Merge pull request #1407 from girder/speed-up-tile-output

Speed up tile output.

CHANGELOG.md

@@ -10,6 +10,9 @@
 - Add a utility function for getting loggers ([#1403](../../pull/1403))
 - Get bioformats jar version if bioformats was started ([#1405](../../pull/1405))
 - Improve thread safety of concurrent first reads using bioformats ([#1406](../../pull/1406))
+- Read more metadata from DICOMweb ([#1378](../../pull/1378))
+- Remove logic for determining DICOMweb transfer syntax ([#1393](../../pull/1393))
+- Speed up tile output ([#1407](../../pull/1407))
 
 ### Changes
 - Use an enum for priority constants ([#1400](../../pull/1400))

large_image/tilesource/tiledict.py

@@ -173,10 +173,11 @@ def __getitem__(self, key, *args, **kwargs):
             else:
                 tileData = self._retileTile()
 
-            pilData = _imageToPIL(tileData)
-
+            pilData = None
             # resample if needed
             if self.resample not in (False, None) and self.requestedScale:
+                pilData = _imageToPIL(tileData)
+
                 self['width'] = max(1, int(
                     pilData.size[0] / self.requestedScale))
                 self['height'] = max(1, int(
@@ -206,7 +207,7 @@ def __getitem__(self, key, *args, **kwargs):
                     tileData, _ = _imageToNumpy(tileData)
                     tileFormat = TILE_FORMAT_NUMPY
                 elif TILE_FORMAT_PIL in self.format:
-                    tileData = pilData
+                    tileData = pilData if pilData is not None else _imageToPIL(tileData)
                     tileFormat = TILE_FORMAT_PIL
                 elif TILE_FORMAT_IMAGE in self.format:
                     tileData, mimeType = _encodeImage(
@@ -217,7 +218,7 @@ def __getitem__(self, key, *args, **kwargs):
                         'Cannot yield tiles in desired format %r' % (
                             self.format, ))
             else:
-                tileData = pilData
+                tileData = pilData if pilData is not None else _imageToPIL(tileData)
                 tileFormat = TILE_FORMAT_PIL
 
             self['tile'] = tileData

large_image/tilesource/utilities.py

@@ -32,6 +32,7 @@
     'GREEN': '#00ff00',
     'BLUE': '#0000ff',
 }
+modesBySize = ['L', 'LA', 'RGB', 'RGBA']
 
 
 class ImageBytes(bytes):
@@ -187,7 +188,7 @@ def _imageToPIL(image, setMode=None):
             # Fallback for hyperspectral data to just use the first three bands
             if image.shape[2] > 4:
                 image = image[:, :, :3]
-            mode = ['L', 'LA', 'RGB', 'RGBA'][image.shape[2] - 1]
+            mode = modesBySize[image.shape[2] - 1]
         if len(image.shape) == 3 and image.shape[2] == 1:
             image = np.resize(image, image.shape[:2])
         if image.dtype == np.uint32:
@@ -220,6 +221,17 @@ def _imageToNumpy(image):
     :param image: input image.
     :returns: a numpy array and a target PIL image mode.
     """
+    if isinstance(image, np.ndarray) and len(image.shape) == 3 and 1 <= image.shape[2] <= 4:
+        return image, modesBySize[image.shape[2] - 1]
+    if (simplejpeg and isinstance(image, bytes) and image[:3] == b'\xff\xd8\xff' and
+            b'\xff\xc0' in image[:1024]):
+        idx = image.index(b'\xff\xc0')
+        if image[idx + 9:idx + 10] in {b'\x01', b'\x03'}:
+            try:
+                image = simplejpeg.decode_jpeg(
+                    image, colorspace='GRAY' if image[idx + 9:idx + 10] == b'\x01' else 'RGB')
+            except Exception:
+                pass
     if not isinstance(image, np.ndarray):
         if not isinstance(image, PIL.Image.Image):
             image = PIL.Image.open(io.BytesIO(image))
@@ -232,7 +244,8 @@ def _imageToNumpy(image):
             image = np.asarray(image)
     else:
         if len(image.shape) == 3:
-            mode = ['L', 'LA', 'RGB', 'RGBA'][(image.shape[2] - 1) if image.shape[2] <= 4 else 3]
+            mode = modesBySize[(image.shape[2] - 1) if image.shape[2] <= 4 else 3]
+            return image, mode
         else:
             mode = 'L'
     if len(image.shape) == 2:

sources/dicom/large_image_source_dicom/dicom_metadata.py

@@ -78,7 +78,7 @@ def extract_specimen_metadata(dataset):
         for prep in getattr(specimen, 'SpecimenPreparationSequence', []):
             steps = {}
             for step in getattr(prep, 'SpecimenPreparationStepContentItemSequence', []):
-                # Only extract entires that have both a name and a value
+                # Only extract entries that have both a name and a value
                 if (len(getattr(step, 'ConceptCodeSequence', [])) > 0 and
                         len(getattr(step, 'ConceptNameCodeSequence', [])) > 0):
                     name = step.ConceptNameCodeSequence[0].CodeMeaning

sources/multi/large_image_source_multi/__init__.py

@@ -970,6 +970,7 @@ def _addSourceToTile(self, tile, sourceEntry, corners, scale):
         x = y = 0
         # If there is no transform or the diagonals are positive and there is
         #   no sheer, use getRegion with an appropriate size (be wary of edges)
+        # TODO: when affine is generalized, only use this if scale is 1
         if (transform is None or
                 transform[0][0] > 0 and transform[0][1] == 0 and
                 transform[1][0] == 0 and transform[1][1] > 0):