First, we need to read the ASCII header file that describes the raw data file contents. On the right, this header is shown as it will be opened by ImageJ via drag and drop.

We open a buffered reader to parse the ASCII file:

BufferedReader br = new BufferedReader(new FileReader(MHDfilename));

Next, we read the first line, to initialize the String line

line = br.readLine();

Now we have to go through the file row by row to find the relevant information. We sub-divide each line into variable-name and variable-value. Having done that, we save the value in a predefined variable.

The for us relevant variables are as followed: 

• BinaryDataByteOrderMSB
  String [] split = line.split(" = ");
  if (line.contains("BinaryDataByteOrderMSB")){
    boolean value = Boolean.parseBoolean(split[1]);
    intelByteOrder = !value;
  }

•  Offset
  if (line.contains("Offset")){
    String [] split2 = split[1].split(" ");
    offsets = new double [split2.length];
    for (int i=0; i < split2.length; i++){
      offsets[i] = Double.parseDouble(split2[i]);
    }
  }
  
  
• ElementSpacing
  if (line.contains("ElementSpacing")){
    String [] split2 = split[1].split(" ");
    spacings = new double [split2.length];
    for (int i=0; i < split2.length; i++){
      spacings[i] = Double.parseDouble(split2[i]);
    }
  }

• DimSize
  if (line.contains("DimSize")){
    String [] split2 = split[1].split(" ");
    width = Integer.parseInt(split2[0]);
    height = Integer.parseInt(split2[1]);
    nImages = Integer.parseInt(split2[2]);
  }
  
  
• ElementType
  if (line.contains("ElementType")){
  if (split[1].equals("MET_USHORT")) fileType = FileInfo.GRAY16_UNSIGNED;
  
  
• ElementDataFile
  if (line.contains("ElementDataFile")){
    datafile = split[1];
  }