Merge pull request #91 from joeranbosma/patch-1

Hydra env update
Closes https://github.com/MIC-DKFZ/nnDetection/issues/88

scripts/consolidate.py

@@ -172,8 +172,8 @@ def main():
     # invoke new parameter sweeps
     cfg = OmegaConf.load(str(target_dir / "config.yaml"))
     ov = ov if ov is not None else []
-    ov.append("host.parent_data=${env:det_data}")
-    ov.append("host.parent_results=${env:det_models}")
+    ov.append("host.parent_data=${oc.env:det_data}")
+    ov.append("host.parent_results=${oc.env:det_models}")
     if ov is not None:
         cfg.merge_with_dotlist(ov)
 

scripts/predict.py

@@ -210,8 +210,8 @@ def main():
     cfg["exp"] = set_arg(cfg["exp"], "id", model, force_args=force_args)
 
     overwrites = ov if ov is not None else []
-    overwrites.append("host.parent_data=${env:det_data}")
-    overwrites.append("host.parent_results=${env:det_models}")
+    overwrites.append("host.parent_data=${oc.env:det_data}")
+    overwrites.append("host.parent_results=${oc.env:det_models}")
     cfg.merge_with_dotlist(overwrites)
 
     for imp in cfg.get("additional_imports", []):

scripts/utils.py

@@ -59,8 +59,8 @@ def boxes2nii():
     training_dir = get_training_dir(task_dir / model, fold)
 
     overwrites = overwrites if overwrites is not None else []
-    overwrites.append("host.parent_data=${env:det_data}")
-    overwrites.append("host.parent_results=${env:det_models}")
+    overwrites.append("host.parent_data=${oc.env:det_data}")
+    overwrites.append("host.parent_results=${oc.env:det_models}")
 
     prediction_dir = training_dir / "test_predictions" \
         if test else training_dir / "val_predictions"
@@ -150,8 +150,8 @@ def seg2nii():
     training_dir = get_training_dir(task_dir / model, fold)
 
     overwrites = overwrites if overwrites is not None else []
-    overwrites.append("host.parent_data=${env:det_data}")
-    overwrites.append("host.parent_results=${env:det_models}")
+    overwrites.append("host.parent_data=${oc.env:det_data}")
+    overwrites.append("host.parent_results=${oc.env:det_models}")
 
     prediction_dir = training_dir / "test_predictions" \
         if test else training_dir / "val_predictions"