Interfacing with external programs

[Andy Weller]

Dear all,

Time, and help, permitting I am trying to write a plugin that can
interface with external programs ("libraries"). Basically, I would like
to control our SEM through ImageJ, ultimately in an automated fashion.

Our SEM's documentation says that it's control software has "a dll
library through which external control is routed. This provides a
docu­men­ted set of functions which third-party applications can use to
control the SEM." There is a library for both 16 bit or 32 bit
interfacing, which have an associated header file.

I am a little out of depth here and really have no idea at present
whether such a thing is feasible!?

Does anyone have any experience, pointers, suggestions in doing such things?

Alternatively, does anyone know of any competent coders who may be able
to do this for us (with potential payment)? If they do, they can contact
me off-list.

Thanks, Andy

[Joachim Wesner]

Hi Andy,

I assuming that you are using Windows - right? (But AFAIK what I say below
also applies when trying to call any native libs in Linux, Mac and other
OSses)

Nevertheless, calling external non-Java libraries is not that easy, because
you need to go through the so called Java Native Interface JNI. To make
things worse, you simply cannot translate
the caller list that your library has (which is described by the header
file for C - for example) to a corresponding list in Java and call the
function. This works only for outgoing (from Java to Native)
scalar parameters and the call will add two extra parameters that your DLL
will need to handle resp. will not understand. This is because both adress
spaces of Java and native app are disjunct,
you cannot simply hand over pointers to arrays and so on. So calling a
native function from Java usually would mean writing a new wrapper for any
new function that handles that special case,
which involevs calling special functions from the native (DLL) side back
into the JNI (using the two extra parameters) to copy and convert (do
"marshalling") any complex arguments as pointers/references and feeding
back data from native to Java. Pretty bothersome.

However, there is help, I know of at least 2 commercial helper applications
that claim to do the conversion automatically. If you know Matlab, it´s
very similar to Matlabs DLL call mechanism,
where you hand over the argument list to a special dll cal interface. The
similarity is there because also Matlab also has a virtual machine
architecture with JIT compilation and so on.

(Sorry I don´t have the reference to those commercial applications handy,
I´m just now on trip in China, I will add this later)

Some time ago I proposed here that a project could/should be started on
developing an independent, free alternative for such a DLL caller, I would
be happy to join if there is any
interest in starting this.

Mit freundliche Grüßen / Sincerely

Dr. Joachim Wesner
Leica Microsystems CMS GmbH
Abteilung FTO

Ernst-Leitz-Straße 17-37 | 35578 Wetzlar (Germany)
Tel. [phone] | Fax [phone]

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer: Dr. Martin Haase | Colin Davis | Dr. Wolf-Otto Reuter

http://www.leica-microsystems.com



                                                                           
             Andy Weller                                                  
             <[hidden email]                                            
             .CH>                                                       An
             Gesendet von:              [hidden email]                
             ImageJ Interest                                         Kopie
             Group                                                        
             <[hidden email].                                       Thema
             GOV>                       Interfacing with external programs
                                                                           
                                                                           
             22.05.2007 00:46                                              
                                                                           
                                                                           
              Bitte antworten                                              
                    an                                                    
              ImageJ Interest                                              
                   Group                                                  
             <[hidden email].                                            
                   GOV>                                                    
                                                                           
                                                                           




Dear all,

Time, and help, permitting I am trying to write a plugin that can
interface with external programs ("libraries"). Basically, I would like
to control our SEM through ImageJ, ultimately in an automated fashion.

Our SEM's documentation says that it's control software has "a dll
library through which external control is routed. This provides a
docu­men­ted set of functions which third-party applications can use to
control the SEM." There is a library for both 16 bit or 32 bit
interfacing, which have an associated header file.

I am a little out of depth here and really have no idea at present
whether such a thing is feasible!?

Does anyone have any experience, pointers, suggestions in doing such
things?

Alternatively, does anyone know of any competent coders who may be able
to do this for us (with potential payment)? If they do, they can contact
me off-list.

Thanks, Andy



______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________

[Adrian Daerr]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

> Time, and help, permitting I am trying to write a plugin that can
> interface with external programs ("libraries").

The keyword here is (or was?*) Java Native Interface (JNI), such as
specified here

http://java.sun.com/j2se/1.4.2/docs/guide/jni/spec/jniTOC.html

Links to tutorials and the like can be found e.g. at the bottom of

http://java.sun.com/products/jdk/faq/jnifaq.html

or through google. It's rather easy to use if you once follow a
tutorial. The ImageJ plugin I wrote using JNI-calls is not very
minimalistic, but for what it's worth the source is here:

http://www.msc.univ-paris-diderot.fr/~daerr/progs/index#ScionFGAkiz

HTH,
Adrian

* seems I can't find the Java Native Interface specification of Java 1.5
or 1.6; maybe just searching the wrong places.
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.7 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGUvf7UKl/wQSyHWgRAnj3AJ9snqylZFxZIOs9qeRRhr3Xx3zuaACbBWxm
Lq9/qGuRloDdG3hAert/xPo=
=L/u4
-----END PGP SIGNATURE-----

[ctrueden]

Hi,

Another technology that might be worth checking out is IKVM.NET, a JVM
implementation for .NET and Mono. It can compile Java bytecode into
CLI (i.e., convert JAR to DLL), which lets you use Java code within a
.NET application, or compile a Java application into a .NET
executable. So Java with C, C++ or C# is really straightforward, as
long as it is managed code.

The implementation supports most of Java 1.4 right now, excluding AWT
and Swing, though support for AWT/Swing has been improving a lot
lately.

http://www.ikvm.net/
http://weblog.ikvm.net/CommentView.aspx?guid=e8206772-da68-4753-bb05-1ff5e4a90a8d

I have not tried ImageJ with IKVM.NET, but it might be worth a shot,
as it should be very quick to test.

-Curtis

On 5/22/07, Adrian Daerr <[hidden email]> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> > Time, and help, permitting I am trying to write a plugin that can
> > interface with external programs ("libraries").
>
> The keyword here is (or was?*) Java Native Interface (JNI), such as
> specified here
>
> http://java.sun.com/j2se/1.4.2/docs/guide/jni/spec/jniTOC.html
>
> Links to tutorials and the like can be found e.g. at the bottom of
>
> http://java.sun.com/products/jdk/faq/jnifaq.html
>
> or through google. It's rather easy to use if you once follow a
> tutorial. The ImageJ plugin I wrote using JNI-calls is not very
> minimalistic, but for what it's worth the source is here:
>
> http://www.msc.univ-paris-diderot.fr/~daerr/progs/index#ScionFGAkiz
>
> HTH,
> Adrian
>
> * seems I can't find the Java Native Interface specification of Java 1.5
> or 1.6; maybe just searching the wrong places.
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.7 (Darwin)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFGUvf7UKl/wQSyHWgRAnj3AJ9snqylZFxZIOs9qeRRhr3Xx3zuaACbBWxm
> Lq9/qGuRloDdG3hAert/xPo=
> =L/u4
> -----END PGP SIGNATURE-----
>

[Andy Weller]

Dear all,

I have a macro that initiates with:
setBatchMode(false);

then switches to:
setBatchMode(true);

after some manual editing.

However, during the macro I measure some Fourier descriptors and I can't
seem to close the "Curvature values" window?! In my macro I have:
if(isOpen("Curvature values")) {
    selectWindow("Curvature values");
    run("Close");
    }

but this doesn't help. I end up with many, many "Curvature values"
windows open.

Any ideas? Is there a function to close ALL windows?

I am using 1.39p under Ubuntu.

Thanks, Andy

[Andy Weller]

Alternatively is it possible to set setBatchMode(true) for the whole
macro, but "display" (show?) an image, do something manual to it, then
close it for the macro to continue (with ALL windows closed)?

Thanks.

Andy Weller wrote:

> Dear all,
>
> I have a macro that initiates with:
> setBatchMode(false);
>
> then switches to:
> setBatchMode(true);
>
> after some manual editing.
>
> However, during the macro I measure some Fourier descriptors and I can't
> seem to close the "Curvature values" window?! In my macro I have:
> if(isOpen("Curvature values")) {
>    selectWindow("Curvature values");
>    run("Close");
>    }
>
> but this doesn't help. I end up with many, many "Curvature values"
> windows open.
>
> Any ideas? Is there a function to close ALL windows?
>
> I am using 1.39p under Ubuntu.
>
> Thanks, Andy