[ome-users] Bio-formats exporter bug with .dv file
Kai Schleicher
kai.schleicher at unibas.ch
Thu Sep 22 17:34:07 BST 2016
Hi Curtis,
Thank you also for clarifying the bio-formats update site and including
OMERO 5.2 update site!
I have tested 5.2 and I can login, view and browse my tree without problem.
Once I want to open an image I receive following error: Data Retrieval
Failure (see log below).
That might be because of the version (we have OMERO 5.2.5). When I
uncheck all OMERO update sites, download the latest FIJI-OMERO connector
manually and place it in FIJIs plugin folder it works just fine.
Thanks for your help and cheers,
Kai
java.lang.Exception: java.lang.NoSuchMethodError:
omero.gateway.facility.ROIFacility.getROICount(Lomero/gateway/SecurityContext;J)I
at
org.openmicroscopy.shoola.env.data.views.calls.ROICountLoader$1.doCall(ROICountLoader.java:50)
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:745)
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:289)
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)
at
org.openmicroscopy.shoola.agents.metadata.ROICountLoader.handleException(ROICountLoader.java:110)
at
org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
at
org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
On 09/15/2016 06:47 AM, Curtis Rueden wrote:
> Hi again Kai,
>
> > I will try to find time to update that to OMERO 5.2.x.
>
> I cut a new release of ImageJ-OMERO (0.4.0) built on OMERO 5.2, and
> uploaded it to a newly created OMERO-5.2 update site.
>
> Note that this initial 5.2-compatible version is only very lightly
> tested. Please give it a try and let us know how it goes!
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Sep 14, 2016 at 2:49 PM, Curtis Rueden <ctrueden at wisc.edu
> <mailto:ctrueden at wisc.edu>> wrote:
>
> Hi Kai,
>
> > I realised that updating to the latest version is only possible when
> > Java 8 is check in the update manager while at the same time
> > bio-formats IS NOT checked. If only bio-formats or both are checked,
> > then version 5.1.10 is installed.
>
> The Bio-Formats update site is intended for previewing _unreleased
> and hence unstable_ versions of Bio-Formats.
>
> Unfortunately, it was still configured to build the 5.1.x
> development branch, and hence had fallen out of date compared to
> the Bio-Formats 5.2.x releases which have already taken place.
>
> I have now updated it to build the develop branch (currently
> 5.2.x). So if you update your Fiji with the Bio-Formats update
> site enabled, you should see (as of this writing) Revision
> 011d303e, with release listed as"5.2.2-DEV" (note that unlike
> Maven SNAPSHOTs, this refers to a state _after_ the 5.2.2 release).
>
> > Since we are also running OMERO, I am a big fan of the omero-fiji
> > connector, which works great for me! As we are currently running OMERO
> > 5.2.5, I was wondering whether this connector could also be included
> > in an update site for fiji. Currently we find only 5.0 and 5.1.
>
> Are you talking about the OMERO-5.0 and OMERO-5.1 update sites,
> which ship the ImageJ-OMERO project [1]?
>
> If so, I will try to find time to update that to OMERO 5.2.x.
>
> Regards,
> Curtis
>
> [1] https://github.com/imagej/imagej-omero
> <https://github.com/imagej/imagej-omero>
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> <http://imagej.net/User:Rueden>
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Sep 14, 2016 at 6:12 AM, Kai Schleicher
> <kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch>> wrote:
>
> Hi,
>
> I encountered a bug when using the bio-formats exporter to
> save individual *.tifs (per channel as well as per timepoint)
> from a two channel timelaps hyperstack recorded on a
> Deltavision microscope with softworx (*.dv). I have uploaded
> said image as ID 17340 here:
> https://www.openmicroscopy.org/qa2/qa/feedback/17340/?token=817ba470200e9765b861241874bd8077
> <https://www.openmicroscopy.org/qa2/qa/feedback/17340/?token=817ba470200e9765b861241874bd8077>
>
> In detail I believe that channels and timepoints get mixed up
> as the image for Channel 0 timepoint 1 is actually channel 1
> timepoint 0 and so on.
>
> I am using the latest bio-formats version 5.2.2.
>
> Concerning this I realised that updating to the latest version
> is only possible when Java 8 is check in the update manager
> while at the same time bio-formats IS NOT checked.
> If only bio-formats or both are checked, then version 5.1.10
> is installed.
>
> This seems a bit counter-intuitive to me, if possible I think
> it'd be easiest from a user perspective to keep updating the
> bio-formats from the respective update site.
> Just as a comment, I was also wondering if it'd be possible to
> show the bio-formats version number in the splash screen of
> the importer? This way it'd easier for our facility users to
> find out which version they have installed.
>
> Since we are also running OMERO, I am a big fan of the
> omero-fiji connector, which works great for me! As we are
> currently running OMERO 5.2.5, I was wondering whether this
> connector could also be included in an update site for fiji.
> Currently we find only 5.0 and 5.1.
>
> Thanks for your help and cheers,
> Kai
>
> --
>
> Kai Schleicher, PhD | Research Associate in Advanced Light
> Microscopy | Biozentrum, University of Basel |
> Klingelbergstrasse 50/70 | CH-4056 Basel |
> Phone: +41 61 267 22 50 <tel:%2B41%2061%20267%2022%2050> |
> kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch> |
> www.biozentrum.unibas.ch <http://www.biozentrum.unibas.ch> |
> www.microscopynetwork.unibas.ch
> <http://www.microscopynetwork.unibas.ch>
>
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