Posted by
David Gault (Staff) on
URL: http://imagej.273.s1.nabble.com/Exception-opening-LIF-files-tp5020662p5020671.html
Hi Christian,
As Curtis has suggested this is a Bio-Formats bug caused by the parsing of the decimal separator. I have created a Trello card to track this issue:
https://trello.com/c/Fig1abYV/239-lif-parsedouble-exceptionIf you have a sample which the Bio-Formats can use for testing please upload it to
https://www.openmicroscopy.org/qa2/qa/upload/With Thanks,
David Gault
On 14 May 2018, at 19:29, Curtis Rueden <
[hidden email]<mailto:
[hidden email]>> wrote:
Hi Christian,
I suggest reporting this bug to the Bio-Formats team as described here:
http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.htmlAt first glance, it looks a bug relating to localization—use of commas
versus periods for the decimal separator.
Regards,
Curtis
--
Curtis Rueden
LOCI software architect -
https://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
https://imagej.net/User:RuedenDid you know ImageJ has a forum?
http://forum.imagej.net/On Mon, May 14, 2018 at 6:01 AM, Christian Goosmann <
[hidden email]> wrote:
Dear list
I have a problem with LIF-files from a Leica confocal. These file open
without a problem on different machines running the Leica software in
different versions.
In Fiji, using Bioformats, however they always throw an exception with
this message. Saving them with the Leica software of an older version
doesn't help.
'(Fiji Is Just) ImageJ 2.0.0-rc-65/1.52a; Java 1.8.0_66 [64-bit]; Windows
7 6.1; 44MB of 12163MB (<1%)
java.lang.NumberFormatException: For input string: "4,99907766094816"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecima
l.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.<init>(Double.java:608)
at loci.formats.in.LIFReader.translateLaserLines(LIFReader.java:1603)
at loci.formats.in.LIFReader.translateMetadata(LIFReader.java:1192)
at loci.formats.in.LIFReader.initMetadata(LIFReader.java:606)
at loci.formats.in.LIFReader.initFile(LIFReader.java:549)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.j
ava:499)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745) '
I have tried this with different older Fiji versions e.g. running Java 6
instead of 8 but no luck. Has any one come across this problem or got a
cure? Thank you.
Christian
I have a 3 MB lif that produces the exception here but the list will only
accept messages without attachments.
--
---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388
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