Thank you for the update. I do have two other questions that you may be able to help with.
Is it possible to use higher resolution gas maps for computing the pion emissivity? Or to obtain the quarter degree maps that are used by webrun? I have custom modifications to the GALPROP code and cannot use the online interface.
I am also somewhat confused by the descriptions of how the pion_decay skymap is computed. The gas distributions are cylindrically symmetric in e.g. Moskalenko et al 2002, but clearly the pion decay skymap contains gas structure that would not be part of this model and are presumably based upon the gas surveys. Could you briefly explain how this actually works, especially in the context of a 3-d simulation? I don't quite understand where the 3-d gas models are used and where the surveys are used in the context of pion decay.
EDIT: Question two is answered in detail at
http://iopscience.iop.org/0004-637X/750/1/3/pdf/apj_750_1_3.pdf