macro parameter from command line

[federica viti]

Hi everyone,
I'm working on ImageJ 1.40 in batch mode. I cannot find anywhere if it's
possible passing parameters to a macros directly by command line. I mean
something like this:
./jre/bin/java -jar ij.jar -batch macros/Try.txt  < inputTry

I cannot use dialog box because I'm working without GUI and not
interactively.
Particularly I need to pass the macro the name of a file. I thought to write
the name in a file and use the option of the open function to read it and
open the file .. something like the example I found on line:

run("Open...", "open="+getDirectory("plugins")+"README.txt");

but the name of my file is composed by variables, so I have to include
everything in a script to decode the name and it cannot read as a txt file.

Do you know some way to help me?
thank you very much
Federica

[Michael Schmid]

Hi Federica,

I see two ways: write all of macro from the batch file, e.g.
under windows
   echo run("Open...", "open=%myFile%"); >myMacro.txt
   echo run("Smooth"); >>myMacro.txt
   echo ... >>myMacro.txt
or under Linux
   echo run("Open...", "open=$myFile"); >myMacro.txt
   echo run("Smooth"); >>myMacro.txt
   echo ... >>myMacro.txt
(note that variable substitution such as $myFile takes
place in spite of the double quotes. Single quotes would
prevent it).

And then start ImageJ with that macro "myMacro.txt".
This will be fine for short macros.


The other way is writing the arguments into a file with fixed
name that your macro reads with
   string = File.openAsString(path);
If the file contains arguments delimited by some character,
e.g. tab "\t", newline "\n", etc, you can use
   args = split(string, delimiters)
to get the arguments as args[0], args[1], etc.

The second option is probably the better one for long macros.


By the way, in a macro
   run("Open...", "open=/tmp/anyimage.tif");
could be replaced by the more simple command
   open("/tmp/anyimage.tif");

Hope this helps,

Michael
________________________________________________________________


On 2 Jun 2008, at 15:15, federica viti wrote:

> Hi everyone,
> I'm working on ImageJ 1.40 in batch mode. I cannot find anywhere if  
> it's
> possible passing parameters to a macros directly by command line. I  
> mean
> something like this:
> ./jre/bin/java -jar ij.jar -batch macros/Try.txt  < inputTry
>
> I cannot use dialog box because I'm working without GUI and not
> interactively.
> Particularly I need to pass the macro the name of a file. I thought  
> to write
> the name in a file and use the option of the open function to read  
> it and
> open the file .. something like the example I found on line:
>
> run("Open...", "open="+getDirectory("plugins")+"README.txt");
>
> but the name of my file is composed by variables, so I have to include
> everything in a script to decode the name and it cannot read as a  
> txt file.
>
> Do you know some way to help me?
> thank you very much
> Federica

[Wayne Rasband]

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

On Jun 2, 2008, at 9:15 AM, federica viti wrote:

> Hi everyone,
> I'm working on ImageJ 1.40 in batch mode. I cannot find anywhere if
> it's
> possible passing parameters to a macros directly by command line. I
> mean
> something like this:
> ./jre/bin/java -jar ij.jar -batch macros/Try.txt  < inputTry
>
> I cannot use dialog box because I'm working without GUI and not
> interactively.
> Particularly I need to pass the macro the name of a file. I thought to
> write
> the name in a file and use the option of the open function to read it
> and
> open the file .. something like the example I found on line:
>
> run("Open...", "open="+getDirectory("plugins")+"README.txt");
>
> but the name of my file is composed by variables, so I have to include
> everything in a script to decode the name and it cannot read as a txt
> file.
>
> Do you know some way to help me?
> thank you very much
> Federica
>