Re: [cctbxbb] Request for a fix in CC1/2 calculation in phenix.merging_statistics

Dear Nat, Thank you very much for your reply. As the code passes the regression test, I have committed this change. This sort() may slowdown the runtime, but it seems comparable. For 3,099,125 reflections test case, the difference was marginal (68.6 vs 68.9 sec). Best regards, Keitaro 2013/10/28 Nathaniel Echols :

On Sun, Oct 27, 2013 at 6:36 AM, Keitaro Yamashita wrote:

...

When I changed the cctbx code to sort reflections after mapping to a.s.u., CC1/2 values by phenix.merging_statistics became closer to XSCALE.

In merging_stats.__init__() in iotbx/merging_statistics.py, I inserted a line

...

array = array.sort("packed_indices") after array = array.customized_copy(anomalous_flag=anomalous).map_to_asu()

but I think there would be more correct way to fix this unexpected behavior.

If you can think of a better method, feel free to implement it, but I think the above is quite appropriate. Assuming this passes the regression test (iotbx/regression/tst_merging_statistics.py), it's fine to check in. The only drawback is that it's probably inefficient (especially for arrays that are already sorted), but the entire program isn't very efficient to begin with, and a more comprehensive solution would require a ground-up approach mostly coded in C++. This will definitely become necessary at some point but none of us have time to spare right now.

-Nat

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