_DKR_Measure_Linearized_Spindle.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"{

min_length  = 7;      //length in microns
max_length  = 15;     //length in microns
sort        = "yes"; 
leaveopen   = "yes";

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

  dir2 = dir1+min_length+"_to_"+max_length+"_spindles"+File.separator;
  File.makeDirectory(dir2);
  if (!File.exists(dir2))
      exit("Unable to create directory");

//open each image
for(i=0;i<list.length;i++){
	open(dir1+list[i]);
	selectWindow(list[i]);
	
	getDimensions(width, height, channels, slices, frames);
	getPixelSize(unit, pixelWidth, pixelHeight);
	name = File.name;
	spindleLength = width*pixelWidth;
	
	if(spindleLength > min_length && spindleLength < max_length){
		if(sort == "yes"){
			saveAs("Tiff", dir2+name+".tif");
			}
		else{}
		}
	
	}
	else{
		selectWindow(list[i]);
		close();
		}
	
	
	//decide if the image should be closed
	if(leaveopen == "yes"){
		}
	else{
		selectWindow(list[i]);
		close();
		}
}