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Create simple test.py inference script #40

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plbenveniste opened this issue Jul 6, 2023 · 2 comments · Fixed by #32
Closed

Create simple test.py inference script #40

plbenveniste opened this issue Jul 6, 2023 · 2 comments · Fixed by #32
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@plbenveniste
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plbenveniste commented Jul 6, 2023

similar to https://github.com/ivadomed/model_seg_mouse-sc_wm-gm_t1/blob/main/test.py, but compatible with nnUnet:

  • input NIfTI file
  • create nnUnet compatible folder structure
  • run nnUnet CLI as system call
  • reorganize file
  • delete temp files
  • done

Related to #38

@plbenveniste plbenveniste self-assigned this Jul 7, 2023
@plbenveniste
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Code based on run_inference.py.

@jcohenadad
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Code based on run_inference.py.

this URL points to a code in a branch, which will likely be deleted once the branch is merged (hence will give a 404 error in the futur), so I suggest to instead point to a code in a 'master' version of git. I think that the code in question is this one: https://github.com/ivadomed/utilities/blob/main/packaging/run_nnunet_inference.py

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