[ome-users] [Software Feedback] LOCI plugin bug
Melissa Linkert
melissa at glencoesoftware.com
Wed Feb 20 21:00:33 GMT 2013
Hi Paul,
> I too have a problem with the ics export; although, I thought that it was a problem with the files I am using. I import an ome.tif using LOCI and then export to ics. My problem is that I want a single ics file from a time series, not individual files for each time point. If in the dialogue box I choose NOT to "write each...to a separate file", I get an exception:
>
> 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 ij.Command.runPlugIn(Command.java:148)
> at ij.Command.runCommand(Command.java:97)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403)
> at loci.plugins.out.Exporter.run(Exporter.java:545)
> at loci.plugins.LociExporter.run(LociExporter.java:77)
> at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
> at ij.IJ.runUserPlugIn(IJ.java:187)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 8 more
>
> However, if I choose to export to separate files, it works. Also, if I choose to export the channels and Zs (i.e., frames are NOT present) to separate files and leave the timepoints unchecked it also works.
Running "Help > Update Fiji" should solve this problem, but do note that
there is an outstanding bug in the ICS writer which affects some
multi-channel datasets. We are testing a fix for that now, and should
have it resolved shortly.
Regards,
-Melissa
On Wed, Feb 20, 2013 at 08:28:49AM +0000, Paul Thomas (BIO) wrote:
> I too have a problem with the ics export; although, I thought that it was a problem with the files I am using. I import an ome.tif using LOCI and then export to ics. My problem is that I want a single ics file from a time series, not individual files for each time point. If in the dialogue box I choose NOT to "write each...to a separate file", I get an exception:
>
> 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 ij.Command.runPlugIn(Command.java:148)
> at ij.Command.runCommand(Command.java:97)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0
> at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403)
> at loci.plugins.out.Exporter.run(Exporter.java:545)
> at loci.plugins.LociExporter.run(LociExporter.java:77)
> at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
> at ij.IJ.runUserPlugIn(IJ.java:187)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 8 more
>
> However, if I choose to export to separate files, it works. Also, if I choose to export the channels and Zs (i.e., frames are NOT present) to separate files and leave the timepoints unchecked it also works.
>
> ____________________
> Dr. Paul Thomas, Director,
> The Henry Wellcome Laboratory for Cell Imaging,
> School of Biological Sciences,
> University of East Anglia,
> Norwich Research Park,
> Norwich,
> NR4 7TJ,
> United Kingdom.
>
> e-mail: p.thomas at uea.ac.uk
> Tel: +44-1603-592196
> Fax: +44-1603-592250
> Imaging web-site: http://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab
> Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548
>
> From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden
> Sent: 19 February 2013 19:39
> To: daniel.martins at oncology.ox.ac.uk
> Cc: OME-users mailing list
> Subject: Re: [ome-users] [Software Feedback] LOCI plugin bug
>
> Hi Daniel,
>
> > When you export a time series let's assume with 5 time points, the
> > first time point is exported correctly, but then the following ones
> > have an issue.
>
> Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed.
>
> Regards,
> Curtis
>
>
> On Tue, Feb 12, 2013 at 10:14 AM, <daniel.martins at oncology.ox.ac.uk<mailto:daniel.martins at oncology.ox.ac.uk>> wrote:
> Dear all, I have been using your LOCI plugin to export some ics/ids time-series stacks using FIJI. I have noticed there is a bug on this feature. When you export a time series let's assume with 5 time points, the first time point is exported correctly, but then the following ones have an issue. For example time-point 3 instead of being exported as a single frame, is exported as an ics stack with 3 frames, 2 empty frames and the last one is the actual single frame you would want to be exported to begin with. In summary, each time-point is exported as a stack with a number of frames equal to the time point number. This bug only seems to occur for ics files. If you could help me and look into this it would be greatly appreciated.
>
> All the best,
>
> Daniel Martins
>
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