_DKR_Batch_Split_DV_Channel.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 "_DKR_Batch_Split_DV_Channel"{

//list filetypes to include
filter="";

//which channel do you want to save (start with 0)
channel="1";

//list auto functions here, adjust mode as necessary
function batchfunction();
mode="AUTO";  //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");
	
dir2 = getDirectory("Choose output directory");
if (dir2=="")
      exit("No directory available");
      
//get a list of all the files in this folder 
preList = getFileList(dir1);
size=0;

	

//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++) {
	//open a two color image in separate channel stacks
	run("Bio-Formats Importer", "open="+dir1+list[i]+" view=Hyperstack stack_order=XYCZT split_channels autoscale");
	
	if(mode=="MANUAL"){
		wait(100);
		run("Install...", "install=C:\\ImageJ\\macros\\_DKR_AutoScaleBrightestSlice.txt");
		waitForUser("click OK \nto proceed"); 
		}
	
	else if(mode=="AUTO"){
		new=list[i]+" - C="+channel;
		selectWindow(new);
		print("output: "+dir2+new+".tif");
		saveAs("Tiff", dir2+new+".tif");
//		batchfunction(dir1, list[i]);
		
		
		}

	//close all windows after dialog box is closed
	while (nImages >0) close();
	}
}