Axis Position Logger

Well, that was easy.

can i connect the menu options on the position-logger application with the halpin on the AXIS controller so that i can record the position with an external button (parport input)?

some menus as in the picture

You could import the 'hal' library and create hal pins like this (example here is a digital input pin 'log-trigger'):
 

after launching linuxcnc and the logger this should show up as a hal pin:

 

You can add the actions for these pin to the 'update' function (example triggers a log on pin 'log-trigger' changing from 0->1)
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