The algorithm failed on one or more cases.

The algorithm failed on one or more cases. ¶

By: MachineKim on July 18, 2023, 6:53 a.m.

Hi, can you please tell me what the error log was?

Re: The algorithm failed on one or more cases. ¶

By: giansteve on July 18, 2023, 7:13 a.m.

Hi,

The error message is the following: "sitk::ERROR: The file "/opt/app/nnUNet_Predictions/bc5eae0e-1bc8-468a-98a2-00547e42ed2c.nii.gz" does not exist."

The algorithm produced the following Traceback errors:

2023-07-18T06:12:29.675000+00:00 Traceback (most recent call last):
2023-07-18T06:12:29.675000+00:00   File "/opt/app/./nrrd_to_nii.py", line 37, in <module>
2023-07-18T06:12:29.675000+00:00     nii_image  = sitk.GetArrayFromImage(sitk.ReadImage(oldpath_nii))
2023-07-18T06:12:29.676000+00:00   File "/home/user/.local/lib/python3.9/site-packages/SimpleITK/extra.py", line 355, in ReadImage
2023-07-18T06:12:29.676000+00:00     return reader.Execute()
2023-07-18T06:12:29.676000+00:00   File "/home/user/.local/lib/python3.9/site-packages/SimpleITK/SimpleITK.py", line 8438, in Execute
2023-07-18T06:12:29.676000+00:00     return _SimpleITK.ImageFileReader_Execute(self)
2023-07-18T06:12:29.676000+00:00 RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:97:
2023-07-18T06:12:29.676000+00:00 sitk::ERROR: The file "/input/images_nii/ct/bc5eae0e-1bc8-468a-98a2-00547e42ed2c.nii.gz" does not exist.
2023-07-18T06:12:50.685000+00:00 Traceback (most recent call last):
2023-07-18T06:12:50.685000+00:00   File "/opt/app/process.py", line 97, in <module>
2023-07-18T06:12:50.685000+00:00     Segaalgorithm().process()
2023-07-18T06:12:50.685000+00:00   File "/home/user/.local/lib/python3.9/site-packages/evalutils/evalutils.py", line 183, in process
2023-07-18T06:12:50.685000+00:00     self.process_cases()
2023-07-18T06:12:50.685000+00:00   File "/home/user/.local/lib/python3.9/site-packages/evalutils/evalutils.py", line 191, in process_cases
2023-07-18T06:12:50.685000+00:00     self._case_results.append(self.process_case(idx=idx, case=case))
2023-07-18T06:12:50.685000+00:00   File "/opt/app/process.py", line 46, in process_case
2023-07-18T06:12:50.685000+00:00     predictions = sitk.GetArrayFromImage(sitk.ReadImage('/opt/app/nnUNet_Predictions/'+filename+'.nii.gz'))
2023-07-18T06:12:50.685000+00:00   File "/home/user/.local/lib/python3.9/site-packages/SimpleITK/extra.py", line 355, in ReadImage
2023-07-18T06:12:50.685000+00:00     return reader.Execute()
2023-07-18T06:12:50.685000+00:00   File "/home/user/.local/lib/python3.9/site-packages/SimpleITK/SimpleITK.py", line 8438, in Execute
2023-07-18T06:12:50.685000+00:00     return _SimpleITK.ImageFileReader_Execute(self)
2023-07-18T06:12:50.685000+00:00 RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:97:
2023-07-18T06:12:50.685000+00:00 sitk::ERROR: The file "/opt/app/nnUNet_Predictions/bc5eae0e-1bc8-468a-98a2-00547e42ed2c.nii.gz" does not exist.

Best Gian Marco

Re: The algorithm failed on one or more cases. ¶

By: MachineKim on July 18, 2023, 7:19 a.m.

Thank you for your prompt response. I appreciate it.

But I have another question.

I need the '--ipc=host' tag in my Docker image, but it seems like I don't have control over it.

Is it possible for you to include it or is it already included?

Re: The algorithm failed on one or more cases. ¶

By: apepe on July 18, 2023, 8:29 a.m.

Hi,

The execution of the containers is standardized and limited by the grand-challenge platform.

Is there any special reason for such a flag?

Re: The algorithm failed on one or more cases. ¶

By: MachineKim on July 19, 2023, 7:40 p.m.

Sorry for the confusion. My code required that flag before, but I changed the code and checked that docker runs well.

Thank you again for your kind reply!