Merge pull request #253 from AllenInstitute/develop

Merge develop

Author: RussTorres

asap/pointmatch/create_tilepairs.py

@@ -74,7 +74,8 @@ def run(self):
             excludeCornerNeighbors=self.args['excludeCornerNeighbors'],
             excludeSameLayerNeighbors=self.args['excludeSameLayerNeighbors'],
             excludeCompletelyObscuredTiles=self.args[
-                'excludeCompletelyObscuredTiles'])
+                'excludeCompletelyObscuredTiles'],
+            useRowColPositions=self.args['useRowColPositions'])
 
         self.output({'tile_pair_file': tilepairJsonFile})
 

asap/pointmatch/schemas.py

@@ -65,6 +65,12 @@ class TilePairClientParameters(RenderParameters):
         missing=True,
         description="Exclude tiles that are completely "
         "obscured by reacquired tiles")
+    useRowColPositions = Bool(
+        required=False,
+        default=False,
+        missing=False,
+        description="For montage pairs (zNeighborDistance == 0) "
+        "use layout imageRow and imageCol values instead of tile bounds to identify neighbor tiles")
     output_dir = OutputDir(
         required=True,
         description="Output directory path to save the tilepair json file")

requirements.txt

@@ -1,6 +1,6 @@
 render-python>=2.2.2
-marshmallow<3.0
-argschema<2.0
+marshmallow
+argschema
 numpy
 pillow
 tifffile