_DKR_Sort_linear_spindles.txt

//20090617
//ImageJ macro by ciclistadan
//
//originally designed to take a straightened spindle image with the spindle exactly
//halfway down the image (at height/2)
//
//this macro has been changed to sort through a folder of straightened images, leaving open only those that meet certain criteria, namely length
//alternately, they can be sorted and saved in a new folder

macro "_DKR_Sort_linear_spindles"{

setBatchMode(true);
//creates folders 0 to length1, len1 to len2, len2 to len3
length1  = 4.5;      //length in microns
length2  = 10;     //length in microns
length3  = 15;
sort        = "yes"; 
leaveopen   = "no";

//batch functions, comment out for indivudual use
dir1 = getDirectory("Choose source directory");
if (dir1=="")
      exit("No directory available");
list = getFileList(dir1);

  dir2 = dir1+"0_to_"+length1+"um_spindles"+File.separator;
  dir3 = dir1+length1+"_to_"+length2+"um_spindles"+File.separator;
  dir4 = dir1+length2+"_to_"+length3+"um_spindles"+File.separator;
  
  File.makeDirectory(dir2);
  if (!File.exists(dir2))
      exit("Unable to create directory2");
  File.makeDirectory(dir3);
  if (!File.exists(dir3))
      exit("Unable to create directory3");
  File.makeDirectory(dir4);
  if (!File.exists(dir4))
      exit("Unable to create directory4");

//open each image
for(i=0;i<list.length;i++){
	showProgress(i/list.length);
	if(File.isDirectory(dir1+list[i])){
		}
	else{
		open(dir1+list[i]);
		selectWindow(list[i]);
		
		getDimensions(width, height, channels, slices, frames);
		getPixelSize(unit, pixelWidth, pixelHeight);
		name = list[i];
		spindleLength = width*pixelWidth;
		
		if(spindleLength < length1){
			run("Subtract Background...", "rolling=50");
			saveAs("Tiff", dir2+name);
			selectWindow(list[i]);
			close();
			}
		else if(spindleLength >= length1 && spindleLength < length2){
						run("Subtract Background...", "rolling=50");
			saveAs("Tiff", dir3+name);
			selectWindow(list[i]);
			close();
			}
		else if(spindleLength >= length2 && spindleLength < length3){
			run("Subtract Background...", "rolling=50");
			saveAs("Tiff", dir4+name);
			selectWindow(list[i]);
			close();
			}
		
		else{
			selectWindow(list[i]);
			close();
			}
		
		}
	}

	print('images sorted');
		
}