`No such file or directory` error when running test.sh

[pzSuen]

I have tested process.py successfully out of the docker.
But when I run test.sh,
As seen in the image, there is no such file called mitotic-figures.json.

Did I miss something?
How to deal with this problem?

[maubreville]

Hey there,

it appears that the save()-function of process.py is not run or does not including saving to the json file, as in the template:

https://github.com/DeepPathology/MIDOG_reference_docker/blob/6bdd60294828a1166a819951ba7aa4cb18da7352/process.py#L61

This may have several reasons. Our template class inherits from evalutil's DetectionAlgorithm, which inherits in itself the process() method from its superclass Algorithm:

https://github.com/comic/evalutils/blob/73ba4ceae361557c70992245b16463159d6bfba0/evalutils/evalutils.py#L180

This is where self.save() is executed from self.process(), which should be run in your process.py.

Another reason might be that you changed the path of the output file. Please make sure that the absolute path is /output/mitotic-figures.json:

https://github.com/DeepPathology/MIDOG_reference_docker/blob/6bdd60294828a1166a819951ba7aa4cb18da7352/process.py#L34

[kabbas570]

@maubreville
I got a similar error while running the test.sh on the window with CPU. However, the error is gone if I run the test.bat file.
Maybe there is some path issue if we want to access mitotic-figures.json using a window ?

Cheers
Abbas

[maubreville]

This is very possible, @kabbas570. The path settings in batch files are, however, subject to a lot of different factors in Windows, especially if you use things like special command line interfaces ("anaconda prompt"), which do change the path settings. In any case, I would use the .bat files in Windows and the .sh files on linux :-)

Can you tell if the processing really proceeds without errors? It could also be that the input image is not available to the inference script, which would also explain the error.

[kabbas570]

@maubreville Thanks for the reply.
Yes, processing works fine with test.bat files, I am getting similar errors for many other challenges I am working on if I run ./test from any of the GitHub.
Got a similar error for this as well.
https://github.com/DIAGNijmegen/picai_nnunet_gc_algorithm

[kabbas570]

The error with ./test.sh is

What's Next?
View summary of image vulnerabilities and recommendations → docker scout quickview
mitosisdetection-output
docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: error running hook #0: error running hook: exit status 1, stdout: , stderr: Auto-detected mode as 'legacy'
nvidia-container-cli: initialization error: WSL environment detected but no adapters were found: unknown.
./test.sh: line 17: python: command not found
cat: /output/mitotic-figures.json: No such file or directory
Traceback (most recent call last):
File "", line 1, in
FileNotFoundError: [Errno 2] No such file or directory: '/output/mitotic-figures.json'
Expected output was not found...
mitosisdetection-output

[maubreville]

To me this looks clearly like a WSL / docker interaction problem.