//Kalen edits
//12/1/14 added option for Nothing Markers in previous images
//12/2/14 changed 


//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 "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){
		    if (n != currentimage) {
				firstonimage=ojFirstObject(n);
				relativeid=ojnum+firstonimage-1;
				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 = ""
	
	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();
			
	}
	
	// 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];
	}
	

	// ask the user for some confirmation
	
	var alignMeStr = "";
	for (anI = 0; anI < alignMe.length-1; anI++)
	{
		alignMeStr = alignMeStr + alignMe[anI] + ",";
	}
	if (alignMe.length != 0)
	{
		alignMeStr = alignMeStr + alignMe[alignMe.length-1];
	}
	
	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");
	}
	//for (anI = 0; anI < alignMe.length; anI++)
	//{
	//	toAlign = parseInt(alignMe[anI]);
	//	if (theOrigin != toAlign)
	//	{
	//		showMessage("aligning " + toAlign + " with origin " + theOrigin);
			//call("PtRegger.class.registerTwo", toAlign, theOrigin);
			//call("PtRegger.class.applyPoints", toAlign, theOrigin);
	//	}
	//}

}

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 "Move markers to one channel Action Tool - C059T3e16M " {
	channel=getNumber("Move all markers to channel: ", 1);
	imnum=1;
	totalimages=ojNImages();
	first=ojFirstObject(imnum);
	next=ojFirstObject(imnum+1);
	idlast=-1;

//the below fills out the column headers
	if (nResults>=0) run("Clear Results");     // Check whether the results table is empty, if not clear it.
		i = nResults;    // variable for counting, initialising with 0
		setResult("Marker", 0, 0);
		setResult("Imageid", 0,0 );
		setResult("X", 0, 0);
		setResult("Y", 0, 0);
		setResult("Z", 0, 0);
	setResult("SpineWithPSD",0,0 );
	setResult("InhibitoryShaft",0,0 );
	setResult("SpineWithInhibitorySynapse",0,0 );	
	setResult("NudeSpine",0,0 );
	setResult("Nothing",0,0 );
	setResult("Landmark",0,0); 


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

		if (n==next){
			imnum++;
			ojShowImage(imnum);
			wait(20);
			next=ojFirstObject(imnum+1);
		}


		setResult("Marker", n-1, n);
		setResult("Imageid", n-1, imnum );
		
		ojShowObject(n);
   
		X=ojXPos(1);
		Y=ojYPos(1);
		Z=ojZPos(1);
		//subtract remainder to equal ch1
		//ex slice 1=ch1 2 ch2 3 ch3 4 ch1 chose ch1 to set so 4-(4-1)%3=4 5-(5-1)%3=4 =6-(6-1)%3=4
		//channel -1 sets to 4 if ch1 5 if ch2 and 6 if ch3
		Z=Z-(Z-1)%3+(channel-1);
		setResult("X", n-1, X);
		setResult("Y", n-1, Y);
		setResult("Z", n-1, Z);
		setResult(ojSelectedItemName(), n-1,1 );
   }
   updateResults();
   ojDeleteAllObjects();

	idlast=0;
	for (n=0; n<nResults; n++){
	
	
		id=getResult("Imageid", n);
		if (idlast < id) {
	
        		ojShowImage(id);
				idlast=id;
		}
		setSlice(getResult("Z", n));
	

		if (getResult("SpineWithPSD", n)==1){
			name="SpineWithPSD";
		} else if (getResult("InhibitoryShaft", n)==1){
			name="InhibitoryShaft";
		} else if (getResult("SpineWithInhibitorySynapse", n)==1){
			name="SpineWithInhibitorySynapse";
		} else if (getResult("NudeSpine", n)==1){
			name="NudeSpine";
		} else if (getResult("Nothing", n)==1){
			name="Nothing";
		} else if (getResult("Landmark", n)==1){
			name="Landmark";
		}
    
		ojSwitchToItem(name);
		ojSetMarker(abs(getResult("X", n)), abs(getResult("Y", n)));
	}
	
updateResults();
}

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);
			}
	}
}