Task #12177 (closed)
Opened 10 years ago
Closed 10 years ago
BUG: IJ-plugin and Fiji
Reported by: | pwalczysko | Owned by: | mlinkert |
---|---|---|---|
Priority: | major | Milestone: | 5.0.2 |
Component: | Bio-Formats | Version: | 5.0.0 |
Keywords: | n.a. | Cc: | ux@…, jamoore, jmoore, mlinkert-x, mlinkert, graemeball@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
Graeme has found out during a drop-in session on 03 April 2014 that his insight-ii plugin in Fiji does not start at all and he cannot relieve this situation by updating Fiji either. Also, his updater/Manage Update Sites window shows Bio-formats 4 and Bio-formats 5 boxes as well as Bio-formats (with no number) box. His Bio-formats version shows 5.0.0-DEV and his OMERO.insigh-ij plugin is 5.0.0 (5.0.0 - release version). The error see below.
He pointed out that the situation is not urgent for him, because the same setup works with freshly downloaded Fiji. But I just wondered whether people trying to keep using their old Fiji will run into these problems as well ?
Graeme's setup
Bio-Formats for ImageJ rev c0951f7: 5.0.0-DEV
/Applications/Fiji?.app/plugins/OMERO.insight-ij-5.0.0-ice35-b19
ls /Applications/Fiji?.app/jars/bio-formats/
formats-api.jar jai_imageio-4.4.10.jar ome-xml-5.0.0.jar
formats-bsd-5.0.0.jar mdbtools-java-5.0.0.jar specification-5.0.0.jar
formats-common-5.0.0.jar metakit-5.0.0.jar turbojpeg-5.0.0.jar
formats-gpl-5.0.0.jar ome-poi-5.0.0.jar
Stack trace:
(Fiji Is Just) ImageJ 1.48t; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2; 23MB of 12279MB (<1%) java.lang.NoSuchFieldError: IS_OS_WINDOWS_7 at org.openmicroscopy.shoola.util.ui.UIUtilities.isWindowsOS(UIUtilities.java:2072) at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildLogin(ScreenLogin.java:677) at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildGUI(ScreenLogin.java:772) at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:1047) at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:176) at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:241) at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123) at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59) at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:99) at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:276) at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:486) at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:429) at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:245) at ij.IJ.runUserPlugIn(IJ.java:199) at ij.IJ.runPlugIn(IJ.java:163) at ij.Executer.runCommand(Executer.java:131) at ij.Executer.run(Executer.java:64) at java.lang.Thread.run(Thread.java:695)
Change History (2)
comment:1 Changed 10 years ago by pwalczysko
comment:2 Changed 10 years ago by mlinkert
- Resolution set to wontfix
- Status changed from new to closed
If there are mixed 4.4.x and 5.0.x jars in Fiji, then it's pretty much a guarantee that very bad things will happen. Fully up to date versions of Fiji are expected to only have a single Bio-Formats update site (see http://fiji.sc/Bio-Formats#Daily_builds); having a Bio-Formats 4 option indicates that Fiji is not up to date. The updater often needs to be run several times to make sure that all updates are applied, and in some cases the 4.4.x jars need to be manually selected for removal in the updater window.
There isn't much that we can do with this, so closing.
As indicated by Graeme, the bug is specific for the update for SPIM viewer in Fiji - when this is done, above bug appears with insight-ii plugin. Otherwise, no bug appears. The bug is not a version-specific one though.