//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;


//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 = "";
	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();
			
	}
	// confirm that the assumption of the origin having the most possible landmarks is true
		numOrigin=ojLastObject(theOrigin)-ojFirstObject(theOrigin)+1;
		
	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] + ",";
		}
		//error check for origin length
		numAlign=ojLastObject(alignMe[anI])-ojFirstObject(alignMe[anI])+1;
		if(numAlign>numOrigin){
			numAlignErrorString=numAlignErrorString+ alignMe[anI] + ",";
			numAlignErrorBool=true;
		}
	}
	if (numAlignErrorBool){
		showMessageWithCancel("Potential Error","The following list of images have more objects than the origin you specified.\n They will be deleted if you press ok. Pressing Cancel will not alter your project. \n\n     Error Images = "+numAlignErrorString);
	}
		

	for (i=0;i<lengthOf(alignMe)
	

	// 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");
	}

}

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);
			}
	}
}