batch mode generates macro failure

Posted by Josep M. Lanau on Aug 05, 2008; 11:08am
URL: http://imagej.273.s1.nabble.com/batch-mode-generates-macro-failure-tp3695456.html

I have recently programmed a macro for measuring objects. Each object
(gray) in the image contains a white particle (background is black). I
measure the shortest and largest distance (if any) from this particle to
the object's surface, along with some other parameters (areas, etc.). This
macro works fine.

Now I want to run this macro in a large amount of images, so I have built
another macro that calls first one and iterates for all images in a
directory.

Everything works perfect, but as soon as add a "setBatchMode(true);" line
in any of the two macros, the first macro does not work.

Can anyone help? I do atach the macros in case you should need them.

Thank you in advance.

Josep M. Lanau

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//                ***** MESURA BOLETS *****
// Creat: JML 01-Març-2008
// Últim modificat el: 5/08/08

macro "Mesura bolets" {

//setBatchMode(true);
nom=getTitle();

print("Imatge, Numbolet, AreaBarret, DiamBarret, PerimBarret, XBarret,
YBarret, AreaCama, XCama, YCama, DiamCama, PerimCama, Lateralitat,
Antilateralitat");

//Neteja roiManager i deselecciona tot

seleccions=roiManager("count")

if (seleccions>0) {
   roiManager("Select", 0);
   roiManager("Delete");

   seleccions=roiManager("count");
   if (seleccions>0) {
      roiManager("Combine");
      roiManager("Delete");
   }
}

// Poso a escala
// run("Set Scale...", "distance=296 known=5 pixel=1 unit=cm global");
// Compto el número de partícules.

run("Set Measurements...", "area centroid perimeter feret's limit display
redirect=None decimal=3");
run("Clear Results");
run("Select None");
setThreshold(35, 255);
run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00
show=Nothing display clear include summarize add");

// Agafo Núm partícules i iterar:

numparticules=roiManager("count");

cas=0;
do {
  run("Set Measurements...", "area centroid perimeter feret's limit display
redirect=None decimal=3");
  roiManager("Select", cas);

  //Duplico,

  run("Enlarge...", "enlarge=1");
  run("Duplicate...", "title=[barretikama"+cas+".jpg]");
  run("Enlarge...", "enlarge=-1");
  run("Colors...", "foreground=white background=black selection=yellow");
  run("Clear Outside");

  // Selecciono blanc, Mesuro cama

  setThreshold(250, 255);
  run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00
show=Nothing display clear include");
  AreaCama=getResult("Area");
  PerimCama=getResult("Perim.");
  DiamCama=getResult("Feret");
  XCama=getResult("X");
  YCama=getResult("Y");
  run("Select None");

  // Seleciono blanc +gris, mesuro barret

  setThreshold(50, 249);
  run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00
show=Nothing display clear include");
  AreaBarret=getResult("Area");
  PerimBarret=getResult("Perim.");
  DiamBarret=getResult("Feret");
  XBarret=getResult("X");
  YBarret=getResult("Y");

  //Miro si hi ha forat

  run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00
show=Nothing display clear");
  diferencia=AreaBarret-getResult("Area");

  lateralitat=0;

  // si hi ha forat mesuro lateralitat

  if (diferencia!=0) {
    run("Duplicate...", "title=[distancies.jpg]");
    run("Colors...", "foreground=black background=white selection=yellow");
    setThreshold(50, 255);
    run("Make Binary", "thresholded remaining black");
    run("Distance Map");
    run("Invert");
    // wait(1500);
    selectWindow("barretikama"+cas+".jpg");

    setThreshold(250, 255);
    run("Create Selection");
    run("Set Measurements...", " min limit display redirect=distancies.jpg
decimal=3");
    run("Measure");
    lateralitat=getResult("Min");
    selectWindow("distancies.jpg");  
    close();  
  }


  selectWindow("barretikama"+cas+".jpg");
  run("Select None");
  run("Duplicate...", "title=[distancies2.jpg]");
  run("Colors...", "foreground=black background=white selection=yellow");
  setThreshold(50, 254);
  run("Make Binary", "thresholded remaining black");
  run("Distance Map");
  run("Invert");
  // wait(1500);
  selectWindow("barretikama"+cas+".jpg");
  setThreshold(50, 254);
  run("Create Selection");
  run("Set Measurements...", " min limit display redirect=distancies2.jpg
decimal=3");
  run("Measure");
  antilateralitat=getResult("Max");
  selectWindow("distancies2.jpg");  
  close();  
 
  selectWindow("barretikama"+cas+".jpg");
  close();

  // imprimeixo resultats a log window

  print(nom, cas+1, AreaBarret, DiamBarret, PerimBarret, XBarret, YBarret,
AreaCama, XCama, YCama, DiamCama, PerimCama, lateralitat, antilateralitat );
  cas=cas+1;

} while (cas<numparticules);

--------


//                ***** BATCH PREPARA I MESURA BOLETS *****

macro "Batch Mesura bolets" {



    dir = getDirectory("Escull el directori a mesurar");
    list = getFileList(dir);

//setBatchMode(true);

    for (i=0; i<list.length; i++) {
        path = dir+list[i];
        showProgress(i, list.length);
        if (!endsWith(path,"/")) open(path);
          if (nImages>=1) {
            run("Run...", "run=[C:\\Program
Files\\ImageJ\\macros\\XOP_MesuraBolets.txt]");
          }
          wait(500);
          selectWindow(list[i]);
          close();
        }
    }

}