// Batch convert TIA or Gatan dm3 image file to tiff
// by Zhou XU
// 2020/05/05
// at Monash Centre for Electron Microscopy
// Windows 10 Enterprise Ver. 1803
// ImageJ ver. 1.52p

ImgNumber=0;
ImgFormat= ".ser";



//open directory of images
input = getDirectory("location where images are stored");
output = getDirectory("Location for results");

// determine number of Files of given FileFormat
list = getFileList(input);

for (i=0; i<list.length; i=i+1) {
	if (endsWith(list[i], ".ser")) {
	 	ImgNumber=ImgNumber+1;
		filename = input + list[i];
		print(filename);
		run("TIA Reader", ".ser-reader...=filename");
		
		// get the pixel size and unit of image, TIA reader should have set the scale when import in
		getPixelSize (unit, pixelWidth, pixelHeight);
		imageWidth = getWidth();
		HFW = imageWidth * pixelWidth;
		
		filename_short = substring(list[i], 0, lastIndexOf(list[i], "."));
		exportFile = output + filename_short +"_HFW"+ HFW + unit + ".tif";
		saveAs("Tiff", exportFile);
		run("Close All");
	}

}



//run("DM3 Reader...", "load=[]");