MCIB3D Plugins -> ClassCastException when running Convex Hull plugin

[SteveWest]

Hi,

I am sure this is an easy fix, but I am getting the following error when trying to run the Convex Hull plugin in the mcib3D plugin suite:

(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51k; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.6; 47MB of 6966MB (<1%)
 
java.lang.ClassCastException: org.scijava.vecmath.Point3f cannot be cast to javax.vecmath.Point3f
        at mcib3d.geom.Object3DSurface.translateTool(Object3DSurface.java:2068)
        at mcib3d.geom.Object3D.computeMeshSurface(Object3D.java:3061)
        at mcib3d.geom.Object3D.getConvexSurface(Object3D.java:3395)
        at mcib3d.geom.Object3D.getConvexObject(Object3D.java:3412)
        at mcib_plugins.Convex_Hull3D.run(Convex_Hull3D.java:66)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
        at ij.IJ.runUserPlugIn(IJ.java:219)
        at ij.IJ.runPlugIn(IJ.java:181)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)


I understand this is a problem with Java3D, and that its not compatible with Java8.  I have also followed the instructions of running 3D_viewer plugin.  I can the 3D viewer plugin to work using either the 3D viewer which comes with FIJI, or by even downloading the zip archive from the mcib3D ImageJ Suite page:

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

But when I run the Convex Hull I still get the same error.

Can someone let me know how I can get the 3D suite to access the Java3D libraries please?

Thanks - any help would be great!

Steve.

[SteveWest]

Hi all,

So it turns out I was using an older version of MCIB3D plugins and core (3.6).  I updated to 3.9, and have run the 3D Viewer (4.0.1) to make sure Java3D is installed, and I tried to run the convex hull again and I get a new error:

java.lang.NoClassDefFoundError: com/github/quickhull3d/QuickHull3D
        at mcib3d.geom.Object3DSurface.computeConvexHull3D(Object3DSurface.java:325)
        at mcib3d.geom.Object3D.getConvexSurface(Object3D.java:3592)
        at mcib3d.geom.Object3D.getConvexObject(Object3D.java:3607)
        at mcib3d.geom.Object3D.getConvexObject(Object3D.java:3623)
        at mcib_plugins.Convex_Hull3D.run(Convex_Hull3D.java:62)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
        at ij.IJ.runUserPlugIn(IJ.java:219)
        at ij.IJ.runPlugIn(IJ.java:181)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: com.github.quickhull3d.QuickHull3D
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 12 more

Which is bizarre, as the new MCIB3D plugins package comes with quickhull3d.jar embedded within it!

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

I thin the problem is the MCIB3D plugin for convex hull expects the QuickHull3D class to be in the com.github.quickhull3d package, but apparently it is not (path seems to be quickhull3d.QuickHull3D).

Any help with getting this plugin to calculate the convex hull of objects would be greatly appreciated!

Thanks,

Steve.

[Thomas Boudier-4]

Hi Steve,

Sorry for the trouble, actually in the 3D suite the convex hull is just
a wrap to this original plugin :

https://imagej.nih.gov/ij/plugins/3d-convex-hull/index.html

I will try to update the 3D suite to avoid this problem.

Best,

Thomas



On 24/04/2017 03:57, SteveWest wrote:

> Hi all,
>
> So it turns out I was using an older version of MCIB3D plugins and core
> (3.6).  I updated to 3.9, and have run the 3D Viewer (4.0.1) to make sure
> Java3D is installed, and I tried to run the convex hull again and I get a
> new error:
>
> java.lang.NoClassDefFoundError: com/github/quickhull3d/QuickHull3D
> at
> mcib3d.geom.Object3DSurface.computeConvexHull3D(Object3DSurface.java:325)
> at mcib3d.geom.Object3D.getConvexSurface(Object3D.java:3592)
> at mcib3d.geom.Object3D.getConvexObject(Object3D.java:3607)
> at mcib3d.geom.Object3D.getConvexObject(Object3D.java:3623)
> at mcib_plugins.Convex_Hull3D.run(Convex_Hull3D.java:62)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
> at ij.IJ.runUserPlugIn(IJ.java:219)
> at ij.IJ.runPlugIn(IJ.java:181)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.lang.ClassNotFoundException:
> com.github.quickhull3d.QuickHull3D
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 12 more
>
> Which is bizarre, as the new MCIB3D plugins package comes with
> quickhull3d.jar embedded within it!
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start
>
> I thin the problem is the MCIB3D plugin for convex hull expects the
> QuickHull3D class to be in the com.github.quickhull3d package, but
> apparently it is not (path seems to be quickhull3d.QuickHull3D).
>
> Any help with getting this plugin to calculate the convex hull of objects
> would be greatly appreciated!
>
> Thanks,
>
> Steve.
>
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/MCIB3D-Plugins-ClassCastException-when-running-Convex-Hull-plugin-tp5018589p5018592.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BII (BioInformatics Institute)/UMI 2955 IPAL, Singapore.
/**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[SteveWest]

Hi Thomas,

Thanks for your reply.  I have tried to download the 3D convex Hull plugin, but the link does not seem to work for me, so I have not been able to test if placing this into the Plugins menu helps.  However, I have the updated version of 3D Convex Hull - 3D Shape - in my plugins directory, which does not seem to help.

I presume its just a problem with an import statement in your Object3DSurface class, where the quickhull3d package is in the com.github package on github, but not in ImageJ?

Anyway thanks for taking the time to solve this problem.

All the best,

Steve.

[Thomas Boudier-4]

Hi Steve,

The problem is fixed in the latest update of 3D Suite in Fiji.

Best,

Thomas


On 24/04/2017 17:21, SteveWest wrote:

> Hi Thomas,
>
> Thanks for your reply.  I have tried to download the 3D convex Hull plugin,
> but the link does not seem to work for me, so I have not been able to test
> if placing this into the Plugins menu helps.  However, I have the updated
> version of 3D Convex Hull - 3D Shape - in my plugins directory, which does
> not seem to help.
>
> I presume its just a problem with an import statement in your
> Object3DSurface class, where the quickhull3d package is in the com.github
> package on github, but not in ImageJ?
>
> Anyway thanks for taking the time to solve this problem.
>
> All the best,
>
> Steve.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/MCIB3D-Plugins-ClassCastException-when-running-Convex-Hull-plugin-tp5018589p5018599.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
  /***************************************************************/
       Thomas Boudier, Associate Professor, UPMC,
       Université Pierre et Marie Curie, Paris, France.
       BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html