[cctbxbb] correlation function for cctbx.miller.array

[Gabor Bunkoczi]

Hi Pavel,

On 2013-10-23 10:55, Pavel Afonine wrote:
> From a quick look I could not see a difference between
> http://en.wikipedia.org/wiki/Cross_correlation and usual correlation
> coefficient that everyone uses... though I did not look very
> carefully..

The difference is that the correlation coefficient is a number, while 
the cross-correlation is actually a function. In fact, the 
cross-correlation of two maps is the phased translation function, and 
the reason I need a map is that the peaks corresponding to potential 
translations could be found. So although the computation is exactly the 
same, the map_correlation method takes this a step further, and 
calculates the integral of the map, removing all spatial information.

BW, Gabor

> 
> All the best,
> Pavel
> 
> On 10/23/13 12:12 AM, Gabor Bunkoczi wrote:
>> On 2013-10-22 18:25, Pavel Afonine wrote:
>>> Hi Gabor,
>>> 
>>> I coded "map_correlation" method in
>>> cctbx_project/cctbx/miller/__init__.py based on (if I recall it
>>> correctly):
>>> 
>>> Acta Cryst. (1993). D49, 530-533
>>> Mean phase error and the map-correlation coefficient
>>> Lunin and Woolfson
>>> 
>>> I'm not aware of functionality you described...
>>> 
>>> I guess you can create a clone of "map_correlation" with 
>>> modifications
>>> you want, and add a corresponding method with some (long)
>>> self-explicable name and a regression test along with it.
>> 
>> Thanks for confirming this. I go ahead and add it, since this is a
>> generic operation between two functions. I will possibly call it
>> "cross_correlation_map".
>> 
>> http://en.wikipedia.org/wiki/Cross_correlation
>> 
>> BW, Gabor
>> 
>> 
>>> 
>>> Pavel
>>> 
>>> 
>>> On 10/22/13 10:01 AM, Gabor Bunkoczi wrote:
>>>> Hi,
>>>> 
>>>> I need to calculate the correlation function between two maps, both 
>>>> of
>>>> them are stored as miller.array objects. There is a map_correlation
>>>> method, which does something similar to what I want, but this 
>>>> calculates
>>>> the total correlation coefficient, while what I need is another
>>>> miller.array with amplitudes = f1*f2 and phases = p2-p1 (where f1, 
>>>> f2
>>>> are amplitudes and p1, p2 are phases of map1 and map2, 
>>>> respectively),
>>>> i.e. not just the sum of these. Is this available somewhere?
>>>> 
>>>> There is the additional complication that the hkl-list for map1 and 
>>>> map2
>>>> may not be fully identical, but the intersect of the two maps could 
>>>> be
>>>> taken.
>>>> 
>>>> Thanks, Gabor
>>>> 
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>>