These are chat archives for fiji/fiji

20th
Nov 2017
tpietzsch
@tpietzsch
Nov 20 2017 13:08
I'm getting the following exception (when importing .czi in BigStitcher):
Including file /mnt/data1/Tess_A/2017-06-28_Tess_A_Cleared_test.czi in dataset.
ZeissCZIReader initializing /mnt/data1/Tess_A/2017-06-28_Tess_A_Cleared_test.czi
There was a problem with the class loci.common.DataTools which can be found here:
/home/pietzsch/Desktop/Fiji.app/jars/bio-formats/formats-common-5.1.10.jar
/home/pietzsch/Desktop/Fiji.app/jars/bio-formats/ome-common-5.3.2.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.common.DataTools.parseInteger(Ljava/lang/String;)Ljava/lang/Integer;
    at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2927)
    at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1870)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1110)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at loci.formats.ImageReader.setId(ImageReader.java:839)
    at spim.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFile(FileListDatasetDefinitionUtil.java:946)
    at spim.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFiles(FileListDatasetDefinitionUtil.java:891)
    at spim.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:657)
    at spim.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:111)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:99)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:86)
    at spim.fiji.plugin.Stitching_Explorer.run(Stitching_Explorer.java:41)
    at ij.IJ.runUserPlugIn(IJ.java:217)
    at ij.IJ.runPlugIn(IJ.java:181)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at java.lang.Thread.run(Thread.java:745)

java.lang.NoSuchMethodException: Could not find method loci.common.DataTools.parseInteger(Ljava/lang/String;)Ljava/lang/Integer;
There was a problem with the class loci.common.DataTools which can be found here:
/home/pietzsch/Desktop/Fiji.app/jars/bio-formats/formats-common-5.1.10.jar
/home/pietzsch/Desktop/Fiji.app/jars/bio-formats/ome-common-5.3.2.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.common.DataTools.parseInteger(Ljava/lang/String;)Ljava/lang/Integer;
    at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2927)
    at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1870)
    at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:1110)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at loci.formats.ImageReader.setId(ImageReader.java:839)
    at spim.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFile(FileListDatasetDefinitionUtil.java:946)
    at spim.fiji.datasetmanager.FileListDatasetDefinitionUtil.detectViewsInFiles(FileListDatasetDefinitionUtil.java:891)
    at spim.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:657)
    at spim.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:111)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:99)
    at spim.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:86)
    at spim.fiji.plugin.Stitching_Explorer.run(Stitching_Explorer.java:41)
    at ij.IJ.runUserPlugIn(IJ.java:217)
    at ij.IJ.runPlugIn(IJ.java:181)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at java.lang.Thread.run(Thread.java:745)
Does anybody have an idea? Is this duplicate loci.common.DataTools class "normal"?
Curtis Rueden
@ctrueden
Nov 20 2017 15:15
I replied in scifio/scifio.
tpietzsch
@tpietzsch
Nov 20 2017 17:29
Ok, I'm also going there...