Re: Macro has slowed down dramatically when run in background

Posted by nelssara on
URL: http://imagej.273.s1.nabble.com/Macro-has-slowed-down-dramatically-when-run-in-background-tp5013659p5013661.html

Also, here is the code for the macro I am running. I have the batchmode as false, because otherwise it throws an error (and I am working with two monitors, so I can just leave imagej up and flashing away while I do other things...).

dir = getDirectory("Choose a Directory to PROCESS");    
    list = getFileList(dir);                                                    
dir2 = getDirectory("Choose a Directory for SAVING the PLA Image");
dir3 = getDirectory("Choose a Directory for SAVING the speckled PLA Image");  
   


 setBatchMode(false);              
    for (f=0; f<list.length; f++) {
        path = dir+list[f];                      
print(path);                                    
        showProgress(f, list.length);    
        if (!endsWith(path,"/")) open(path);
if (nImages>=1) {                                        
  if (endsWith(path,"f")) {

   t=getTitle();                                      
   s=lastIndexOf(t, '.');                          
   ts=substring(t, 0,s);
 
 
  ts2= ts +' PLA';
  ts3= ts + ' speck';
  ts4= ts + ' mask';                                                                                      

//Split channels
        run("Split Channels");
        selectWindow(t + " (blue)");
        close();
        selectWindow(t + " (green)");
        close();
        selectWindow(t + " (red)");
        run("Subtract Background...", "rolling=50");
        run("Duplicate...", " ");
        selectWindow(t + " (red)-1");
        run("Gray Morphology", "radius=3.5 type=circle operator=erode");
        run("Gray Morphology", "radius=3.5 type=circle operator=dilate");
        imageCalculator("Subtract create", t + " (red)", t + " (red)-1");
        selectWindow("Result of " + t + " (red)");
        rename(ts3);                                      
    saveAs("Tiff",  dir3 + ts3);
    run("Duplicate...", " ");
    setAutoThreshold("Triangle dark");
    setOption("BlackBackground", false);
    run("Convert to Mask");
        run("Make Binary");
        run("Divide...", "value=255");
        saveAs("Tiff",  dir3 + ts4);
        setMinAndMax(0, 1);
        imageCalculator("multiply create", ts3 + ".tif", ts4 + ".tif");
        selectWindow("Result of " + ts3 +".tif");
        run("Brightness/Contrast...");
   run("32-bit");
   run("Divide...", "value=255");
   run("Brightness/Contrast...");
   setMinAndMax(0,1);
   run("Set Measurements...", "integrated limit display redirect=None decimal=1");
   run("Measure");
   rename(ts3);                                      
   saveAs("Tiff",  dir3 + ts3);
   selectWindow(t + " (red)");
   rename(ts2);
   saveAs("Tiff", dir2 + ts2);
   run("Close All");
               

       }                                
  }
}      

selectWindow("Results");
saveAs("results", dir2 + "PLA Intensity values 2.xls");