Thanks Robin I have asked there and Otmar has responded. He proposed an IRAF method I had already tried but it seems ISIS did not like the 1D result. It could have been a specific issue with the data I had.
In any even I have cracked the key issues in getting a Python program to read the data so I can write it out in an acceptable FITS format. Just need to complete the program and test it out.
Thanks for the advice.
Regards Andrew