fix: 🐛 Fix datasplit._neuroglancer bug that happened with binarized…

… arrays.

Also set GT to automatically be a segmentation layer in neuroglancer, for run.visualize_pipeline

dacapo/experiments/datasplits/datasets/arrays/constant_array.py

@@ -438,7 +438,8 @@ def _neuroglancer_source(self):
             This method is used to return the source array for neuroglancer.
         """
         # return self._source_array._neuroglancer_source()
-        return np.ones_like(self.source_array.data, dtype=np.uint64) * self._constant
+        shape = self.source_array[self.source_array.roi].shape[-3:]
+        return np.ones(shape, dtype=np.uint64) * self._constant
 
     def _combined_neuroglancer_source(self) -> neuroglancer.LocalVolume:
         """

dacapo/experiments/run.py

@@ -1,4 +1,3 @@
-from dacapo.store.create_store import create_array_store
 from .datasplits import DataSplit
 from .tasks.task import Task
 from .architectures import Architecture
@@ -230,6 +229,8 @@ def visualize_pipeline(self):
                 "Only GunpowderTrainer is supported for visualization"
             )
         if not hasattr(self.trainer, "_pipeline"):
+            from ..store.create_store import create_array_store
+
             array_store = create_array_store()
             self.trainer.build_batch_provider(
                 self.datasplit.train,

dacapo/experiments/trainers/gunpowder_trainer.py

@@ -544,7 +544,12 @@ def load_batch(event):
                         dimensions=dims,
                     )
 
-                    s.layers[str(name)] = neuroglancer.ImageLayer(source=local_vol)
+                    if name == self._gt_key:
+                        s.layers[str(name)] = neuroglancer.SegmentationLayer(
+                            source=local_vol
+                        )
+                    else:
+                        s.layers[str(name)] = neuroglancer.ImageLayer(source=local_vol)
 
                 s.layout = neuroglancer.row_layout(
                     [

examples/distance_task/synthetic_example.py

@@ -173,7 +173,7 @@
     csv_path,
     input_resolution,
     output_resolution,
-    binarize_gt=True,
+    binarize_gt=True,  # Binarize the ground truth data to convert from instance segmentation to semantic segmentation
 ).compute()
 
 datasplit = datasplit_config.datasplit_type(datasplit_config)