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

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

macro "Stack Reformatter"{
	startTime = getTime();
	run("Bio-Formats Macro Extensions");
	setBatchMode(true)
	input = getDirectory("Choose Input Directory");
	output = getDirectory("Choose Output Directory");
	list = getFileList(input);
	Dialog.create("Huygens Browser");
	Dialog.addNumber("Number of channels:", 3);
	Dialog.addString("File extension:", ".tif");
	Dialog.show();
	channels = Dialog.getNumber();
	extension = Dialog.getString();

	i = -1;
	thisType = "false";
	while(thisType == "false"){
		i++;
		file = directory + fileList[i];
		Ext.isThisType(file, thisType);
	}

	Ext.setId(fileList[i]);
	Ext.getSizeC(sizeC);
	Ext.getSeriesCount(sCount);
	Ext.getDimensionOrder(dimOrder);
	IJ.log("Number of series: " + sCount);
	IJ.log("Number of channels: " + sizeC);
	IJ.log("Dimension order: " + dimOrder);

	for(s = 1; s <= sCount; s++){
		reformat(input, output, list[i], channels, s);
		print(round(s * 100.0 / sCount) + "% done");
	}

	setBatchMode(false);
	close("*");
	duration = (getTime() - startTime) / 1000;
	hours = floor(duration / 3600);
	minutes = floor((duration - hours * 3600) / 60);
	seconds = floor(duration - hours * 3600 - minutes * 60);
	print("100% Done: " + hours + ":" + minutes + ":" + seconds);
	
	function reformat(input, output, filename, channels, series) {
		fullInputFilename = input + filename;
		fullOutputFilename = output + filename + ".tif";
		print ("Reading " + fullInputFilename + " series " + series);
		run("Bio-Formats Importer", "open=[" + fullInputFilename + "] autoscale color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT series_list=" + series);
		//slices = nSlices() / channels;
		//run("Stack to Hyperstack...", "order=xyzct channels=" + channels + " slices=" + slices + " frames=1 display=Composite");
		print ("Writing " + fullOutputFilename);
		//run("Bio-Formats Exporter", "save=[" + fullOutputFilename + "] compression=LZW");
		saveAs("Tiff", fullOutputFilename);
	}
}