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Batch processes through plugins

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jswalker

Batch processes through plugins

Hi all,

I'm trying to do a couple operations on many files in a folder, but these operations must be done through plugins (eg BioFormats, or ND2Reader).

The recorder spits this out:

run("Bio-Formats Importer", "open=[C:\\file\\path\\file.tif] insertoptionshere");

How do I make this perform the same action on all files in a list? I understand how to do this when I'm not doing it through a plugin -- my question is specifically about doing this within the plugin syntax shown above.

I'm working with the following script:

   requires("1.33s"); 
   dir = getDirectory("Choose a Directory: ");
   setBatchMode(true);
   count = 0;
   countFiles(dir);
   n = 0;
   processFiles(dir);
   //print(count+" files processed");
   
   function countFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              countFiles(""+dir+list[i]);
          else
              count++;
      }
  }

   function processFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFiles(""+dir+list[i]);
          else {
             showProgress(n++, count);
             path = dir+list[i];
             processFile(path);
          }
      }
  }

  function processFile(path) {
       if (endsWith(path, ".tif")) {
           [COMMAND GOES HERE]
           close();
      }
  }

I've tried universalizing the line that the recorder spits out, but it gives me an error.

I tried looking for this in the archives but may have been using the wrong search terms -- sorry if so. Many thanks in advance!

Aryeh Weiss

Re: Batch processes through plugins

On 8/5/15 10:34 PM, jswalker wrote:

> Hi all,
>
> I'm trying to do a couple operations on many files in a folder, but these
> operations must be done through plugins (eg BioFormats, or ND2Reader).
>
> The recorder spits this out:
>
> run("Bio-Formats Importer", "open=[C:\\file\\path\\file.tif]
> insertoptionshere");
>
> How do I make this perform the same action on all files in a list? I
> understand how to do this when I'm not doing it through a plugin -- my
> question is specifically about doing this within the plugin syntax shown
> above.

You can get your file list and insert the string variables into the
argument string, Here is an example from something I wrote:

run("Bio-Formats Importer", "open=["+inputPath+"] autoscale
color_mode=Default view=Hyperstack stack_order=XYCZT series_"+d2s(j,0));

your argument list will look different, but the idea is the same. In my
example, I have variable for the input path (a complete path to my
file). Since I needed to loop over a set of fields in a multifield
image, I also have "series_"+d2s(j,0) which constructs the correct
argument to get a particular field (i is a loop variable)

hope this helps
--aryeh

> I'm working with the following script:
>
>
>
> I've tried universalizing the line that the recorder spits out, but it gives
> me an error.
>
> I tried looking for this in the archives but may have been using the wrong
> search terms -- sorry if so. Many thanks in advance!
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Batch-processes-through-plugins-tp5013914.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph: 972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

jswalker

Re: Batch processes through plugins

Aryeh,

Yes, that's perfect, thank you. Thanks for the example, too -- I've got it now!

Cheers,

Jill

From: Aryeh Weiss [via ImageJ] <ml-node+[hidden email]>
Sent: Thursday, August 6, 2015 12:40 AM
To: Walker, Jillian S
Subject: Re: Batch processes through plugins

On 8/5/15 10:34 PM, jswalker wrote:

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph: 972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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