mlcommons / mlcommons/inference

Assertion error

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Description

python3 preprocess.py
--raw_data_dir ~/3D\ UNET/kits19/data
--results_dir ~/3D\ UNET/build/preprocessed_data
--num_proc 4
/home/sahaas/3D UNET/mlc-inference/vision/medical_imaging/3d-unet-kits19/preprocess.py:29: DeprecationWarning: Please import zoom from the scipy.ndimage namespace; the scipy.ndimage.interpolation namespace is deprecated and will be removed in SciPy 2.0.0.
from scipy.ndimage.interpolation import zoom
Preprocessing /home/sahaas/3D UNET/kits19/data...
Traceback (most recent call last):
File "/home/sahaas/3D UNET/mlc-inference/vision/medical_imaging/3d-unet-kits19/preprocess.py", line 694, in
main()
File "/home/sahaas/3D UNET/mlc-inference/vision/medical_imaging/3d-unet-kits19/preprocess.py", line 683, in main
preprocess_with_multiproc(args)
File "/home/sahaas/3D UNET/mlc-inference/vision/medical_imaging/3d-unet-kits19/preprocess.py", line 529, in preprocess_with_multiproc
cases = preproc.collect_cases()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sahaas/3D UNET/mlc-inference/vision/medical_imaging/3d-unet-kits19/preprocess.py", line 249, in collect_cases
collected_set == target_set
AssertionError: Some of the target inference cases were found: {'case_00400'}

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Research direction

Reproduce the command from the issue with the 3D UNet KiTS19 data and inspect preprocess.py, especially collect_cases() around line 249 and its caller at line 529. Investigate why case_00400 appears in the collected set despite the target inference cases assertion; done should mean preprocessing proceeds without this assertion.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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