Dear List
FigureJ seems to be broken. When trying to send an image to a panel, it throws an exception with the message: Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; at utilities.MyImageMath.getPixels(MyImageMath.java:53) at FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) at FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) at FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6289) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6054) at java.awt.Container.processEvent(Container.java:2041) at java.awt.Component.dispatchEventImpl(Component.java:4652) at java.awt.Container.dispatchEventImpl(Container.java:2099) at java.awt.Component.dispatchEvent(Component.java:4482) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) at java.awt.Container.dispatchEventImpl(Container.java:2085) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4482) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:603) at java.awt.EventQueue$1.run(EventQueue.java:601) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:617) at java.awt.EventQueue$2.run(EventQueue.java:615) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:614) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Then it behaves like described in Alessandros message from October 2013 on this list: >"...the selection is not inserted. On the main ImageJ panel there is an >indication "Scaling Image" with three asterisks moving left-right and I'm >assuming that the software is trying to scale the image in order to fit it >into the frame but even after one hour, nothing happens." I am using an up to date FIJI on Win7-32, no difference on another machine with the 64 bit version. Only an older Version of FIJI last updated March 2014 still has FigureJ working. I tried manually adding imagescience.jar to the plugins folder (as suggested by Jerome in reply to Alessandro in 2013) but no difference. Any hints? Christian -- --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Christian, dear all,
You're getting this error message because FigureJ makes use of the imagescience.jar library that provides high quality image transforms. To be more precise, it uses the Affine.run method, the signature of which changed at some point in imagescience. From your error message, I'd guess that you've upgraded imagescience, but not figurej to their latest versions. As you're running Fiji, the easiest way to upgrade is through the updater, just make sure to subscribe to the current update sites that provides ImageScience and FigureJ: *ImageScience* http://sites.imagej.net/ImageScience/ *IBMP-CNRS* http://sites.imagej.net/Mutterer/If you're not using the updater for some reason, you can get the latest versions of the needed file from: http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start#installation_details_for_imagej Sincerely, Jerome On 5 February 2016 at 13:10, Christian Goosmann < [hidden email]> wrote: > Dear List > FigureJ seems to be broken. When trying to send an image to a panel, it > throws an exception with the message: > > Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: > imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; > at utilities.MyImageMath.getPixels(MyImageMath.java:53) > at FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) > at FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) > at > FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) > at > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > at > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > at > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > at > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > at > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) > at > java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) > at java.awt.Component.processMouseEvent(Component.java:6289) > at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) > at java.awt.Component.processEvent(Component.java:6054) > at java.awt.Container.processEvent(Container.java:2041) > at java.awt.Component.dispatchEventImpl(Component.java:4652) > at java.awt.Container.dispatchEventImpl(Container.java:2099) > at java.awt.Component.dispatchEvent(Component.java:4482) > at > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) > at > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) > at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) > at java.awt.Container.dispatchEventImpl(Container.java:2085) > at java.awt.Window.dispatchEventImpl(Window.java:2478) > at java.awt.Component.dispatchEvent(Component.java:4482) > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) > at java.awt.EventQueue.access$000(EventQueue.java:85) > at java.awt.EventQueue$1.run(EventQueue.java:603) > at java.awt.EventQueue$1.run(EventQueue.java:601) > at java.security.AccessController.doPrivileged(Native Method) > at > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > at > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) > at java.awt.EventQueue$2.run(EventQueue.java:617) > at java.awt.EventQueue$2.run(EventQueue.java:615) > at java.security.AccessController.doPrivileged(Native Method) > at > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:614) > at > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > at > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > Then it behaves like described in Alessandros message from October 2013 on > this list: > > "...the selection is not inserted. On the main ImageJ panel there is an >> indication "Scaling Image" with three asterisks moving left-right and I'm >> assuming that the software is trying to scale the image in order to fit it >> into the frame but even after one hour, nothing happens." >> > > I am using an up to date FIJI on Win7-32, no difference on another machine > with the 64 bit version. Only an older Version of FIJI last updated March > 2014 still has FigureJ working. I tried manually adding imagescience.jar to > the plugins folder (as suggested by Jerome in reply to Alessandro in 2013) > but no difference. > Any hints? > Christian > > -- > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Jerome Mutterer CNRS - Institut de biologie moléculaire des plantes 12, rue du Général Zimmer 67084 Strasbourg Cedex www.ibmp.cnrs.fr -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Christian,
As Jerome alluded to, ImageScience moved out of core Fiji and onto its own update site. See: http://imagej.net/2016-01-05_-_ImageScience_is_moving_to_an_update_site 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 Fri, Feb 5, 2016 at 7:24 AM, Jerome Mutterer < [hidden email]> wrote: > Dear Christian, dear all, > > You're getting this error message because FigureJ makes use of the > imagescience.jar library that provides high quality image transforms. To be > more precise, it uses the Affine.run method, the signature of which changed > at some point in imagescience. From your error message, I'd guess that > you've upgraded imagescience, but not figurej to their latest versions. > As you're running Fiji, the easiest way to upgrade is through the updater, > just make sure to subscribe to the current update sites that provides > ImageScience and FigureJ: > *ImageScience* http://sites.imagej.net/ImageScience/ > *IBMP-CNRS* http://sites.imagej.net/Mutterer/If you're not using the > updater for some reason, you can get the latest versions of the needed file > from: > > http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start#installation_details_for_imagej > > Sincerely, > > Jerome > > > > > On 5 February 2016 at 13:10, Christian Goosmann < > [hidden email]> wrote: > > > Dear List > > FigureJ seems to be broken. When trying to send an image to a panel, it > > throws an exception with the message: > > > > Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: > > > imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; > > at utilities.MyImageMath.getPixels(MyImageMath.java:53) > > at FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) > > at FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) > > at > > > FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) > > at > > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > > at > > > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > > at > > > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > > at > > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > > at > > > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) > > at > > java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) > > at java.awt.Component.processMouseEvent(Component.java:6289) > > at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) > > at java.awt.Component.processEvent(Component.java:6054) > > at java.awt.Container.processEvent(Container.java:2041) > > at java.awt.Component.dispatchEventImpl(Component.java:4652) > > at java.awt.Container.dispatchEventImpl(Container.java:2099) > > at java.awt.Component.dispatchEvent(Component.java:4482) > > at > > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) > > at > > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) > > at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) > > at java.awt.Container.dispatchEventImpl(Container.java:2085) > > at java.awt.Window.dispatchEventImpl(Window.java:2478) > > at java.awt.Component.dispatchEvent(Component.java:4482) > > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) > > at java.awt.EventQueue.access$000(EventQueue.java:85) > > at java.awt.EventQueue$1.run(EventQueue.java:603) > > at java.awt.EventQueue$1.run(EventQueue.java:601) > > at java.security.AccessController.doPrivileged(Native Method) > > at > > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at > > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) > > at java.awt.EventQueue$2.run(EventQueue.java:617) > > at java.awt.EventQueue$2.run(EventQueue.java:615) > > at java.security.AccessController.doPrivileged(Native Method) > > at > > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at java.awt.EventQueue.dispatchEvent(EventQueue.java:614) > > at > > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > > at > > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > > at > > > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > > at > > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > > at > > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > > at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > > > Then it behaves like described in Alessandros message from October 2013 > on > > this list: > > > > "...the selection is not inserted. On the main ImageJ panel there is an > >> indication "Scaling Image" with three asterisks moving left-right and > I'm > >> assuming that the software is trying to scale the image in order to fit > it > >> into the frame but even after one hour, nothing happens." > >> > > > > I am using an up to date FIJI on Win7-32, no difference on another > machine > > with the 64 bit version. Only an older Version of FIJI last updated March > > 2014 still has FigureJ working. I tried manually adding imagescience.jar > to > > the plugins folder (as suggested by Jerome in reply to Alessandro in > 2013) > > but no difference. > > Any hints? > > Christian > > > > -- > > --- > > Christian Goosmann > > Mikroskopie > > Max-Planck-Institut für Infektionsbiologie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > Tel.: +49 30 28460 388 > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Curtis, and Jerome
thank you for pointing it out. However, adding the 'Imagescience' update site and updating didn't improve things. Next, I tried installing a fresh download of Fiji and updating it only once with 'IBMP-CNRS' and 'Imagescience' added to the updater (I had to use the December 2015 lifeline Version, because the current download didn't even launch on win-32). But FigureJ also didn't work, with the difference that I got no error message when it crashed. I can only guess there is an issue between the updater and the new situation with Imagescience moving out. Can anyone reproduce? Regards Christian --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 Curtis Rueden wrote: > Hi Christian, > > As Jerome alluded to, ImageScience moved out of core Fiji and onto its own > update site. > > See: > http://imagej.net/2016-01-05_-_ImageScience_is_moving_to_an_update_site > > 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 Fri, Feb 5, 2016 at 7:24 AM, Jerome Mutterer < > [hidden email]> wrote: > >> Dear Christian, dear all, >> >> You're getting this error message because FigureJ makes use of the >> imagescience.jar library that provides high quality image transforms. To be >> more precise, it uses the Affine.run method, the signature of which changed >> at some point in imagescience. From your error message, I'd guess that >> you've upgraded imagescience, but not figurej to their latest versions. >> As you're running Fiji, the easiest way to upgrade is through the updater, >> just make sure to subscribe to the current update sites that provides >> ImageScience and FigureJ: >> *ImageScience* http://sites.imagej.net/ImageScience/ >> *IBMP-CNRS* http://sites.imagej.net/Mutterer/If you're not using the >> updater for some reason, you can get the latest versions of the needed file >> from: >> >> http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start#installation_details_for_imagej >> >> Sincerely, >> >> Jerome >> >> >> >> >> On 5 February 2016 at 13:10, Christian Goosmann < >> [hidden email]> wrote: >> >>> Dear List >>> FigureJ seems to be broken. When trying to send an image to a panel, it >>> throws an exception with the message: >>> >>> Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: >>> >> imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; >>> at utilities.MyImageMath.getPixels(MyImageMath.java:53) >>> at FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) >>> at FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) >>> at >>> >> FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) >>> at >>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) >>> at >>> >> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) >>> at >>> >> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) >>> at >>> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) >>> at >>> >> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) >>> at >>> java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) >>> at java.awt.Component.processMouseEvent(Component.java:6289) >>> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) >>> at java.awt.Component.processEvent(Component.java:6054) >>> at java.awt.Container.processEvent(Container.java:2041) >>> at java.awt.Component.dispatchEventImpl(Component.java:4652) >>> at java.awt.Container.dispatchEventImpl(Container.java:2099) >>> at java.awt.Component.dispatchEvent(Component.java:4482) >>> at >>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) >>> at >>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) >>> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) >>> at java.awt.Container.dispatchEventImpl(Container.java:2085) >>> at java.awt.Window.dispatchEventImpl(Window.java:2478) >>> at java.awt.Component.dispatchEvent(Component.java:4482) >>> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) >>> at java.awt.EventQueue.access$000(EventQueue.java:85) >>> at java.awt.EventQueue$1.run(EventQueue.java:603) >>> at java.awt.EventQueue$1.run(EventQueue.java:601) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at >>> >> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) >>> at >>> >> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) >>> at java.awt.EventQueue$2.run(EventQueue.java:617) >>> at java.awt.EventQueue$2.run(EventQueue.java:615) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at >>> >> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) >>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:614) >>> at >>> >> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) >>> at >>> >> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) >>> at >>> >> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) >>> at >>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) >>> at >>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) >>> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) >>> >>> Then it behaves like described in Alessandros message from October 2013 >> on >>> this list: >>> >>> "...the selection is not inserted. On the main ImageJ panel there is an >>>> indication "Scaling Image" with three asterisks moving left-right and >> I'm >>>> assuming that the software is trying to scale the image in order to fit >> it >>>> into the frame but even after one hour, nothing happens." >>>> >>> I am using an up to date FIJI on Win7-32, no difference on another >> machine >>> with the 64 bit version. Only an older Version of FIJI last updated March >>> 2014 still has FigureJ working. I tried manually adding imagescience.jar >> to >>> the plugins folder (as suggested by Jerome in reply to Alessandro in >> 2013) >>> but no difference. >>> Any hints? >>> Christian >>> >>> -- >>> --- >>> Christian Goosmann >>> Mikroskopie >>> Max-Planck-Institut für Infektionsbiologie >>> Campus Charité Mitte >>> Charitéplatz 1 >>> 10117 Berlin >>> Tel.: +49 30 28460 388 >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> >> -- >> Jerome Mutterer >> CNRS - Institut de biologie moléculaire des plantes >> 12, rue du Général Zimmer >> 67084 Strasbourg Cedex >> www.ibmp.cnrs.fr >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi Jerome
I followed your suggestion, but even with bioformats update (I checked, bio-formats_plugins.jar is present in the plugins folder) figureJ still crashes. But now it becomes complicated. It doesn't crash when the image opened in FigureJ is a jpg file but it does (every time so far) when it is a tif file. Even files that were changed and saved as tiff by imageJ make it crash, so it shouldn't be a question of compressed tiff. Needless to say that all the files open with no problem to ImageJ at all and it doesn't matter if they are 10MB or 2 MB. And then the type of crash is maybe not a crash really (don't know the official terms enough): the windows loose their content when they are moved on the screen, no more menu commands work, the cpu keeps working at around 50% until I kill ImageJ in the task manager (maybe it would finish by itself if given a very long time). I checked only now if opening Jpgs is successful in my original updated (not fresh) install. But it is still the situation described where I started the thread. So I have one more workaround now: saving images as 'jpg' before using them. FigureJ, as many here have stated, is after all a very useful tool. Best regards Christian --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 Jerome Mutterer wrote: > Hi Christian, > Please try adding the Bio-Formats update site as well, as Bioformats > is used to load images in FigureJ. > *Bio-Formats* http://sites.imagej.net/Bio-Formats/ > > This should fix your issue with the fresh lifeline version. > Jerome > > > On 8 February 2016 at 16:42, Christian Goosmann > <[hidden email] <mailto:[hidden email]>> > wrote: > > Hi Curtis, and Jerome > thank you for pointing it out. However, adding the 'Imagescience' > update site and updating didn't improve things. Next, I tried > installing a fresh download of Fiji and updating it only once with > 'IBMP-CNRS' and 'Imagescience' added to the updater (I had to use > the December 2015 lifeline Version, because the current download > didn't even launch on win-32). But FigureJ also didn't work, with > the difference that I got no error message when it crashed. > I can only guess there is an issue between the updater and the new > situation with Imagescience moving out. > Can anyone reproduce? > Regards > Christian > > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> > > Curtis Rueden wrote: > > Hi Christian, > > As Jerome alluded to, ImageScience moved out of core Fiji and > onto its own > update site. > > See: > http://imagej.net/2016-01-05_-_ImageScience_is_moving_to_an_update_site > > 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 Fri, Feb 5, 2016 at 7:24 AM, Jerome Mutterer < > [hidden email] > <mailto:[hidden email]>> wrote: > > Dear Christian, dear all, > > You're getting this error message because FigureJ makes > use of the > imagescience.jar library that provides high quality image > transforms. To be > more precise, it uses the Affine.run method, the signature > of which changed > at some point in imagescience. From your error message, > I'd guess that > you've upgraded imagescience, but not figurej to their > latest versions. > As you're running Fiji, the easiest way to upgrade is > through the updater, > just make sure to subscribe to the current update sites > that provides > ImageScience and FigureJ: > *ImageScience* http://sites.imagej.net/ImageScience/ > *IBMP-CNRS* http://sites.imagej.net/Mutterer/If you're not > using the > updater for some reason, you can get the latest versions > of the needed file > from: > > http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start#installation_details_for_imagej > > Sincerely, > > Jerome > > > > > On 5 February 2016 at 13:10, Christian Goosmann < > [hidden email] > <mailto:[hidden email]>> wrote: > > Dear List > FigureJ seems to be broken. When trying to send an > image to a panel, it > throws an exception with the message: > > Exception in thread "AWT-EventQueue-0" > java.lang.NoSuchMethodError: > > imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; > > at > utilities.MyImageMath.getPixels(MyImageMath.java:53) > at > FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) > at > FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) > at > > FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) > > at > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > at > > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > > at > > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > > at > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > at > > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) > > at > java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) > at > java.awt.Component.processMouseEvent(Component.java:6289) > at > javax.swing.JComponent.processMouseEvent(JComponent.java:3267) > at > java.awt.Component.processEvent(Component.java:6054) > at > java.awt.Container.processEvent(Container.java:2041) > at > java.awt.Component.dispatchEventImpl(Component.java:4652) > at > java.awt.Container.dispatchEventImpl(Container.java:2099) > at > java.awt.Component.dispatchEvent(Component.java:4482) > at > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) > at > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) > at > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) > at > java.awt.Container.dispatchEventImpl(Container.java:2085) > at > java.awt.Window.dispatchEventImpl(Window.java:2478) > at > java.awt.Component.dispatchEvent(Component.java:4482) > at > java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) > at java.awt.EventQueue.access$000(EventQueue.java:85) > at java.awt.EventQueue$1.run(EventQueue.java:603) > at java.awt.EventQueue$1.run(EventQueue.java:601) > at > java.security.AccessController.doPrivileged(Native Method) > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) > > at java.awt.EventQueue$2.run(EventQueue.java:617) > at java.awt.EventQueue$2.run(EventQueue.java:615) > at > java.security.AccessController.doPrivileged(Native Method) > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at > java.awt.EventQueue.dispatchEvent(EventQueue.java:614) > at > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > > at > > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > at > java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > Then it behaves like described in Alessandros message > from October 2013 > > on > > this list: > > "...the selection is not inserted. On the main ImageJ > panel there is an > > indication "Scaling Image" with three asterisks > moving left-right and > > I'm > > assuming that the software is trying to scale the > image in order to fit > > it > > into the frame but even after one hour, nothing > happens." > > I am using an up to date FIJI on Win7-32, no > difference on another > > machine > > with the 64 bit version. Only an older Version of FIJI > last updated March > 2014 still has FigureJ working. I tried manually > adding imagescience.jar > > to > > the plugins folder (as suggested by Jerome in reply to > Alessandro in > > 2013) > > but no difference. > Any hints? > Christian > > -- > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Jerome
indeed. Update offered to update IBMP-CNRS and after that FigureJ works with tiffs and jpgs as good as new. Thank you Christian --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 Jerome Mutterer wrote: > Hi Christian, > Could you update Fiji and apply changes from IBMP update site ? > Let me know if this improves. > > Jerome > > On 9 February 2016 at 12:39, Christian Goosmann > <[hidden email] <mailto:[hidden email]>> > wrote: > > Hi Jerome > I followed your suggestion, but even with bioformats update (I > checked, bio-formats_plugins.jar is present in the plugins folder) > figureJ still crashes. But now it becomes complicated. It doesn't > crash when the image opened in FigureJ is a jpg file but it does > (every time so far) when it is a tif file. Even files that were > changed and saved as tiff by imageJ make it crash, so it shouldn't > be a question of compressed tiff. Needless to say that all the > files open with no problem to ImageJ at all and it doesn't matter > if they are 10MB or 2 MB. And then the type of crash is maybe not > a crash really (don't know the official terms enough): the windows > loose their content when they are moved on the screen, no more > menu commands work, the cpu keeps working at around 50% until I > kill ImageJ in the task manager (maybe it would finish by itself > if given a very long time). I checked only now if opening Jpgs is > successful in my original updated (not fresh) install. But it is > still the situation described where I started the thread. > So I have one more workaround now: saving images as 'jpg' before > using them. FigureJ, as many here have stated, is after all a very > useful tool. > Best regards > Christian > > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> > > Jerome Mutterer wrote: > > Hi Christian, > Please try adding the Bio-Formats update site as well, as > Bioformats is used to load images in FigureJ. > *Bio-Formats* http://sites.imagej.net/Bio-Formats/ > > This should fix your issue with the fresh lifeline version. > Jerome > > > On 8 February 2016 at 16:42, Christian Goosmann > <[hidden email] > <mailto:[hidden email]> > <mailto:[hidden email] > <mailto:[hidden email]>>> wrote: > > Hi Curtis, and Jerome > thank you for pointing it out. However, adding the > 'Imagescience' > update site and updating didn't improve things. Next, I tried > installing a fresh download of Fiji and updating it only > once with > 'IBMP-CNRS' and 'Imagescience' added to the updater (I had > to use > the December 2015 lifeline Version, because the current > download > didn't even launch on win-32). But FigureJ also didn't > work, with > the difference that I got no error message when it crashed. > I can only guess there is an issue between the updater and > the new > situation with Imagescience moving out. > Can anyone reproduce? > Regards > Christian > > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> > <tel:%2B49%2030%2028460%20388> > > Curtis Rueden wrote: > > Hi Christian, > > As Jerome alluded to, ImageScience moved out of core > Fiji and > onto its own > update site. > > See: > http://imagej.net/2016-01-05_-_ImageScience_is_moving_to_an_update_site > > 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 Fri, Feb 5, 2016 at 7:24 AM, Jerome Mutterer < > [hidden email] > <mailto:[hidden email]> > <mailto:[hidden email] > <mailto:[hidden email]>>> wrote: > > Dear Christian, dear all, > > You're getting this error message because FigureJ > makes > use of the > imagescience.jar library that provides high > quality image > transforms. To be > more precise, it uses the Affine.run method, the > signature > of which changed > at some point in imagescience. From your error > message, > I'd guess that > you've upgraded imagescience, but not figurej to their > latest versions. > As you're running Fiji, the easiest way to upgrade is > through the updater, > just make sure to subscribe to the current update > sites > that provides > ImageScience and FigureJ: > *ImageScience* http://sites.imagej.net/ImageScience/ > *IBMP-CNRS* http://sites.imagej.net/Mutterer/If > you're not > using the > updater for some reason, you can get the latest > versions > of the needed file > from: > > http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start#installation_details_for_imagej > > Sincerely, > > Jerome > > > > > On 5 February 2016 at 13:10, Christian Goosmann < > [hidden email] <mailto:[hidden email]> > <mailto:[hidden email] > <mailto:[hidden email]>>> wrote: > > Dear List > FigureJ seems to be broken. When trying to send an > image to a panel, it > throws an exception with the message: > > Exception in thread "AWT-EventQueue-0" > java.lang.NoSuchMethodError: > > imagescience.transform.Affine.run(Limagescience/image/Image;Limagescience/transform/Transform;IZZ)Limagescience/image/Image; > > at > utilities.MyImageMath.getPixels(MyImageMath.java:53) > at > FigureJ_Tool.transferROIDataToPanel(FigureJ_Tool.java:451) > at > FigureJ_Tool.cleanGUIandTransferROI(FigureJ_Tool.java:1984) > at > > FigureJ_Tool$FigureControlPanel$22.actionPerformed(FigureJ_Tool.java:1195) > > at > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) > at > > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) > > at > > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) > > at > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) > at > > javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) > > at > java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) > at > java.awt.Component.processMouseEvent(Component.java:6289) > at > javax.swing.JComponent.processMouseEvent(JComponent.java:3267) > at > java.awt.Component.processEvent(Component.java:6054) > at > java.awt.Container.processEvent(Container.java:2041) > at > java.awt.Component.dispatchEventImpl(Component.java:4652) > at > java.awt.Container.dispatchEventImpl(Container.java:2099) > at > java.awt.Component.dispatchEvent(Component.java:4482) > at > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) > at > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) > at > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) > at > java.awt.Container.dispatchEventImpl(Container.java:2085) > at > java.awt.Window.dispatchEventImpl(Window.java:2478) > at > java.awt.Component.dispatchEvent(Component.java:4482) > at > java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644) > at > java.awt.EventQueue.access$000(EventQueue.java:85) > at > java.awt.EventQueue$1.run(EventQueue.java:603) > at > java.awt.EventQueue$1.run(EventQueue.java:601) > at > java.security.AccessController.doPrivileged(Native Method) > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) > > at > java.awt.EventQueue$2.run(EventQueue.java:617) > at > java.awt.EventQueue$2.run(EventQueue.java:615) > at > java.security.AccessController.doPrivileged(Native Method) > at > > java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) > > at > java.awt.EventQueue.dispatchEvent(EventQueue.java:614) > at > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) > > at > > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) > > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) > at > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) > at > java.awt.EventDispatchThread.run(EventDispatchThread.java:122) > > Then it behaves like described in Alessandros > message > from October 2013 > > on > > this list: > > "...the selection is not inserted. On the main > ImageJ > panel there is an > > indication "Scaling Image" with three > asterisks > moving left-right and > > I'm > > assuming that the software is trying to > scale the > image in order to fit > > it > > into the frame but even after one hour, > nothing > happens." > > I am using an up to date FIJI on Win7-32, no > difference on another > > machine > > with the 64 bit version. Only an older Version > of FIJI > last updated March > 2014 still has FigureJ working. I tried manually > adding imagescience.jar > > to > > the plugins folder (as suggested by Jerome in > reply to > Alessandro in > > 2013) > > but no difference. > Any hints? > Christian > > -- > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 > <tel:%2B49%2030%2028460%20388> <tel:%2B49%2030%2028460%20388> > > -- > ImageJ mailing list: > http://imagej.nih.gov/ij/list.html > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr> > <http://www.ibmp.cnrs.fr> > > -- > ImageJ mailing list: > http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr> > <http://www.ibmp.cnrs.fr/> > > > > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Free forum by Nabble | Edit this page |