== Generating Masks ==

All scripts can currently only run on 32bit machines

 * Mask each band of a raw Specim file separately
   * Run seperate_band_mask.py -d <directory>|-f <filename> -s <save_path> -l|-o
   -d specify directory from which to read raw files (or specify directory using "-f <filename>")[[BR]]
   -f specify single raw file to read (or specify directory using "-d <directory>")[[BR]]
   -s specify path to save masks (required)[[BR]]
   -o specify overflow mask (or specify low signal mask using -l)[[BR]]
   -l specify low signal mask (or specify overflow mask using -o)[[BR]]

    Creates a bil with the same number of bands as the raw file.  Masked pixels are marked as 1, everywhere else is 0.

 * Combine masks of each band of a raw Specim file into a single layer
   * Run combined_band_mask.py -d <directory>|-f <filename> -s <save_path> -l|-o
   Options the same as 1st script

    Saves as a png

 * Combine masks of each band of a raw Specim file into a a single layer overlayed onto an RGB image
   * Run overlay_combined_band_mask.py -d <directory>|-f <filename> -s <save_path> -l|-o
   Options the same as 1st script

    Saves as a png