zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
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Export as TSF: error in Fiji #1

Closed zitmen closed 9 years ago

zitmen commented 9 years ago
What steps will reproduce the problem?
1. INstall ThunderSTORM in the latest Fiji
2. Run an analysis
3. Export results as TSF

What is the expected output? What do you see instead?
I expect a .tsf file to be created and saved. Instead I get this error:

There was a problem with the class org.apache.commons.io.IOUtils which can be found
here:
/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/jars/batik.jar
/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/plugins/Thunder_STORM.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: org.apache.commons.io.IOUtils.closeQuietly(Ljava/io/Closeable;)V
    at cz.cuni.lf1.lge.ThunderSTORM.ImportExport.TSFImportExport.importFromFile(TSFImportExport.java:179)
    at cz.cuni.lf1.lge.ThunderSTORM.ImportExportPlugIn.importFromFile(ImportExportPlugIn.java:268)
    at cz.cuni.lf1.lge.ThunderSTORM.ImportExportPlugIn.runImport(ImportExportPlugIn.java:235)
    at cz.cuni.lf1.lge.ThunderSTORM.ImportExportPlugIn.run(ImportExportPlugIn.java:102)
    at ij.IJ.runUserPlugIn(IJ.java:199)
    at ij.IJ.runPlugIn(IJ.java:163)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:695)
Could not find method org.apache.commons.io.IOUtils.closeQuietly(Ljava/io/Closeable;)V
(See Log for details)

Notably a .tsf file is indeed created but I'm not sure it is not corrupted. If I try
to re-import it, I get the same error and it is not imported in ThunderSTORM.

What version of the product are you using? On what operating system?
I'm using ThunderSTORM 1.1 in Fiji (ImageJ 1.48q), Java 1.6.0_65 (64b) on OSX 10.9.1

Please provide any additional information below.
Thanks for this great tool!
Christophe Leterrier, Marseille

Original issue reported on code.google.com by lechristophe on 2014-02-11 15:48:36

zitmen commented 9 years ago
Thanks for feedback.
It should be ok in development version dev-2014-02-19-b1. Fixed in commit 4061dbb27aa1.

Original issue reported on code.google.com by vmodrosedem on 2014-02-19 15:11:13