roiManager and Batch mode

[Luciano Marpegan]

Hi everybody,

I'm writing a macro to remove big particles from my images. Most of
these particles have irregular shapes, are over twice bigger than the
particles I'm interested in and their intensity is
homogeneous although sometimes they overlap with the particles I'm
measuring. I need to do batch processing because I usually work with
image sequences with over 10k frames and it is very time consuming to
do it manually.
The macro is based on the "BatchProcessFolders" macro from the ImageJ
macros web page and works fine as far as I don't use the setBatchMode
function. When I use it, the roiManager doesn't reset and seems to
keep adding the selections instead of deleting the ones of the
previous cycle. making it short, does the roiManager("reset")
function work while in batch mode?
I will really appreciate any help Best.
Luciano

Following is the macro 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++;
        setBatchMode(false);
         }
}

    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")) {
            open(path);
            run("Divide...", "value=1023");
            run("8-bit");
            setThreshold(1, 255);
            run("Analyze Particles...", "size=250-Infinity
circularity=0.00-1.00 show=Nothing add");
            roiManager("Combine");
            run("Subtract...", "value=1");
            roiManager("Reset");
            setThreshold(1, 255);
            run("Analyze Particles...", "size=125-Infinity
circularity=0.03-1.00 show=Nothing add");
            roiManager("Combine");
            run("Subtract...", "value=1");
            roiManager("Reset");
     subdir=getDirectory ("image");
     newdir=subdir+"Filtered"+File.separator;
     File.makeDirectory(newdir);
     fname=File.getName(path) ;
     saveAs("tiff", newdir+ "filtered"+getTitle);
            close();

       }
   }







Luciano Marpegan, Ph. D.,
Postdoctoral Fellow,
Biology Department, Washington University,
PO Box 1137,1 Brookings Drive, St. Louis,MO 63130
Office Phone: [phone]
Email: [hidden email]

[Wayne Rasband]

In the ImageJ 1.41b daily build, the particle analyzer, when run from a
batch mode macro, no longer opens the ROI Manager window when "Add to
Manager" is enabled, resulting in faster and more reliable operation.

-wayne

On Apr 28, 2008, at 8:01 PM, Luciano Marpegan wrote:

> Hi everybody,
>
> I'm writing a macro to remove big particles from my images. Most of
> these particles have irregular shapes, are over twice bigger than the
> particles I'm interested in and their intensity is
> homogeneous although sometimes they overlap with the particles I'm
> measuring. I need to do batch processing because I usually work with
> image sequences with over 10k frames and it is very time consuming to
> do it manually.
> The macro is based on the "BatchProcessFolders" macro from the ImageJ
> macros web page and works fine as far as I don't use the setBatchMode
> function. When I use it, the roiManager doesn't reset and seems to
> keep adding the selections instead of deleting the ones of the
> previous cycle. making it short, does the roiManager("reset") function
> work while in batch mode?
> I will really appreciate any help Best.
> Luciano
>
> Following is the macro 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++;
>        setBatchMode(false);
>         }
> }
>
>    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")) {
>            open(path);
>            run("Divide...", "value=1023");
>            run("8-bit");
>            setThreshold(1, 255);
>            run("Analyze Particles...", "size=250-Infinity
> circularity=0.00-1.00 show=Nothing add");
>            roiManager("Combine");
>            run("Subtract...", "value=1");
>            roiManager("Reset");
>            setThreshold(1, 255);
>            run("Analyze Particles...", "size=125-Infinity
> circularity=0.03-1.00 show=Nothing add");
>            roiManager("Combine");
>            run("Subtract...", "value=1");
>            roiManager("Reset");
>     subdir=getDirectory ("image");
>     newdir=subdir+"Filtered"+File.separator;
>     File.makeDirectory(newdir);
>     fname=File.getName(path) ;
>     saveAs("tiff", newdir+ "filtered"+getTitle);
>            close();
>
>       }
>   }
>
>
>
>
>
>
>
> Luciano Marpegan, Ph. D.,
> Postdoctoral Fellow,
> Biology Department, Washington University,
> PO Box 1137,1 Brookings Drive, St. Louis,MO 63130
> Office Phone: [phone]
> Email: [hidden email]
>