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Merged
ctrueden merged 2 commits into from
Aug 9, 2024
Merged

Add Mesh Visualization example #260

ctrueden merged 2 commits into from
Aug 9, 2024

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@gselzer
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@gselzer gselzer commented Aug 8, 2024 •
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This PR writes up a RTD example page for a script that creates a mesh from a binary image and displays it using the 3D Viewer plugin.

TODO: I had trouble running this script after the first time I ran it, due to the following error. I'll try again on Windows - can anyone else replicate?

java.lang.UnsatisfiedLinkError: Couldn't load library 'gluegen_rt' generically including [], nor as [/home/g/Applications/Fiji.app/lib/linux64/libgluegen_rt.so, /home/g/Applications/Fiji.app/libgluegen_rt.so, /home/g/Applications/Fiji.app/natives/linux-amd64/libgluegen_rt.so]
    at com.jogamp.common.jvm.JNILibLoaderBase.loadLibraryInternal(JNILibLoaderBase.java:634)
    at com.jogamp.common.jvm.JNILibLoaderBase.access$000(JNILibLoaderBase.java:64)
    at com.jogamp.common.jvm.JNILibLoaderBase$DefaultAction.loadLibrary(JNILibLoaderBase.java:107)
    at com.jogamp.common.jvm.JNILibLoaderBase.loadLibrary(JNILibLoaderBase.java:488)
    at com.jogamp.common.os.DynamicLibraryBundle$GlueJNILibLoader.loadLibrary(DynamicLibraryBundle.java:427)
    at com.jogamp.common.os.Platform$1.run(Platform.java:321)
    at com.jogamp.common.util.SecurityUtil.doPrivileged(SecurityUtil.java:80)
    at com.jogamp.common.os.Platform.<clinit>(Platform.java:290)
    at com.jogamp.opengl.GLProfile.<clinit>(GLProfile.java:154)
    at jogamp.opengl.ThreadingImpl$1.run(ThreadingImpl.java:83)
    at jogamp.opengl.ThreadingImpl$1.run(ThreadingImpl.java:66)
    at com.jogamp.common.util.SecurityUtil.doPrivileged(SecurityUtil.java:80)
    at jogamp.opengl.ThreadingImpl.<clinit>(ThreadingImpl.java:66)
    at com.jogamp.opengl.Threading.disableSingleThreading(Threading.java:164)
    at org.scijava.java3d.JoglPipeline.initialize(JoglPipeline.java:130)
    at org.scijava.java3d.Pipeline.createPipeline(Pipeline.java:92)
    at org.scijava.java3d.MasterControl.loadLibraries(MasterControl.java:837)
    at org.scijava.java3d.VirtualUniverse.<clinit>(VirtualUniverse.java:274)
    at org.scijava.java3d.NodeRetained.dirtyBoundsCache(NodeRetained.java:974)
    at org.scijava.java3d.Shape3DRetained.setGeometry(Shape3DRetained.java:368)
    at org.scijava.java3d.Shape3D.setGeometry(Shape3D.java:253)
    at customnode.CustomMesh.update(CustomMesh.java:95)
    at customnode.CustomMesh.<init>(CustomMesh.java:78)
    at customnode.CustomTriangleMesh.<init>(CustomTriangleMesh.java:55)
    at customnode.CustomTriangleMesh.<init>(CustomTriangleMesh.java:49)
    at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
    at meshvis.opsMeshToCustomMesh(meshvis.groovy:59)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
    at java.base/java.lang.reflect.Method.invoke(Method.java:580)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
    at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:165)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$3.invokeMethod(GroovyScriptEngineImpl.java:315)
    at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
    at meshvis.run(meshvis.groovy:62)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:331)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:161)
    at org.scijava.plugins.scripting.groovy.GroovyScriptLanguage$1.eval(GroovyScriptLanguage.java:97)
    at java.scripting/javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:262)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
    at java.base/java.lang.Thread.run(Thread.java:1583)

TODO: Add an image (on media.scijava.org)

@gselzer
WIP: Mesh Visualization document
100c616 
TODO: Add an image (on media.scijava.org)
@gselzer gselzer added the docs Issues relating to documentation of the Ops framework label Aug 8, 2024
@gselzer gselzer requested review from ctrueden, elevans and hinerm August 8, 2024 18:43
@gselzer gselzer self-assigned this Aug 8, 2024
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gselzer commented Aug 8, 2024

TODO: I had trouble running this script after the first time I ran it, due to the following error. I'll try again on Windows - can anyone else replicate?

I could not replicate this error on Windows

TODO: Add an image (on media.scijava.org)

Done! See 4ea470d

@gselzer gselzer marked this pull request as ready for review August 8, 2024 20:03
@ctrueden ctrueden merged commit 0314ee6 into main Aug 9, 2024
@ctrueden ctrueden deleted the docs/mesh-example branch August 9, 2024 19:08
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