Re: Macro to run Laplacian on stacks

Posted by Stoyan Pavlov on Apr 29, 2017; 8:55pm
URL: http://imagej.273.s1.nabble.com/Macro-to-run-Laplacian-on-stacks-tp5018607p5018637.html

Hi,
The problem is that featureJ is producing a new image with name
<originalimage>-Laplacian. And you need to account for that.
I' ve  just the macro you need. As a basis I used an old batch processing
macro created by porifera.net. It will ask about source folder, destination
folder and filter size and will process all images in the source folder
with the preselected filter size of the Lap[lacian of Gaussian  and save
them to the destination.
Best regards,
Stoyan

//Macro START
//----------------

//Batch Processor

// ***Select macro(s) used here ***
// Just replace "bmp" by "jpeg" or any other standard image file format here
//to select output type of your filtered image

macro "Batch Convert to TIFF" {convert("tif");}

//Function Batch processing
 function convert(format) {
     requires("1.34m");

// *** General Settings ***


// Close log window if open
       if (isOpen("Log")) {
        selectWindow("Log");
        run("Close");
       }

//Variables
       var abort,dir1,dir2,dir3,rad,list;

// Instruction
       showMessage("Instruction", "Choose source directory containing
source-files \nand destination directories for Filtered IMAGE. \n \nBrougt
to you 2007 by porifera.net\n \n");

// ### Input your values for specific functions here ###

// ### End Input specific functions ###


// Choose directories
     dir1 = getDirectory("Choose source image directory ");
     dir2 = getDirectory("Choose FILTERED IMAGE destination directory ");
     list = getFileList(dir1);
    b = getNumber("Gaussian blur radius (in scaled units):", 2);

// Protocol start
       print("ImageJ macro 'Batch_Processor' by porifera.net \n \n");
       print("initial file source directory: ",dir1, "\n");
       print("filtered file destination directory: ", dir2,"\n");
       print("Number of files:", list.length, "\n \n");

// Batch processing
     setBatchMode(true);
     count = 0;
               countFiles(dir1);
               n = 0;
               processFiles(dir1);

     function countFiles(dir1) {
       list = getFileList(dir1);
       for (i=0; i<list.length; i++) {
         if (endsWith(list[i], "/"))
             countFiles(""+dir1+list[i]);
         else
             count++;
       }
               }



  function processFiles(dir1) {
     list = getFileList(dir1);
     for (i=0; i<list.length; i++) {
         if (endsWith(list[i], "/"))
             processFiles(""+dir1+list[i]);
         else {
            showProgress(n++, count);
            path = dir1+list[i];
            processFile(path);
               }
               }
       }

 function processFile(path) {
      if (endsWith(path, "")) {
          open(path);


initimage = getTitle();

// *** Insertion specific operations ***

run("FeatureJ Laplacian", "compute smoothing=&b");
selectImage(initimage);
close();
selectImage(initimage+" Laplacian");
rename(initimage);

// *** End Insertion specific operations ***

// Save and close images

       // Safe and close FILTERED IMAGE
         selectWindow(initimage);
         saveAs(format, dir2+"Laplacian_of_Gaussian_r"+b+"_"+list[i]);  //
Safe with a prefix indicating filter radius
         close();


//Print progress report
print("processed file ", list[i]);

     }
 }

//Final message progress report
print("successfully processed ", list.length, " files");
showMessage("Batch processing finished");

 }


macro "Abort" {
      abort = true;
}

//-----------
//Macro END


---
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]

2017-04-26 0:45 GMT+03:00 Ved Sharma <[hidden email]>:

> You can use Process > Batch > Macro...
>
> Put the run(FeatureJ, options) in the text box and you should be good to
> go. You can use macro recorder to generate this line.
>
> Ved
>
> ___________________________________
> Ved Sharma, PhD
> Department of Anatomy and Structural Biology
> Albert Einstein College of Medicine
> Bronx, New York
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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