run macro in command line

[Lee S]

Dear,

I would like to know how to run imageJ with my images for linking with an
external homemade program.

For example, I have an image in c:\program files\imageJ\1.tif (image file)
and 1smacro.txt (macro).
When I typed,  "java -cp ij.jar;.RunMacro 1smacro.txt" in command line of
c:\program files\imageJ, java could not found "1smacro.txt".
Would you give me an example for my purpose?
How can I let ImageJ know 1.tif as the input parameter?

Best,

S. Lee

[dscho]

Hi,

On Fri, 2 Oct 2009, Lee S wrote:

> I would like to know how to run imageJ with my images for linking with an
> external homemade program.
>
> For example, I have an image in c:\program files\imageJ\1.tif (image file)
> and 1smacro.txt (macro).

        java -cp ij.jar ij.ImageJ -macro 1smacro.txt

> How can I let ImageJ know 1.tif as the input parameter?

You have to specify it in the macro.  You can run

        java -cp ij.jar ij.ImageJ 1.tif -macro 1smacro.txt

too, but there is no guarantee that 1.tif has been fully loaded before the
macro is evaluated.

Hth,
Dscho

[Jim Passmore]

ImageJ Interest Group <[hidden email]> wrote on 10/02/2009 10:51:36
AM:
> Hi,
>
> On Fri, 2 Oct 2009, Lee S wrote:
>
> > I would like to know how to run imageJ with my images for linking with
an
> > external homemade program.
> >
> > For example, I have an image in c:\program files\imageJ\1.tif (image
file)

> > and 1smacro.txt (macro).
>
>    java -cp ij.jar ij.ImageJ -macro 1smacro.txt
>
> > How can I let ImageJ know 1.tif as the input parameter?
>
> You have to specify it in the macro.  You can run
>
>    java -cp ij.jar ij.ImageJ 1.tif -macro 1smacro.txt
>
> too, but there is no guarantee that 1.tif has been fully loaded before

the
> macro is evaluated.
>
> Hth,
> Dscho

Coincidentally, I was mulling over this just this morning, and found the
following from Wayne (6/2/08):

> You can run a macro from the command line and pass a string argument
> using the -macro or -batch command line options. As an example, here is
> a macro that opens an image in the 'images' directory in the users home
> directory:
>
>    name = getArgument;
>    if (name=="") exit ("No argument!");
>    path = getDirectory("home")+"images"+File.separator+name;
>    setBatchMode(true);
>    open(path);
>    print(getTitle+": "+getWidth+"x"+getHeight);
>
> Assume it is named 'OpenImage.txt' and is located in the macros folder.
> Run the command
>
>      java -jar ij.jar -macro OpenImage blobs.tif
>
> and ImageJ will launch and "blobs.tif: 256x254" is displayed in the Log
> window. Note that ImageJ assumed the '.txt' extension and the
> Image/macros directory. Or run
>
>      java -jar ij.jar -batch OpenImage blobs.tif
>
> and the ImageJ window is not opened and the "blobs.tif: 256x254" output
> is displayed in the terminal window.
>
> -wayne

This approach allows you to specify the file on the command line, but use
the macro to open it, avoiding the timing problem.

Jim

----------------------------------------------
Jim Passmore
Research Associate
Sealed Air Corporation
----------------------------------------------

[Wayne Rasband]

 > I would like to know how to run imageJ with my images for
 > linking with an external homemade program.
 >
 > For example, I have an image in c:\program
 > files\imageJ\1.tif (image file) and 1smacro.txt (macro).
 > When I typed,  "java -cp ij.jar;.RunMacro 1smacro.txt" in
 > command line of c:\program files\imageJ, java could not
 > found "1smacro.txt". Would you give me an example for my
 > purpose? How can I let ImageJ know 1.tif as the input
 > parameter?

You can pass the image name or path to the macro as an argument using

    java -jar <path to ij.jar> -ijpath <path to ImageJ folder> -macro
1smacro 1.tif

The macro can retrieve the argument using the getArgument() function

   path = getArgument();
   if (path=="")
       exit("Argument is missing");
   open(path);

Here is a tested example that assumes the ImageJ folder is in
/Applications and that the "1smacro.txt" macro is in
/Applications/ImageJ/macros:

   java -jar /Applications/imagej/ij.jar -ijpath /Applications/ImageJ
-macro 1smacro abe.tif

ImageJ assumes the ".txt" extension if it is omitted. The ImageJ
command line options are described at the beginning of the source file
at

      http://rsb.info.nih.gov/ij/source/ij/ImageJ.java

-wayne