Sc@`s dZddlmZmZmZddlZddlZddlZddlm Z ddl j j Z ddl j jZddlj jZddlmZmZmZddl mZmZddlmZmZddlj jZddlmZmZejdd kr)ejZej d Znej Zej d ZiZ!iZ"eZ#e#dZ$d Z%d e&fd YZ'dfdYZ(e(dZ)dZ*ddZ+dZ,dZ-dZ.dZ/dZ0dZ1dZ2dZ3dZ4dZ5dddZ6dZ7dZ8e9d Z:d!Z;d"Z<d#fd$YZ=d%fd&YZ>d'fd(YZ?d)fd*YZ@d+fd,YZAd-fd.YZBd/fd0YZCd1fd2YZDeAe jEd3e@d3ZEeAe jFd4e?d3ZFeAe jGd4e?d3ZGeAe jHZHeAe jIZIeAe jJZJeAe jKZKeAe jLd3e>d ZLeAe jMd3e=d5d4ZMeAe jNd3e=d5d4ZNeAe jOZOeAe jPZPeAe jQd4e@d4ZQeAe jRd3e=d5d6d4d6ZReAe jSZSeAe jTZTeAe jUZUeAe jVZVeAe jWZWeAe jXZXd7ZYeAejZZ[eAe j\Z\eAe j]Z]eAe j^Z^eDe j_Z_eDe j`Z`e9e`_ eDe jad d ZaeCe jbeBdd ZbeCe jceBdd ZceCe jdeBdd ZdeCe jeeBdd ZeeCe jfeBdd ZfeDe jgZgeDe jhd3d4Zhe9eh_ eDe jiZie9ei_ eDe jjZje9ej_ eDe jkZke9ek_ eDe jlZle9el_ eDe jmZme9em_ eDe jnZne9en_ eDe joZoeDe jod d j ZpeDe jqZqeqj ZreDe jsZseDe jtZteDe juZueDe jvZvd8Zwd9Zxe9d:Zyd;ezfd<YZ{e{Z|d=Z}e}Z~e}Zd d>d?d@Zd dAZd>d?d dBZd dCZe9d e9dDZeZdEZdFZdGZdHZe9dIZdJZe9dKZedLZedMZe9dNZe9dOZe$e9dPZe9e9dQZe9e9dRZe9e9ddSZdTZe9dUdVZd dWZd dXZd dYZd dZZd d[Zd d\Zd d]Zd d^Zd d_Zd`ZdaZddbZdcZe9e9dUddZe9deZdUdfZdgZdhZeZdiZeZdjZdke9dlZdmfdnYZeZdofdpYZeZdke9dqZddd drZddd e9e9dsZdke9e9dtZdke9e9duZdke9e9dvZdwZe9dxZdyZdzZeepe|_eere|_eee|_eee|_eee|_eeee|_eee|_d{Zeee|_[e9d|Zeee|_e9e9d}Zeee|_[eeIe|_e|_Ieee|_e9e9e9d~Zeee|_e9e9e9dZeee|_eee|_eee|_eee|_eee|_eeee|_eee|_eee|_e9e9dZeee|_[e9e9dZeee|_[eee|_eeee|_eee|_eeYe|_Yeee|_e9e9dZeee|_eee|_eee|_eee|_eee|_eee|_eee|_dZeee|_eeee|_eee|_dZeee|_eee|_eee|_eee|_eee|_e9e9e9dZe9e9e9dZeee|_eee|_eee|_ee[e|_[[e{dedd ZddZde9ddZddZdS(s1MA: a facility for dealing with missing observations MA is generally used as a numpy.array look-alike. by Paul F. 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Adapted for numpy_core 2005 by Travis Oliphant and (mainly) Paul Dubois. i(tdivisiontabsolute_importtprint_functionN(treduce(tnewaxistndarraytinf(tamaxtamin(tbool_t typecodes(tbytestlongiigz8tMAErrorcB`s#eZddZdZeZRS(cC`s(t|ts|f}n||_dS(sCreate an exceptionN(t isinstancettupletargs(tselfR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt__init__.s cC`st|jdS(s#Calculate the string representationi(tstrR(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt__str__5sN(t__name__t __module__tNoneRRt__repr__(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR -s  t_MaskedPrintOptioncB`sMeZdZdZdZdZdZddZdZeZ RS(s<One instance of this class, masked_print_option, is created.cC`s|j|d|_dS(s&Create the masked print option object.iN(t set_displayt_enabled(Rtdisplay((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR<s cC`s|jS(s#Show what prints for masked values.(t_display(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRAscC`s ||_dS(s2set_display(s) sets what prints for masked values.N(R(Rts((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyREscC`s|jS(s(Is the use of the display value enabled?(R(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytenabledIsicC`s ||_dS(sSet the enabling flag to flag.N(R(Rtflag((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytenableMscC`s t|jS(N(RR(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRQs( RRt__doc__RRRRR!RR(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR:s      s--g@xDyt-i?Bt?cC`st|trtSt|ts1t|tr5tSt|trHtSt|tr[t St|t syt|t r|j j }|tdkrtS|tdkrtS|tdkrt S|tdkrtS|tdkrtjtStStSdS(s7Function to calculate default fill value for an object.tFloattIntegertComplext CharactertUnsignedIntegerN(Rtfloattdefault_real_fill_valuetintR tdefault_integer_fill_valueR tdefault_character_fill_valuetcomplextdefault_complex_fill_valuet MaskedArrayRtdtypetcharR tumathtabsolutetdefault_object_fill_value(tobjtx((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytdefault_fill_value`s,  cC`st|trtjSt|ts4t|tr8tSt|tsVt|tr|j j }|t dkrytjS|t dkrtS|t dkrtSn t ddS(sDFunction to calculate default fill value suitable for taking minima.R%R&R)s(Unsuitable type for calculating minimum.N( RR*tnumericRR,R t_MAXINTR1RR2R3R t TypeError(R7R8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytminimum_fill_valuezs cC`st|trt St|ts2t|tr7t St|tsUt|tr|jj }|t dkrvt S|t dkrt S|t dkrdSn t ddS(sDFunction to calculate default fill value suitable for taking maxima.R%R&R)is(Unsuitable type for calculating maximum.N( RR*RR,R R;R1RR2R3R R<(R7R8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmaximum_fill_values cC`s t|r|j|ndS(s,Set fill value of a if it is a masked array.N(t isMaskedArraytset_fill_value(tat fill_value((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR@s cC`s!t|tr|jStSdS(sMask of values in a; could be nomask. Returns nomask if a is not a masked array. To get an array for sure use getmaskarray.N(RR1traw_masktnomask(RA((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytgetmasks cC`s0t|}|tkr(tt|S|SdS(sMask of values in a; an array of zeros if mask is nomask or not a masked array, and is a byte-sized integer. Do not try to add up entries, for example. N(RERDtmake_mask_nonetshape(RAtm((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt getmaskarrays  cC`s-y|jjtkSWntk r(tSXdS(s;Is m a legal mask? Does not check contents, only type. N(R2ttypetMaskTypetAttributeErrortFalse(RH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytis_masks cC`s|tkrtSt|trp|jjtkr^|rUtj|dtd|}qm|}q|jt}nt |t jt}|rt j t j | rtS|SdS(smake_mask(m, copy=0, flag=0) return m as a mask, creating a copy if necessary or requested. Can accept any sequence of integers or nomask. Does not check that contents must be 0s and 1s. if flag, return nomask if m contains no true elements. R2tcopyN(RDRRR2RJRKR:tarraytastypetfilledtTruet fromnumerictsometruetravel(RHROR tresult((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt make_masks  cC`s"tj|dt}||_|S(s&Return a mask of all zeros of shape s.R2(R:tzerosRKRG(RRW((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRFs cC`s^|tkrt|S|tkr,t|S||krHt|rH|Sttj||S(sLogical or of the mask candidates m1 and m2, treating nomask as false. Result may equal m1 or m2 if the other is nomask. (RDRXRNR4t logical_or(tm1tm2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmask_ors  cC`slt|tr|j|St|tr<|jdr<|St|tr[tj|dStj|SdS(sa as a contiguous numeric array with any masked areas replaced by value if value is None or the special element "masked", get_fill_value(a) is used instead. If a is already a contiguous numeric array, a itself is returned. filled(a) can be used to be sure that the result is numeric when passing an object a to other software ignorant of MA, in particular to numeric itself. t CONTIGUOUStON(RR1RRRtflagstdictR:RP(RAtvalue((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRRs  cC`s+t|r|j}n t|}|S(sb The fill value of a, if it has one; otherwise, the default fill value for that type. (R?RBR9(RARW((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytget_fill_values  cC`s,t|}t|}||kr(|SdS(s:The common fill_value of a and b, if there is one, or NoneN(RcR(RAtbtt1tt2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytcommon_fill_values    tdomain_check_intervalcB`s eZdZdZdZRS(s9domain_check_interval(a,b)(x) = true where x < a or y > bcC`s||_||_dS(s9domain_check_interval(a,b)(x) = true where x < a or y > bN(ty1ty2(RRiRj((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs cC`s.tjtj||jtj||jS(sExecute the call behavior.(R4RZtgreaterRjtlessRi(RR8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt__call__s(RRR"RRm(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRh s t domain_tancB`s eZdZdZdZRS(s/domain_tan(eps) = true where abs(cos(x)) < eps)cC`s ||_dS(s/domain_tan(eps) = true where abs(cos(x)) < eps)N(teps(RRo((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRscC`s%tjtjtj||jS(sExecute the call behavior.(R4RlR5tcosRo(RR8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRms(RRR"RRm(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRns tdomain_greatercB`s eZdZdZdZRS(s(domain_greater(v)(x) = true where x <= vcC`s ||_dS(s(domain_greater(v)(x) = true where x <= vN(tcritical_value(RRr((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR%scC`stj||jS(sExecute the call behavior.(R4t less_equalRr(RR8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRm)s(RRR"RRm(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRq#s tdomain_greater_equalcB`s eZdZdZdZRS(s-domain_greater_equal(v)(x) = true where x < vcC`s ||_dS(s-domain_greater_equal(v)(x) = true where x < vN(Rr(RRr((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR/scC`stj||jS(sExecute the call behavior.(R4RlRr(RR8((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRm3s(RRR"RRm(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRt-s tmasked_unary_operationcB`s)eZdddZdZdZRS(icC`sl||_||_||_t|dt||_t|dt||_|t|<|ft|d4Z?d5Z@d6ZAd7ZBd8ZCd_d9ZDd:ZEd;ZFd_d<ZGd=ZHd>ZId?ZJd@ZKdAZLdBZMdCZNdDZOePdEeOdFdGZQdHZRePdEeRdFdIZSdJZTd_dKZUdLZVePeVdFeWjXjYjZYdMZZePdEeZdFdNZ[dOZ\ePdEe\dFdPZ]dQZ^dRZ_d_dSZ`d_dTZadUZbdVZcdWZddXZeePe e dFdYZfePe edFdZZgePeedFd[ZhePeedFd\ZieiZjePedd_dFd]ZkePeed_dFd^ZlRS(`sArrays with possibly masked values. Masked values of 1 exclude the corresponding element from any computation. Construction: x = array(data, dtype=None, copy=True, order=False, mask = nomask, fill_value=None) If copy=False, every effort is made not to copy the data: If data is a MaskedArray, and argument mask=nomask, then the candidate data is data.data and the mask used is data.mask. If data is a numeric array, it is used as the candidate raw data. If dtype is not None and is != data.dtype.char then a data copy is required. Otherwise, the candidate is used. If a data copy is required, raw data stored is the result of: numeric.array(data, dtype=dtype.char, copy=copy) If mask is nomask there are no masked values. Otherwise mask must be convertible to an array of booleans with the same shape as x. fill_value is used to fill in masked values when necessary, such as when printing and in method/function filled(). The fill_value is not used for computation within this module. g333333$@c C`s|dkrd}ntj|}|}t|tr|j} |dkrZ| j}n|| jkrrt}n|tkr|j}q|tk rt}qnxt|t r|} |dkr| j}q|| jkrt}qn0t }tj |d|dtd|} | j}|rk|| jkrVtj | d|dtd||_ qt| j ||_ n | |_ |tkrt|_d|_n3t||_|jtkrd|_n |j|k|_t|j} t|j } | | kr| dkr1tj|j|j j|_d|_q| dkrptj|j |jj|_ |jj|j _qtdnI| dkrt|jt|j kr|j|j j|j_n|j|dS(sarray(data, dtype=None, copy=True, order=False, mask=nomask, fill_value=None) If data already a numeric array, its dtype becomes the default value of dtype. R2ROtorderiisMask and data not compatible.N(RR:R2RR1tdataRSRDtmaskRRMRPt_dataRQt_maskt _shared_maskRXRRTtresizeRGR t unshare_maskR@( RRR2RORRRBttctneed_data_copiedtctnmtnd((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR*sb             ! '         * cC`s|jtk rtj|jjr|dkrGtjd|jS|\}}}t j |}|dkrt d|n|j ||Sqt|_d|_ n|r|jj|S|jSdS(s:Special hook for numeric. Converts to numeric if possible.siCannot automatically convert masked array to numeric because data is masked in one or more locations.s%s not known to maiN(RRDRTRVtanyRtwarningstwarnRR{tgetR RRRRQ(RRtcontexttfuncRtitfills((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt __array__ls     c C`s'|dkr"t|dtdtS|d \}}t|}ttg|D]}t|^qI}|dk rt||g|D]}t|d|^q}n|tk ry |j }Wnt k rqX|j |krttg|D]}t |^q}qnt|dtd|S(spSpecial hook for ufuncs. Wraps the numpy array and sets the mask according to context. RORiRN( RR1RMRDRzRR]RERyRGRLRI( RRPRRRRxRARHRG((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt__array_wrap__s   (  +   .cC`s |jjS(sReturn the current shape.(RRG(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt _get_shapescC`s@||j_|jtk r<|jj|_||j_ndS(sSet the array's shape.N(RRGRRDRO(Rtnewshape((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt _set_shapes cC`sf|jtkr4t|jjdtd|jSt|jjd|jjd|jSdS(s"Calculate the flat value. RRBN(RRDR}RRVRB(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt _get_flats  cC`s|j}||(dS(sx.flat = valueN(RV(RRbty((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt _set_flats cC`sZ|jtkr1t|jjdtd|jSt|jjd|jd|jSdS(s%Get the real part of a complex array.RRBN(RRDR}RtrealRB(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt _get_reals  cC`s|j}||dsN(RRRGRRDRRtlisttonesRTRVRQR,RR4Rtsum( RRRHRtlsRRtwtn1tn2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytcounts0             cC`s t||S(s%s.dot(other) = innerproduct(s, other)(t innerproduct(RR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytdotscC`s|jS(sGet the current fill value.(R(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRBscC`s|j}|j}|tkr<|jdr/|S|jSn|dkrT|j}n|}|tkrxtj |}ny,tj |d|j dd}|||g:0yE>c C`stt|t|}t|}t|}tt|ddd||jt}tt|ddd|djt} tjtj|| ||tj| } t j t j | S(s Returns true if all components of a and b are equal subject to given tolerances. If fill_value is 1, masked values considered equal. If fill_value is 0, masked values considered unequal. The relative error rtol should be positive and << 1.0 The absolute error atol comes into play for those elements of b that are very small or zero; it says how small a must be also. ROiRi( R]RERRRPRQR*R4RsR5RTtalltrueRV( RARdRBtrtoltatolRHRRR8RR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytallcloses   **0cC`stt|t|}|tkrgt|}t|}tj||}tjtj|S|rt|}t|}tj||}t |d|dd}tjtjt|dSdSdS(s True if all entries of a and b are equal, using fill_value as a truth value where either or both are masked. RROiiN( R]RERDRRR4RRTR=RVRP(RARdRBRHR8RRR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytallequals     cC`stj}t||}t|jjtjrtj|||||||}t |dd}t |d|d|d|St ||d|SdS(s masked_values(data, value, rtol=1.e-5, atol=1.e-8) Create a masked array; mask is nomask if possible. If copy==0, and otherwise possible, result may share data values with original array. Let d = filled(data, value). Returns d masked where abs(data-value)<= atol + rtol * abs(value) if d is of a floating point type. Otherwise returns masked_object(d, value, copy) R iRRORBN( R4R5RRt issubclassR2RJR:tfloatingRsRXRPt masked_object(RRbR>R?ROtabsRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt masked_valuess *cC`sIt||}ttj||dd}t|d|d|d|S(s5Create array masked where exactly data equal to valueR iRRORB(RRRXR4RRP(RRbRORR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRDscC`sttj||||S(soJust like range() except it returns a array whose type can be specified by the keyword argument dtype. (RPR:R(tstarttstoptstepR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRscC`sttj||S(sAConstruct a masked array from a string. Result will have no mask.(R}R:t fromstring(RR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRJscC`sft|}|tkr:tjt||}t|Stjt|d|}t||SdS(sLeft shift n bitsiN(RERDR4RRRR}(RARRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs    cC`sft|}|tkr:tjt||}t|Stjt|d|}t||SdS(sRight shift n bitsiN(RERDR4RRRR}(RARRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs    cC`sht|}|tk r-tj||}nttjt||d|}|jt||S(swresize(a, new_shape) returns a new array with the specified shape. The original array's total size can be any size.R(RERDRTRRPRRR@Rc(RAt new_shapeRHRW((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs   $cC`st|}t|trV|dkr3|j}n |j|}t|g|}nt|}|tk rt j |||}nt j |||}t ||}|j t ||S(srepeat elements of a repeats times along axis repeats is a sequence of length a.shape[axis] telling how many times to repeat each element. N(RRRR,RRRGRRERDRTtrepeatR}R@Rc(RAtrepeatsRtaftnumRHRRW((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt new_repeats      cC`sttj|S(s<identity(n) returns the identity matrix of shape n x n. (RPR:tidentity(R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRQscC`sttj||S(sindices(dimensions,dtype=None) returns an array representing a grid of indices with row-only, and column-only variation. (RPR:tindices(t dimensionsR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRR"scC`sttj||S(sPzeros(n, dtype=float) = an array of all zeros of the given length or shape.(RPR:RY(RGR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRY(scC`sttj||S(sNones(n, dtype=float) = an array of all ones of the given length or shape.(RPR:R(RGR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR-scC`st|}|j|S(s?Count of the non-masked elements in a, or along a certain axis.(R}R(RAR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR2s c C`s|dk rtdnt|}t|}t||}t|d}t|d}|jjtdkrtt j |||St t j |ddd}t||}|t krtt j ||Stj|d|}tt j |||SdS(sa**bs3-argument power not supported.iR&iR N(RR RER]RRR2R3R R}R4RRXRlRDR:R( RARdRRRRHtfatfbtmd((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR7s    cC`st|d|ddd|S(s]masked_array(a, mask=nomask) = array(a, mask=mask, copy=0, fill_value=fill_value) RROiRB(RP(RARRB((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR}JscC`s4|dkr!t|}d}ntj|||S(Ni(RRVRR(RRR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRPs   cC`s4|dkr!t|}d}ntj|||S(Ni(RRVRR(RRR2((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytproductVs   c C`st|}|j}|j}|d kr3d}n|d kr||tkr|d krtj|jj}td|d}qyt |dj}t jj|jj|}t jj|}~q;|d kr*tj|j}t j |dj}t jj|}~q;t t |dtd|j}tj|j|}tj|}~n|tkr|d kr||d}t jj|j|}q;t |d}|j} | dkrd} n| |kr?tj |tdd}tj|||}tj||}~q;| ||fkrtgt|} td d d| | value(RoRk(R8RbRO((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmasked_greaterscC`stt||||S(s:masked_greater_equal(x, value) = x masked where x >= value(RoR (R8RbRO((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmasked_greater_equalscC`stt||||S(s0masked_less(x, value) = x masked where x < value(RoRl(R8RbRO((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt masked_lessscC`stt||||S(s7masked_less_equal(x, value) = x masked where x <= value(RoRs(R8RbRO((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmasked_less_equalscC`sLt|d}tj||}t|t|}t|d|d|S(s6masked_not_equal(x, value) = x masked where x != valueiRRO(RRR4RR]RERP(R8RbRORRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmasked_not_equalscC`sLt|d}tj||}t|t|}t|d|d|S(s{masked_equal(x, value) = x masked where x == value For floating point consider masked_values(x, value) instead. iRRO(RRR4RR]RERP(R8RbRORRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt masked_equal scC`s||kr!|}|}|}nt|d}tjtj||tj||}t|t|}t|d|d|S(sjx with mask of all values of x that are inside [v1,v2] v1 and v2 can be given in either order. iRRO(RRR4RRsR R]RERP(R8tv1tv2RORRRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyt masked_insides  *cC`s||kr!|}|}|}nt|d}tjtj||tj||}t|t|}t|d|d|S(skx with mask of all values of x that are outside [v1,v2] v1 and v2 can be given in either order. iRRO(RRR4RZRlRkR]RERP(R8RvRwRORRRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytmasked_outside s  *cG`sWt|}t|j|}|tkr7t|St|dtj||SdS(sCopy of a with a new shape.RN(RERRRRDR}R:(RARRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR-s    cC`sTt|}tjt|}|tkr7t|St|dtj|SdS(s-a as one-dimensional, may share data and maskRN(RERTRVRRRDR}R:(RARHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRV6s    cC`sg}x!|D]}|jt|q Wtj||}x.|D]}t|tk rCPqCqCWt|Sg}x!|D]}|jt|qzWtj||}t|d|S(s+Concatenate the arrays along the given axisR(tappendRRR:t concatenateRERDR}RI(tarraysRRR8R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR{?s    cC`sxt|}t|j}|tkrCtdtj|||Stdtj|||dtj|||SdS(NRR(RER}RRDR:tswapaxes(RAtaxis1taxis2RHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR}Os   cC`srt|}t|j}|tkr@ttj|||Sttj|||dtj|||SdS(s"returns selection of items from a.RN(RER}RRDR:ttake(RARRRRkRlRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pytnew_takeYs   cC`sft|}t|}|tkr:ttj||Sttj||dtj||SdS(s!reorder dimensions per tuple axesRN(RERRRDR}R:R2(RAtaxesRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR2ds    cC`sy|j}t|}t|}tj|||t|}|tk ru|jtj|j|dndS(snsets storage-indexed locations to corresponding values. Values and indices are filled if necessary. iN(R%RRR:R#RERDRRC(RARRR RlRR"R(RH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR#os      cC`sl|tkrdStj|j||t|}|tkrEdS|jtj|j|ddS(s3putmask(a, mask, values) sets a where mask is true.Ni(RDR:R$R%RERRC(RARR RH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR$~s    cC`svt|d}t|d}t|jdkr?d|_nt|jdkr`d|_nttj||S(sinner(a,b) returns the dot product of two arrays, which has shape a.shape[:-1] + b.shape[:-1] with elements computed by summing the product of the elements from the last dimensions of a and b. 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Masked values in condition are considered false. i(RRRERDR:R R}(RbR8t dimensionRkRRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR s   t_minimum_operationcB`s8eZdZdZddZddZdZRS(sObject to calculate minimacC`sdS(s`minimum(a, b) or minimum(a) In one argument case returns the scalar minimum. N((R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRscC`s|dkrut|}|tkr@tt|j}|S|j}t|dkrbtSt|j Snt t ||||SdS(sExecute the call behavior.iN( RRERDRRRRVR RRR%RRl(RRARdRHRtac((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRms    icC`st|}|tkr=t|}ttjj||Stjjt|t||}tjj||}t||t |SdS(s#Reduce target along the given axis.N( RERDRRR}R4tminimumRR=RRc(RRRRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs   $cC`st|}t|}|tkr9|tkr9t}n*t|}t|}tj||}tjjt|t|}t||S(s<Return the function applied to the outer product of a and b.( RERDRIRZRR4RRRR}(RRARdRRRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs     !N(RRR"RRRmRR(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs    t_maximum_operationcB`s8eZdZdZddZddZdZRS(sObject to calculate maximacC`sdS(s`maximum(a, b) or maximum(a) In one argument case returns the scalar maximum. N((R((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRscC`s|dkrut|}|tkr@tt|j}|S|j}t|dkrbtSt|j Snt t ||||SdS(sExecute the call behavior.iN( RRERDRRRRVR RRR%RRk(RRARdRHRR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRms    icC`st|}|tkr=t|}ttjj||Stjjt|t||}tjj||}t||t |SdS(s#Reduce target along the given axis.N( RERDRRR}R4tmaximumRR>RRc(RRRRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs   $cC`st|}t|}|tkr9|tkr9t}n*t|}t|}tj||}tjjt|t|}t||S(s<Return the function applied to the outer product of a and b.( RERDRIRZRR4RRRR}(RRARdRRRHR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR s     !N(RRR"RRRmRR(((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs    cC`sk|dkrt|}nt||}tj||}t|tkrXt|St||ddS(sIf x does not have a mask, return a masked array formed from the result of numeric.sort(x, axis). Otherwise, fill x with fill_value. Sort it. Set a mask where the result is equal to fill_value. Note that this may have unintended consequences if the data contains the fill value at a non-masked site. If fill_value is not given the default fill value for x's type will be used. ROiN( RR9RRRTtsortRERDR}RF(R8RRBRR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyRs  cC`sftjt||||}t|}|tkrCt||St|tj||||SdS(s9diagonal(a,k=0,axis1=0, axis2=1) = the k'th diagonal of aN(RTtdiagonalRRRERDR}(RAtkR~RRRH((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR-s    cC`st||||jd|S(s~trace(a,offset=0, axis1=0, axis2=1) returns the sum along diagonals (defined by the last two dimenions) of the array. R2(RR(RAtoffsetR~RR2Rk((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyttrace6scC`st||}tj||S(sTreating masked values as if they have the value fill_value, return sort indices for sorting along given axis. if fill_value is None, use get_fill_value(x) Returns a numpy array. (RRRTtargsort(R8RRkRBR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyR<scC`st||}tj||S(sTreating masked values as if they have the value fill_value, return indices for minimum values along given axis. if fill_value is None, use get_fill_value(x). Returns a numpy array if x has more than one dimension. Otherwise, returns a scalar index. (RRRTtargmin(R8RRkRBR((sM/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/oldnumeric/ma.pyREscC`sO|dkr0t|}y | }Wq0q0Xnt||}tj||S(s&Treating masked values as if they have the value fill_value, return sort indices for maximum along given axis. if fill_value is None, use -get_fill_value(x) if it exists. 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