How to convert a VTK example from java to clojure?
Antonio Recio
The original java:
import vtk.*;
public class Cone5 {
static {
System.loadLibrary("vtkCommonJava");
System.loadLibrary("vtkFilteringJava");
System.loadLibrary("vtkIOJava");
System.loadLibrary("vtkImagingJava");
System.loadLibrary("vtkGraphicsJava");
System.loadLibrary("vtkRenderingJava");
}
public static void main (String []args) throws Exception {
vtkConeSource cone = new vtkConeSource();
cone.SetHeight( 3.0 );
cone.SetRadius( 1.0 );
cone.SetResolution( 10 );
vtkPolyDataMapper coneMapper = new vtkPolyDataMapper();
coneMapper.SetInputConnection(cone.GetOutputPort());
vtkActor coneActor = new vtkActor();
coneActor.SetMapper(coneMapper);
vtkRenderer ren1 = new vtkRenderer();
ren1.AddActor(coneActor);
ren1.SetBackground(0.1, 0.2, 0.4);
vtkRenderWindow renWin = new vtkRenderWindow();
renWin.AddRenderer( ren1 );
renWin.SetSize(300, 300);
ren1.ResetCamera();
ren1.GetActiveCamera().Azimuth(90);
vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin);
vtkInteractorStyleTrackballCamera style =
new vtkInteractorStyleTrackballCamera();
iren.SetInteractorStyle(style);
iren.Initialize();
iren.Start();
}
}
My modified version in clojure with errors:
(ns project.core
(:import (vtk vtkConeSource vtkPolyDataMapper vtkRenderWindow
vtkRenderWindowInteractor vtkCamera vtkActor vtkRenderer
vtkInteractorStyleTrackballCamera)))
(defn main []
(let [cone (doto (vtkConeSource.)
(.SetHeight 3.0)
(.SetRadius 1.0)
(.SetResolution 10))
coneMapper (doto (vtkPolyDataMapper.)
(.SetInputConnection(.GetOutputPort cone)))
coneActor (doto (vtkActor.)
(.SetMapper coneMapper))
ren (doto (vtkRenderer.)
(.AddActor coneActor)
(.SetBackground 0.1 0.2 0.4)
(.ResetCamera)
(.GetActiveCamera.Azimuth 90))
renWin (doto (vtkRenderWindow.)
(.AddRenderer ren)
(.SetSize 300 300))
iren (doto (.vtkRenderWindowInteractor.)
(.SetRenderWindow renWin)
(.SetInteractorStyle vtkInteractorStyleTrackballCamera.)
(.Initialize)
(.Start))
]))
Tassilo Horn
Hi Antonio,
> My modified version in clojure with errors:*
The errors would be interesting as well. But I found at least two
obvious glitches.
> (defn main []
> (let [cone (doto (vtkConeSource.)
> (.SetHeight 3.0)
> (.SetRadius 1.0)
> (.SetResolution 10))
> coneMapper (doto (vtkPolyDataMapper.)
> (.SetInputConnection(.GetOutputPort cone)))
> coneActor (doto (vtkActor.)
> (.SetMapper coneMapper))
> ren (doto (vtkRenderer.)
> (.AddActor coneActor)
> (.SetBackground 0.1 0.2 0.4)
> (.ResetCamera)
> (.GetActiveCamera.Azimuth 90))
This has to be: (-> (.GetActiveCamera) (.Azimuth 90))
> renWin (doto (vtkRenderWindow.)
> (.AddRenderer ren)
> (.SetSize 300 300))
> iren (doto (.vtkRenderWindowInteractor.)
> (.SetRenderWindow renWin)
> (.SetInteractorStyle vtkInteractorStyleTrackballCamera.)
This has to be: (.SetInteractorStyle (vtkInteractorStyleTrackballCamera.))
> (.Initialize)
> (.Start))
> ]))
HTH,
Tassilo
Antonio Recio
(:import (vtk vtkConeSource vtkPolyDataMapper vtkRenderWindow
vtkRenderWindowInteractor vtkCamera vtkActor vtkRenderer
vtkInteractorStyleTrackballCamera)))
(let [cone (doto (vtkConeSource.)
(.SetHeight 3.0)
(.SetRadius 1.0)
(.SetResolution 10))
coneMapper (doto (vtkPolyDataMapper.)
(.SetInputConnection(.GetOutputPort cone)))
coneActor (doto (vtkActor.)
(.SetMapper coneMapper))
ren (doto (vtkRenderer.)
(.AddActor coneActor)
(.SetBackground 0.1 0.2 0.4)
(.ResetCamera)
renWin (doto (vtkRenderWindow.)
(.AddRenderer ren)
(.SetSize 300 300))
(.SetRenderWindow renWin)
(.SetInteractorStyle (vtkInteractorStyleTrackballCamera.))
(.Initialize)
(.Start))
]))
But in the REPL I obtain this error.
user=> (main)
UnsatisfiedLinkError vtk.vtkConeSource.VTKInit()J vtk.vtkConeSource.VTKInit (vtkConeSource.java:-2)
I can view any gui, do you think that I need to use java swing JFrame JPanel?
Meikel Brandmeyer
you are missing the static part from the Java source. Add the (System/loadLibrary "vtkCommonJava") etc. between the ns clause and the definition of main.
Sincerely
Meikel
Antonio Recio
(ns project.core
(:import (javax.swing JButton JFrame JPanel)
(vtk vtkConeSource vtkPolyDataMapper vtkRenderWindow
vtkRenderWindowInteractor vtkCamera vtkActor vtkRenderer
vtkInteractorStyleTrackballCamera)))
(System/loadLibrary "vtkFilteringJava")
(System/loadLibrary "vtkIOJava")
(System/loadLibrary "vtkImagingJava")
(System/loadLibrary "vtkGraphicsJava")
(System/loadLibrary "vtkRenderingJava")
(defn main []
(let [cone (doto (vtkConeSource.)
(.SetHeight 3.0)
(.SetRadius 1.0)
(.SetResolution 10))
coneMapper (doto (vtkPolyDataMapper.)
(.SetInputConnection(.GetOutputPort cone)))
coneActor (doto (vtkActor.)
(.SetMapper coneMapper))
ren (doto (vtkRenderer.)
(.AddActor coneActor)
(.SetBackground 0.1 0.2 0.4)
(.ResetCamera)
(-> (.GetActiveCamera) (.Azimuth 90)))
renWin (doto (vtkRenderWindow.)
(.AddRenderer ren)
(.SetSize 300 300))
iren (doto (vtkRenderWindowInteractor.)
(.SetRenderWindow renWin)
(.SetInteractorStyle (vtkInteractorStyleTrackballCamera.))
(.Initialize)
(.Start))
]))
But I still get the same error. I think that I have problems to add the "LD_LIBRARY_PATH" to my REPL.
user => (project.core/main)
Antonio Recio
(System/setProperty "java.library.path" "/usr/local/lib/vtk-5.9/")
Antonio Recio
$ java -Djava.library.path=/usr/local/lib/vtk-5.9/ -Djava.ext.dirs=/usr/share/java -cp clojure.jar:src clojure.main main.clj
Exception in thread "main" java.lang.ClassNotFoundException: vtk.vtkConeSource (main.clj:1)
at clojure.lang.Compiler.eval(Compiler.java:5440)
at clojure.lang.Compiler.eval(Compiler.java:5415)
at clojure.lang.Compiler.load(Compiler.java:5857)
at clojure.lang.Compiler.loadFile(Compiler.java:5820)
at clojure.main$load_script.invoke(main.clj:221)
at clojure.main$script_opt.invoke(main.clj:273)
at clojure.main$main.doInvoke(main.clj:354)
at clojure.lang.RestFn.invoke(RestFn.java:409)
at clojure.lang.Var.invoke(Var.java:365)
at clojure.lang.AFn.applyToHelper(AFn.java:163)
at clojure.lang.Var.applyTo(Var.java:482)
at clojure.main.main(main.java:37)
Caused by: java.lang.ClassNotFoundException: vtk.vtkConeSource
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at clojure.lang.DynamicClassLoader.findClass(DynamicClassLoader.java:58)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at project.core$eval3$loading__4410__auto____4.invoke(main.clj:1)
at project.core$eval3.invoke(main.clj:1)
at clojure.lang.Compiler.eval(Compiler.java:5424)
... 11 more
Aaron Cohen
classpath as well.
Add the path to your VTK java files to the "cp" parameter you are
invoking clojure with.
Antonio Recio
My /usr/local/bin/clojure:
#!/bin/sh
export JAVA_HOME=/usr/lib/jvm/java-6-sun/
export LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.26/jre/lib/amd64/:/usr/local/lib/:/usr/local/lib/vtk-5.9/:/usr/local/lib/cmake/ITK-4.0/WrapITK/lib/
export CLASSPATH=/usr/share/java/clojure-contrib.jar:/usr/local/lib/vtk-5.9/java/vtk.jar:.
if [ "x$CLASSPATH" = "x" ] ; then
extra_classpath=""
else
extra_classpath=":$CLASSPATH"
fi
while true ; do
case "$1" in
-cp | -classpath)
extra_classpath=":$2"
shift 2 ;;
--)
shift
break ;;
*)
break ;;
esac
done
if [ "x$1" = "x" -a "x`which rlwrap`" != "x" ] ; then
rlwrap="rlwrap -r -c -C clojure -f /etc/rlwrap/clojure-b (){}[],^%\$#@\"\";:''|\\"
fi
exec rlwrap --complete-filenames --quote-characters='"' --prompt-colour=Red java -cp /usr/share/java/clojure.jar"$extra_classpath" clojure.main "$@"
When I execute the application:
$ clojure main.clj
Exception in thread "main" java.lang.RuntimeException: java.lang.UnsatisfiedLinkError: vtk.vtkConeSource.VTKInit()J
at clojure.lang.Util.runtimeException(Util.java:153)
at clojure.lang.Compiler.eval(Compiler.java:6417)
at clojure.lang.Compiler.load(Compiler.java:6843)
at clojure.lang.Compiler.loadFile(Compiler.java:6804)
at clojure.main$load_script.invoke(main.clj:282)
at clojure.main$script_opt.invoke(main.clj:342)
at clojure.main$main.doInvoke(main.clj:426)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.lang.Var.invoke(Var.java:401)
at clojure.lang.AFn.applyToHelper(AFn.java:161)
at clojure.lang.Var.applyTo(Var.java:518)
at clojure.main.main(main.java:37)
Caused by: java.lang.UnsatisfiedLinkError: vtk.vtkConeSource.VTKInit()J
at vtk.vtkConeSource.VTKInit(Native Method)
at vtk.vtkObject.<init>(vtkObject.java:96)
at vtk.vtkAlgorithm.<init>(vtkAlgorithm.java:794)
at vtk.vtkPolyDataAlgorithm.<init>(vtkPolyDataAlgorithm.java:163)
at vtk.vtkConeSource.<init>(vtkConeSource.java:114)
at project.core$main.invoke(main.clj:14)
at project.core$eval26.invoke(main.clj:38)
at clojure.lang.Compiler.eval(Compiler.java:6406)
... 10 more
Aaron Cohen
is this just a bunch of stuff you've been trying?
I usually just use -Djava.library.path=<whatever>. On linux you also
may have to be sure that your shared libraries are +x for your user.
--Aaron
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Antonio Recio
Aaron Cohen
> java -Djava.library.path=/usr/local/lib/vtk-5.9/
This is the directory that contains: libvtkCommonJava.so,
libvtkFilteringJava.so, libvtkIOJava.so, libvtkImagingJava.so,
libvtkGraphicsJava.so, and libvtkRenderingJava.so ?
They all are executable for the user you are running your program as?
Does the Java example in your initial mail actually run for you?
--Aaron
Antonio Recio
Java and c++ examples work fine.
Aaron Cohen
slightly complicated problem.
What is happening is that the vtk java files and your clojure code are
using different classloaders (clojure uses its own classloader).
System/loadLibrary is kind of crippled in that it always loads the
library into the ClassLoader of the _invoking class's_ classLoader. I
was hoping it would use the Thread's context classloader, but it does
not.
There isn't any straightforward way to load a library using a
particular classloader either, so you have 2 options.
1) Make a java class that exposes a "loadLibrary" method. This java
class will be in the same classLoader as VTK and as a result,
loadLibrary calls from there will be visible to VTK.
public class Loader {
public static void loadLibrary(String lib) {
// Hack to load a library outside of Clojure's classloader
System.loadLibrary(lib);
}
}
2) Expose the package-private "Runtime/loadLibrary0" method and call it.
; This function is in clojure-contrib, reproduced here for convenience
(defn wall-hack-method
"Calls a private or protected method.
params is a vector of class which correspond to the arguments to the method
obj is nil for static methods, the instance object otherwise
the method name is given as a symbol or a keyword (something Named)"
[class-name method-name params obj & args]
(-> class-name (.getDeclaredMethod (name method-name) (into-array
Class params))
(doto (.setAccessible true))
(.invoke obj (into-array Object args))))
(defn load-lib [class lib]
"Loads a native library in the same classLoader as \"class\" was
loaded in. \"lib\" is a string with the OS-appropriate name of the
library. For instance, to load libvtk.so on Linux, lib should be
\"vtk\""
(wall-hack-method java.lang.Runtime "loadLibrary0" [Class String]
(Runtime/getRuntime) class lib))
; Load vtkCommonJava library in the same classLoader as vtkConeSource
(load-lib vtkConeSource "vtkCommonJava")
--------
I actually think clojure should probably add a method to its RT class
that does option 1 above, that way there's a straightforward way to
load native libraries in the correct classloader.
--Aaron
Antonio Recio
Aaron Cohen
> I have tried to use wall-hack-method but I still obtain the
> error: UnsatisfiedLinkError vtk.vtkConeSource.VTKInit()J
> vtk.vtkConeSource.VTKInit (vtkConeSource.java:-2). What I am doing wrong?
> (ns project.core
> (:import (javax.swing JButton JFrame JPanel)
> (vtk vtkConeSource vtkPolyDataMapper vtkRenderWindow
> vtkRenderWindowInteractor vtkCamera vtkActor vtkRenderer
> vtkInteractorStyleTrackballCamera)))
> (System/loadLibrary "vtkCommonJava")
> (System/loadLibrary "vtkFilteringJava")
> (System/loadLibrary "vtkIOJava")
> (System/loadLibrary "vtkImagingJava")
> (System/loadLibrary "vtkGraphicsJava")
> (System/loadLibrary "vtkRenderingJava")
You need to replace all of these with the appropriate (load-lib
vtkConeSource "libraryName"). The vtkConeSource there is fairly
arbitrary, it's just any class that was loaded by the correct
ClassLoader.
> (defn wall-hack-method
> [class-name method-name params obj & args]
> (-> class-name (.getDeclaredMethod (name method-name) (into-array Class
> params))
> (doto (.setAccessible true))
> (.invoke obj (into-array Object args))))
> (defn load-lib [class vtk]
> (wall-hack-method java.lang.Runtime "vtkCommonJava" [Class String]
Where did this "vtkCommonJava" come from? It must be "loadLibrary0".
You're trying to call a method that doesn't exist.
To be clear, the top of your file should look like:
(defn wall-hack-method
"Calls a private or protected method.
params is a vector of class which correspond to the arguments to the method
obj is nil for static methods, the instance object otherwise
the method name is given as a symbol or a keyword (something Named)"
[class-name method-name params obj & args]
(-> class-name (.getDeclaredMethod (name method-name) (into-array
Class params))
(doto (.setAccessible true))
(.invoke obj (into-array Object args))))
(defn load-lib [class lib]
"Loads a native library in the same classLoader as class was
loaded in, lib is a string with the OS-appropriate name of the
library. For instance, to load libvtk.so on Linux, lib should be
\"vtk\""
(wall-hack-method java.lang.Runtime "loadLibrary0" [Class String]
(Runtime/getRuntime) class lib))
(load-lib vtkConeSource "vtkCommonJava")
(load-lib vtkConeSource "vtkFilteringJava")
(load-lib vtkConeSource "vtkIOJava")
(load-lib vtkConeSource "vtkImagingJava")
(load-lib vtkConeSource "vtkGraphicsJava")
(load-lib vtkConeSource "vtkRenderingJava")
Antonio Recio
Nils Blum-Oeste
Aaron Cohen
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