ó ù™xTc@ sddlmZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd „ƒYZd efd „ƒYZd efd „ƒYZdefd„ƒYZ de fd„ƒYZ defd„ƒYZ de fd„ƒYZ defd„ƒYZ defd„ƒYZdS(iÿÿÿÿ(tdivisiont ReaderBasecB s°eZdZd„Zd„Zdd„Zdd„Zdd„Zdd„Z dd„Z dd „Z dd „Z dd „Z dd „Zdd „Zdd„Zdd„ZRS(sThe imageset reader base class.cC sdS(N((tself((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__init__scC sdS(N((Rtother((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__cmp__scC sdS(N((Rtindices((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_image_pathssicC sdS(N((Rtpanel((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_image_sizescC sdS(N((Rtindex((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt get_formatscC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_format_class scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_path#scC sdS(N((RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytis_valid&scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytread)scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_detectorbase,scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt get_detector/scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_goniometer2scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_beam5scC sdS(N((RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytget_scan8sN(t__name__t __module__t__doc__RRtNoneRR R R R RRRRRRR(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRs             t NullReadercB s•eZdZd„Zd„Zd d„Zd d„Zd d„Zd d„Z d d„Z d„Z d d „Z d d „Z d d „Zd d „ZRS(s A placeholder reader. cC stj|ƒ||_dS(N(RRt _filenames(Rt filenames((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR?s cC s t|tƒS(s Compare with another reader. (t isinstanceR(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRCscC s&|dkrt|jƒS|j|ƒS(s Get the image paths. N(RtlistR(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRGs  cC sdS(s Get the format. N(R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR MscC sdS(s Get the format class. N(R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR QscC s"|dkr|jdS|j|S(s Get an image path. iN(Rt_pathR(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR Us  cC stS(s% Return whether the reader is valid. (tTrue(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR[scC stdƒ‚dS(Ns"NullReader doesn't have image data(t RuntimeError(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR_scC stdƒ‚dS(sGet the detector instance.s%NullReader doesn't have detector dataN(R (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRbscC stdƒ‚dS(sGet the beam instance.s!NullReader doesn't have beam dataN(R (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRfscC stdƒ‚dS(sGet the goniometer instance.s'NullReader doesn't have goniometer dataN(R (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRjscC stdƒ‚dS(sGet the scan instance.s!NullReader doesn't have scan dataN(R (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRnsN(RRRRRRRR R R RRRRRR(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR<s           tSingleFileReadercB s¹eZdZdd„Zd„Zd„Zd„Zdd„Zdd„Z dd„Z dd„Z dd „Z dd „Z dd „Zdd „Zdd „Zdd„Zdd„ZRS(sThe single file reader class.cC stj|ƒ||_dS(sInitialise the reader class.N(RRt_format(Rtformat_instance((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRvs cC s|j|jkS(s%Compare the reader to another reader.(R"(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR}scC s|jj|jjƒfS(N(R"t __class__tget_image_file(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt __getstate__scC s|d|dƒ|_dS(Nii(R"(Rtstate((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt __setstate__„scC scgt|jjƒƒD]}|jj|ƒ^q}|dkrD|Sg|D]}||^qKSdS(s$Get the image paths within the file.N(trangeR"tget_num_imagesR%R(RRtiR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR‡s 1 cC s|jS(sGet the format instance(R"(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR ”scC s |jjS(sGet the format class(R"R$(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR ˜scC s|jj|ƒS(s'Get the image file for the given index.(R"R%(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR œscC stS(sEnsure the reader is valid.(R(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR scC s|jj|ƒS(sGet the image data.(R"t get_raw_data(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR¤scC s|jj|ƒS(sGet the detector base instance.(R"R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR¨scC s|jj|ƒS(sGet the detector instance.(R"R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR¬scC s|jj|ƒS(sGet the beam instance.(R"R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR°scC s|jj|ƒS(sGet the goniometer instance.(R"R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR´scC s|jj|ƒS(sGet the scan instance.(R"R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR¸sN(RRRRRRR&R(RR R R RRRRRRR(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR!ss              tMultiFileStatecB sMeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z RS(s1A class to keep track of multi file reader state.cC s||_d|_dS(sInitialise with format class.N(t _format_classRt_current_format_instance(Rt format_class((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRÀs cC s|jS(sGet the format class.(R.(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR0ÅscC se|jƒdks*||jƒjƒkra|j|ƒ}|j|ƒsUtdƒn||_ndS(s&Load the file with the given filename.sFormat is invalid.N(R RR%R.t_is_format_validR R/(RtfilenameR#((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt load_fileÉs  cC s|jS(s Get the current format instance.(R/(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR ÚscC s|j|jƒƒS(s$Check if the format object is valid.(t understandR%(RR#((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR1ÞscC s<|jdk r!|jjƒ}nd}i|jd6|d6S(s7 Save the current image and format class for pickling. R0tcurrent_filenameN(R/RR%R.(RR5((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR&âs  cC s>|d|_d|_|ddk r:|j|dƒndS(s* Set the format class and load the image. R0R5N(R.RR/R3(RR'((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR(ës  ( RRRRR0R3R R1R&R((((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR-½s      tNullFormatCheckercB seZd„ZRS(cC stS(N(R(Rtfmt((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__call__ôs(RRR8(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR6óstMultiFileReadercB s¼eZdZdd„Zd„Zdd„Zd„Zdd„Zdd„Z dd„Z dd „Z dd „Z dd „Z dd „Zdd „Zdd„Zdd„Zdd„ZRS(s@A multi file reader class implementing the ReaderBase interface.cC sƒtj|ƒddl}|dks+t‚t|ƒdksCt‚||_t|ƒ|_|dkrs||_ n t ƒ|_ dS(s<Initialise the reader with the format and list of filenames.iÿÿÿÿNi( RRtosRtAssertionErrortlenRR-t_stateR1R6(RR0Rt formatcheckerR:((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRûs     cC s.|jƒ|jƒko-|jƒ|jƒkS(s5Compare the reader by format class and filename list.(R R(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRscC s;|dkrt|jƒSg|D]}|j|^q SdS(sGet the list of image paths.N(RRR(RRR+((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRs  cC s |jjƒS(sGet the format class.(R=R0(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR sicC s|jƒjƒ|jƒS(sGet the image size.(R RR (RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR !scC s+|dkr|jƒjƒS|j|SdS(sGet the path the given index.N(RR R%R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR %s cC s|j|ƒjƒS(s.Get the detector base instance at given index.(R R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR,scC s|j|ƒjƒS(s)Get the detector instance at given index.(R R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR0scC s|j|ƒjƒS(s%Get the beam instance at given index.(R R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR4scC s|j|ƒjƒS(s+Get the goniometer instance at given index.(R R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR8scC s|j|ƒjƒS(s%Get the scan instance at given index.(R R(RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR<scC sy|j|ƒ}t|jƒƒ}|dks3t‚|dkrI|jƒStgt|ƒD]}|j|ƒ^qYƒSdS(s(Read the image frame at the given index.iiN(R R<RR;R,ttupleR)(RR R#tnpanelsR+((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR@s   cC s|j|ƒjƒS(s"Get the format at the given index.(t _update_stateR (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR OscC s`|dk r(|jj|j|ƒƒn1|jjƒdkrY|jj|jdƒƒn|jS(s.Update the state and load file at given index.iN(RR=R3R R (RR ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRASs  cC s‚ddl}|dkr0tt|jƒƒ}nxK|D]C}y|j|ƒ}Wntk rf}tSX|j|ƒs7tSq7Wt S(sEnsure imageset is valid.iÿÿÿÿN( R:RR)R<RR t IndexErrortFalseR1R(RRR:R R#R ((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR\s   N(RRRRRRRR R R RRRRRRR RAR(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR9øs               tImageSetcB seZdZddd„Zd„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z de d „Zd dd „Zdd „Zdd„Zdd„Zdd„Zdd„Zdd„Zdd„Zdd„Zd„Zd„Zd„Zdd„Zd„ZRS(s4 A class exposing the external image set interface. cC sy|stdƒ‚n||_|r0||_n!tt|jƒjƒƒƒ|_|dkrltƒ|_ n ||_ dS(s† Initialise the ImageSet object. Params: reader The reader object array_range The image range (first, last) sImageSet needs a reader!N( t ValueErrort_readert_indicesR)R<treaderRRtdictt_models(RRHRtmodels((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRys   ! cC sSt|tƒr5|j|}t|jƒ||jƒS|jƒj|j|ƒSdS(s` Get an item from the image set stream. If the item is an index, read and return the image at the given index. Otherwise, if the item is a slice, then create a new ImageSet object with the given number of array indices from the slice. Params: item The index or slice Returns: An image or new ImageSet object N(RtsliceRGRDRHRJR(RtitemR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt __getitem__”s cC s t|jƒS(s0 Return the number of images in this image set. (R<RG(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__len__¨scC st|jƒƒS(s8 Return the array indices of the image set as a string. (tstrtpaths(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__str__¬scc s,x%|jD]}|jƒj|ƒVq WdS(s= Iterate over the array indices and read each image in turn. N(RGRHR(Rtf((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt__iter__°scC s|jƒ|jƒkS(s$ Compare this image set to another. (RH(RR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRµscC s t|jƒS(s& Return the indices in the image set. (RRG(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR¹scC s0|jƒjƒ}g|jD]}||^qS(s4 Return a list of filenames referenced by this set. (RHRRG(RRR+((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRQ½scC s|jƒj|jƒS(sA Validate all the images in the image set. Can take a long time. (RHRRG(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRÂscC sk|j|ƒ}||jkr`i}|s(|j|ƒ}y|jƒj|ƒ|d^siisindex out of rangeN(RxRtsumRGRHRR*RB(RR ((Rs</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRZs% ! cC s ||_dS(s Set the beam. N(Rl(RRW((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR`fscC s ||_dS(s Set the goniometer model N(Rw(RRV((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRajscC s ||_dS(s Set the detector model. N(Rk(RRU((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR_nscC sP|jdgkrC|jƒ|jd|jddksCt‚n||_dS(s Set the scan model. iiÿÿÿÿiN(RGR*R;Rx(RRX((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRbrs1c C s4t|jƒd|jd|jd|jd|jƒS(s: Return the set of all images (i.e. not just the subset). RWRURVRX(RvRHRlRkRwRx(R((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyRcys!cC s-|dkr|j|ƒS|j||ƒSdS(so Read all the files in the sweep and convert them into an array of the appropriate dimensions. The required array is allocated first, this has he useful property that if you've been lazy and just got a sweep and extracted the array without consideration for the amount of memory available on your machine, you'll get an exception straight away. TODO: Currently uses numpy for fast copying of arrays, try to do this using flex arrays. Params: item The index item (frame 0, frame n), (z0, z1, y0, y1, x0, x1) Returns: The sweep image data as an array. N(Rt _to_array_allt_to_array_w_range(RRMR((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pytto_array~s  c C s-ddlm}t|ƒ}|jƒj|ƒd}|jƒj|ƒd}|dksr|dksr|dkrtdƒ‚n|j|j|||ƒƒ}x‡t|ƒD]y\}}t |t ƒsÓ|f}n||} | j |jd| j ƒŒƒ| |||d…dd…dd…fddl}ddlm} ddlm} t|ƒ}|jdƒ} | dkrµ|jdƒd} |jdƒd} d| |jdƒ| f}g|D]}||^qœ}nd}|g}t|ƒ}|d}|j j|ƒ\}}|d}t |ƒdt |ƒf}|dk r?||j ƒks?t ‚n|dkrg|rg| j|dƒ}n|dkr |dk r‘t||ƒ}nt|ƒ}nvt|| ƒræt|ƒdksÇt ‚||dƒ}t|ƒ}n0|dk søt ‚t||ƒ}t||ƒ}t|d |d |d |d |ƒ}|S( sCreate a sweepiÿÿÿÿN(R°(R³R²is %s%%0%dd%siRWRURVRX(R:R´R°R¸R³R£RµR¶RR\RÄRÅR}R;R·RnRR¹R<R!R9Rv(RqRR0RWRURVRXR»R:R°R³RµR¼R½R¾R RRÆRÇRÈRÉRrRHR#R¿((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt make_sweep"sN            N(RRRt staticmethodRCR¯RRRÀR¨RÂRÁRÊRË(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyR§=s'<(6 N(t __future__RtobjectRRR!R-R6R9RDRdRnRvRšR§(((s</public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/imageset.pyt s.7J6~¬¦9ûA