/*
Author: Ahsen Chaudhry
Last updated: June 14, 2019
This macro will add each mitochondrial object in 3D stacks to the ROI manager. The assigned number labels to the mitochondria 
correspond to the results of the 3D Analysis command.
*/

macro Display3DMitoROI
{
	inputName = getTitle();
	if (checkIfThresholded(inputName)==false) exit("Needs a thresholded input");

	
	Stack.getDimensions(w, h, channels, slices, frames);
	if (slices==1) exit("Needs 3D input");
	if (frames>1) 
	{
		Stack.getPosition(channel, slice, frame);
		run("Duplicate...", "duplicate");
		inputName = inputName + " Frame: " + frame;
		rename(inputName);
	}
	
	var mitoCount;
	setBatchMode(true);
	
	run("3D OC Options", "volume surface nb_of_obj._voxels mean_distance_to_surface dots_size=5 font_size=10 " + 
	"redirect_to=none");
	getVoxelSize(width, height, depth, unit);
	voxel = width*height*depth;
	sizeFilter = 0.05 / voxel;
	run("3D Objects Counter", "threshold=50 slice=1 min.=" + sizeFilter + " max.=13369344 objects statistics summary");
	mitoCount = Table.size("Results");
	close("Results");
	
	run("3D Manager");
	selectWindow("Objects map of " + inputName);
	Ext.Manager3D_AddImage();	
	
	/* There is currently a bug in the 3D ImageJ Suite. A fix is being awaited.
	for (i = 0; i < mitoCount;i++)
	{
		Ext.Manager3D_Select(i);
		newName = inputName + " Mito # " + (i+1);
		newNum = i + 1;
		Ext.Manager3D_Rename(newName );
	}
	*/
	close("Objects map of " + inputName);
	setBatchMode(false);
	selectWindow(inputName);


	
	function checkIfThresholded (image)
	{
		var thres = false;

		selectWindow(image);
		run("Z Project...", "projection=[Max Intensity]");
		getHistogram(values,counts,256);
		counter = 0;
		for (i = 0; i < values.length; i++) {if (counts[i]>1) counter++;}
		if (counter<=2) thres = true;
		close("MAX_" + inputName);
		selectWindow(image);

		return thres;
	}
}