Merge pull request #1365 from girder/fix-series-detection

Fix series detection for some bioformats files
girder · Nov 9, 2023 · 6685ba9 · 6685ba9
2 parents d63c892 + 04ca2e8
commit 6685ba9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@
 
 ### Bug Fixes
 - Default to "None" for the DICOM assetstore limit ([#1359](../../pull/1359))
+- Fix series detection for some bioformats files ([#1365](../../pull/1365))
 
 ## 1.26.0
 

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -99,7 +99,7 @@ def _reduceLogging():
             'org/slf4j/LoggerFactory', 'getLogger',
             '(Ljava/lang/String;)Lorg/slf4j/Logger;', rootLoggerName)
         logLevel = javabridge.get_static_field(
-            'ch/qos/logback/classic/Level', 'WARN', 'Lch/qos/logback/classic/Level;')
+            'ch/qos/logback/classic/Level', 'ERROR', 'Lch/qos/logback/classic/Level;')
         javabridge.call(rootLogger, 'setLevel', '(Lch/qos/logback/classic/Level;)V', logLevel)
     except Exception:
         pass
@@ -352,7 +352,7 @@ 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']):
                     frameList.append([idx])
                     if nextSeriesNum == idx:
                         nextSeriesNum = idx + 1