// 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);

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

	Ext.setId(file);
	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 = 0; s < sCount; s++){
		reformat(input, output, list[i], s);
		print(round((s+1) * 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, series) {
		fullInputFilename = input + filename;
		fullOutputFilename = output + filename + "_series_" + series + ".tif";
		print ("Reading " + fullInputFilename + " series " + series);
		//Ext.setSeries(series);
		//Ext.openImagePlus(fullInputFilename);
		Ext.openImage(fullOutputFilename, series);
		print ("Writing " + fullOutputFilename);
		saveAs("Tiff", fullOutputFilename);
	}
}