//Make a list of open images
function getOpenima(id){
openim=newArray(nImages);
if(nImages==0) exit("no image open");
for(i=1;i<=nImages;i++) { 
	selectImage(i);
          if(id==true) openim[i-1]=getImageID();
          else openim[i-1]=getTitle;
      } 
return openim;
}



//Close windows except those spécified
function closeWindowexept(openim,exept){
ima=getOpenima(true);
for(i=0;i<ima.length;i++){
	closed=1;
	for(j=0;j<exept.length;j++){
			if(ima[i]==exept[j]) closed=0;
		}
	for(k=0;k<openim.length;k++){
			if(ima[i]==openim[k]) closed=0;
		}
	if(closed==1){
		selectImage(ima[i]);
		close();
		}
	}
}


//Create a dialogue box to choose the images
function getChoiceim(){
list=getOpenima(false);
Dialog.create("Images selection");
Dialog.addChoice("Mask (8-bit binary image, backgroung=black)",list);
Dialog.addChoice("Image to process (16 bit)",list);
Dialog.show;
cmask=Dialog.getChoice(); 
selectImage(cmask);
imask=getImageID();
cima=Dialog.getChoice(); 
selectImage(cima);
iima=getImageID();
choice=newArray(imask,iima);
return choice;
}


//Evaluate type of the image to be treated 
function getType(choice){
type=newArray(4);
selectImage(choice[0]);
type[0]=bitDepth();
type[2]=nSlices();
selectImage(choice[1]);
type[1]=bitDepth();
type[3]=nSlices;
return type;
}


//Show an error message if image to be treated are not in te corrected type
function showErrorchoice(type){
if(type[0]!=8){
	exit("mask (black background) image must be 8-bit type"); 
	}
if(type[1]!=16){
	exit("image to be treated must be 16-bit type"); 
	}
if(type[2]!=type[3]){
	exit("image and mask must have the same number of slices");
	}
}


//Apply by subtraction the mask to the image
function applyMask(mask,im,openim){
selectImage(mask);
run("Duplicate...", "title=inter duplicate");
inter=getImageID();
run("16-bit");
run("Divide...", "stack value=255");
imageCalculator("Multiply create stack", inter,im);
rename("result");
res=getImageID();
exept=newArray(1); exept[0]=res;
closeWindowexept(openim, exept);
return res;
}


macro "apply mask"{
openim=getOpenima(true);
choice=getChoiceim();
showErrorchoice(getType(choice));
applyMask(choice[0],choice[1],openim);
run("Tile");

}




macro"help"{
message1= "Use this macro to create a image in which the background is set at zero whereas the particles of interest, that are specified by a mask, keep their original intensity. ";
message2= "Image informations:\n \t-Image must be 16-bit type \n \t-Mask is a binary black background image to specify pixels that belong to the particles of interest";
message=message1+"\n"+message2;
showMessage("help",message);
}