update release flow; bugfix

Author: wasserth

resources/anonymise_nnunet_pkl_v2.py

@@ -0,0 +1,43 @@
+import os
+import sys
+import pickle
+import shutil
+from pathlib import Path
+
+
+if __name__ == "__main__":
+    """
+    Remove elements with Subject IDs from nnunet results.
+
+    Also deleting the training log because in there are also the IDs.
+
+    usage:
+
+    cd $RESULTS_FOLDER
+    anonymise_nnunet_pkl_v2.py nnUNet/3d_fullres/Dataset291_TotalSegmentator_part1_organs_1559subj/nnUNetTrainerNoMirroring__nnUNetPlans__3d_fullres
+    nnUNet_export_model_to_zip -t 291 -o dataset_291_upload.zip -c 3d_fullres -tr nnUNetTrainerV2 --not_strict
+    """
+    dir_in = Path(sys.argv[1])
+
+    folds = sorted(list(dir_in.glob("fold_*")))
+    print(f"Nr of folds found: {len(folds)}")
+
+    # Anonymise model_final_checkpoint.model.pkl for all folds
+    for fold_dir in folds:
+
+        # Remove unneeded files and directories
+        for dir in [fold_dir / "validation"]:
+            if dir.exists():
+                print(f"Deleting: {dir}")
+                shutil.rmtree(dir)
+    
+        for file in [fold_dir / "checkpoint_best.pth"]:
+            if file.exists():
+                print(f"Deleting: {file}")
+                os.remove(file)
+
+        training_logs = fold_dir.glob("training_log_*")
+        for log in training_logs:
+            if log.exists():
+                print(f"Deleting: {log}")
+                os.remove(log)

resources/package_management.md

@@ -26,5 +26,9 @@ INFO: Now all done by `release.sh`
 
 
 ## Release new weights
+* `cd /mnt/nvme/data/multiseg/weights_upload/totalsegmentator_v2`
+* `cp -r $nnUNet_results/Dataset527_breasts_1559subj .`
+* `python ~/dev/TotalSegmentator/resources/anonymise_nnunet_pkl_v2.py Dataset527_breasts_1559subj/nnUNetTrainer_DASegOrd0_NoMirroring__nnUNetPlans__3d_fullres`
+* `zip -r Dataset527_breasts_1559subj.zip Dataset527_breasts_1559subj`
 * Click on "Draft a new release" on github
 * Create new tag ending with -weights and upload weights

totalsegmentator/libs.py

@@ -301,7 +301,7 @@ def download_pretrained_weights(task_id):
         WEIGHTS_URL = url + "/v2.4.0-weights/Dataset008_HepaticVessel.zip"
     elif task_id == 913:
         weights_path = config_dir / "Dataset913_lung_nodules"
-        WEIGHTS_URL = url + "/v2.4.0-weights/Dataset913_lung_nodules.zip"  # TODO: correct url
+        WEIGHTS_URL = url + "/v2.5.0-weights/Dataset913_lung_nodules.zip"
 
     # Commercial models
     elif task_id == 304: