Modify ref_build to take ref file not list

I modified the ref_build function of that AIAFile class, so that you can pass
in different types of reference files rather than a list of file names. This
was to accomodate the reference files from AMDIS, which put all reference info
into a single file. This required some modifications to the data.py and
calibration.py files as well.
Modified the mass extraction from the cdf file

I noticed that there were rounding errors with some of the masses, which I
think was causing some small problems. For example, although most masses
seemed to be 1 amu apart and slightly larger than their intended mass, some
masses appeared slightly below the intended mass. When forcing these to be
integers, they would round down instead of up. I changed the behavior to use
Numpy's round function, which rounds using the normal rounding rules.

I still found that some values were duplicated. Used Pandas groupby to average
values with the same mass. This is way overkill, and I can probably redo this
algorithm on my own with less overhead than importing all of Pandas library.
Tried some memory/speed optimization with data types

The intensity array was getting forced to a double precision floating point
array. However, the input array was already float32. Just changed it so that
there was no type conversion. This did not help with speed, but will most
likely help with memory usage.

For the groupby operation, I changed the masses to be integers instead of
floats. That made a small difference in execution speed. Something to think
about when I optimize that section of the code later.