Merge pull request #1515 from girder/speed-up-tifffile

Speed up some tifffile and multi source access cases

CHANGELOG.md

@@ -6,9 +6,11 @@
 - Improve uint16 image scaling ([#1511](../../pull/1511))
 - Read some untiled tiffs using the tiff source ([#1512](../../pull/1512))
 - Speed up multi source compositing in tiled cases ([#1513](../../pull/1513))
+- Speed up some tifffile and multi source access cases ([#1515](../../pull/1515))
 
 ### Changes
 - Limit internal metadata on multi-source files with huge numbers of sources ([#1514](../../pull/1514))
+- Make DICOMweb assetstore imports compatible with Girder generics ([#1504](../../pull/1504))
 
 ## 1.28.1
 

sources/multi/large_image_source_multi/__init__.py

@@ -828,7 +828,8 @@ def _openSource(self, source, params=None):
         with self._lastOpenSourceLock:
             if (hasattr(self, '_lastOpenSource') and
                     self._lastOpenSource['source'] == source and
-                    self._lastOpenSource['params'] == params):
+                    (self._lastOpenSource['params'] == params or (
+                        params == {} and self._lastOpenSource['params'] is None))):
                 return self._lastOpenSource['ts']
         if not len(large_image.tilesource.AvailableTileSources):
             large_image.tilesource.loadTileSources()
@@ -841,6 +842,7 @@ def _openSource(self, source, params=None):
         if params is None:
             params = source.get('params', {})
         ts = openFunc(source['path'], **params)
+        source['sourceName'] = ts.name
         with self._lastOpenSourceLock:
             self._lastOpenSource = {
                 'source': source,

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -474,19 +474,12 @@ def _nonemptyLevelsList(self, frame=0):
             sidx = frame // self._basis['P'][0]
         else:
             sidx = 0
-        series = self._tf.series[self._series[sidx]]
         nonempty = [None] * self.levels
         nonempty[self.levels - 1] = True
+        series = self._tf.series[self._series[sidx]]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
         for ll in range(1, len(series.levels)):
             scale = round(math.log(max(za[0].shape[xidx] / za[ll].shape[xidx],
                                        za[0].shape[yidx] / za[ll].shape[yidx])) / math.log(2))
@@ -497,6 +490,19 @@ def _nonemptyLevelsList(self, frame=0):
         self._nonempty_levels_list[frame] = nonempty
         return nonempty
 
+    def _getZarrArray(self, series, sidx):
+        with self._zarrlock:
+            if sidx not in self._zarrcache:
+                if len(self._zarrcache) > 10:
+                    self._zarrcache = {}
+                za = zarr.open(series.aszarr(), mode='r')
+                hasgbs = hasattr(za[0], 'get_basic_selection')
+                if not hasgbs and math.prod(series.shape) < 256 * 1024 ** 2:
+                    za = series.asarray()
+                self._zarrcache[sidx] = (za, hasgbs)
+            za, hasgbs = self._zarrcache[sidx]
+        return za, hasgbs
+
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         frame = self._getFrame(**kwargs)
@@ -507,14 +513,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         else:
             sidx = 0
         series = self._tf.series[self._series[sidx]]
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
         if hasgbs: