[ome-users] Exception trying to open Nikon confocal image with Bio-formats 5.1 (was working with version 5.0)

[Pierre Muller]

Hi Melissa,

  thank you very much for this answer.

I changed my update site to get updates directly from ome site.
I hope to be able to confirm that your patch fixes the issue
I see as soon as it is merged.

Best regards,

Pierre Muller

> -----Message d'origine-----
> De : Melissa Linkert [mailto:melissa.linkert at gmail.com] De la part de
> Melissa Linkert
> Envoyé : mercredi 22 avril 2015 22:18
> À : Pierre Muller
> Cc : ome-users at lists.openmicroscopy.org.uk
> Objet : Re: [ome-users] Exception trying to open Nikon confocal image
> with Bio-formats 5.1 (was working with version 5.0)
> 
> Hi Pierre,
> 
> > Each time I try to open a ICS or IDS file generated by
> >
> > Nikon confocal microscope software
> >
> > EZ-C1,   Silver Version 3.91 build 880,
> >
> > I get this exception with 5.1 plugin (while 5.0 allows opening of
> this
> > file):
> >
> >
> >
> > (Fiji Is Just) ImageJ 2.0.0-rc-29/1.49q; Java 1.6.0_24 [64-bit];
> Windows 7
> > 6.1; 23MB of 6127MB (<1%)
> >
> > java.lang.NullPointerException
> >
> >                 at
> >
> loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.jav
> a:598
> > )
> >
> >                 at
> > loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)
> 
> Thank you very much for reporting this problem, and for investigating
> the cause.  We are reviewing a fix:
> 
> https://github.com/openmicroscopy/bioformats/pull/1756
> 
> This will unfortunately not be included in the forthcoming 5.1.1
> release, but I would expect it to be included in the 5.1.2 release.
> 
> If you wish to try the fix prior to 5.1.2, you can do so by enabling
> the
> Bio-Formats update site in Fiji.  Once the status of the above changes
> from "Open" to "Merged", updating Fiji should install a pre-release
> version of Bio-Formats that contains the fix.  For instructions, see:
> 
> http://imagej.net/Bio-formats#Daily_builds
> 
> Regards,
> -Melissa
> 
> On Tue, Apr 21, 2015 at 04:29:51PM +0200, Pierre Muller wrote:
> > Each time I try to open a ICS or IDS file generated by
> >
> > Nikon confocal microscope software
> >
> > EZ-C1,   Silver Version 3.91 build 880,
> >
> > I get this exception with 5.1 plugin (while 5.0 allows opening of
> this
> > file):
> >
> >
> >
> > (Fiji Is Just) ImageJ 2.0.0-rc-29/1.49q; Java 1.6.0_24 [64-bit];
> Windows 7
> > 6.1; 23MB of 6127MB (<1%)
> >
> > java.lang.NullPointerException
> >
> >                 at
> >
> loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.jav
> a:598
> > )
> >
> >                 at
> > loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)
> >
> >                 at
> > loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
> >
> >                 at
> > loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
> >
> >                 at
> > loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
> >
> >                 at
> >
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
> >
> >                 at
> loci.plugins.in.Importer.readPixels(Importer.java:146)
> >
> >                 at loci.plugins.in.Importer.run(Importer.java:85)
> >
> >                 at
> loci.plugins.LociImporter.run(LociImporter.java:78)
> >
> >                 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:662)
> >
> >
> >
> >
> >
> > I am using FIJI and was not able to compile the plugin to get more
> detailed
> > debug information.
> >
> > But from comparison of 5.0 source and 5.1 source, I suspect that this
> > change:
> >
> > @@ -575,9 +575,19 @@ public class ImagePlusReader implements
> >
> >      r.setSeries(series);
> >
> >
> >
> >      final int[] zct = r.getZCTCoords(ndx);
> >
> > -    final int[] subC = r.getChannelDimLengths();
> >
> > -    final String[] subCTypes = r.getChannelDimTypes();
> >
> > +    final int sizeC = r.getSizeC();
> >
> >      final StringBuffer sb = new StringBuffer();
> >
> > +
> >
> > +    int[] subC;
> >
> > +    String[] subCTypes;
> >
> > +    Modulo moduloC = r.getModuloC();
> >
> > +    if (moduloC.length() > 1) {
> >
> > +      subC = new int[] {r.getSizeC() / moduloC.length(),
> moduloC.length()};
> >
> > +      subCTypes = new String[] {moduloC.parentType, moduloC.type};
> >
> > +    } else {
> >
> > +      subC = new int[] {r.getSizeC()};
> >
> > +      subCTypes = new String[] {FormatTools.CHANNEL};
> >
> > +    }
> >
> >
> >
> >      boolean first = true;
> >
> >      if (cCount > 1) {
> >
> >       if (first) first = false;
> >
> >       else sb.append("; ");
> >
> >       int[] subCPos = FormatTools.rasterToPosition(subC, zct[1]);
> >
> >       for (int i=0; i<subC.length; i++) {
> >
> > >>>> Line 598 of exception >>>>        boolean ch =
> > subCTypes[i].equals(FormatTools.CHANNEL);
> >
> >         sb.append(ch ? "c" : subCTypes[i]);
> >
> >         sb.append(":");
> >
> >
> >
> > might be the cause of the exception, if SubCTypes array ends up
> having less
> > elements than subC array.
> >
> >
> >
> >   Please add me a CC as I am not subscribed to this mailing list.
> >
> >
> >
> >   I can provide a example file if needed.
> >
> >
> >
> > Pierre Muller
> >
> > Institut Charles Sadron
> >
> > 23 rue du Loess
> > BP 84047
> > 67034 STRASBOURG Cedex 2
> > tél 33 (0)3 88 41 40 07
> >
> > email : pierre.muller at ics-cnrs.unistra.fr
> >
> >
> >
> >
> >
> 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
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