Merge pull request #1333 from girder/tiffile-assoc-images

Improve tifffile associated image detection.

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Improvements
 - Style can specify a dtype of 'source' to maintain the original dtype even when compositing frames ([#1326](../../pull/1326))
 - Max Merge option in Frame Selector ([#1306](../../pull/1306), [#1330](../../pull/1330))
+- Improve tifffile associated image detection ([#1333](../../pull/1333))
 
 ### Changes
 - Prohibit bioformats and vips from reading mrxs directly ([#1328](../../pull/1328))

large_image/tilesource/utilities.py

@@ -292,7 +292,7 @@ def _vipsCast(image, mustBe8Bit=False, originalScale=None):
     if image.format not in formats or (image.format == pyvips.BandFormat.USHORT and not mustBe8Bit):
         return image
     target, offset, multiplier = formats[image.format]
-    if image.format == pyvips.BandFormat.DOUBLE:
+    if image.format == pyvips.BandFormat.DOUBLE or image.format == pyvips.BandFormat.FLOAT:
         maxVal = image.max()
         # These thresholds are higher than 256 and 65536 because bicubic and
         # other interpolations can cause value spikes

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -240,10 +240,11 @@ def _findAssociatedImages(self):
         Find associated images from unused pages and series.
         """
         pagesInSeries = [p for s in self._tf.series for ll in s.pages.levels for p in ll.pages]
+        hashes = [p.hash for p in pagesInSeries if p.keyframe is not None]
         self._associatedImages = {}
         for p in self._tf.pages:
             if (p not in pagesInSeries and p.keyframe is not None and
-                    not len(set(p.axes) - set('YXS'))):
+                    p.hash not in hashes and not len(set(p.axes) - set('YXS'))):
                 id = 'image_%s' % p.index
                 entry = {'page': p.index}
                 entry['width'] = p.shape[p.axes.index('X')]