Exception opening LIF-files

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Exception opening LIF-files

Christian Goosmann-2
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(FloatingDecimal.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.java: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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Exception opening LIF-files

ctrueden
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.html

At 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/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Exception opening LIF-files

David Gault (Staff)
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-exception
If 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.html

At 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/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did 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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


The University of Dundee is a registered Scottish Charity, No: SC015096

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Exception opening LIF-files Case Closed

Christian Goosmann-2
In reply to this post by Christian Goosmann-2
Thanks to Curtis, who gave me a hint. The problem was in the regional
settings of the OS (Win 7). Although it was set to 'English (US)' there
was an additional setting change that set the decimal separator back to
comma. This led to LIF files that bio formats could not open.

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

On 14.05.2018 13:01, Christian Goosmann 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(FloatingDecimal.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.java: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.
>

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Re: Exception opening LIF-files

Christian Goosmann-2
In reply to this post by David Gault (Staff)
Hi David

thanks for taking this up. I uploaded a 3 MB lif under this number:


    QA Bug | 21092 (new)

afterwards I tried to comment, but was not allowed. Maybe because I am
not registered.
As stated earlier today, we have found a workaround to prevent files
with this problem in future. But it would still be an improvement if bio
formats could be made tolerant to this.

Best regards

Christian


---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

On 15.05.2018 13:07, David Gault (Staff) wrote:

> 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-exception
> If 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.html
>
> At 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/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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