From a50998173b7de3fdd2f390b0ad55958a9d23e84d Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 17 Jun 2024 11:08:16 +0200
Subject: [PATCH] [segmentation.scripts] Fix saved files extensions
---
src/mednet/libs/segmentation/engine/evaluator.py | 2 +-
src/mednet/libs/segmentation/scripts/predict.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/mednet/libs/segmentation/engine/evaluator.py b/src/mednet/libs/segmentation/engine/evaluator.py
index 01917104..6da6282c 100644
--- a/src/mednet/libs/segmentation/engine/evaluator.py
+++ b/src/mednet/libs/segmentation/engine/evaluator.py
@@ -364,7 +364,7 @@ def _evaluate_sample_worker(
retval = _sample_measures(prediction, target, mask, steps)
if output_folder is not None:
- fullpath = output_folder / name / f"{stem}.csv"
+ fullpath = output_folder / name / f"{pathlib.Path(stem).stem}.csv"
tqdm.write(f"Saving {fullpath}...")
fullpath.parent.mkdir(parents=True, exist_ok=True)
retval.to_csv(fullpath)
diff --git a/src/mednet/libs/segmentation/scripts/predict.py b/src/mednet/libs/segmentation/scripts/predict.py
index e96d25a3..b91400ac 100644
--- a/src/mednet/libs/segmentation/scripts/predict.py
+++ b/src/mednet/libs/segmentation/scripts/predict.py
@@ -115,7 +115,7 @@ def predict(
for split_name, split in predictions.items():
pred_paths = []
for sample in split:
- hdf5_path = output_folder / f"{sample[0]}.hdf5"
+ hdf5_path = output_folder / f"{pathlib.Path(sample[0]).stem}.hdf5"
_save_hdf5(sample[3], sample[1], sample[2], hdf5_path)
pred_paths.append([str(sample[0]), str(hdf5_path)])
json_predictions[split_name] = pred_paths
--
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