Sc @`sdZddlmZmZmZdZddlZddlZddlZ ddl j j Z ddlmZddlmZmZmZmZmZddlmZmZe j jjZe jZddljZddlm Z m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&m'Z'ej j(Z(d d d d d dgZ)ddddgZ*dZ+e,dZ-dZ.d e!e/fdYZ0dZ1e0Z2e,e,e,e,e,e3e,e,dZe,e,e,e,e,e3e,e,e#d ZdZ4dZ5e,dde,e,dZ6e,dZ7dS( s#:mod:`numpy.ma..mrecords` Defines the equivalent of :class:`numpy.recarrays` for masked arrays, where fields can be accessed as attributes. Note that :class:`numpy.ma.MaskedArray` already supports structured datatypes and the masking of individual fields. :author: Pierre Gerard-Marchant i(tdivisiontabsolute_importtprint_functionsPierre GF Gerard-MarchantN(t basestring(tbool_tdtypetndarraytrecarraytarray(t fromarrayst fromrecords(tMAErrort MaskedArraytmaskedtnomaskt masked_arraytgetdatat getmaskarraytfilledt MaskedRecordst mrecarrayR R t fromtextfiletaddfieldt_datat_maskt _fieldmaskRcC`st|dr9djg|jjD]}|d^q"Sd}xi|D]a}tj|}|t|jj7}t|jjt j r|t |j 7}n|d7}qFW|d S(sKReturns the formats of each array of arraylist as a comma-separated string.Rt,iti( thasattrtjoinRtdescrtnptasarrayt_typestrttypet issubclasstntypestflexibletreprtitemsize(tdatatdesctformatstobj((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt _getformats3s* c C`s[t|}gt|D]}d|^q}|dkrD|}n~t|ttfrb|}n7t|tr|jd}ntdt |t|}||kr|||7}ng}xt |||j D]l\}}} |t kr3| dt kr#|j || dfqJ|j | q|j || dfqWtj|S(sChecks that the field names of the descriptor ``descr`` are not some reserved keywords. If this is the case, a default 'f%i' is substituted. If the argument `names` is not None, updates the field names to valid names. sf%iRsillegal input names %siiN(tlentrangetNonet isinstancettupletlisttstrtsplitt NameErrorR&tzipRtreserved_fieldstappendRR( Rtnamestndescrtit default_namest new_namestnnamestntdtt((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt _checknamesAs( #     % cC`s]g|jjD]}|df^q }tj|jd|}ttgt||_|S(Ns|b1R( RR9RtemptytshapeR1tFalseR-tflat(tselfR?tmdescrtfdmask((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt_get_fieldmask`s%cB`s eZdZddddddddeeedeedZdZdZ e de Z dZ e de Z dZdZd Zd Zd Zd Zd ZdddZdZdZdZddZdZdZdZRS(s *IVariables*: _data : {recarray} Underlying data, as a record array. _mask : {boolean array} Mask of the records. A record is masked when all its fields are masked. _fieldmask : {boolean recarray} Record array of booleans, setting the mask of each individual field of each record. _fill_value : {record} Filling values for each field. icK`stj||d|d|d|d|d|d|d|d| d |  }tj|j}| tksvtj|  r|stt gt ||_ qn&tj | d |} | j |j krI|j| j}}|d krtj| |j } nD||kr tj| |j } n d d }t|||ft}n|sh|j| t|_n\| j|kr| }n;tj g| D]}t|gt |^qd|}||_ |S(NRtbuftoffsettstridesR*R9ttitlest byteordertalignedtcopyis/Mask and data not compatible: data size is %i, smask size is %i.(Rt__new__tmatmake_mask_descrRRRtsizeR1RER-RRRDtresizetreshapeR tTruet __setmask__t _sharedmask(tclsRDRRKRLRMR*R9RNRORPtmaskt hard_maskt fill_valuet keep_maskRQtoptionsRGtmdtypetndtnmtmsgRtm((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRRus8!  "      2  cC`st|dd}|dkrt|dt}tj|d}|tkritj|jd|}qtj|}t g|D]}t |gt |^qd|j t }n|j}|jd||j||dtkrt |d}ddj|Sgtg|jjD]}t||^qD]2}ddjg|D]}t|^q^q}ddj|SdS(s%Calculates the string representation.is(%s)Rs[%s]s, s%sN(RUR6RR9RgRR3(RGtftsR;tmstr((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt__str__JsddcC`s|jj}dtg|D]}t|^qdf}g|jjD]}||t||f^qI}|jdd|j|d|jfdgtdj |S(s#Calculates the repr representation.s %%%is : %%siismasked_records(s fill_values )s ( RR9tmaxR-RgtinserttextendR^R3R(RGt_namesR?tfmtRtreprstr((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt__repr__Us 02 cC`s|dkr?|dkr*tj|}q(tj||}n|dkry@t|trxtj||}d}ntj||}Wq(tk rtj|}|jdkr|jj d}|j j||}|j |ntj||}d|_ q(Xntj|||}t |dttk r|tj|j}|jj|t|_|j|j_n|S(s Returns a view of the mrecarray.iRN(R/RRkR#R|RRR{t __class__t __bases__t __array__RnRxRgRRSRTRRD(RGRR"toutputtbasetypeRa((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRk_s0     cC`s t|_dS(sForces the mask to hardN(RXt _hardmask(RG((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt harden_maskscC`s t|_dS(sForces the mask to softN(RER(RG((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt soften_maskscC`s=|j}|jjjt|}|jj|_|S(s$Returns a copy of the masked record.(RlRRQRkR"R(RGRtcopied((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRQs cC`sf|dk r|j|jSt|jjdt}t|jj}d||<|jS(sLCopy the data portion of the array to a hierarchical python list and returns that list. Data items are converted to the nearest compatible Python type. Masked values are converted to fill_value. If fill_value is None, the corresponding entries in the output list will be ``None``. RN(R/RttolistRjRyR(RGR^tresultR\((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRs  cC`s@d|j|j|jj|jj|jj|jf}|S(sOReturn the internal state of the masked array, for pickling purposes. i(RDRtflagstfncRttostringRRx(RGtstate((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt __getstate__s    c C`s|\}}}}}}}tj|||||ftg|jjD]\} } | tf^qG} |jdj|| ||f||_dS(sbRestore the internal state of the masked array, for pickling purposes. ``state`` is typically the output of the ``__getstate__`` output, and is a 5-tuple: - class name - a tuple giving the shape of the data - a typecode for the data - a binary string for the data - a binary string for the mask. RN(Rt __setstate__RRRRlR^( RGRtvertshpttyptisftrawtmsktflvtkt_Ra((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRs 1 cC`s%t|j|jddf|jfS(s6Return a 3-tuple for pickling a MaskedArray. itb(i(t_mrreconstructRRfR(RG((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt __reduce__sN(t__name__t __module__t__doc__R/RERRXRRRrRstpropertyRRuRRwRhRRRRRRkRRRQRRRR(((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRgs4     %     - 5   &      cC`sOtj|||j|}tjt|d}|j||d|d|S(sbInternal function that builds a new MaskedArray from the information stored in a pickle. tb1R\R(RRRRk(tsubtypet baseclasst baseshapeRRR((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRsc C`sg|D]} t| ^q} g|D]} tjt| ^q&} t| d|d|d|d|d|d|d|jt} tt| | j _ |dk r|| _ n| S( sCreates a mrecarray from a (flat) list of masked arrays. Parameters ---------- arraylist : sequence A list of (masked) arrays. Each element of the sequence is first converted to a masked array if needed. If a 2D array is passed as argument, it is processed line by line dtype : {None, dtype}, optional Data type descriptor. shape : {None, integer}, optional Number of records. If None, shape is defined from the shape of the first array in the list. formats : {None, sequence}, optional Sequence of formats for each individual field. If None, the formats will be autodetected by inspecting the fields and selecting the highest dtype possible. names : {None, sequence}, optional Sequence of the names of each field. fill_value : {None, sequence}, optional Sequence of data to be used as filling values. Notes ----- Lists of tuples should be preferred over lists of lists for faster processing. RRDR*R9RNRPRON( RRt atleast_1dRt recfromarraysRkRR2R6RRFR/R^( t arraylistRRDR*R9RNRPROR^txtdatalisttmasklistt_array((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyR s(   c C`st|dd } yt|d} Wn$tk rLt|dj} nXt|trt|tr|jj t}n|d kr|j}n|j }nt |d|d|d|d|d|d|d |j t } |d k r|| _ n| tk rtj| d t} t| j} | rF| | j_qt| jd krg| D]}t|^qb| j_q| j| n| d k r| | j(n| S( sHCreates a MaskedRecords from a list of records. Parameters ---------- reclist : sequence A list of records. Each element of the sequence is first converted to a masked array if needed. If a 2D array is passed as argument, it is processed line by line dtype : {None, dtype}, optional Data type descriptor. shape : {None,int}, optional Number of records. If None, ``shape`` is defined from the shape of the first array in the list. formats : {None, sequence}, optional Sequence of formats for each individual field. If None, the formats will be autodetected by inspecting the fields and selecting the highest dtype possible. names : {None, sequence}, optional Sequence of the names of each field. fill_value : {None, sequence}, optional Sequence of data to be used as filling values. mask : {nomask, sequence}, optional. External mask to apply on the data. Notes ----- Lists of tuples should be preferred over lists of lists for faster processing. RiRRDR*R9RNRPRORQiN(RgR/R-R|RR0RR RRkRtrecfromrecordsRR^RRRRERRFRDR1RY(treclistRRDR*R9RNRPROR^R\RtnfieldstmrectmaskrecordlengthRe((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyR s6        (  cC`s*g}tj|}t|jdkr7|d}n$t|jdkr[tdnx|D]}yt|Wntk r yt|Wn[tk ryt|}Wn!tk r|j|j qX|jtj tq"X|jtj tqbX|jtj tqbW|S(sTries to guess the dtypes of the str_ ndarray `arr`, by testing element-wise conversion. Returns a list of dtypes. The array is first converted to ndarray. If the array is 2D, the test is performed on the first line. An exception is raised if the file is 3D or more. iisThe array should be 2D at most!( RR R-RDRtinttfloattcomplexR8R(tarrtvartypesRR((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt_guessvartypesKs*     cC`st|dr|Syt|}Wn!tk rFtd|nX|jd dkrq|jdd|S|jtddS(s%Opens the file handle of file `fname`treadlinesNo such file: '%s'is\xisWow, binary fileN(RtopentIOErrorRtseektcloseR(tfnameR((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pytopenfileks  t#Rc C`s2t|}xTtrb|j}||j| j}|j|} t| dkrPqqW|dkrx| }ntg|D]=}|d|krt|dkr|jj|^q} | j \} } |j |dkrt | d}ntg|D]} t j | ^q}t|| krtd}|d7}tj|t|| ft | d}ngt||D]\}}||f^q}g|D]}tj|^q}| j|k}gt| j|||D]0\}}}}t|d|d|d|^q}t|d|S( sCreates a mrecarray from data stored in the file `filename`. Parameters ---------- filename : {file name/handle} Handle of an opened file. delimitor : {None, string}, optional Alphanumeric character used to separate columns in the file. If None, any (group of) white spacestring(s) will be used. commentchar : {'#', string}, optional Alphanumeric character used to mark the start of a comment. missingchar : {'', string}, optional String indicating missing data, and used to create the masks. varnames : {None, sequence}, optional Sequence of the variable names. If None, a list will be created from the first non empty line of the file. vartypes : {None, sequence}, optional Sequence of the variables dtypes. If None, it will be estimated from the first non-commented line. Ultra simple: the varnames are in the header, one lineiis&Attempting to %i dtypes for %i fields!s Reverting to default.R\RR^N(RRXRtfindtstripR4R-R/RRDRRRRtwarningstwarnR6RStdefault_fill_valuetTR (Rt delimitort commentchart missingchartvarnamesRRtlinet firstlinet _varnamest _variablesRRtvRdR?RHtmfillvRtaReRAt _datalist((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyR|s6     @  " ."Lc C`s|j}|j}|dks*|tkr@dt|j}ntj|}tj|jj ||jfg}t |j |}g|jj j D]!}|j|j||^q|j|j|jj ||jt}tjg|jD]}|tf^q} t |j | } g|jj j D]!}| j|j||^q:| jt|| jj || |_|S(sAdds a new field to the masked record array, using `newfield` as data and `newfieldname` as name. If `newfieldname` is None, the new field name is set to 'fi', where `i` is the number of existing fields. sf%iN(RRR/R7R-RRSRRRRRDR{tvaluesRR~RkRR9RR( tmrecordtnewfieldt newfieldnameRRtnewdtypetnewdataRR?t newmdtypetnewmask((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyRs&  %5+5 (8Rt __future__RRRt __author__RRtnumpyRtnumpy.core.numerictypestcoret numerictypesR$t numpy.compatRRRRRRRjtnumpy.core.recordsR RR Rtrecordst_byteorderconvR!tnumpy.maRSR R R RRRRRt_check_fill_valuet__all__R7R,R/RBRJRyRRRRERRRR(((sK/opt/xtal/ccp4-6.5-linux32/lib/python2.7/site-packages/numpy/ma/mrecords.pyt sF    ( :    g    (  @  B