Merge pull request #892 from girder/faster-styling

Speed up styling by doing less

CHANGELOG.md

@@ -12,6 +12,7 @@
 - Store the id of job results for easier post-job work ([887](../../pull/887))
 - Harden style compositing of partial tiles ([889](../../pull/889))
 - Cache read_tiff calls to speed up restyling ([891](../../pull/891))
+- Speed up styling by doing less ([892](../../pull/892))
 
 ### Changes
 - Be more consistent in source class name attribute assignment ([884](../../pull/884))

large_image/tilesource/base.py

@@ -1128,7 +1128,7 @@ def _applyStyle(self, image, style, x, y, z, frame=None):  # noqa
         output = numpy.zeros((image.shape[0], image.shape[1], 4), float)
         mainImage = image
         mainFrame = frame
-        for entry in style:
+        for eidx, entry in enumerate(style):
             dtype = dtype if dtype is not None else entry.get('dtype')
             axis = axis if axis is not None else entry.get('axis')
             bandidx = 0 if image.shape[2] <= 2 else 1
@@ -1213,13 +1213,17 @@ def _applyStyle(self, image, style, x, y, z, frame=None):  # noqa
                             clrs = palette[numpy.floor(band * len(palette)).astype(int).clip(
                                 0, len(palette) - 1), channel]
                 if composite == 'multiply':
-                    output[:keep.shape[0], :keep.shape[1], channel] = numpy.multiply(
-                        output[:keep.shape[0], :keep.shape[1], channel],
-                        numpy.where(keep, clrs / 255, 1))
+                    if eidx:
+                        output[:keep.shape[0], :keep.shape[1], channel] = numpy.multiply(
+                            output[:keep.shape[0], :keep.shape[1], channel],
+                            numpy.where(keep, clrs / 255, 1))
                 else:
-                    output[:keep.shape[0], :keep.shape[1], channel] = numpy.maximum(
-                        output[:keep.shape[0], :keep.shape[1], channel],
-                        numpy.where(keep, clrs, 0))
+                    if not eidx:
+                        output[:keep.shape[0], :keep.shape[1], channel] = numpy.where(keep, clrs, 0)
+                    else:
+                        output[:keep.shape[0], :keep.shape[1], channel] = numpy.maximum(
+                            output[:keep.shape[0], :keep.shape[1], channel],
+                            numpy.where(keep, clrs, 0))
         if dtype == 'uint16':
             output = (output * 65535 / 255).astype(numpy.uint16)
         elif dtype == 'float':
@@ -1287,7 +1291,8 @@ def _outputTile(self, tile, tileEncoding, x, y, z, pilImageAllowed=False,
         mode = None
         if (numpyAllowed == 'always' or tileEncoding == TILE_FORMAT_NUMPY or
                 (applyStyle and getattr(self, 'style', None)) or isEdge):
-            tile, mode = self._outputTileNumpyStyle(tile, applyStyle, x, y, z, kwargs.get('frame'))
+            tile, mode = self._outputTileNumpyStyle(
+                tile, applyStyle, x, y, z, self._getFrame(**kwargs))
         if isEdge:
             contentWidth = min(self.tileWidth,
                                sizeX - (maxX - self.tileWidth))
@@ -1491,6 +1496,21 @@ def getBandInformation(self, statistics=False, **kwargs):
             self._bandInfo = bandInfo
         return self._bandInfo
 
+    def _getFrame(self, frame=None, **kwargs):
+        """
+        Get the current frame number.  If a style is used that completely
+        specified the frame, use that value instead.
+
+        :param frame: an integer or string with the frame number.
+        :returns: an integer frame number.
+        """
+        frame = int(frame or 0)
+        if (hasattr(self, 'style') and 'bands' in self.style and
+                len(self.style['bands']) and
+                all(entry.get('frame') is not None for entry in self.style['bands'])):
+            frame = int(self.style['bands'][0]['frame'])
+        return frame
+
     def _xyzInRange(self, x, y, z, frame=None, numFrames=None):
         """
         Check if a tile at x, y, z is in range based on self.levels,

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -478,7 +478,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         ft = fc = fz = 0
         fseries = self._metadata['frameSeries'][0]
         if kwargs.get('frame') is not None:
-            frame = int(kwargs.get('frame'))
+            frame = self._getFrame(**kwargs)
             fc = frame % self._metadata['sizeC']
             fz = (frame // self._metadata['sizeC']) % self._metadata['sizeZ']
             ft = (frame // self._metadata['sizeC'] //

sources/multi/large_image_source_multi/__init__.py

@@ -906,7 +906,7 @@ def _addSourceToTile(self, tile, sourceEntry, corners, scale):
 
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, len(self._frames) if hasattr(self, '_frames') else None)
         scale = 2 ** (self.levels - 1 - z)
         corners = [[

sources/nd2/large_image_source_nd2/__init__.py

@@ -254,7 +254,7 @@ def getInternalMetadata(self, **kwargs):
 
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, self._framecount)
         x0, y0, x1, y1, step = self._xyzToCorners(x, y, z)
         tileframe = self._nd2array

sources/ometiff/large_image_source_ometiff/__init__.py

@@ -324,7 +324,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 x, y, z, pilImageAllowed=pilImageAllowed,
                 numpyAllowed=numpyAllowed, sparseFallback=sparseFallback,
                 **kwargs)
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         if frame < 0 or frame >= len(self._omebase['TiffData']):
             raise TileSourceError('Frame does not exist')
         subdir = None

sources/test/large_image_source_test/__init__.py

@@ -170,7 +170,7 @@ def getInternalMetadata(self, **kwargs):
 
     @methodcache()
     def getTile(self, x, y, z, *args, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, len(self._frames) if hasattr(self, '_frames') else None)
 
         if not (self.minLevel <= z <= self.maxLevel):

sources/tiff/large_image_source_tiff/__init__.py

@@ -544,7 +544,7 @@ def getInternalMetadata(self, **kwargs):
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 sparseFallback=False, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, len(self._frames) if hasattr(self, '_frames') else None)
         if frame > 0:
             if self._frames[frame]['dirs'][z] is not None:
@@ -641,7 +641,7 @@ def getTileFromEmptyDirectory(self, x, y, z, **kwargs):
         basez = z
         scale = 1
         dirlist = self._tiffDirectories
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         if frame > 0:
             dirlist = self._frames[frame]['dirs']
         while dirlist[z] is None:
@@ -662,7 +662,7 @@ def getTileFromEmptyDirectory(self, x, y, z, **kwargs):
                 subtile = self.getTile(
                     x * scale + newX, y * scale + newY, z,
                     pilImageAllowed=True, numpyAllowed=False,
-                    sparseFallback=True, edge=False, frame=kwargs.get('frame'))
+                    sparseFallback=True, edge=False, frame=frame)
                 if not isinstance(subtile, PIL.Image.Image):
                     subtile = PIL.Image.open(io.BytesIO(subtile))
                 tile.paste(subtile, (newX * self.tileWidth,

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -365,7 +365,7 @@ def _getAssociatedImage(self, imageKey):
 
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, self._framecount)
         x0, y0, x1, y1, step = self._xyzToCorners(x, y, z)
         if len(self._series) > 1:

sources/vips/large_image_source_vips/__init__.py

@@ -184,7 +184,7 @@ def getNativeMagnification(self):
 
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
-        frame = int(kwargs.get('frame') or 0)
+        frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, len(self._frames))
         img = self._getFrameImage(frame)
         x0, y0, x1, y1, step = self._xyzToCorners(x, y, z)