//Macro to stictch a DV-collected panel data set.
//Chris Gell 11-07-2018
//Version 1


//open a series from a .dv file, save them out so sinple Fiji stitching works.
//currently only supports single channels.




setBatchMode(true); 
open();

//get the size of the panel in tiles
xsize=getNumber("Enter the number of columns", 17);
ysize=getNumber("Enter the number of columns", 31);


//see if any images are open.
if (nImages<=1) {
	//
	Dialog.create("");
	Dialog.addMessage("Too few images open, open at least 2 images.");
	Dialog.show();
	exit; 
}
//where to save everything
dir = getDirectory("Choose a Directory for saving");

 //create an array with a list of open window names
 n = nImages; 
    
setBatchMode(true); 
    for (i=1; i<=n; i++) { 
        selectImage(i);
        rename("tile_"+i);
       title = getTitle;
       saveAs("tiff", dir+title); 

    }

 setBatchMode(false);
 
 //edit the grid size in this line 
 run("Grid/Collection stitching", "type=[Grid: snake by rows] order=[Right & Down                ] grid_size_x="+xsize+" grid_size_y="+ysize+" tile_overlap=1 first_file_index_i=1 directory="+dir+" file_names=tile_{i}.tif output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]");