ojRecalculate();
totalImages=ojNImages();
ojNumCheck=newArray(totalImages);
for (i=1;i<=totalImages;i++){
	first=ojFirstObject(i);
	last=ojLastObject(i);
	ojNumCheck[i-1]=last-first+1;
}
for (i=1;i<lengthOf(ojNumCheck);i++){
	if (ojNumCheck[i-1]!=ojNumCheck[i]){
		exit("Aborted because you don't have the same number of objects on every image.")
	};
}

//the below fills out the column headers
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("ojj File Name", 0,"" );

markers = newArray(ojNColumns());
index=0;
for (i=1;i<=ojNColumns();i++){
	if(endsWith(ojGetColumnTitle(i),"xpos")){
		markers[index]=substring(ojGetColumnTitle(i), 0, indexOf(ojGetColumnTitle(i), "_"));//find the name before the _
		index++;
	}
}
markers=Array.trim(markers,index);
for (n=1;n<=totalImages;n++)	
	setResult("S "+n,0," ");

//
//	setResult("xpos S1",0,0);
//	setResult("ypos S1",0,0);	
//	setResult("zpos S1",0,0);	


for (n=1;n<=totalImages;n++){	
	setResult("Original S"+n,0," ");
	setResult("Checked S"+n,0," ");	
	setResult("Final S"+n,0," ");
}

for (n=1;n<=totalImages;n++){
	setResult("xpos S"+n,0,0);
	setResult("ypos S"+n,0,0);	
	setResult("zpos S"+n,0,0);	
}


path=ojGetProjectPath();
name=ojGetProjectName();

var markerNameCodes=call("ij.Prefs.get","marker.nameCode","");
if(markerNameCodes=="")
	showMessage("Set marker name value pairs in edit object settings of the action bar if you don't want to use the marker names themselves.");
else
	List.setList(markerNameCodes);

for (n=1; n<=ojNumCheck[0]; n++) {
	session=0; 
	setResult("Marker", n-1, n);

	for (imageOffset=0;imageOffset<=(totalImages-1)*ojNumCheck[0];imageOffset=imageOffset+ojNumCheck[0]){
		session++;
		setResult("ojj File Name", n-1,name );

		type="";
		for (i=0; i<lengthOf(markers);i++){

			column=markers[i]+"_"+"xpos";
			test=ojResult(column,n+imageOffset);
			if ( test>0 ) {			
				if(markerNameCodes=="")							
					type=markers[i];
				else{
					type=List.get( markers[i]);
					List.set(type,markers[i]);
				}
			}

			//print("n"+n+" imageoffset "+imageOffset+" test="+test+" type="+type);
		}

		if (type==""){exit("Something is wrong with the columns in your object file. They may not match the names of your markers");}

		setResult("Final S"+session,n-1,type);
		setResult("S "+session,n-1,type);	

		if(markerNameCodes=="")	{
			X=round(ojResult(type+"_xpos",n+imageOffset));
			Y=round(ojResult(type+"_ypos",n+imageOffset));
			Z=round(ojResult(type+"_zpos",n+imageOffset));
		}else{
			//print(n+imageOffset);
			X=round(ojResult(List.get(type)+"_xpos",n+imageOffset));
			Y=round(ojResult(List.get(type)+"_ypos",n+imageOffset));
			Z=round(ojResult(List.get(type)+"_zpos",n+imageOffset));
		}

		setResult("xpos S"+session, n-1, X);
		setResult("ypos S"+session, n-1, Y);	
		setResult("zpos S"+session, n-1, Z);

		//blank by default
		setResult("Original S"+session,n-1," ");
		setResult("Checked S"+session,n-1," ");
		if (ojColumnNumber("OrigType")>0){  //check if the track changes mode is on
			temp=ojResultString("OrigType",n+imageOffset);
			setResult("Original S"+session,n-1,List.get(temp));
		}
		if (ojColumnNumber("CheckedType")>0){ 
			temp=ojResultString("CheckedType",n+imageOffset);
			setResult("Checked S"+session,n-1,List.get(temp));		
		}

	}

}

updateResults();

saveAs("results",path+name+".csv");


if (startsWith(getInfo("os.name"), "Windows")){
	// forward slash is an escape character btw. need those quotations
	//print("copy "+ "\""+ojGetProjectPath()+"*.csv\" "+"\""+ojGetProjectPath()+"CombinedResults.csv\"");	
	//print("cmd.exe /C type NUL > "+"\""+ojGetProjectPath()+"CombinedResults.csv\"");
	
	exec("cmd.exe /C type NUL > "+"\""+ojGetProjectPath()+"CombinedResults.csv\"");
	exec("cmd.exe /C copy  /y "+ "\""+ojGetProjectPath()+"*.csv\" "+"\""+ojGetProjectPath()+"CombinedResults.csv\"");
// below is messy but gets rid of other headers
	open(ojGetProjectPath()+"CombinedResults.csv");
	updateResults();
	delArray=newArray();
	for(n=0;n<nResults;n++){
		test=getResult("Marker",n);	
		if (isNaN(test))
			delArray=Array.concat(delArray,n) ;		
	}
	
	Array.reverse(delArray);
	for (n=0;n<lengthOf(delArray);n++)
		call("ij.IJ.deleteRows", delArray[n],delArray[n]);						
	updateResults();
	saveAs("results",path+"CombinedResults.csv");
}