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

[Pierre Muller]

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.java: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

 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150421/5f25572d/attachment.html>