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> -lo

-d specify directory from which to read raw files (or specify directory using "-f <filename>")
-f specify single raw file to read (or specify directory using "-d <directory>")
-s specify path to save masks (required)
-o specify overflow mask (or specify low signal mask using -l)
-l specify low signal mask (or specify overflow mask using -o)

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> -lo

Options the same as 1st script

Saves as a png. Masked areas appear white and everywhere else black.

• 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> -lo

Options the same as 1st script

Saves as a png. Overflows are red, low values are blue.