Doubts about using the Imagej library

[Vishnu_Bhai]

Hi All,

I have been wanting to use the Imagej library to write an independent application that demarcates cancerous regions in a tissue. But the thing is that I was not able to setup the environment properly to use Imagej as a library. So instead I decided to write the whole thing as a plugin so that I could use the in-built Imagej environment for compiling the program. Now my concern is, if I set up the environment correctly, will I be able to turn the plugin into an independent java program that uses the Imagej library and does not require the Imagej software. Is that possible?

Regards,
Vishnu

[dscho]

Hi,

On Mon, 26 Jul 2010, Vishnu_Bhai wrote:

> I have been wanting to use the Imagej library to write an independent
> application that demarcates cancerous regions in a tissue. But the thing
> is that I was not able to setup the environment properly to use Imagej
> as a library. So instead I decided to write the whole thing as a plugin
> so that I could use the in-built Imagej environment for compiling the
> program. Now my concern is, if I set up the environment correctly, will
> I be able to turn the plugin into an independent java program that uses
> the Imagej library and does not require the Imagej software. Is that
> possible?

It depends how you wrote your plugin. We have some guidelines in Fiji how
to write plugins so that they can be reused by other plugins (i.e. in a
library-like manner):

        http://pacific.mpi-cbg.de/wiki/index.php/PlugIn_Design_Guidelines

Basically, you must never show() images or result tables, except in the
run() method.

There is a further complication if you used constructions imitating
interactive usage of ImageJ, such as calling something like
IJ.run("Duplicate", "title=another-one"); -- in this case, using the
current image (there is no current image in a library) and relying on the
WindowManager to get the resulting image (there must not be any window
manager in a library).

Hth,
Johannes

[Gluender-4]

Dear experts,

very much I should like to receive some advice concerning calling a
UNIX-binary from an ImageJ (1.44) macro by use of "exec( )" on MacOS
10.4.

The UNIX-binary has been installed with MacPorts and resides at

        /opt/local/bin/

 From the OSX-Terminal I can call, e.g. its help text, as usual by

        MyMac:~ me$ theBinary -h

or by

        MyMac:~ me$ /opt/local/bin/theBinary -h



 From an ImageJ macro I can open (start) the UNIX-binary by

        exec( "open", "/opt/local/bin/theBinary" );

but I can't call, e.g. its help text, neither by

        exec( "theBinary", "-h" );

nor by

        exec( "/opt/local/bin/theBinary", "-h" );


What am I doing wrong?

Any help is highly appreciated!

Best
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[karo03]

Try perhaps
exec( "/opt/local/bin/theBinary -h" );

Regards

Am 27.07.2010 um 15:18 schrieb Gluender:

> exec( "/opt/local/bin/theBinary", "-h" );

Karsten
[hidden email]

[Gluender-4]

Thanks Karsten,

but that doesn't the trick.
I think I tried the obvious "permutations" but without success yet.

>Try perhaps
>exec( "/opt/local/bin/theBinary -h" );
>
>Regards
>
>Am 27.07.2010 um 15:18 schrieb Gluender:
>
>>  exec( "/opt/local/bin/theBinary", "-h" );
>
>Karsten
>[hidden email]

Best greetings by this "local call"
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[karo03]

Hmm, the "perhaps" was only an exaggeration!
On my Macosx 10.6.4 ImageJ 1.44e4 it does the trick! Although it does not with the comma separation! Possibly a thing how the options are read into the executable. By the way, I am using gmic(.sourceforge.net) as executable.

Thanks for the "local", typically Neuherberg or Garching are never local for Munich!

Karsten

Am 27.07.2010 um 15:59 schrieb Gluender:

> Thanks Karsten,
>
> but that doesn't the trick.
> I think I tried the obvious "permutations" but without success yet.
>
>> Try perhaps
>> exec( "/opt/local/bin/theBinary -h" );
>>
>> Regards
>>
>> Am 27.07.2010 um 15:18 schrieb Gluender:
>>
>>> exec( "/opt/local/bin/theBinary", "-h" );
>>
>> Karsten
>> [hidden email]
>
> Best greetings by this "local call"
> --
>
>                  Herbie
>
>         ------------------------
>         <http://www.gluender.de>

Karsten
[hidden email]

[Vishnu_Bhai]

Hi Johannes,

Well, I have not used the run method or any other Imagej functionality anywhere in the plugin. Does this mean I am fine a far as writing an independent application goes?

[Gluender-4]

The problem is solved, at least what concerns the UNIX-binary's main
function. It is only the help page that isn't shown by use of "-h".
Strange.

>Dear experts,
>
>very much I should like to receive some advice concerning calling a
>UNIX-binary from an ImageJ (1.44) macro by use of "exec( )" on MacOS
>10.4.
>
>The UNIX-binary has been installed with MacPorts and resides at
>
> /opt/local/bin/
>
>From the OSX-Terminal I can call, e.g. its help text, as usual by
>
> MyMac:~ me$ theBinary -h
>
>or by
>
> MyMac:~ me$ /opt/local/bin/theBinary -h
>
>
>
>From an ImageJ macro I can open (start) the UNIX-binary by
>
> exec( "open", "/opt/local/bin/theBinary" );
>
>but I can't call, e.g. its help text, neither by
>
> exec( "theBinary", "-h" );
>
>nor by
>
> exec( "/opt/local/bin/theBinary", "-h" );
>
>
>What am I doing wrong?
>
>Any help is highly appreciated!

Best
--

                   Herbie

          ------------------------
          <http://www.gluender.de>