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Bug 1047 - cannot read lif files
cannot read lif files
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
All Mac OS
: P5 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-04-01 23:03 CDT by maimisa8
Modified: 2015-04-06 10:44 CDT
3 users (show)

See Also:
Description maimisa8 2015-04-01 23:03:58 CDT 
when try to open lif files i got the following error and have no idea what to fix. Any help is appreciated. Thank you

(Fiji Is Just) ImageJ 2.0.0-rc-28/1.49q; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 22MB of 5129MB (<1%)
 
java.lang.NumberFormatException: empty String
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:992)
	at java.lang.Double.valueOf(Double.java:475)
	at java.lang.Double.<init>(Double.java:567)
	at loci.formats.in.LIFReader.translateFilterSettings(LIFReader.java:1507)
	at loci.formats.in.LIFReader.translateMetadata(LIFReader.java:1018)
	at loci.formats.in.LIFReader.initMetadata(LIFReader.java:517)
	at loci.formats.in.LIFReader.initFile(LIFReader.java:459)
	at loci.formats.FormatReader.setId(FormatReader.java:1395)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
	at loci.plugins.in.Importer.showDialogs(Importer.java:137)
	at loci.plugins.in.Importer.run(Importer.java:75)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:447)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:66)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
	at ij.io.Opener.openImage(Opener.java:360)
	at ij.io.Opener.openImage(Opener.java:239)
	at ij.io.Opener.open(Opener.java:106)
	at ij.io.Opener.openAndAddToRecent(Opener.java:288)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:695)
Comment 1 Mark Hiner 2015-04-02 13:19:17 CDT 
If you haven't already, try enabling the Bio-Formats update site[1]. That will upgrade to Bio-Formats 5.1 which may already fix this bug.

If that doesn't work, Bio-Formats has its own bug tracking[2] - they have additional instructions for troubleshooting and reporting issues.

[1] http://imagej.net/How_to_follow_a_3rd_party_update_site
[2] https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html
Comment 2 Curtis Rueden 2015-04-06 10:44:48 CDT 
As Mark says, this is an issue with Bio-Formats, and should be reported to the Bio-Formats team.

http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html