Fix issue #772, Incorrect zeros included in emsd average when particles are dropped

[vivarose]

I've tested this code with imsd() and emsd() on test data and it works, and on actual movie data and it is more accurate but it doesn't make as big a difference as I feared it would. So Issue #772 isn't so bad unless there are a lot of gaps in the data.

Pros of accepting my pull-request: Slightly more accurate emsd data! If there are a lot of gaps, then it's MUCH MUCH more accurate.

Cons: It takes slightly more time to run. With timit, I see 30.6 ms ± 1.55 ms per loop before my edits versus 32.1 ms ± 1.43 ms per loop after my edits.

Issue #772 occurs when there are gaps in the data, so the problem shows up in _msd_gaps().

Here are the edits:
I updated _msd_gaps() with "skipna=False" on the sum() function. This way values based on a lack of data will show up as NaN (instead of showing up as zero).

I also added some code to reset the estimated number of datapoints N to be 0 if there is no data.
result['N'] = np.where(result['msd'].isna(), 0, result['N'])

I was hoping this would be enough but it created another problem that I had to take care of: When the emsd is calculated, there's a problem because we are averaging in a NaN (albeit weighted as N=0), and it turns out NaN * 0 = NaN. I wanted it to come out to zero. So I had to reset the NaN to zero again. Awkward, but it works. Then it's 0*0 = 0, which is the weight I wanted, and it calculates the emsd correctly.

# remove np.nan because it would make the rest of the calculation break
msds['msd'] = np.where(msds['msd'].isna(), 0, msds['msd'])

So this update does provide a more accurate emsd() calculation, and it removes the weird DROPS that show up in the imsd data (see Walkthrough output 31).

I plan to use this version going forward because I can't stand inaccuracies!

[vivarose]

It looks like the NaN makes the tests unhappy.

I prefer the NaN because an MSD of 0 means that there was a particle that didn't move, but we are really dealing with a situation of a particle that wasn't observed. But if it makes the tests unhappy, then, what can I do?

[vivarose]

I see that my attempt to appease the checks (#774) didn't work. That makes me think that my pull-request isn't the problem. Maybe there is something else going on.

I'm re-opening this pull-request. If you are trying to decide whether to incorporate one of these pull-requests, this is the one that leaves NaN in the imsd whereas #774 is the one that uses 0 instead. Both versions fix Issue #772.