_DKR_Batch_split_mosaic.txt

// created by Dan Rozelle 20091005
//used to quickly open each DV movie, and wait to do some simple manual function or paste another macro as a function


macro "split"{

//list auto functions here, adjust mode as necessary
function batchfunction();
mode="MANUAL";  //use "MANUAL" or "AUTO" or "BOTH"

if(nImages>0) exit ("close all images before proceeding");


dir1 = getDirectory("Choose source directory");
if (dir1=="")
      exit("No directory available");

//get a list of all the files in this folder 
preList = getFileList(dir1);
size=0;

//include only certain filetypes
	filter=".zvi";
	

//count each '*filter*' files
for(place=0;place<preList.length;place++){
	if(endsWith(preList[place],filter)){
		size++;
	}
}
//create a new array and populate with filtered images
list=newArray(size);
position=0;
for(place=0;place<preList.length;place++){
	if(endsWith(preList[place],filter)){
		list[position]=preList[place];
		position++;
		}
	}



//starting with the first image, we increment through each image until we have done 6, or finish our list, whichever comes first
  for(i=0; i<list.length; i++) {
	
	run("Bio-Formats Importer", "open="+dir1+list[i]+" color_mode=Composite view=Hyperstack stack_order=XYCZT ");
	base = File.nameWithoutExtension;


	selectWindow(list[i]);
	rename("current");
	batchfunction(base,dir1);

	
	//close the window after dialog box is closed
	selectWindow("current");
	close();
	}
}

showMessage("done")



function batchfunction(base, dir1)
{

selectWindow("current");
run("Enhance Contrast", "saturated=0.35");
run("Specify...", "width=2688 height=2048 x=0 y=0 slice=1");
run("Duplicate...", "title="+base+"-1.zvi duplicate channels=1-3 frames=1-7");
selectWindow(base+"-1.zvi");
saveAs("Tiff", dir1+base+"-1.tif");
selectWindow(base+"-1.tif");
close();

selectWindow("current");
run("Specify...", "width=2688 height=2048 x=2688 y=0 slice=1");
run("Duplicate...", "title="+base+"-2.zvi duplicate channels=1-3 frames=1-7");
selectWindow(base+"-2.zvi");
saveAs("Tiff", dir1+base+"-2.tif");
selectWindow(base+"-2.tif");
close();

selectWindow("current");
run("Specify...", "width=2688 height=2048 x=0 y=2048 slice=1");
run("Duplicate...", "title="+base+"-3.zvi duplicate channels=1-3 frames=1-7");
selectWindow(base+"-3.zvi");
saveAs("Tiff", dir1+base+"-3.tif");
selectWindow(base+"-3.tif");
close();

selectWindow("current");
run("Specify...", "width=2688 height=2048 x=2688 y=2048 slice=1");
run("Duplicate...", "title="+base+"-4.zvi duplicate channels=1-3 frames=1-7");
selectWindow(base+"-4.zvi");
saveAs("Tiff", dir1+base+"-4.tif");
selectWindow(base+"-4.tif");
close();
}