ó
űxTc           @   sJ   d  d l  m Z d  d l m Z d  d l m Z d e f d     YZ d S(   i˙˙˙˙(   t   division(   t   Format(   t
   FormatHDF5t   FormatHDF5Nexusc           B   s   e  Z e d     Z d   Z d   Z d   Z d   Z d   Z d   Z	 d   Z
 d d  Z d d	  Z d d
  Z d d  Z d   Z d d  Z RS(   c         C   s÷   y t  j |  d  j d  } Wn t k
 r5 } t SX| d k rF t Sd d  l } | j |  d  } d | k rt t Sd | d k r | j   t S| d d j } | d d j	 j
 d  } | j   | sŃ t S| d	 k ró t |  d
 k ró t St S(   Nt   rbi   s   HDF

i˙˙˙˙t   rt   entryt
   definitiont   versiont   NXmxg      đ?(   R   t	   open_filet   readt   IOErrort   Falset   h5pyt   Filet   closet   valuet   attrst   gett   floatt   True(   t
   image_filet   tagt   eR   t	   h5_handleR   R   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt
   understand   s*    

c         C   s)   |  j  |  s t  t j |  |  d  S(   N(   R   t   AssertionErrorR   t   __init__(   t   selfR   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyR   /   s    c         C   sÁ   d d  l  } | j |  j   d  |  _ |  j d } | d } d | k rV d |  _ n! d | k rn d |  _ n	 t d  t | |  j d j d	  } d d
 l m	 } | | d d d  |  _
 d  S(   Ni˙˙˙˙R   R   t   samplet   poset   transformationss#   cannot find pose or transformationst   CBF_axis_omegat   vector(   t   align_reference_framei   i    (   i   i    i    (   i    i    i˙˙˙˙(   i    i    i   (   R   R   t   get_image_filet
   _h5_handlet
   _pose_namet   RuntimeErrort   tupleR   t$   rstbx.cftbx.coordinate_frame_helpersR#   t   _R(   R   R   R   R   t   axisR#   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   _start3   s    
	c         C   sR   |  j  d } | d } | |  j } t | d j d  } |  j j |  j |  S(   s    Get the rotation axis. R   R   R!   R"   (   R%   R&   R(   R   t   _goniometer_factoryt
   known_axisR*   (   R   R   R   R   R+   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   _goniometerN   s
    
c         C   sá  d d l  m } |  j d } | d } | d } | |  j } | d } | d } | j d } | d	 }	 | j | j d
  j   }
 | j d  } | j d  } d | j | d	 |	 |
 d	 | d |	 |
 d | d |	 |
 d f  } | j | j d
  j   }
 | d	 } |
 j | d t } |  j	 | | j   } |  j	 | | j   } |  j	 | | } d | d j
 d | d j
 f } t | d  t | d  f } d | d d	 f } |  j j d | | | | | |  S(   Ni˙˙˙˙(   t   matrixR   t
   instrumentt   detectort   translationt   rotationt   offseti    R"   g      đ?g        ič  i   i   t   degt   x_pixel_sizet   y_pixel_sizet   x_pixel_offsett   y_pixel_offsett   saturation_valuet    (   g      đ?g        g        (   g        g      đ?g        (   t   scitbxR0   R%   R&   R   t   colt	   normalizet$   axis_and_angle_as_r3_rotation_matrixR   R*   R   t   lent   _detector_factoryt   make_detector(   R   R0   R   R1   R2   R   R3   R4   R5   t   transR"   t   fastt   slowt   origt   anglet   m_rott
   pixel_sizet
   image_sizet   trusted_range(    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt	   _detectorW   s:    





	c         C   s   d d l  m } |  j d } | d } | d } d | k rJ | d } n d | k rc | d } n  |  j j |  j | j d	  | d  S(
   sj    Nexus defines beam along z axis, i.e. from source to sample (i.e. reversed
    w.r.t. imgCIF convention).i˙˙˙˙(   R0   R   R   t   beamt
   wavelengtht   incident_wavelengthi    (   i    i    i˙˙˙˙(   R=   R0   R%   t   _beam_factoryt   simple_directionalR*   R>   (   R   R0   R   R   RN   RO   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   _beam   s    

	c         C   sR  d d l  } |  j d } | d } | |  j } | d } | d | d | d f } d t |  f } | d } | d	 }	 |	 d
 }
 |	 d } | d } | j j d  } | j | d d  } | j |  t d | d  } i | d 6} x4 t	 | d   D]" \ } } | | | | | d <qW|  j
 j | t |
  | t |  d t S(   s    Get the scan. i˙˙˙˙NR   R   R!   i    i   R1   R2   t
   count_timet
   frame_timet
   start_timet   .s   %Y-%m-%dT%H:%M:%Ss   0.%sR6   (   t   timeR%   R&   RA   R   t   splitt   strptimet   mktimeR   t	   enumeratet   _scan_factoryt	   make_scant   listR   (   R   RX   R   R   R   t   anglest   oscillationt   image_rangeR1   R2   t   exposure_timesRU   RV   t	   time_ssect   time_structt   epochst   it   t(    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   _scan   s0    






!		c         C   s&   |  j  d } | d d } | j d S(   NR   t   datai    (   R%   t   shape(   R   R   Rj   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   get_num_imagesś   s    c         C   s   t  j |   S(   N(   R   t   get_goniometer(   R   t   index(    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyRm   ť   s    c         C   s   t  j |   S(   N(   R   t   get_detector(   R   Rn   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyRo   ž   s    c         C   s   t  j |   S(   N(   R   t   get_beam(   R   Rn   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyRp   Á   s    c         C   s4   | d  k r t j |   St j |   } | | Sd  S(   N(   t   NoneR   t   get_scan(   R   Rn   t   scan(    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyRr   Ä   s    c         C   sQ   d d l  m } |  j d } | d d } | j | | d  d   d  d   f  S(   Ni˙˙˙˙(   t   flexR   Rj   (   t   scitbx.array_familyRt   R%   t   int(   R   Rn   Rt   R   Rj   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   get_raw_dataË   s    c         C   s   t  j |   S(   N(   R   R$   (   R   Rn   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyR$   Ń   s    N(   t   __name__t
   __module__t   staticmethodR   R   R,   R/   RM   RS   Ri   Rl   Rq   Rm   Ro   Rp   Rr   Rw   R$   (    (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyR      s   (					-				N(   t
   __future__R    t   dxtbx.format.FormatR   t   dxtbx.format.FormatHDF5R   R   (    (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatHDF5Nexus.pyt   <module>   s   