fix neuroglancer from CartesianSpace to CoordinateSpace

seung-lab · May 3, 2022 · 2ac2f6c · 2ac2f6c
1 parent 231588e
commit 2ac2f6c
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/chunkflow/chunk/base.py b/chunkflow/chunk/base.py
@@ -418,6 +418,10 @@ def properties(self) -> dict:
             props['voxel_size'] = self.voxel_size
         return props 
 
+    @property
+    def size(self):
+        return self.array.size
+
     @property
     def slices(self) -> tuple:
         """

diff --git a/chunkflow/flow/neuroglancer.py b/chunkflow/flow/neuroglancer.py
@@ -55,7 +55,7 @@ def _append_synapse_annotation_layer(self, viewer_state: ng.viewer_state.ViewerS
         viewer_state.layers.append(
             name=name,
             layer=ng.LocalAnnotationLayer(
-                dimensions=ng.CartesianSpace(names=['z', 'y', 'x'], units="nm", scales=(1,1,1)),
+                dimensions=ng.CoordinateSpace(names=['z', 'y', 'x'], units="nm", scales=(1,1,1)),
                 annotation_properties=[
                     ng.AnnotationPropertySpec(
                         id='color',
@@ -94,7 +94,7 @@ def _append_point_annotation_layer(self, viewer_state: ng.viewer_state.ViewerSta
         viewer_state.layers.append(
             name=name,
             layer=ng.LocalAnnotationLayer(
-                dimensions=ng.CartesianSpace(names=['z', 'y', 'x'], units="nm", scales=(1, 1, 1)),
+                dimensions=ng.CoordinateSpace(names=['z', 'y', 'x'], units="nm", scales=(1, 1, 1)),
                 annotation_properties=[
                     ng.AnnotationPropertySpec(
                         id='color',
@@ -119,7 +119,7 @@ def _append_point_annotation_layer(self, viewer_state: ng.viewer_state.ViewerSta
 
     def _append_image_layer(self, viewer_state: ng.viewer_state.ViewerState, chunk_name: str, chunk: Chunk):
         voxel_size = self._get_voxel_size(chunk)
-        dimensions = ng.CartesianSpace(
+        dimensions = ng.CoordinateSpace(
             scales=voxel_size,
             units=['nm', 'nm', 'nm'],
             names=['z', 'y', 'x']
@@ -149,7 +149,7 @@ def _append_segmentation_layer(self, viewer_state: ng.viewer_state.ViewerState,
             assert chunk.min() >= 0
             chunk = chunk.astype(np.uint64)
         voxel_size = self._get_voxel_size(chunk)
-        dimensions = ng.CartesianSpace(
+        dimensions = ng.CoordinateSpace(
             scales=voxel_size,
             units=['nm', 'nm', 'nm'],
             names=['z', 'y', 'x']
@@ -191,7 +191,7 @@ def _append_probability_map_layer(self, viewer_state: ng.viewer_state.ViewerStat
             toNormalized(getDataValue(2))));
 }
 """
-        dimensions = ng.CartesianSpace(
+        dimensions = ng.CoordinateSpace(
             scales=(1, ) + voxel_size,
             units=['', 'nm', 'nm', 'nm'],
             names=['c^', 'z', 'y', 'x']

diff --git a/chunkflow/flow/read_precomputed.py b/chunkflow/flow/read_precomputed.py
@@ -55,6 +55,7 @@ def __init__(self,
             mip=self.mip,
             cache=False,
             green_threads=True)
+            #parallel=True,
 
     def __call__(self, output_bbox: BoundingBox):
         # if we do not clone this bounding box, 

diff --git a/chunkflow/flow/write_precomputed.py b/chunkflow/flow/write_precomputed.py
@@ -46,6 +46,7 @@ def __init__(self,
             cache=False,
             green_threads=True,
             progress=True)
+            #parallel=True,
 
         if upload_log:
             log_path = os.path.join(volume_path, 'log')