Eliminated sending indices into tracmass

Stopped the unnecessary practice of sending ia, ja, ka into tracmass since they can be inferred from xstart, ystart, zstart. This meant deleted several pieces of code in run.py. Also changed tools.convert_indices() to not expect i, j when converting indices.

By chance, also noticed that zsave in run.py was a little out of date and updated it so that it uses map_coordinates, similar to what happens at the end of each loop to call tracmass.