// author: Matthias Muelke; Institut für Experimentelle Unfallchirurgie Gießen

dir1=getDirectory("Input");
dir2=getDirectory("Working directory");


Dialog.create("settings");
Dialog.addNumber("scale [pixels/µm] (microscope)", 1.55);
Dialog.addNumber("downsizing", 0.25);
Dialog.addMessage("");
Dialog.addCheckbox("Thickness", true);
Dialog.addCheckbox("Separation", true);
Dialog.addCheckbox("Area", true);
	Dialog.show();
scale = Dialog.getNumber();
downsizing = Dialog.getNumber();;
mode_Th = Dialog.getCheckbox();;;
mode_Sep = Dialog.getCheckbox();;;;
mode_Area = Dialog.getCheckbox();;;;;


s=scale*downsizing ;

if(File.exists(dir2+"Thickness")) {
	print("folder already exists");
}else{
	myDir3=dir2+"Thickness"+File.separator;
	File.makeDirectory(myDir3);
	print("new folder created");
}

dir3=dir2+"Thickness\\";

if(File.exists(dir2+"Separation")) {
	print("folder already exists");
}else{
	myDir4=dir2+"Separation"+File.separator;
	File.makeDirectory(myDir4);
	print("new folder created");
}
dir4=dir2+"Separation\\";


setBatchMode(false);

list = getFileList(dir1);
for (j=0; j<list.length; j++) {
file1=dir1+list[j];

if (mode_Th==1) {
open(file1);

run("Set Scale...", "distance=s known=1 pixel=1 unit=µm");
run("Clear Outside");
setOption("BlackBackground", true);
run("Make Binary");
run("Thickness", "thickness graphic");


saveAs("Tiff", dir3+list[j]+"1.tif");
close();
close();
setResult("measurement", j, "Thickness"); 
}
if (mode_Sep==1 && mode_Th==1) {
	setResult(" ", j, " "); 
}

if (mode_Sep==1) {
open(file1);

run("ROI Manager...");
roiManager("Add");
setBackgroundColor(0, 0, 0);
run("Clear Outside");
run("Invert");


run("Set Scale...", "distance=s known=1 pixel=1 unit=µm");

run("Make Binary");
run("Invert");
run("Thickness", "spacing graphic");


saveAs("Tiff", dir4+list[j]+"2.tif");
close();
close();
setResult("measurement ", j, "Separation"); 
}

   while (nImages>0) { 
          selectImage(nImages); 
          close(); 
      } 
}


     MonthNames = newArray("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec");
     DayNames = newArray("Sun", "Mon","Tue","Wed","Thu","Fri","Sat");
     getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
     TimeString =DayNames[dayOfWeek]+"_";
     if (dayOfMonth<10) {TimeString = TimeString+"0";}
     TimeString = TimeString+dayOfMonth+"-"+MonthNames[month]+"-"+year+"_";
     if (hour<10) {TimeString = TimeString+"0";}
     TimeString = TimeString+hour+"-";
     if (minute<10) {TimeString = TimeString+"0";}
     TimeString = TimeString+minute+"-";
     if (second<10) {TimeString = TimeString+"0";}
     TimeString = TimeString+second;
     
if (mode_Sep==0 && mode_Th==0) {
	}else{
	if (mode_Sep==1 && mode_Th==1) {	
saveAs("Results", dir2+"Results_Thickness+Separation_"+TimeString+".xls");
	}else{
	if (mode_Th==1) {
	saveAs("Results", dir2+"Results_Thickness_"+TimeString+".xls");	
	}
	if (mode_Sep==1) {
	saveAs("Results", dir2+"Results_Separation_"+TimeString+".xls");	
	}
	}
selectWindow("Results");
run("Close");
if (mode_Sep==1) {
selectWindow("ROI Manager");
run("Close"); 
}
}


if (mode_Area==1) {

list = getFileList(dir1);
setBatchMode( true );
run("Set Measurements...", "area area_fraction redirect=None decimal=3");
for (j=0; j<list.length; j++) {
	
open(dir1+list[j]);
l=3*j;

run("Set Scale...", "distance=s known=1 pixel=1 unit=µm");
run("Measure");
run("Clear Outside");
run("Make Binary");
run("Invert");


// id values of each class in the classified image 
classLabels = newArray( 0, 1  );


run("Set Measurements...", "area area_fraction redirect=None decimal=3");

for( i=0; i<classLabels.length; i ++ )
{
minTh = classLabels[ i ];
maxTh = classLabels[ i ];
  if( i < classLabels.length - 1 )
  maxTh = classLabels[ i+1 ] -1;
else // last value is assumed to be 255
  {
minTh = classLabels[ i-1 ] +1;
  maxTh = classLabels[ i ];
}
  selectWindow(list[j]);
  run("Duplicate...", "title=[to-be-thresholded]"); selectWindow("to-be-thresholded");
  setThreshold( minTh, maxTh );
run("Convert to Mask");
  run("Measure");
close();
}
close();
new=getResult("Area",l);
new2=getResult("Area",l+1);
new3=getResult("%Area",l+1);
setResult("Tb.Ar/T.Ar", l, new3/(new/new2));
setResult("name", l, list[j]); 
}


saveAs("Results", dir2+"Results_Area_"+TimeString+".xls");
selectWindow("Results");
run("Close");
}