Added APR read options #135
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Following previous PR, the format for APR tracking files has changed. I've added a small section that will read these files (if they exist) and output a df that contains the information that would be needed for plotting.
This routine went into read_phantom.py because it required the dump filename (this is safer than using the time in the simulation). By producing a df with the position and size of the APR region, the user can choose exactly how it is plotted. This also circumvents the rotation problem; both sdf_sinks and sdf_apr will require rotation to be taken into account somehow but both can be treated the same when that is done. Naturally allows for multiple APR regions.
I'll edit the documentation to include an example if you're happy with the above changes.