JNI in ImageJ

[Dale Thayer]

Has anyone gone to the trouble of creating a JNI interface to many of the
ImageJ functions?  I see a few very specific examples, but no
comprehensive effort to make a general purpose JNI interface that allows
access to all (or at least the most popular) functions.  I have a lot of
code written in C that analyzes ROI's from images and I would like to, as
a simple example, display an image, draw a ROI, send the ROI from ImageJ
to my C code, analyze the ROI, then send results back to ImageJ for
plotting or other things.  Therefore, I would prefer to use JNI than
rewrite all my C code in Java.

[Joachim Wesner]

HI,

I´ve started playing around a bit with JNI for surporting new frame
grabbers. As I understand you are mostly interested in calling foreign
functions in a
DLL from ImageJ and returning results, not trying to call ImageJ functions
back from C, true? Or what are those "popular functions"?

In that case one could think about a general dll interface as in the newer
versions of Matlab, which is pretty nifty. Before that, you had to write a
new
MEX interface for each external function you wanted to use and convert from
and to the internal data representation of Matlab variables and arrays.
Now, Matlab can parse a .h file that describes the external dll for
functions and will "automagically" invoke a wrapper that allocates, copies
and converts the arguments and the return values to and from the dll, so no
change to the dll and no extra glue code needed. Really nice.

I think if you somehow wisely limited the allowed complexity of the
function definitions (Matalb even does understand typedefs in the .h) for a
first version such an interface to ImageJ could be doable, I already was
thinking about adding such an interface to Euler (a free Matlab clone) some
day.

Joachim





                                                                                                                                       
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                      24.04.2006 23:33                                                                                                
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Has anyone gone to the trouble of creating a JNI interface to many of the
ImageJ functions?  I see a few very specific examples, but no
comprehensive effort to make a general purpose JNI interface that allows
access to all (or at least the most popular) functions.  I have a lot of
code written in C that analyzes ROI's from images and I would like to, as
a simple example, display an image, draw a ROI, send the ROI from ImageJ
to my C code, analyze the ROI, then send results back to ImageJ for
plotting or other things.  Therefore, I would prefer to use JNI than
rewrite all my C code in Java.



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[Dale Thayer]

Hello Joachim,

Yes, I meant to say that I am interested in using functions in DLL from
ImageJ.

For example,

1.  Open a TIFF image in ImageJ
2.  Draw a ROI using ImageJ.
3.  Call DLL function from ImageJ that "transfers" the pixels in the ROI
through a generic JNI interface.
4.  Process the pixels in C code.
4.  Return a few variables of results (perhaps float's, int's, or array of
data) back to ImageJ via a generic JNI defined return function.
5.  Display results in a dialog box from within ImageJ.

As I understand it, I would write some Java plug-in that does step 3,
sends ROI via JNI interface to DLL, then receives say a pointer to a
structure with results, and then the plug-in would display the results, or
plot the results.  In other words, if a JNI "data transfer" interface
could be written, then I could easily move data back and forth to my C
code.  One of the variables being passed to the C code could be a simple
number that tells the C code which C function to execute, that way I don't
have to define a JNI interface for every DLL function.  Maybe there's a
better way.  Perhaps the ImageJ community has some ideas.

Thanks for your response.  I'll look into the Matlab suggestion.

Dale





Joachim Wesner <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
04/24/2006 05:24 PM
Please respond to
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Subject
Antwort: JNI in ImageJ






HI,

I´ve started playing around a bit with JNI for surporting new frame
grabbers. As I understand you are mostly interested in calling foreign
functions in a
DLL from ImageJ and returning results, not trying to call ImageJ functions
back from C, true? Or what are those "popular functions"?

In that case one could think about a general dll interface as in the newer
versions of Matlab, which is pretty nifty. Before that, you had to write a
new
MEX interface for each external function you wanted to use and convert
from
and to the internal data representation of Matlab variables and arrays.
Now, Matlab can parse a .h file that describes the external dll for
functions and will "automagically" invoke a wrapper that allocates, copies
and converts the arguments and the return values to and from the dll, so
no
change to the dll and no extra glue code needed. Really nice.

I think if you somehow wisely limited the allowed complexity of the
function definitions (Matalb even does understand typedefs in the .h) for
a
first version such an interface to ImageJ could be doable, I already was
thinking about adding such an interface to Euler (a free Matlab clone)
some
day.

Joachim





 
                      Dale Thayer  
                      <dale.thayer@TER         An: [hidden email]    
 
                      ADYNE.COM>               Kopie:   (Blindkopie:
Joachim Wesner/DEWET/LMSCentral/Leica)
                      Gesendet von:            Thema:   JNI in ImageJ      
 
                      ImageJ Interest  
                      Group  
                      <[hidden email]  
                      .GOV>  
 
 
                      24.04.2006 23:33  
                      Bitte antworten  
                      an ImageJ  
                      Interest Group  
 




Has anyone gone to the trouble of creating a JNI interface to many of the
ImageJ functions?  I see a few very specific examples, but no
comprehensive effort to make a general purpose JNI interface that allows
access to all (or at least the most popular) functions.  I have a lot of
code written in C that analyzes ROI's from images and I would like to, as
a simple example, display an image, draw a ROI, send the ROI from ImageJ
to my C code, analyze the ROI, then send results back to ImageJ for
plotting or other things.  Therefore, I would prefer to use JNI than
rewrite all my C code in Java.



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[Arnaud DIEUDONNE]

You can try to use java.lang.Runtime to launch processes.
I use it to launch C programs from plugins, you can manage messages and errors
from the program through a StreamGobbler class (found on the web)...

Arnaud

Quoting Dale Thayer <[hidden email]>:

> Has anyone gone to the trouble of creating a JNI interface to many of the
> ImageJ functions?  I see a few very specific examples, but no
> comprehensive effort to make a general purpose JNI interface that allows
> access to all (or at least the most popular) functions.  I have a lot of
> code written in C that analyzes ROI's from images and I would like to, as
> a simple example, display an image, draw a ROI, send the ROI from ImageJ
> to my C code, analyze the ROI, then send results back to ImageJ for
> plotting or other things.  Therefore, I would prefer to use JNI than
> rewrite all my C code in Java.
>

--
Arnaud Dieudonné
Doctorant en Physique Médicale
Laboratoire QUANT.I.F.
Faculté de Médecine et Pharmacie de Rouen
Tel: [phone]

[lakshmi]

Hi,

I have been trying to write c plugins for ImageJ, I made the .dll file using .c and .h and I have included it in the ImageJ folder. When I try to compile the java file I get this error:-

java.lang.UnsatisfiedLinkError: H_.sayHello()V
        at H_.sayHello(Native Method)
        at H_.run(H_.java:18)
        at ij.IJ.runUserPlugIn(IJ.java:183)
        at ij.ImageJ.runUserPlugIn(ImageJ.java:268)
        at ij.plugin.PlugInExecuter.run(Compiler.java:264)
        at java.lang.Thread.run(Thread.java:619)

Can anyone please suggest what might be the mistake?