//Kalen edits
//12/1/14 added option for Nothing Markers in previous images
//12/2/14 changed ("SpineWithInhibitorySynapse" category names
//12/5/14 added error checking to the alignment option;

// 1/7/14 added stats result window showing number objects and image start stop points

//2/23/15 changed C button to turn channels on or off only
//Vars have to be defined at the top of the file, else some hard to fix errors occur.
//variable below saves Z state


var Zext = 0;
var ALock = 0;
var tempSave = 0;
//Variables here are for Emad's functions below
var alignMe = newArray(); 
var theOrigin = -1;
var alignmentOption = "";
var applyMarkersToPrevious = "Yes";




//Gets the toolbar ready for objectJ analysis
macro "Lock Alt Key On or Off for Scrolling ESC aborts Action Tool - C037T0b11AT8b09cTcb09t" {
	run("Action Bar","/plugins/ActionBar/_Kalensbar.txt");
}

macro "Count object types in each image in the current object file Action Tool - C037T0b11CT8b09nTcb09t" {
	Landmark=0;
	SpineWithPSD=0; 
	InhibitoryShaft=0; 
	SpineWithInhibitorySynapse=0; 
	NudeSpine=0; 
	Nothing=0;
	lastLandmarkImage=0;



	markers = newArray("Landmark","SpineWithPSD","InhibitoryShaft","SpineWithInhibitorySynapse","NudeSpine","Nothing"); 
	valArray= newArray(Landmark,SpineWithPSD,InhibitoryShaft,SpineWithInhibitorySynapse,NudeSpine,Nothing); 
	imageTemp=1; 

	for (n=1;n<=ojNObjects();n++){ 

		column="Landmark_X"; 
		if( ojResult(column,ojIndexToRow(n)) >0){ 
			lastLandmarkImage++;
		}

		for(markTypeNum=0;markTypeNum<6;markTypeNum++){ 
			column=markers[markTypeNum]+"_X"; 
			if( ojResult(column,ojIndexToRow(n)) >0){ 
				valArray[markTypeNum]=valArray[markTypeNum]+1; 
			} 

		}
 
		if(n==ojLastObject(imageTemp)){ 


			setResult("First Object", imageTemp-1, ojFirstObject(imageTemp));
			setResult("Last Object", imageTemp-1, ojLastObject(imageTemp));
			setResult("Last Landmark Object", imageTemp-1, lastLandmarkImage);

			for(markTypeNum=0;markTypeNum<6;markTypeNum++){ 
				setResult(markers[markTypeNum]+"#", imageTemp-1, valArray[markTypeNum]); 
			} 
			setResult("Label",imageTemp-1,ojGetImageName(imageTemp)); 

			//Reseting for the next image	
			imageTemp++;
			lastLandmarkImage=n;
			 
			valArray= newArray(Landmark,SpineWithPSD,InhibitoryShaft,SpineWithInhibitorySynapse,NudeSpine,Nothing); 
		}
	}
	IJ.renameResults("Synaptic Counts Per Image")
}


macro "Go to Object Action Tool - C037O00aaL99ff" {
//This finds markers based on what they are labeled as on an image
	//if (isKeyDown("shift")) 
		ojnum=getNumber("Go to Object # on all sessions ", 0);
		currentimage=ojImageLink();
		firstoncurrentimage=ojFirstObject(currentimage);
		zoom=getZoom();
		//print("after get zoom");
		totalimages=ojNImages();
		for (n=1; n<=totalimages; n=n+1){
			
		    firstonimage=ojFirstObject(n);
			relativeid=ojnum+firstonimage-1;
			// the below makes sure this isnt the image I was on, that it is open, and that it has the mark I want. 
		    if (n != currentimage && ojGetImageValue(n, "ID")!=0 && ojLastObject(n)>=relativeid) {
				//ojShowImage(n);
				ojShowObject(relativeid);
				yoj=ojYPos(1);
				xoj=ojXPos(1);
				ojZoom(zoom,xoj,yoj);
			}
			
		}
		// To return the view to the start
			ojShowImage(currentimage);
			ojShowObject(ojnum+firstoncurrentimage-1);
			yoj=ojYPos(1);
			xoj=ojXPos(1);
			ojZoom(zoom,xoj,yoj);
}

macro "Set all channels Action Tool - C059T3e16C" {
//This finds markers based on what they are labeled as on an image
		currentimage=ojImageLink();
		var min=newArray(3);
		var max=newArray(3);
		ok = getBoolean("The display range of the current\n"
        +"image will be propagated to all open images.");
   		 if (!ok) exit();
   		 
		for (i=0; i<3; i++){
			Stack.setChannel(i+1);
			getMinAndMax(min[i], max[i]);
		}

		totalimages=ojNImages();
		for (n=1; n<=totalimages; n=n+1){
		    if (n != currentimage) {
			ojShowImage(n);
				for (i=0; i<3; i++){
					Stack.setChannel(i+1);
					setMinAndMax(min[i], max[i]);
				}
			}
		}
		// To return the view to the start
			ojShowImage(currentimage);
			Stack.setChannel(2)
;
}

//These are EMADS tools to do alignment inside ImageJ
//These are EMADS tools to do alignment inside ImageJ
macro "Align select images Action Tool - C059T3e16A " {
	var alignMeStr = "";
	var numAlignErrorBool=false;
	var numAlignErrorString = "";
	
	while (alignMe.length == 0 || theOrigin == -1)
	{
		// turn alignMe into a string
		for (anI = 0; anI < alignMe.length-1; anI++)
		{
			alignMeStr = alignMeStr + alignMe[anI] + ",";
		}
		if (alignMe.length != 0)
		{
			alignMeStr = alignMeStr + alignMe[alignMe.length-1];
		}
	
		showMessage("Error", "You haven't designated images that you want to align, or you haven't chosen an origin. Fix that.");
		
		// prompt for values
		//KB removed need for 0 indexing
		var alignChoices = newArray("No", "Yes");
		Dialog.create("Set origin and images to align");
		Dialog.addNumber("Number of origin image", theOrigin);
		Dialog.addString("Comma separated values of images to align ie 1,2,3,4", alignMeStr, 24);
		Dialog.addChoice("Overwrite non Landmark points in non Origin images above?", alignChoices, alignmentOption);
		Dialog.addChoice("Place empty markers in previous sessions?", alignChoices, applyMarkersToPrevious);
		Dialog.show();
	
		theOrigin = Dialog.getNumber();
		alignMe = split(Dialog.getString(), ",");
		alignmentOption = Dialog.getChoice();
		applyMarkersToPrevious = Dialog.getChoice();
			
	}
	for (anI = 0; anI < alignMe.length; anI++)
	{
		// turn alignMe into a string that doesn't end in a comma
		if (anI==alignMe.length){
			alignMeStr = alignMeStr + alignMe[anI];
		}else{
			alignMeStr = alignMeStr + alignMe[anI] + ",";
		}

	}
	
// confirm that the assumption of the origin having the most possible landmarks is true
		numOrigin=ojLastObject(theOrigin)-ojFirstObject(theOrigin)+1;
		
 	//error check for origin length
		for(i=1;i<=ojNImages();i++){
			numAlign=ojLastObject(i)-ojFirstObject(i)+1;
			if(numAlign>numOrigin){
				numAlignErrorString=numAlignErrorString+ i + ",";
				numAlignErrorBool=true;
			}
		}
		
		
	if (numAlignErrorBool){
		showMessageWithCancel("Potential Error","The following list of images have more objects than the origin you specified.\n "
			+"If any of these images are ones you wanted to align to, they will be deleted if you press ok.\n "
			+"If the image is not in your list to align, but you have enabled the place empty markers in previous sessions, "
			+"I haven't found an issue...YET. \n"
			+"I would think about whatever you thought you were going to do if I were you. "
			+"Pressing Cancel will not alter your project. \n\n"     
			+"Images with more objects than the origin you chose are: "
			+numAlignErrorString);
	}
		
	// ask the user for some confirmation
	if (getBoolean("You are about to align the following images: [" + alignMeStr + "] with image number " + theOrigin + " as the origin. Are you sure?"))
	{
		run("ptReg ", "command=doAlign align="+ alignMeStr + " origin=" + theOrigin + " overwrite=" + alignmentOption+ " emptyMarkers="+ applyMarkersToPrevious);
		showMessage("done");
	}

}

macro "Align select images Action Tool Options" {
	// turn alignMe into a string
	var alignMeStr = "";
	for (anI = 0; anI < alignMe.length-1; anI++)
	{
		alignMeStr = alignMeStr + alignMe[anI] + ",";
	}
	if (alignMe.length != 0)
	{
		alignMeStr = alignMeStr + alignMe[alignMe.length-1];
	}

	var alignChoices = newArray("No", "Yes");
	var alignChoices2 = newArray("No", "Yes");
	Dialog.create("Set origin and images to align");
	Dialog.addNumber("Number of origin image", theOrigin);
	Dialog.addString("Comma separated values of images to align", alignMeStr, 24);
	Dialog.addChoice("Overwrite non Landmark points in non Origin images above?", alignChoices, alignmentOption);
	Dialog.addChoice("Place empty markers in previous sessions?", alignChoices2, applyMarkersToPrevious);
	Dialog.show();
	
	theOrigin = Dialog.getNumber();
	alignMe = split(Dialog.getString(), ",");
	alignmentOption = Dialog.getChoice();
	applyMarkersToPrevious = Dialog.getChoice();
}
macro "Extend Z Action Tool - C059T3e16Z " {
	if (Zext == 0){
		Zext = 1;
		numberper=getNumber("Value visible +- marked Z plane : ", 1);

		ojExtendVisibilityDepth(numberper, numberper);
	} else {
		Zext = 0;
		ojExtendVisibilityDepth(0, 0);
	}

}


macro "Open and or move all other images in project to same location as current image Action Tool - C059T3e16S " {
	currentimage=ojImageLink();
	totalimages=ojNImages();
	getLocationAndSize(x, y, width, height);
	for (n=1; n<=totalimages; n=n+1){
		    if (n != currentimage) {
			ojShowImage(n);
			wait(15);
			setLocation(x, y);
			}
	}
}