Split up refine_time into two functions so the calculation can be called separately

Closes #159

See merge request !97

Camilla Compton authored 4 years ago and Jameson Rollins committed 4 years ago

This is mainly a copy/paste to split the refine.py function refine_time into two functions:

* find_transition: Takes an input of the time window and dictionary containing information about the channel needed for refinement (channel, std, min); then outputs the threshold used and refined time.
* refine_time: Does the job of the old refine_time function but calls new find_transition function to do the actual refinement calculation.

The reason for this change is that in the future I would like add a plugin to look at speed or order of light falling off PDs. This plugin could then call the function refine_calculate rather than copy/pasting refinement code.

Only change made to logic is on lines 58-60, where now if the refinement has already been done, the previously refined time will be used to center the search window rather than the transition_gps. This will not make a difference for the normal refinement but should speed up future plugins that use the refinement calculation as the search window could be smaller.

Closes #159

until issues resolved