[ome-users] Problem opening VSI file
Emil Rozbicki
emil at glencoesoftware.com
Tue Nov 18 13:59:41 GMT 2014
Hi Filipe,
Quick update on your issue with the .VSI format. The files you have sent us are in MetaSystems format which is currently not supported. I've CC'd you on the Task for supporting it: http://trac.openmicroscopy.org.uk/ome/ticket/12483
Cheers,
Emil
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
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20141118/e898d0b3/attachment.html>
More information about the ome-users
mailing list