Re: batch processing across folders

Posted by dpoburko on Jan 22, 2009; 11:08pm
URL: http://imagej.273.s1.nabble.com/batch-processing-across-folders-tp3693993p3693995.html

G. Esteban Fernandez wrote:

> Damon,
>  
> When you get a list of names inside a folder, subfolder names end with
> "/".  Thus, what I've done in the past to process subfolders is run a
> for loop to parse through the list of names in a folder and for each
> name that ends with "/" run another for loop to parse through the
> files in that subfolder.  The code looks something like this:
> mainDir = getDirectory("Choose a main directory ");
> mainList = getFileList(mainDir);
>  
> for (i=0; i<mainList.length; i++) {  // for loop to parse through
> names in main folder
>      if(endsWith(mainList[i], "/")){   // if the name is a subfolder...
>  
>           subDir = mainDir + mainList[i];
>           subList = getFileList(subDir);
>  
>           for (j=0; j<subList.length; j++) {  // for loop to parse
> through names in subfolder
>  
>                // DO STUFF
>  
>           }
>      }
> }
>
>  
> Good luck!
>  
> -Esteban
>  
>  
> On Thu, Jan 22, 2009 at 1:56 PM, Damon Poburko <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi All,
>      I have a some analysis that I would like to batch process. I have
>     a macro that runs and saves my analysis for images in a given
>     folder. What I would like to do is set up a parent macro, or
>     expand the macro, to start in a user-defined parent folder,
>     generate a list of subfolders and then apply the analysis to each
>     of those subfolders.  I'm not sure if IJ's macro language will
>     allow this , or if it  requires a proper  pluggin.
>     Thanks,
>     Damon
>
>
>     --
>
>     Damon Poburko, PhD
>     Postdoctoral Research Fellow
>     Stanford University School of Medicine
>     Dept. of Molecular & Cellular Physiology
>     279 Campus Dr., Beckman B103, Stanford, CA 94305
>     Ph: 650 725 7564, fax: [phone]
>
>
>
>
> --
> G. Esteban Fernandez, Ph.D.
> Associate Director
> Molecular Cytology Core Facility
> University of Missouri
> 120 Bond Life Sciences Center
> Columbia, MO  65211
>
> http://www.biotech.missouri.edu/mcc/
>
> 573-882-4895
> 573-884-9395 fax
>

Esteban,

   That was exactly what I needed. Many thanks!

Damon