Merge pull request #1367 from girder/fix-series-detection

Only keep bioformats series that are the same dimensions.
girder · Nov 9, 2023 · f04147d · f04147d
2 parents 2d3794b + 084bb06
commit f04147d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,7 @@
 
 ### Bug Fixes
 - Default to "None" for the DICOM assetstore limit ([#1359](../../pull/1359))
-- Fix series detection for some bioformats files ([#1365](../../pull/1365))
+- Fix series detection for some bioformats files ([#1365](../../pull/1365), [#1367](../../pull/1367))
 
 ## 1.26.0
 

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -352,17 +352,20 @@ def _getSeriesStarts(self, rdr):  # noqa
             for idx in range(1, self._metadata['seriesCount']):
                 rdr.setSeries(idx)
                 if (rdr.getSizeX() == self._metadata['sizeX'] and
-                        rdr.getSizeY() == self._metadata['sizeY']):
+                        rdr.getSizeY() == self._metadata['sizeY'] and
+                        rdr.getImageCount() == self._metadata['imageCount']):
                     frameList.append([idx])
                     if nextSeriesNum == idx:
                         nextSeriesNum = idx + 1
                     lastX, lastY = self._metadata['sizeX'], self._metadata['sizeY']
-                if (rdr.getSizeX() * rdr.getSizeY() >
-                        self._metadata['sizeX'] * self._metadata['sizeY']):
+                if (rdr.getSizeX() * rdr.getSizeY() * rdr.getImageCount() >
+                        self._metadata['sizeX'] * self._metadata['sizeY'] *
+                        self._metadata['imageCount']):
                     frameList = [[idx]]
                     nextSeriesNum = idx + 1
                     self._metadata['sizeX'] = self.sizeX = lastX = rdr.getSizeX()
                     self._metadata['sizeY'] = self.sizeY = lastY = rdr.getSizeY()
+                    self._metadata['imageCount'] = rdr.getImageCount()
                 if (lastX and lastY and
                         nearPowerOfTwo(rdr.getSizeX(), lastX) and rdr.getSizeX() < lastX and
                         nearPowerOfTwo(rdr.getSizeY(), lastY) and rdr.getSizeY() < lastY):