<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Filipe,<div><br></div><div>Thanks you for reporting the issue. I have created a ticket and CC'd you on it.</div><div><a href="https://trac.openmicroscopy.org.uk/ome/ticket/12643">https://trac.openmicroscopy.org.uk/ome/ticket/12643</a></div><div><br></div><div>Regards,</div><div>Emil Rozbicki<div apple-content-edited="true"><br class="Apple-interchange-newline">
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<br><div><div>On 17 Nov 2014, at 21:02, Filipe De Vadder <<a href="mailto:filipe.devadder@gmail.com">filipe.devadder@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">Hello,</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">I have had some trouble opening VSI files on FIJI. If I try to open them using Bioformats on hyper stack (but the other options are not working either), here is the message that I get: <br class="">(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49k; Java 1.6.0_65 [64-bit]; Mac OS X 10.10; 22MB of 1067MB (2%) <br class=""> <br class="">java.lang.IllegalArgumentException: Invalid series: 0 <br class=""> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) <br class=""> at loci.formats.FormatReader.setSeries(FormatReader.java:927) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) <br class=""> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) <br class=""> at loci.formats.FormatReader.setId(FormatReader.java:1317) <br class=""> at loci.formats.ImageReader.setId(ImageReader.java:753) <br class=""> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406) <br class=""> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:252) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:335) <br class=""> at io.scif.AbstractParser.parse(AbstractParser.java:52) <br class=""> at io.scif.AbstractReader.setSource(AbstractReader.java:270) <br class=""> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90) <br class=""> at io.scif.img.ImgOpener.createReader(ImgOpener.java:542) <br class=""> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144) <br class=""> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266) <br class=""> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250) <br class=""> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78) <br class=""> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50) <br class=""> at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134) <br class=""> at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327) <br class=""> at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150) <br class=""> at ij.IJ.runPlugIn(IJ.java) <br class=""> at ij.Executer.runCommand(Executer.java:131) <br class=""> at ij.Executer.run(Executer.java:64) <br class=""> at java.lang.Thread.run(Thread.java:695) <br class=""><br class="">I have tried to open on Windows but still the same message.</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">If I try to open it using BIOP plugin, I also get a "macro error" message: <br class="">Relative Path, adding Path to Fiji <br class="">Full path to BIOPLib :/Applications/Fiji.app/plugins/BIOP/BIOPLib.ijm <br class="">Empty Library. Adding BIOPLib Library. <br class="">java.lang.reflect.InvocationTargetException <br class=""> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) <br class=""> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) <br class=""> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) <br class=""> at java.lang.reflect.Method.invoke(Method.java:597) <br class=""> at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:83) <br class=""> at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288) <br class=""> at ij.macro.Functions.doExt(Functions.java:4261) <br class=""> at ij.macro.Functions.getStringFunction(Functions.java:267) <br class=""> at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283) <br class=""> at ij.macro.Interpreter.getString(Interpreter.java:1262) <br class=""> at ij.macro.Interpreter.doStatement(Interpreter.java:277) <br class=""> at ij.macro.Interpreter.doBlock(Interpreter.java:598) <br class=""> at ij.macro.Interpreter.runUserFunction(Interpreter.java:307) <br class=""> at ij.macro.Interpreter.doUserFunctionAssignment(Interpreter.java:877) <br class=""> at ij.macro.Interpreter.doAssignment(Interpreter.java:717) <br class=""> at ij.macro.Interpreter.doStatement(Interpreter.java:241) <br class=""> at ij.macro.Interpreter.doStatements(Interpreter.java:214) <br class=""> at ij.macro.Interpreter.run(Interpreter.java:111) <br class=""> at ij.macro.Interpreter.run(Interpreter.java:81) <br class=""> at ij.macro.MacroRunner.run(MacroRunner.java:139) <br class=""> at java.lang.Thread.run(Thread.java:695) <br class="">Caused by: java.lang.IllegalArgumentException: Invalid series: 0 <br class=""> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) <br class=""> at loci.formats.FormatReader.setSeries(FormatReader.java:927) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) <br class=""> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) <br class=""> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) <br class=""> at loci.formats.FormatReader.setId(FormatReader.java:1317) <br class=""> at loci.formats.ImageReader.setId(ImageReader.java:753) <br class=""> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) <br class=""> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) <br class=""> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) <br class=""> at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:402) <br class=""> ... 21 more <br class=""><br class="">I have ticked the updates from both Bioformats, LOCI and BIOP and my software is up to date. I really don't know what is going on. My bioformats version is the latest release.</div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">If you want, you can access the file I am trying to open (and all other files in the same folder) at: <a href="http://dl.free.fr/gNluLSgVz" class="">http://dl.free.fr/gNluLSgVz</a></div><div id="message5010477" class="message-text adbayes-content" style="cursor: text; overflow-x: auto;">I hope this is enough to know what is going on.<br class="">Your help will be very much appreciated. <br class="">Thanks a lot, <br class="">Filipe</div><div class=""><br class=""></div><div class=" ad" style="clear: both; margin: 2em 0px 1em; visibility: visible !important; height: auto !important; position: static !important; top: auto !important; left: auto !important; width: 675px !important;"><div class="div752938" style="font-family: Verdana, Geneva, Helvetica, Arial, sans-serif; font-size: 13px; width: 336px; float: left; clear: none;"></div><div class="div601350" style="font-family: Verdana, Geneva, Helvetica, Arial, sans-serif; font-size: 13px; width: 336px; float: left; clear: none;"></div></div></div>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></div></body></html>