The first change I implemented to the 3D correlation function was setting up the masks in two coordinate systems. In the 2D code the mask is simply in ra and dec (because we are taking an angular correlation function in those dimensions). In the 3D code the correlation calculation is done in comoving coordinates, however the data mask is still in ra and dec because this is how we scan the sky. Therefore the continuous space that the data lives in is in ra, dec, redshift, but the space in which we are doing the correlation calculation in is x, y, z. Because we need to apply the same mask to the randoms in our correlation function as we do to the data, I need to apply a mask in ra, dec, redshift space... but then convert to x, y, z space for the calculation. I was thinking it was somewhere in this conversion where my problems were in my code. However in the first set of changes I made, I just added two masks (in the two coordinate systems) instead of one. And I got the following result:
I am really confused how my correlation function could be off by over 10 orders of magnitude by simply changing the number of input masks. I am not actually changing the values of the masks between this version of the code and the last version I plotted. Both are taking a data set which is contiguous in x, y, z, and therefore using a mask in x, y, z for the randoms and not changing yet to ra, dec, redshift space. There should not be any difference in the actual calculation. Time to revert back to "working" version and implement the masks more slowly I guess. I hate this!
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