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get current image filename/directory for macros

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get current image filename/directory for macros

Dan Siegal-Gaskins-2
Hello all,

After a couple of years of playing with ImageJ, I'm only now starting to
write macros.  What I have is a stack of 9 images, and I'd like to:

1. run the Image CorrelationJ plugin on the first slice
2. save the output to a text file
3. skip to the next slice
4. run the Image CorrelationJ plugin
5. go back to step 2 and loop through until the end of the stack

Using the macro recorder, the command for running Image CorrelationJ is:

--------------
run("Image CorrelationJ 1o", "target=filename.tif source=filename.tif
correlation=[Fix slide (Source)] statistic=Average markers=Circle local=1
decimal=2");
--------------

So my first question is, how do I replace filename.tif with the a variable
name of the current active image?  I'm assuming there is some 'get filename'
command that I could run, and then I could assign the result to a variable
that I could use in the above statement.  After that I need to save the
data.  The macro recorder shows this as:

--------------
saveAs("Text", "active directory/foo.bar");
--------------

Similar to my first question, how do I use a variable for the directory
which I can assign the directory to be the current working directory?

Thanks,
Dan
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Re: get current image filename/directory for macros

Christine Labno
Hi Dan,

I think the commands you want are below.  For a list of other
built in macro commands, look here:
http://rsb.info.nih.gov/ij/developer/macro/functions.html

  dir = getDirectory("image");

will get the directory of the current image and assign it to
the variable "dir"

  name=getTitle;

will get the name of the current image and assign it to the
variable "name"


  saveAs("Text", dir);

will save the .txt file to the same directory as the current
image, without a name.

  path = dir+name;
     
will create a path to the current directory and lead the
command saveAs("Text", path); below to include the current
image name.  For some reason, saveAs("Text", dir+name); will
not work.  Maybe someone more experienced can explain why.


So your macro should read:

dir = getDirectory("image");
  name=getTitle;
  path = dir+name;

//run commands, etc. here with variables substituted in (i.e.
//target=name).    

saveAs("Text", dir); OR
saveAs("Text", path);


Best,
Christine



---- Original message ----
>Date: Tue, 5 Aug 2008 18:08:56 -0400
>From: Dan Siegal-Gaskins <[hidden email]>  
>Subject: get current image filename/directory for macros  
>To: [hidden email]
>
>Hello all,
>
>After a couple of years of playing with ImageJ, I'm only now
starting to
>write macros.  What I have is a stack of 9 images, and I'd
like to:
>
>1. run the Image CorrelationJ plugin on the first slice
>2. save the output to a text file
>3. skip to the next slice
>4. run the Image CorrelationJ plugin
>5. go back to step 2 and loop through until the end of the stack
>
>Using the macro recorder, the command for running Image
CorrelationJ is:
>
>--------------
>run("Image CorrelationJ 1o", "target=filename.tif
source=filename.tif
>correlation=[Fix slide (Source)] statistic=Average
markers=Circle local=1
>decimal=2");
>--------------
>
>So my first question is, how do I replace filename.tif with
the a variable
>name of the current active image?  I'm assuming there is some
'get filename'
>command that I could run, and then I could assign the result
to a variable
>that I could use in the above statement.  After that I need
to save the
>data.  The macro recorder shows this as:
>
>--------------
>saveAs("Text", "active directory/foo.bar");
>--------------
>
>Similar to my first question, how do I use a variable for the
directory
>which I can assign the directory to be the current working
directory?
>
>Thanks,
>Dan
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