x14c220d351e0>, <monai.data.image_reader.NrrdReader object at 0x14c220d34820>, <monai.data.image_reader.NumpyReader object at 0x14c220d34e20>, <monai.data.image_reader.PILReader object at 0x14c220d35990>, <monai.data.image_reader.NibabelReader object at 0x14c220d35570>].