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</o:shapelayout></xml><![endif]--></head><body lang=FR link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Each time I try to open a ICS or IDS file generated by<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Nikon confocal microscope software <o:p></o:p></span></p><p class=MsoNormal><span lang=DE>EZ-C1, Silver Version 3.91 build 880,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>I get this exception with 5.1 plugin (while 5.0 allows opening of this file):<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>(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%)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>java.lang.NullPointerException<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.constructSliceLabel(ImagePlusReader.java:598)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:385)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.Importer.readPixels(Importer.java:146)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.in.Importer.run(Importer.java:85)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at ij.IJ.runUserPlugIn(IJ.java:199)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at ij.IJ.runPlugIn(IJ.java:163)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at ij.Executer.runCommand(Executer.java:131)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at ij.Executer.run(Executer.java:64)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> at java.lang.Thread.run(Thread.java:662)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I am using FIJI and was not able to compile the plugin to get more detailed debug information.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>But from comparison of 5.0 source and 5.1 source, I suspect that this change:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>@@ -575,9 +575,19 @@ public class ImagePlusReader implements<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> r.setSeries(series);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> final int[] zct = r.getZCTCoords(ndx);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>- final int[] subC = r.getChannelDimLengths();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>- final String[] subCTypes = r.getChannelDimTypes();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ final int sizeC = r.getSizeC();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> final StringBuffer sb = new StringBuffer();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ int[] subC;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ String[] subCTypes;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ Modulo moduloC = r.getModuloC();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ if (moduloC.length() > 1) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ subC = new int[] {r.getSizeC() / moduloC.length(), moduloC.length()};<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ subCTypes = new String[] {moduloC.parentType, moduloC.type};<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ } else {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ subC = new int[] {r.getSizeC()};<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ subCTypes = new String[] {FormatTools.CHANNEL};<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>+ }<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> boolean first = true;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> if (cCount > 1) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> if (first) first = false;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> else sb.append("; ");<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> int[] subCPos = FormatTools.rasterToPosition(subC, zct[1]);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> for (int i=0; i<subC.length; i++) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>>>>> Line 598 of exception >>>> boolean ch = subCTypes[i].equals(FormatTools.CHANNEL);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> sb.append(ch ? "c" : subCTypes[i]);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> sb.append(":");<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>might be the cause of the exception, if SubCTypes array ends up having less elements than subC array.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> Please add me a CC as I am not subscribed to this mailing list.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> I can provide a example file if needed.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal>Pierre Muller<o:p></o:p></p><p class=MsoNormal>Institut Charles Sadron<o:p></o:p></p><p class=MsoNormal>23 rue du Loess<br>BP 84047<br>67034 STRASBOURG Cedex 2 <br>tél 33 (0)3 88 41 40 07<o:p></o:p></p><p class=MsoNormal>email : pierre.muller@ics-cnrs.unistra.fr<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>