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simple scripts for eval and pred with nnunet #183

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merged 5 commits into from
Jun 25, 2024
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scarere
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@scarere scarere commented Jun 20, 2024

Feature

Short Description

Simple scripts for prediction and evaluation.

  • The prediction script is specific to generating predicted segmentation maps for for nnUNet models
  • The evaluation script generates the metrics used in the PICAI challenge, but could be applied to any set of predictions and ground truths. These are the metrics we aim to use when evaluating prostate segmentation models.

from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor


def main() -> None:
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Similar to the last PR, can you could add a section to the README with a description of the purpose of the script, what it does and an example invocation

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for the predict and eval script

y_true_dir=args.gt_path,
)

# Print metrics
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Maybe worth mentioning in the comments here or in the README what the metrics being computed are. If its a lot of info you can give a short overview and link to the picai documentation or somewhere else that expands on the metrics

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Other than the request to add some documentation in the README about the scripts and an example invoking them, I think this looks good! Feel free to add that and then merge this in

@scarere scarere merged commit 70fa23d into main Jun 25, 2024
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@scarere scarere deleted the picai_pred_and_eval branch June 25, 2024 17:57
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2 participants