Running the template for Docker

Hello, As a first step, I am just running the base template (./test.sh) provided at https://github.com/apepe91/SEGA2023/tree/main/SegaAlgorithm And getting the following error; can anyone help with this, please? I am running it locally with WSL on Windows. A similar issue I found here, https://github.com/DeepMicroscopy/MIDOG_reference_docker/issues/5

segaalgorithm-output-aaf39bf52fdd663bc5ff7159ad0777c0 Traceback (most recent call last): File "/usr/local/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/local/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "/opt/app/process.py", line 72, in Segaalgorithm().process() File "/home/user/.local/lib/python3.8/site-packages/evalutils/evalutils.py", line 181, in process self.load() File "/home/user/.local/lib/python3.8/site-packages/evalutils/evalutils.py", line 123, in load self._cases[key] = self._load_cases( File "/home/user/.local/lib/python3.8/site-packages/evalutils/evalutils.py", line 157, in _load_cases raise FileLoaderError( evalutils.exceptions.FileLoaderError: Could not load any files in /input/images/ct with . cat: /output/results.json: No such file or directory Expecting value: line 1 column 1 (char 0) Traceback (most recent call last): File "", line 1, in FileNotFoundError: [Errno 2] No such file or directory: '/output/results.json' Expected output was not found... segaalgorithm-output-aaf39bf52fdd663bc5ff7159ad0777c0gorithm-output-aaf39bf52fdd663bc5ff7159ad0777c0

Hi! I have the exact same issue, but I could not find any solution yet...

Did you find any solution? Thanks

Dear Abbas and Helene,

it appears that your problem relates to the input folder "FileLoaderError: Could not load any files in /input/images/ct". You would need to adapt the input paths to fit those on your machines or adapt your folder structure. The paths/interfaces in the template are those required for the docker submission to work.

Once the algorithm executes without errors, it should also generate the missing file "results.json".

Let me know if this fixes your issue

Best Antonio

Dear Antonio, Thanks for the response, I solved the path issue in process.py and now getting the following error.

Could not load 1.0.000.000000.0.00.0.0000000000.0000.0000000000.000.zraw using . Could not load expected_output.json using . Cheers Abbas

Dear Abbas,

These are warning generated by the original evalutils template, you can ignore them. The reason is that in your local system you have files represented as zraw+mha.

The remote system loads the files as .mha (single file). You can locally replace them also with nrrd files. There is no difference if you use the ITK loader. Keep this in mind in case you use a different loader.

Best, Antonio

Dear Antonio, Thanks for your reply; I have solved the problem locally.

Cheers Abbas