Submission problem

Hello,

Unfortunately, I still cannot upload my algorithm due to unknown problem. All the pretests before the submission are passed. Could you please send me the recent error report?

Hi

I think you are trying to read the folder ( "/opt/algorithm/CXR_cropped_nodules/") with simpleITK ???

The error is below:

2021-12-24T11:15:58+00:00 Could not load nodules.json using . 2021-12-24T11:18:06+00:00 HDF5-DIAG: Error detected in HDF5 (1.10.6) thread 0: 2021-12-24T11:18:06+00:00 #000: /tmp/SimpleITK-build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c line 370 in itk_H5Fis_hdf5(): unable open file 2021-12-24T11:18:06+00:00 major: File accessibilty 2021-12-24T11:18:06+00:00 minor: Not an HDF5 file 2021-12-24T11:18:06+00:00 #001: /tmp/SimpleITK-build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c line 830 in itk_H5F__is_hdf5(): unable to locate file signature 2021-12-24T11:18:06+00:00 major: File accessibilty 2021-12-24T11:18:06+00:00 minor: Not an HDF5 file 2021-12-24T11:18:06+00:00 #002: /tmp/SimpleITK-build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDint.c line 126 in itk_H5FD_locate_signature(): unable to read file signature 2021-12-24T11:18:06+00:00 major: Low-level I/O 2021-12-24T11:18:06+00:00 minor: Unable to initialize object 2021-12-24T11:18:06+00:00 #003: /tmp/SimpleITK-build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDint.c line 205 in itk_H5FD_read(): driver read request failed 2021-12-24T11:18:06+00:00 major: Virtual File Layer 2021-12-24T11:18:06+00:00 minor: Read failed 2021-12-24T11:18:06+00:00 #004: /tmp/SimpleITK-build/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c line 725 in H5FD_sec2_read(): file read failed: time = Fri Dec 24 11:18:06 2021 2021-12-24T11:18:06+00:00 , filename = '/opt/algorithm/CXR_cropped_nodules/', file descriptor = 3, errno = 21, error message = 'Is a directory', buf = 0x7fffccdf4158, total read size = 8, bytes this sub-read = 8, bytes actually read = 18446744073709551615, offset = 0 2021-12-24T11:18:06+00:00 major: Low-level I/O 2021-12-24T11:18:06+00:00 minor: Read failed 2021-12-24T11:18:06+00:00 Traceback (most recent call last): 2021-12-24T11:18:06+00:00 File "/usr/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main 2021-12-24T11:18:06+00:00 "main", mod_spec) 2021-12-24T11:18:06+00:00 File "/usr/local/lib/python3.7/runpy.py", line 85, in _run_code 2021-12-24T11:18:06+00:00 exec(code, run_globals) 2021-12-24T11:18:06+00:00 File "/opt/algorithm/process.py", line 127, in 2021-12-24T11:18:06+00:00 Nodulegeneration().process() 2021-12-24T11:18:06+00:00 File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 183, in process 2021-12-24T11:18:06+00:00 self.process_cases() 2021-12-24T11:18:06+00:00 File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 191, in process_cases 2021-12-24T11:18:06+00:00 self._case_results.append(self.process_case(idx=idx, case=case)) 2021-12-24T11:18:06+00:00 File "/home/algorithm/.local/lib/python3.7/site-packages/evalutils/evalutils.py", line 273, in process_case 2021-12-24T11:18:06+00:00 segmented_nodules = self.predict(input_image=input_image) 2021-12-24T11:18:06+00:00 File "/opt/algorithm/process.py", line 106, in predict 2021-12-24T11:18:06+00:00 cxr_nodule = sitk.GetArrayFromImage(sitk.ReadImage(os.path.join(cxr_path,file_name))) 2021-12-24T11:18:06+00:00 File "/home/algorithm/.local/lib/python3.7/site-packages/SimpleITK/extra.py", line 346, in ReadImage 2021-12-24T11:18:06+00:00 return reader.Execute() 2021-12-24T11:18:06+00:00 File "/home/algorithm/.local/lib/python3.7/site-packages/SimpleITK/SimpleITK.py", line 8015, in Execute 2021-12-24T11:18:06+00:00 return _SimpleITK.ImageFileReader_Execute(self) 2021-12-24T11:18:06+00:00 RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:105: 2021-12-24T11:18:06+00:00 sitk::ERROR: Unable to determine ImageIO reader for "/opt/algorithm/CXR_cropped_nodules/"