ó
k™xTc           @   s‚   d  d l  m Z d  d l m Z d  d l m Z d  d l m Z d  d l	 m
 Z
 m Z d „  Z d e f d „  ƒ  YZ d	 „  Z d
 S(   iÿÿÿÿ(   t   division(   t   flex(   t   correlation(   t   math(   t   fftpackt   simplexc         C   sU   |  j  ƒ  } t | d ƒ } t j t j | ƒ ƒ } t j | | | ƒ } | | f S(   Ni    (   t   coefst   absR   t   sumt   normt   smatht   sqrt(   t	   nlm_arrayt   coeft   meant   vart   sigma(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyt   get_mean_sigma   s
    t   alignc           B   sY   e  Z d  d d d  e e e d „ Z d	 d „ Z d „  Z d „  Z d d „ Z d „  Z	 RS(
   i
   i   c
         C   sV  | |  _  | |  _ | |  _ t j d t | d ƒ t j t | ƒ ƒ |  _	 | |  _
 t d | d d | ƒ |  _ |  j | d d |  _ t j d |  j d |  _ | |  _ | |  _ | |  _ t |  _ |	 |  _ g  |  _ t j ƒ  |  _ t j ƒ  |  _ t | | | d ƒ |  _ |  j ƒ  |  j }
 |  j j |
 d |
 d |
 d |  j ƒ |  _ d  S(   Ng       @i   i    i   i
   (   t   nmaxt   fixedt   movingR
   t   pit   floatR   t   doublet   ranget   betat   nbt   maxt   padt   ngridt   dxt   topnt   refinet   check_inversiont   Falset	   inversiont   show_resultt	   top_alignt
   top_scorest   scoresR   t   cc_objt   scant   best_eat   rotate_moving_objt
   moving_nlm(   t   selfR   R   R   t   n_betaR   R    R!   R"   R%   t   ea(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyt   __init__   s(    			1							
	c         C   sb   | d  k r |  j } n  t |  j ƒ \ } } t |  j ƒ \ } } | | | | | |  _ |  j S(   N(   t   Nonet
   best_scoreR   R   R   t   cc(   R.   t
   this_scoret   fix_meant   fix_st   mov_meant   mov_s(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyt   get_cc)   s    c         C   s€  t  j |  j |  j ƒ } t } xš |  j D]� } |  j j | ƒ |  j j d | ƒ } |  j d k r} |  j j |  j | ƒ } n  | } | j	 | ƒ j
 ƒ  } |  j j t j | ƒ ƒ |  _ q( Wt j |  j ƒ |  _ t j |  j |  j ƒ |  _ |  j r
t } t j ƒ  } xš |  j D]� } |  j j | ƒ |  j j d | ƒ } |  j d k rg|  j j |  j | ƒ } n  | j ƒ  } | j	 | ƒ j
 ƒ  } | j t j | ƒ ƒ } qWt j | ƒ } t j | | ƒ }	 |	 |  j k  rþ| |  _ | |  _ |	 |  _ t |  _ q
t |  _ n  |  j |  j |  j }
 |  j |  j |  j |
 |  j } |  j |  j |  j |
 |  j | } |  j |
 }
 t j d t | ƒ |  j d } t j d t | ƒ |  j d } | |
 | f |  _ |  j |  j ƒ |  j r|g  |  _  g  |  _! t j ƒ  |  _" x† |  j# D]{ } |  j$ | ƒ } |  j  j% | ƒ |  j" j% |  j& |  j' | ƒ ƒ ƒ |  j! j% |  j j( | d | d | d |  j ƒ ƒ qWt j) |  j" t ƒ } |  j" | d |  _ |  j* rd GHxS t+ |  j ƒ D]? } | | } | } | Gd Gt, |  j  | ƒ Gd G|  j" | GHq×Wn  |  j  | d } | d | d | d f |  _ |  j j( | d | d | d |  j ƒ |  _- n  d  S(   Ni    g       @i   i   s   refined results:t   :(.   R   t   complex_to_complex_2dR   R#   R   R)   t   set_betat   mm_coefR   t   backwardt   as_1dR(   t   concatenateR   R	   t	   min_indext	   best_indxR
   R   R3   R"   t   TrueR   t	   deep_copyt   scoreR$   R   R   R+   t   find_topR    R!   t   refinedt   refined_moving_nlmt   refined_scoreR&   t   run_simplext   appendR:   t   targetR,   t   sort_permutationR%   R   t   listR-   (   R.   t   fftR$   R   t   mmt	   fft_inputR(   t   inversion_scorest   inv_best_indxt   inv_best_scoret   bt   at   gt   tt   rt   orderst   iit   oR0   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyR*   2   sv    #				"&""			"8	
0c         C   s  t  j |  j ƒ } xþ t | ƒ D]ð } | | } | |  j |  j } | |  j |  j | |  j } | |  j |  j | |  j | } |  j | } t j d t | ƒ |  j d } t j d t | ƒ |  j d } |  j	 j
 t  j | | | f ƒ ƒ |  j j
 |  j | ƒ q Wd  S(   Ng       @i   (   R   RN   R(   R   R   R   R
   R   R   R&   RL   R   R'   (   R.   R    R[   R\   R]   RV   RW   RX   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyRG   ~   s    
#"""iô  c         C   s‰   d } | g } x= t  | ƒ D]/ } | j | t j | ƒ d d |  j ƒ q Wt j d | d | d |  d | d d	 ƒ } | j ƒ  } | S(
   Ni   i   i   t	   dimensiont   matrixt	   evaluatort   max_itert	   tolerancegñhãˆµøä>(   R   RL   R   t   random_doubleR   R   t   simplex_optt   get_solution(   R.   t   startRa   t   dimt   starting_matrixR\   t	   optimizert   result(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyRK   �   s    	-	c         C   s5   |  j  j | d | d | d |  j ƒ } t | ƒ S(   Ni    i   i   (   R)   t   calc_correlationR$   R   (   R.   t   vR4   (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyRM   š   s    *N(
   t   __name__t
   __module__R#   R1   R2   R:   R*   RG   RK   RM   (    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyR      s   		L	c          C   s   t  j d d g ƒ }  d  S(   Niÿÿÿÿi   (   iÿÿÿÿiÿÿÿÿiÿÿÿÿ(   i   i   i   (   R   t   vec3_double(   t   xyz(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyt   tstŸ   s    N(   t
   __future__R    t   scitbx.array_familyR   t   scitbx.mathR   t   stdlibR   R
   t   scitbxR   R   R   t   objectR   Rq   (    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/math/zernike_align_fft.pyt   <module>   s   	�