From 7b405bd7ede840e2a7bb2fc14f72711126316811 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 18 Jun 2024 11:30:29 +0200
Subject: [PATCH] [segmentation] Fix issue with output file paths
---
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 6da6282c..5f947b5d 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"{pathlib.Path(stem).stem}.csv"
+ fullpath = (output_folder / name / f"{stem}").with_suffix(".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 023b0162..04b3d57d 100644
--- a/src/mednet/libs/segmentation/scripts/predict.py
+++ b/src/mednet/libs/segmentation/scripts/predict.py
@@ -116,7 +116,7 @@ def predict(
for split_name, split in predictions.items():
pred_paths = []
for sample in split:
- hdf5_path = output_folder / f"{pathlib.Path(sample[0]).stem}.hdf5"
+ hdf5_path = (output_folder / f"{sample[0]}").with_suffix(".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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