Merge pull request #994 from girder/nd2-dask-threads

Don't use dask threads when using nd2 to fetch tiles

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Improvements
 - Better control dtype on multi sources ([#993](../../pull/993))
+- Don't use dask threads when using nd2 to fetch tiles ([#994](../../pull/994))
 
 ### Bug Fixes
 - Use open.read rather than download to access files in Girder ([#989](../../pull/989))

sources/nd2/large_image_source_nd2/__init__.py

@@ -140,7 +140,7 @@ def __init__(self, path, **kwargs):
                 raise TileSourceFileNotFoundError(self._largeImagePath) from None
             raise TileSourceError('File cannot be opened via nd2reader.')
         # We use dask to allow lazy reading of large images
-        self._nd2array = self._nd2.to_dask(copy=False)
+        self._nd2array = self._nd2.to_dask(copy=False, wrapper=False)  # ##DWM::
         arrayOrder = list(self._nd2.sizes)
         # Reorder this so that it is XY (P), T, Z, C, Y, X, S (or at least end
         # in Y, X[, S]).
@@ -260,7 +260,8 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             tileframe = tileframe[fp // fc]
             fp = fp % fc
         with self._tileLock:
-            tile = tileframe[y0:y1:step, x0:x1:step].compute().copy()
+            # Have dask use single-threaded since we are using a lock anyway.
+            tile = tileframe[y0:y1:step, x0:x1:step].compute(scheduler='single-threaded').copy()
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)