[ome-users] Problem opening VSI file
Emil Rozbicki
emil at glencoesoftware.com
Tue Nov 18 11:49:17 GMT 2014
Hi Filipe,
Thanks you for reporting the issue. I have created a ticket and CC'd you on it.
https://trac.openmicroscopy.org.uk/ome/ticket/12643
Regards,
Emil Rozbicki
On 17 Nov 2014, at 21:02, Filipe De Vadder <filipe.devadder at gmail.com> wrote:
> Hello,
> 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:
> (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%)
>
> java.lang.IllegalArgumentException: Invalid series: 0
> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198)
> at loci.formats.FormatReader.setSeries(FormatReader.java:927)
> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179)
> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97)
> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456)
> at loci.formats.FormatReader.setId(FormatReader.java:1317)
> at loci.formats.ImageReader.setId(ImageReader.java:753)
> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388)
> at io.scif.AbstractParser.parse(AbstractParser.java:252)
> at io.scif.AbstractParser.parse(AbstractParser.java:335)
> at io.scif.AbstractParser.parse(AbstractParser.java:52)
> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
> at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
> at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
> at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
> at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
> at ij.IJ.runPlugIn(IJ.java)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:695)
>
> I have tried to open on Windows but still the same message.
> If I try to open it using BIOP plugin, I also get a "macro error" message:
> Relative Path, adding Path to Fiji
> Full path to BIOPLib :/Applications/Fiji.app/plugins/BIOP/BIOPLib.ijm
> Empty Library. Adding BIOPLib Library.
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:83)
> at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)
> at ij.macro.Functions.doExt(Functions.java:4261)
> at ij.macro.Functions.getStringFunction(Functions.java:267)
> at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283)
> at ij.macro.Interpreter.getString(Interpreter.java:1262)
> at ij.macro.Interpreter.doStatement(Interpreter.java:277)
> at ij.macro.Interpreter.doBlock(Interpreter.java:598)
> at ij.macro.Interpreter.runUserFunction(Interpreter.java:307)
> at ij.macro.Interpreter.doUserFunctionAssignment(Interpreter.java:877)
> at ij.macro.Interpreter.doAssignment(Interpreter.java:717)
> at ij.macro.Interpreter.doStatement(Interpreter.java:241)
> at ij.macro.Interpreter.doStatements(Interpreter.java:214)
> at ij.macro.Interpreter.run(Interpreter.java:111)
> at ij.macro.Interpreter.run(Interpreter.java:81)
> at ij.macro.MacroRunner.run(MacroRunner.java:139)
> at java.lang.Thread.run(Thread.java:695)
> Caused by: java.lang.IllegalArgumentException: Invalid series: 0
> at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198)
> at loci.formats.FormatReader.setSeries(FormatReader.java:927)
> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179)
> at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97)
> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456)
> at loci.formats.FormatReader.setId(FormatReader.java:1317)
> at loci.formats.ImageReader.setId(ImageReader.java:753)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
> at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:402)
> ... 21 more
>
> 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.
> If you want, you can access the file I am trying to open (and all other files in the same folder) at: http://dl.free.fr/gNluLSgVz
> I hope this is enough to know what is going on.
> Your help will be very much appreciated.
> Thanks a lot,
> Filipe
>
> _______________________________________________
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> ome-users at lists.openmicroscopy.org.uk
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