Generate masks for training volume if denoted

htem · Nov 30, 2023 · 0a7e95d · 0a7e95d
1 parent 7245e30
commit 0a7e95d
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/src/autoseg/train_job.py b/src/autoseg/train_job.py
@@ -1,5 +1,5 @@
 from .train import mtlsd_train, aclsd_train, stelarr_train
-from .utils import tiff_to_zarr
+from .utils import tiff_to_zarr, create_masks
 
 
 def train_model(
@@ -8,8 +8,9 @@ def train_model(
     warmup: int = 100000,
     raw_file: str = "path/to/.zarr/or/.n5/or/.tiff",
     rewrite_file: str = "./rewritten.zarr",
-    rewrite_ds: str = "training_raw",
+    rewrite_ds: str = "volumes/training_raw",
     out_file: str = "./raw_predictions.zarr",
+    generate_masks: bool = False,
     voxel_size: int = 33,
     save_every=2500,
 ) -> None:
@@ -21,7 +22,9 @@ def train_model(
                      out_ds=rewrite_ds)
         raw_file: str = rewrite_file
 
-
+    if generate_masks:
+        create_masks(raw_file, "volumes/training_gt_labels")
+
     model_type: str = model_type.lower()
     if model_type == "mtlsd":
         mtlsd_train(