From ed745aecd1dce07bb7b3b00e571d28c8b5df6c54 Mon Sep 17 00:00:00 2001
From: Yehuda Warszawer <36595323+yw7@users.noreply.github.com>
Date: Sat, 16 Nov 2024 01:15:28 +0200
Subject: [PATCH] Change checkpoint_latest to checkpoint_best in inference
 script

Fixes #78

Change `checkpoint_latest.pth` to `checkpoint_best.pth` in the inference script.

* Update line 301 in `totalspineseg/inference.py` to use `checkpoint_best.pth` instead of `checkpoint_latest.pth`.
* Update line 552 in `totalspineseg/inference.py` to use `checkpoint_best.pth` instead of `checkpoint_latest.pth`.

---

For more details, open the [Copilot Workspace session](https://copilot-workspace.githubnext.com/neuropoly/totalspineseg/issues/78?shareId=XXXX-XXXX-XXXX-XXXX).
---
 totalspineseg/inference.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/totalspineseg/inference.py b/totalspineseg/inference.py
index 162e1e2..4142f85 100644
--- a/totalspineseg/inference.py
+++ b/totalspineseg/inference.py
@@ -298,7 +298,7 @@ def main():
     # Get the nnUNet parameters from the results folder
     nnUNetTrainer, nnUNetPlans, configuration = next((nnUNet_results / step1_dataset).glob('*/fold_*')).parent.name.split('__')
     # Check if the final checkpoint exists, if not use the latest checkpoint
-    checkpoint = 'checkpoint_final.pth' if (nnUNet_results / step1_dataset / f'{nnUNetTrainer}__{nnUNetPlans}__{configuration}' / f'fold_{fold}' / 'checkpoint_final.pth').is_file() else 'checkpoint_latest.pth'
+    checkpoint = 'checkpoint_final.pth' if (nnUNet_results / step1_dataset / f'{nnUNetTrainer}__{nnUNetPlans}__{configuration}' / f'fold_{fold}' / 'checkpoint_final.pth').is_file() else 'checkpoint_best.pth'
 
     if not quiet: print('\n' 'Running step 1 model:')
     subprocess.run([
@@ -549,7 +549,7 @@ def main():
         # Get the nnUNet parameters from the results folder
         nnUNetTrainer, nnUNetPlans, configuration = next((nnUNet_results / step2_dataset).glob('*/fold_*')).parent.name.split('__')
         # Check if the final checkpoint exists, if not use the latest checkpoint
-        checkpoint = 'checkpoint_final.pth' if (nnUNet_results / step2_dataset / f'{nnUNetTrainer}__{nnUNetPlans}__{configuration}' / f'fold_{fold}' / 'checkpoint_final.pth').is_file() else 'checkpoint_latest.pth'
+        checkpoint = 'checkpoint_final.pth' if (nnUNet_results / step2_dataset / f'{nnUNetTrainer}__{nnUNetPlans}__{configuration}' / f'fold_{fold}' / 'checkpoint_final.pth').is_file() else 'checkpoint_best.pth'
 
         if not quiet: print('\n' 'Running step 2 model:')
         subprocess.run([