// Dave Barry, Francis Crick Institute
// 2018.08.14
// david.barry@crick.ac.uk

// Generates "preview" images of stacks in a directory

macro "Huygens Browser"{
	input = getDirectory("Choose Input Directory");
	list = getFileList(input);
	Dialog.create("Huygens Browser");
	Dialog.addNumber("Number of channels:", 3);
	Dialog.addNumber("Display constrast saturation (0.0 - 1.0):", 0.35);
	Dialog.addString("File extension:", ".tif");
	Dialog.show();
	channels = Dialog.getNumber();
	saturation = Dialog.getNumber();
	extension = Dialog.getString();
	for (i = 0; i < list.length; i++){
		if(endsWith(toLowerCase(list[i]), toLowerCase(extension))){
			makePreview(input, list[i], channels);
			waitForUser("Huygens Browser", "Press OK to open next image.");
		}
	}
	print("Done");
	
	function makePreview(input, filename, channels) {
		fullFilename = input + filename;
		print (fullFilename);
		run("Bio-Formats Importer", "open=fullFilename color_mode=Custom rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
		slices = nSlices() / channels;
		run("Stack to Hyperstack...", "order=xyzct channels=" + channels + " slices=" + slices + " frames=1 display=Composite");
		Stack.setSlice(slices / 2);
		for(c = 1; c <= channels; c++){
			Stack.setChannel(c);
			run("Enhance Contrast", "saturated=" + saturation);
		}
	}
}