Using Turboreg plugin for imagej
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Using Turboreg plugin for imagej
 
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Hi, To install Turboreg I downloaded the Unix distibution and copied the extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, opened an image, used image/Type/RGB stack to convert 2 images of same size to stack image and went to plugins/TurboReg/TurboReg and clicked on the menu and every time I do that with various images I get the following exception in the Exception window ImageJ 1.49p; Java 1.7.0_75 [64-bit]; Linux 3.13.0-46-generic; 3700K of 455MB (<1%) java.lang.IllegalArgumentException: null source at java.util.EventObject.<init>(EventObject.java:56) at java.awt.AWTEvent.<init>(AWTEvent.java:337) at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:285) at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:174) at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) at java.awt.Menu.removeNotify(Menu.java:198) at java.awt.Component.removeNotify(Component.java:6991) at java.awt.Container.remove(Container.java:1199) at java.awt.Container.remove(Container.java:1257) at turboRegPointToolbar.<init>(TurboReg_.java:5645) at turboRegDialog.<init>(TurboReg_.java:1550) at TurboReg_.run(TurboReg_.java:314) 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:745) I copied the source code to plugins folder did plugins/compile and run. I used the PC distribution. Everything I do brings the above exception--I have no idea what I do wrong. Please help. |
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Hi Riyafa,
> Everything I do brings the above exception--I have no idea what I do > wrong. Please help. Did you try the Fiji distribution of ImageJ? It comes with TurboReg installed. If you still have trouble, please provide a minimal, complete, verifiable example [1], including the data you use and a list of steps, ideally a small macro to reproduce. Regards, Curtis [1] http://imagej.net/Bug_reporting_best_practices On Sat, Mar 14, 2015 at 9:24 AM, Riyafa Abdul Hameed <[hidden email]> wrote: > 0 down vote favorite > Hi, > > To install Turboreg <http://bigwww.epfl.ch/thevenaz/turboreg/> I > downloaded the Unix distibution > <http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.tar> and copied the > extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, > opened an image, used image/Type/RGB stack to convert 2 images of same size > to stack image and went to plugins/TurboReg/TurboReg and clicked on the > menu > and every time I do that with various images I get the following exception > in the Exception window > > ImageJ 1.49p; Java 1.7.0_75 [64-bit]; Linux 3.13.0-46-generic; 3700K of > 455MB (<1%) > > java.lang.IllegalArgumentException: null source > at java.util.EventObject.<init>(EventObject.java:56) > at java.awt.AWTEvent.<init>(AWTEvent.java:337) > at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:285) > at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:174) > at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) > at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) > at java.awt.Menu.removeNotify(Menu.java:198) > at java.awt.Component.removeNotify(Component.java:6991) > at java.awt.Container.remove(Container.java:1199) > at java.awt.Container.remove(Container.java:1257) > at turboRegPointToolbar.<init>(TurboReg_.java:5645) > at turboRegDialog.<init>(TurboReg_.java:1550) > at TurboReg_.run(TurboReg_.java:314) > 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:745) > > I copied the source code to plugins folder did plugins/compile and run. I > used the PC distribution > <http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.zip> . Everything I do > brings the above exception--I have no idea what I do wrong. Please help. > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Using-Turboreg-plugin-for-imagej-tp5011964.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi,
I have the same error using Turboreg from a clean and updated Fiji installation. (Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_79 [64-bit]; Linux 3.16.7-031607-generic; 29MB of 6603MB (<1%) java.lang.IllegalArgumentException: null source at java.util.EventObject.<init>(EventObject.java:56) at java.awt.AWTEvent.<init>(AWTEvent.java:337) at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:285) at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:174) at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) at java.awt.Menu.removeNotify(Menu.java:198) at java.awt.Component.removeNotify(Component.java:6991) at java.awt.Container.remove(Container.java:1199) at java.awt.Container.remove(Container.java:1257) at turboRegPointToolbar.<init>(TurboReg_.java:5607) at turboRegDialog.<init>(TurboReg_.java:1501) at TurboReg_.run(TurboReg_.java:383) 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:745) Same error apply for all images (try "Track For Trackmate" for example). Any idea ? Thanks -- Hadrien Mary Ph.D student in Biology Tournier-Gachet Team CNRS - LBCMCP - UMR 5088 Université de Toulouse - Bât. 4R3B1 118, route de Narbonne - 31062 Toulouse On Sun, Mar 15, 2015 at 2:35 PM, Curtis Rueden <[hidden email]> wrote: > Hi Riyafa, > >> Everything I do brings the above exception--I have no idea what I do >> wrong. Please help. > > Did you try the Fiji distribution of ImageJ? It comes with TurboReg > installed. > > If you still have trouble, please provide a minimal, complete, verifiable > example [1], including the data you use and a list of steps, ideally a > small macro to reproduce. > > Regards, > Curtis > > [1] http://imagej.net/Bug_reporting_best_practices > > > On Sat, Mar 14, 2015 at 9:24 AM, Riyafa Abdul Hameed <[hidden email]> > wrote: > >> 0 down vote favorite >> Hi, >> >> To install Turboreg <http://bigwww.epfl.ch/thevenaz/turboreg/> I >> downloaded the Unix distibution >> <http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.tar> and copied the >> extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, >> opened an image, used image/Type/RGB stack to convert 2 images of same size >> to stack image and went to plugins/TurboReg/TurboReg and clicked on the >> menu >> and every time I do that with various images I get the following exception >> in the Exception window >> >> ImageJ 1.49p; Java 1.7.0_75 [64-bit]; Linux 3.13.0-46-generic; 3700K of >> 455MB (<1%) >> >> java.lang.IllegalArgumentException: null source >> at java.util.EventObject.<init>(EventObject.java:56) >> at java.awt.AWTEvent.<init>(AWTEvent.java:337) >> at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:285) >> at java.awt.event.InvocationEvent.<init>(InvocationEvent.java:174) >> at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) >> at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) >> at java.awt.Menu.removeNotify(Menu.java:198) >> at java.awt.Component.removeNotify(Component.java:6991) >> at java.awt.Container.remove(Container.java:1199) >> at java.awt.Container.remove(Container.java:1257) >> at turboRegPointToolbar.<init>(TurboReg_.java:5645) >> at turboRegDialog.<init>(TurboReg_.java:1550) >> at TurboReg_.run(TurboReg_.java:314) >> 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:745) >> >> I copied the source code to plugins folder did plugins/compile and run. I >> used the PC distribution >> <http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.zip> . Everything I do >> brings the above exception--I have no idea what I do wrong. Please help. >> >> >> >> >> -- >> View this message in context: >> http://imagej.1557.x6.nabble.com/Using-Turboreg-plugin-for-imagej-tp5011964.html >> Sent from the ImageJ mailing list archive at Nabble.com. >> >> -- >> 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 |
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Bug seems to be located in this function
(https://github.com/fiji/TurboReg/blob/master/src/main/java/TurboReg_.java#L5607): public turboRegPointToolbar ( final Toolbar previousToolbar ) { previousInstance = previousToolbar; instance = this; final Container container = previousToolbar.getParent(); final Component[] component = container.getComponents(); for (int i = 0; (i < component.length); i++) { if (component[i] == previousToolbar) { container.remove(previousToolbar); // <---- HERE container.add(this, i); break; } } resetButtons(); down[currentTool] = true; setTool(currentTool); setForeground(Color.black); setBackground(gray); addMouseListener(this); container.validate(); } /* end turboRegPointToolbar */ I guess the issue comes from an API breakage. I really don’t know how to fix it … Any help would be nice. I can open a github issue if needed. Thanks — Hadrien Mary Ph.D student in Biology Tournier-Gachet Team CNRS - LBCMCP - UMR 5088 Université de Toulouse - Bât. 4R3B1 118, route de Narbonne - 31062 Toulouse On Thu, May 7, 2015 at 12:36 PM, Hadrien Mary [hidden email] wrote: Hi, I have the same error using Turboreg from a clean and updated Fiji installation. (Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_79 [64-bit]; Linux 3.16.7-031607-generic; 29MB of 6603MB (<1%) java.lang.IllegalArgumentException: null source at java.util.EventObject.(EventObject.java:56) at java.awt.AWTEvent.(AWTEvent.java:337) at java.awt.event.InvocationEvent.(InvocationEvent.java:285) at java.awt.event.InvocationEvent.(InvocationEvent.java:174) at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) at java.awt.Menu.removeNotify(Menu.java:198) at java.awt.Component.removeNotify(Component.java:6991) at java.awt.Container.remove(Container.java:1199) at java.awt.Container.remove(Container.java:1257) at turboRegPointToolbar.(TurboReg.java:5607) at turboRegDialog.(TurboReg.java:1501) at TurboReg.run(TurboReg.java:383) 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:745) Same error apply for all images (try “Track For Trackmate” for example). Any idea ? Thanks — Hadrien Mary Ph.D student in Biology Tournier-Gachet Team CNRS - LBCMCP - UMR 5088 Université de Toulouse - Bât. 4R3B1 118, route de Narbonne - 31062 Toulouse On Sun, Mar 15, 2015 at 2:35 PM, Curtis Rueden [hidden email] wrote: Hi Riyafa, Everything I do brings the above exception—I have no idea what I do wrong. Please help. Did you try the Fiji distribution of ImageJ? It comes with TurboReg installed. If you still have trouble, please provide a minimal, complete, verifiable example [1], including the data you use and a list of steps, ideally a small macro to reproduce. Regards, Curtis [1] http://imagej.net/Bug_reporting_best_practices On Sat, Mar 14, 2015 at 9:24 AM, Riyafa Abdul Hameed [hidden email] wrote: 0 down vote favorite Hi, To install Turboreg http://bigwww.epfl.ch/thevenaz/turboreg/ I downloaded the Unix distibution http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.tar and copied the extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, opened an image, used image/Type/RGB stack to convert 2 images of same size to stack image and went to plugins/TurboReg/TurboReg and clicked on the menu and every time I do that with various images I get the following exception in the Exception window ImageJ 1.49p; Java 1.7.0_75 [64-bit]; Linux 3.13.0-46-generic; 3700K of 455MB (<1%) java.lang.IllegalArgumentException: null source at java.util.EventObject.(EventObject.java:56) at java.awt.AWTEvent.(AWTEvent.java:337) at java.awt.event.InvocationEvent.(InvocationEvent.java:285) at java.awt.event.InvocationEvent.(InvocationEvent.java:174) at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) at java.awt.Menu.removeNotify(Menu.java:198) at java.awt.Component.removeNotify(Component.java:6991) at java.awt.Container.remove(Container.java:1199) at java.awt.Container.remove(Container.java:1257) at turboRegPointToolbar.(TurboReg.java:5645) at turboRegDialog.(TurboReg.java:1550) at TurboReg.run(TurboReg.java:314) 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:745) I copied the source code to plugins folder did plugins/compile and run. I used the PC distribution http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.zip . Everything I do brings the above exception—I have no idea what I do wrong. Please help. — View this message in context: http://imagej.1557.x6.nabble.com/Using-Turboreg-plugin-for-imagej-tp5011964.html Sent from the ImageJ mailing list archive at Nabble.com. — 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 |
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Hi Hadrien,
I did some digging for a while yesterday, but the "null source" error is broad so I didn't get very far. It seems pretty clear that some defensive programming in the source code at that spot would indeed address the issue. If you figure it out and file a PR, that would be great. Or you can file a regular issue so it is not forgotten. But unlikely that LOCI will have time to work on it before end of summer. Regards, Curtis On Fri, May 8, 2015 at 8:49 AM, Hadrien Mary <[hidden email]> wrote: > Bug seems to be located in this function > ( > https://github.com/fiji/TurboReg/blob/master/src/main/java/TurboReg_.java#L5607 > ): > > public turboRegPointToolbar ( > final Toolbar previousToolbar > ) { > previousInstance = previousToolbar; > instance = this; > final Container container = previousToolbar.getParent(); > final Component[] component = container.getComponents(); > for (int i = 0; (i < component.length); i++) { > if (component[i] == previousToolbar) { > container.remove(previousToolbar); // <---- HERE > container.add(this, i); > break; > } > } > resetButtons(); > down[currentTool] = true; > setTool(currentTool); > setForeground(Color.black); > setBackground(gray); > addMouseListener(this); > container.validate(); > } /* end turboRegPointToolbar */ > > I guess the issue comes from an API breakage. I really don’t know how > to fix it … > > Any help would be nice. I can open a github issue if needed. > > Thanks > > — > Hadrien Mary > > Ph.D student in Biology > Tournier-Gachet Team > CNRS - LBCMCP - UMR 5088 > > Université de Toulouse - Bât. 4R3B1 > 118, route de Narbonne - 31062 Toulouse > > On Thu, May 7, 2015 at 12:36 PM, Hadrien Mary [hidden email] > wrote: > > Hi, > > I have the same error using Turboreg from a clean and updated Fiji > installation. > > (Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_79 [64-bit]; Linux > 3.16.7-031607-generic; 29MB of 6603MB (<1%) > > java.lang.IllegalArgumentException: null source > at java.util.EventObject.(EventObject.java:56) > at java.awt.AWTEvent.(AWTEvent.java:337) > at java.awt.event.InvocationEvent.(InvocationEvent.java:285) > at java.awt.event.InvocationEvent.(InvocationEvent.java:174) > at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) > at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) > at java.awt.Menu.removeNotify(Menu.java:198) > at java.awt.Component.removeNotify(Component.java:6991) > at java.awt.Container.remove(Container.java:1199) > at java.awt.Container.remove(Container.java:1257) > at turboRegPointToolbar.(TurboReg.java:5607) > at turboRegDialog.(TurboReg.java:1501) > at TurboReg.run(TurboReg.java:383) > 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:745) > > Same error apply for all images (try “Track For Trackmate” for example). > > Any idea ? > > Thanks > > — > Hadrien Mary > > Ph.D student in Biology > Tournier-Gachet Team > CNRS - LBCMCP - UMR 5088 > > Université de Toulouse - Bât. 4R3B1 > 118, route de Narbonne - 31062 Toulouse > > On Sun, Mar 15, 2015 at 2:35 PM, Curtis Rueden [hidden email] wrote: > > Hi Riyafa, > > Everything I do brings the above exception—I have no idea what I do > wrong. Please help. > > Did you try the Fiji distribution of ImageJ? It comes with TurboReg > installed. > > If you still have trouble, please provide a minimal, complete, verifiable > example [1], including the data you use and a list of steps, ideally a > small macro to reproduce. > > Regards, > Curtis > > [1] http://imagej.net/Bug_reporting_best_practices > > On Sat, Mar 14, 2015 at 9:24 AM, Riyafa Abdul Hameed [hidden email] > wrote: > > 0 down vote favorite > Hi, > > To install Turboreg http://bigwww.epfl.ch/thevenaz/turboreg/ I > downloaded the Unix distibution > http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.tar and copied the > extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, > opened an image, used image/Type/RGB stack to convert 2 images of same size > to stack image and went to plugins/TurboReg/TurboReg and clicked on the > menu > and every time I do that with various images I get the following exception > in the Exception window > > ImageJ 1.49p; Java 1.7.0_75 [64-bit]; Linux 3.13.0-46-generic; 3700K of > 455MB (<1%) > > java.lang.IllegalArgumentException: null source > at java.util.EventObject.(EventObject.java:56) > at java.awt.AWTEvent.(AWTEvent.java:337) > at java.awt.event.InvocationEvent.(InvocationEvent.java:285) > at java.awt.event.InvocationEvent.(InvocationEvent.java:174) > at sun.awt.X11.XBaseMenuWindow.dispose(XBaseMenuWindow.java:907) > at java.awt.MenuComponent.removeNotify(MenuComponent.java:310) > at java.awt.Menu.removeNotify(Menu.java:198) > at java.awt.Component.removeNotify(Component.java:6991) > at java.awt.Container.remove(Container.java:1199) > at java.awt.Container.remove(Container.java:1257) > at turboRegPointToolbar.(TurboReg.java:5645) > at turboRegDialog.(TurboReg.java:1550) > at TurboReg.run(TurboReg.java:314) > 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:745) > > I copied the source code to plugins folder did plugins/compile and run. I > used the PC distribution > http://bigwww.epfl.ch/thevenaz/turboreg/turboreg.zip . Everything I do > brings the above exception—I have no idea what I do wrong. Please help. > > — > View this message in context: > > http://imagej.1557.x6.nabble.com/Using-Turboreg-plugin-for-imagej-tp5011964.html > Sent from the ImageJ mailing list archive at Nabble.com. > > — > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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