From 04ca2e8a842b288c5a4b329b9094cf8163e00a4f Mon Sep 17 00:00:00 2001 From: David Manthey Date: Thu, 9 Nov 2023 09:41:14 -0500 Subject: [PATCH] Fix series detection for some bioformats files --- CHANGELOG.md | 1 + sources/bioformats/large_image_source_bioformats/__init__.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f74318af..585fd62cd 100644 --- 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 index cf7cc582c..9e790fe51 100644 --- 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