// This macro will use Pairwise Stitching to merge mosaic z-stack timelapses into movies.  
// This works on one slice at a time
xTiles = 2;
yTiles = 2;
numFrames = 1;
numSlices = 3;
directory = '\\\\129.98.104.245\\d$\\Images\\Dave\\2015.11.24 - Survival Lung Window POD 1\\02 5x5 Mosaic';
baseFileName = "02 5x5 Mosaic";
overlapPixels = 100;
xBaseShift = 379.72928;
yBaseShift = 399.19302;


//Loop through all of the slices of the mosaic
for(sliceCount=1; sliceCount<=numSlices; sliceCount++)
{	
	//Loop through all of the frames of the mosaic
	numTiles = xTiles * yTiles;
	
	currentSlice = IJ.pad(sliceCount,4);
	print("Current slice: " + currentSlice);
	
	for(frameCount=1; frameCount<=numFrames; frameCount++)
	{
		currentFrame = IJ.pad(frameCount,3);
		for (yCount=1; yCount<=yTiles; yCount++)
		{
			yShift = yBaseShift *  (yCount - 1);
			for(xCount=1; xCount<=xTiles; xCount++)
			{
				xShift = xBaseShift * (xCount - 1);
				// Determine which image to open.
				currentTile = IJ.pad(xCount+((yCount-1)*xTiles),3);
				//Load up the Red, Green and Blue channels of the image
				open(directory + "\\" + baseFileName + "-" + currentFrame + "-Red-" + currentTile + "-" + currentSlice + ".tif");
				rename("Red");
				open(directory + "\\" + baseFileName + "-" + currentFrame + "-Green-" + currentTile + "-" + currentSlice + ".tif");
				rename("Green");
				open(directory + "\\" + baseFileName + "-" + currentFrame + "-Blue-" + currentTile + "-" + currentSlice + ".tif");
				rename("Blue");
				run("Merge Channels...", "c1=Red c2=Green c3=Blue create");
				selectWindow("Composite");
				rename("Tile-" + currentTile);
				getDimensions(width, height, channels, slices, frames);
	
				if(xCount==1)
				{
					rename("Tile-" + IJ.pad(1+((yCount-1)*xTiles),3));
				}
				else
				{			
					selectWindow("Tile-" + IJ.pad(1+((yCount-1)*xTiles),3));
					getDimensions(width1, height1, channels1, slices1, frames1);
					makeRectangle(width1-overlapPixels, 0, overlapPixels, height);
					selectWindow("Tile-" + currentTile);
					makeRectangle(0, 0, overlapPixels, height);
					run("Pairwise stitching", "first_image=Tile-" + IJ.pad(1+((yCount-1)*xTiles),3) + " second_image=Tile-" + currentTile + " fusion_method=[Max. Intensity] fused_image=Fused check_peaks=5 ignore x=&xShift y=0 registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
					selectWindow("Tile-" + IJ.pad(1+((yCount-1)*xTiles),3));
					close();
					selectWindow("Tile-" + currentTile);
					close();
					selectWindow("Fused");
					rename("Tile-" + IJ.pad(1+((yCount-1)*xTiles),3));
				}
			}	
	
			selectWindow("Tile-" + IJ.pad(1+((yCount-1)*xTiles),3));
			rename("Row-" + IJ.pad(yCount,2));
		
			if(yCount>1)
			{
				selectWindow("Row-01");
				getDimensions(width, height, channels, slices, frames);
				makeRectangle(0, height-overlapPixels, width, overlapPixels);
				selectWindow("Row-" + IJ.pad(yCount,2) );
				makeRectangle(0, 25, width, overlapPixels);
	
				run("Pairwise stitching", "first_image=Row-" + IJ.pad(1,2) + " second_image=Row-" + IJ.pad(yCount,2) + " fusion_method=[Max. Intensity] fused_image=Fused check_peaks=5 ignore x=0 y=&yShift registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
				selectWindow("Row-01");
				close();
				selectWindow("Row-" + IJ.pad(yCount,2) );
				close();
				selectWindow("Fused");
				rename("Row-01");
			}
		}
	
		selectWindow("Row-01");
		rename("Frame-" + currentFrame);
	
		if (frameCount==1)
		{
			selectWindow("Frame-" + currentFrame);
			rename("All Frames");
		}
		else
		{
			selectWindow("All Frames");
			getDimensions(width1, height1, channels1, slices1, frames1);
			selectWindow("Frame-" + currentFrame);
			getDimensions(width2, height2, channels2, slices2, frames2);
			newWidth = maxOf(width1, width2);
			newHeight = maxOf(height1, height1);
			selectWindow("All Frames");
			run("Canvas Size...", "width=&newWidth height=&newHeight position=Top-Left zero");
			selectWindow("Frame-" + currentFrame);
			run("Canvas Size...", "width=&newWidth height=&newHeight position=Top-Left zero");
			concatFrameString = "image1='All Frames' " + "image2=Frame-" + currentFrame;
			run("Concatenate...", "  title=[All Frames] " + concatFrameString + " image3=[-- None --]");
		}
	}

	selectWindow("All Frames");
	rename("Slice-" + currentSlice);
	run("Hyperstack to Stack");
		
	if (sliceCount==1)
	{
		concatSliceString = "image1=Slice-" + currentSlice;

	}
	else
	{
		concatSliceString = concatSliceString + " image" + sliceCount + "=Slice-" + currentSlice;
	}
}

if(numSlices>1)
{
run("Concatenate...", "  title=[&baseFileName] " + concatSliceString + " image" + numSlices+1 + "=[-- None --]");
}
run("Stack to Hyperstack...", "order=xyctz channels=3 slices=" + currentSlice + " frames=" + numFrames + " display=Composite");
rename(baseFileName);