xTc@ sddlmZddlZddlZddlZddlmZdefdYZedkrddl Z x#e j dD]Z ej e GHqWndS(i(tdivisionN(t FormatTIFFtFormatTIFFRayonixcB seZdZedZdZdZdZdZdZ dZ dZ d Z d Z d Zd Zd ZdZdZRS(srA class for reading TIFF format Rayonix images, and correctly constructing a model for the experiment from this.cC stj|\}}}}}t|dks6t|tjkrNd}nd}|d}|d}tj||dd!d } tj||dd!d } tj||dd!d } || ks|| ks|| krtStj||dd!d } tj||dd!d } tj||dd!d }tj||dd!d }| dks| d ks|d ks|d krtStS( sCheck to see if this looks like an Rayonix TIFF format image, i.e. we can make sense of it. This simply checks that records which describe the size of the image match with the TIFF records which do the same.ittItiiiPiTiiXi\ipitixi|iiiPiTiTiXiXi\ipititixixi|i|i( Rtget_tiff_headertlentAssertionErrort LITTLE_ENDIANtstructtunpacktFalsetTrue(t image_filetwidththeighttdepthtordertbytestendiant_It_it_widtht_heightt_depthtnimagestorigint orientationtview((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt understands(   $0cC s|j|sttj|\}}}}}d|_|tjkrid|_d|_d|_nd|_d|_d|_tj ||dS( scInitialise the image structure from the given file, including a proper model of the experiment.isIs>is>iiN( RR RRt _header_sizeR RRt_iit__init__(tselfRRRRRR((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR"<s       cC s@tj|ddlm}||j|_|jjdS(Ni(tMARImage(Rt_starttiotbx.detectors.marR$t _image_filet detectorbaset readHeader(R#R$((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR%Ws cC sk|j\}}}}xCtt|D]/}||kr+||||ksZtq+q+W|jjS(sReturn a model for goniometer corresponding to the values stored in the image header. In the first instance assume this is a single axis annd raise exception otherwise.(t_get_rayonix_scan_anglestrangeRR t_goniometer_factoryt single_axis(R#tstartstendstoffsetRtj((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt _goniometer`s  !c C s/|j\}}}}|j}|d|dks>t|ddksTt|ddksjt|ddkst|j}|j\}}|j} |j|jf} tj |j |j dd!d} d} || d|| df} |j j d|| dd | | | | fg S( sReturn a model for a simple detector, which at the moment [NKS does not] insist that the offsets and rotations are all 0.0.igiiihiltCCDs+xs-y(R*t_get_rayonix_detector_rotationsR t_get_rayonix_distancet_get_rayonix_beam_xyt_get_rayonix_pixel_sizet _tiff_widtht _tiff_heightR R Rt_tiff_header_bytest_detector_factorytsimple(R#R.R/R0Rt rotationstdistancetbeam_xtbeam_yt pixel_sizet image_sizetoverloadt underloadtbeam((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt _detectorms"    cC s7tj|j|jdd!dd}|jj|S(s#Return a simple model for the beam.iiigh㈵>(R R RR:t _beam_factoryR<(R#t wavelength((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt_beams!c C s|jjd}|jd}tj|j}|j\}}}}||}|} |jj|j|||| |S(s+Return the scan information for this image.tTIFFi( t _scan_factorytformatt_get_rayonix_timesttimetmktimet_get_rayonix_timestampR*tsingleR'( R#RLt exposure_timetepochR.R/R0Rt osc_startt osc_range((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt_scans   cC s{tj|j|jdd!d}|dkr7|dStj|j|jdd!d}|dkrn|dStddS( sULook in the usual places for the detector distance, return this as a float in mm.iiigMbP?iiscannot find distance in headerN(R R RR:t RuntimeError(R#R>((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR5s  cC s;tj|j|jdd!d \}}|d|dfS(s Get the beam x, y positions which are defined in the standard to be in pixels. X and Y are not defined by the documentation, so taking as a given that these are horizontal and vertical. N.B. the documentation states that the horizontal direction is fast.iiigMbP?(R R R!R:(R#R?R@((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR6s#cC s;tj|j|jdd!d \}}|d|dfS(sGet the pixel sizes in mm.ii igư>(R R R!R:(R#tpixel_xtpixel_y((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR7s#cC s;tj|j|jdd!d \}}|d|dfS(s/Get the integration, exposure times in seconds.iiigMbP?(R R R!R:(R#t integrationtexposure((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyRMs#cC s|jdd!}t|d }t|dd!}t|dd!}t|dd!}t|dd!}t|dd !}tj||||||jS( s$Get the image acquisition timestamp.i@ i` iiiii i i(R:tinttdatetimet timetuple(R#t timestamptmonthtdaythourtminutetyeartsecond((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyRPsc C s|jtjkrd}nd}tj||jdd!d }tj||jdd!d }tj|j|jdd !d }tj|j|jd d !d }g|D]}|d ^q}g|D]}|d ^q} || ||d fS( spGet the scan angles for: twotheta, omega, chi, kappa, phi, delta, gamma. The exact definitions for these are somewhat poorly defined, though I presume that they will come from some kind of standard goniometer definition... Also returns the scan axis offset and the apparent oscillation width, as these are sometimes not properly recorded elsewhere.siiiiiiiiiiiiiiiigMbP?(t_tiff_byte_orderRR R R R:R( R#tiiiiiiit start_anglest end_anglest axis_offsett axis_rangetststarts_degreestet ends_degrees((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR*s cC sb|jtjkrd}nd}tj||jdd!d }g|D]}|d^qH}|S(seGet the recorded rotx, roty, rotz of the detector - which in most cases will probably all be 0.0.siiiiiigMbP?(RfRR R R R:(R#tiiit rot_anglestrt rot_degrees((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyR4s cC s|jtjkstddlm}ddlm}ddlm }t |j dksft|j dj }tj |j}|j|j|||t|d|d}|j dj }|j|j|d|d|S(s^Get the pixel intensities (i.e. read the image and return as a flex array of integers.)i(t streambuf(t read_uint16(tflexii(RfRR R t boost.pythonRttdxtbxRutscitbx.array_familyRvRt get_detectortget_image_sizet open_fileR'treadR R\treshapetgrid(R#RtRuRvtsizetftraw_dataRB((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt get_raw_datas'!(t__name__t __module__t__doc__t staticmethodRR"R%R2RFRIRVR5R6R7RMRPR*R4R(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyRs %          t__main__i( t __future__RRNR]R tdxtbx.format.FormatTIFFRRRtsystargvtargR(((sL/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/format/FormatTIFFRayonix.pyt s