:SKc@sWdZddkZddkZddkZddkZddkZddkZddkZddZ dZ dZ dZ dZdZd Zd Zd Zd Zd ZdZdZeiZdZeidZeidZdZdZdZedZ edZ!ddZ"dZ#dddddeedZ$dddeddZ%ddd Z&ddd!Z'd"dd#d$Z(d%Z)d&Z*e+d'Z,d(ee+d)Z-d(ee+d*Z.d(ee+d+Z/d,Z0d-e1fd.YZ2d/Z3d0Z4dd1Z5e+d2Z6ddd3Z7dS(4s flib.py A collection of useful routines. Date and time: 'str2tm', 'tm', 'tm2str', 'dt2str', 'dt2filename', 'labview2tm' and 'tm2labview' Saving/loading data files: 'loadbinary', 'savebinary', 'loadascii', 'saveascii', 'swapendian', 'savenum', 'loadnum', 'savestr', 'loadstr' String formatting: 'a2str' Array Handling: 'average', 'absdiff', 'finites' Complex numbers: 'phase' Number comparision: 'floatcmp' Plotting: 'plotdate' 7 Jul 2009, Lev Levitin iNcKsC|idpt|d-' where the date is omitted from the time if both and have the same date. s%s-%sN(RRR(tstarttend((sc:\py\lib\flib.pyt timespan2strscCs+ti|pti|}n|dS(s Convert a timestamp, or an array of timestamps from Labview format (seconds since 00:00 1 Jan 1904 UTC) to C and UNIX format (seconds since 00:00 1 Jan 1970 UTC) i%|(RRR(R((sc:\py\lib\flib.pyt labview2tmscCs+ti|pti|}n|dS(s Convert a timestamp, or an array of timestamps from C and UNIX format (seconds since 00:00 1 Jan 1970 UTC) to Labview format (seconds since 00:00 1 Jan 1904 UTC) i%|(RRR(R((sc:\py\lib\flib.pyt tm2labviewscCsItt|}tt|}||jo|Sn |d|SdS(sR Return a string representating of date span of given two moments in time t-N(RR(RR((sc:\py\lib\flib.pytdatespans  cCstS(s> Determines byte order for loading/saving binary data (R(((sc:\py\lib\flib.pyt swapendianssicCsD||}|iiddjo|i}n|i|dS(s Save a number 'n' to a binary file pointed by a handle 'file' optional 'dtype' argument specify a format for a number to be stored in, defaults to unsigned 64 bit integer. Use big endian format. ittNotImplementedErrorR@( RAtfullR*tsRBtversionR8tlttypet nsectionsR+RC((sc:\py\lib\flib.pyt loadbinarysJ   $    ( c Cst|}t|dt}|o|i|ddSn|idjo|i|Sncyti|}Wn#t j ot d|nXti |d|dti ||i SdS(NR'iR s+unsupported data format '%s' in binary fileR-(R5R/R1tseekR tlowerR4RR't TypeErrort ValueErrorR.tuint64titemsize(R*tskiptformattlengthR'((sc:\py\lib\flib.pyRQ4s s%gcCsLti|o ||Snti|o|djodndSndS(s Convert a number into string. Handle special cases: "NaN" for not-a-number "Inf" for positive infinity "-Inf" for negative infinity itInfs-InftNaN(Rtisfinitetisinf(tnumbertfmt((sc:\py\lib\flib.pytn2strs  cCst|ttfo|ii}|djp|d djo tiSn|d djo ti Sn|djp/|djp"|d djp|d d jo tiSn|d jp|d d jo ti Sqnt|tot |i Snt |S( s Converts into float from different formats: 1. if arg is a string, treat as a decimal floating point number. Handle special cases: "NaN", "-1.#IND..." is Not-a-Number "1.#QNAN" is minus Not-a-Number (???) "Inf", "+Inf", "1.#INF...", "+1.#INF..." is Positive Infinity "-Inf","-1.#INF..." is Negative Infinity 2. a real part is taken from a complex number 3. float(arg) is called for anything else. tNANis-1.#INDs1.#QNANtINFs+INFis1.#INFs+1.#INFs-INFs-1.#INF( RRRtstriptupperRRdRctcomplextfloattreal(targRT((sc:\py\lib\flib.pyt smartfloats  < t#icsddkl}|djo h}n|i|} zwg} djo d} nfd} d} xSt| D]E\} }| |joq{n|i|ddi}t|pq{n| djoCg}t| |D]\}}||i|t q~} n|dj oB|i}g}|D]}|| |||qB~}n>g}t| |D]\}}|| ||q~}t|}| i |q{Wt i | t i } t| djo3|djo d | _qdt|f| _n|pm| i\}}|djp |djot||f| _q|djp |djo d | _qn|o| iSn| SWd| |j o| inXdS( sA A CUSTOMISED VERSION OF pylab.load CHANGES FROM PYLAB: if keep2D is set to True: 1. 2D arrays are preserved even if an empty/single line/single column is read. 2a. if en empty file was read and "usecols" is specified, a shape is set to 0,len(usecols) 2.b if an empty file was read and "usecols" is not specified, a shape is set to 0,0 if keep2D is set to False: 1. A single line/single column data is converted into a 1D array (standard pylab behaviour) 2. An empty file is converted into an empty array, does not generate an error (pylab generates an error) Load ASCII data from filename into an array and return the array. The data must be regular, same number of values in every row filename can be a filename or a file handle. Support for gzipped files is automatic, if the filename ends in .gz matfile data is not supported; use scipy.io.mio module Example usage: X = load('test.dat') # data in two columns t = X[:,0] y = X[:,1] Alternatively, you can do the same with "unpack"; see below comments - the character used to indicate the start of a comment in the file delimiter is a string-like character used to seperate values in the file. If delimiter is unspecified or none, any whitespace string is a separator. converters, if not None, is a dictionary mapping column number to a function that will convert that column to a float. Eg, if column 0 is a date string: converters={0:datestr2num} skiprows is the number of rows from the top to skip usecols, if not None, is a sequence of integer column indexes to extract where 0 is the first column, eg usecols=(1,4,5) to extract just the 2nd, 5th and 6th columns unpack, if True, will transpose the matrix allowing you to unpack into named arguments on the left hand side t,y = load('test.dat', unpack=True) # for two column data x,y,z = load('somefile.dat', usecols=(3,5,7), unpack=True) See examples/load_demo.py which exeercises many of these options. i(tcbookt cSs |iS(N(RO(tx((sc:\py\lib\flib.pyt splitfuncscs |iS(N(RO(Rv(t delimiter(sc:\py\lib\flib.pyRwsiiN(ii(i(t matplotlibRtR t to_filehandlet enumerateRORlR0tgetRrtappendRRRLtshapetmaxt transposeR@(RAtcommentsRxt converterstskiprowstusecolstunpacktkeep2DRttfhtXRwt converterseqtitlineRtjtvaltvalst_[2]trowt_[3]tthisLentrtc((Rxsc:\py\lib\flib.pyt loadasciisR7       C 3=    s%.8gs cCs@ddkl}|i|or|o d}nd}tii|} |ido&ddk} | i||d} qt ||} n3t |do|} t }t } n t d zY|dj o$|o| o| i|d nt|tj} ti|}d} |id jo"|i} t|d f|_n|t jp|djo| o|i}nxL|D]D}| i|ig}|D]}|t||q~d qW|t jp|djo| o|i}n| dj o | |_nWd| |j o| inXdS( s A CUSTOMISED VERSION OF pylab.save CHANGES: 1. Allows to add a header to the file. 2. Allows append data to an existing file. It is totally a resposibility of the user to make sure data appended is in the same format as in the initial part of the file. The header is not written down if appending to an existing file. 2. Default number format is '%g' 3. Default delimiter is a tab character ' ' 4. If 'pack' is True, 'X' is transposed before saving (compatible with 'flib.loadascii' and 'pylab.load' with 'unpack=True') If 'pack' is None (default), 'X' is transposed if it is a tuple, and preserved otherwise If 'pack' is False, 'X', transposition is not carried (the default pylab behaviour) Save the data in X to file filename using fmt string to convert the data to strings filename can be a filename or a file handle. If the filename ends in .gz, the file is automatically saved in compressed gzip format. The load() command understands gzipped files transparently. Example usage: save('test.out', X) # X is an array save('test1.out', (x,y,z)) # x,y,z equal sized 1D arrays save('test2.out', x) # x is 1D save('test3.out', x, fmt='%1.4e') # use exponential notation delimiter is used to separate the fields, eg delimiter ',' for comma-separated values i(Rttatws.gzNtbRZs(filename must be a string or file handles i(RyRttis_string_liketostpathtexiststendswithtgzipR:R*thasattrRR]R R2RWttupleRR=tndimR~R0RtjoinRiR@(RARRhRxR8R}tpackRttmodetalready_existsRRtisXtuplet origShapeRRR((sc:\py\lib\flib.pyt saveasciiEsF     !B!  c Csddkl}|i|}d}zZg}xMt|D]?\}}||joq;n|i|o||7}q;Pq;WWd||j o|inX||iS(Ni(RtRG(RyRtRzR{t startswithR@trstrip( RAtcommentRRtRR8RRR((sc:\py\lib\flib.pyt readheaders     cCs|djo|djotdnt|t|jotdnt|djo||fSn|djo$t|t|t|}nf|djo |}nO|djo$t|t|t|}n|djo |}nd}|djoti||g}nti||g}|ii}|i |ddg}|ddg}d}|djod} d} nd} d } xt dt|D]} || d} || d} | | | |d |d |o.| || || || ||d7}q|i | |i | d}qW|djo||fSn ||fSd S( s Reduce size of an array by combining similar points into their centre of mass. 'x' and 'y' are expected to be 1D arrays of the same length, containing the data. If both 'xstep' and 'ystep' are 0, the function deletes multiple occurances of the same points. If 'xstep' is positive, points with similar 'y' and scatter in 'x' smaller than 'xstep' are combined into a single point with an average 'x'. For a negative 'xstep' the absolute value is treated as an xstep, relative to the total span of values in 'x'. If 'ystep' is non-zero, the behaviour is similar to the above, but with the roles of 'x' and 'y' swapped. Both 'xstep' and 'ystep' currently can not be non-zero. is+Only one of xstep and ystep can be non-zerosx and y must be the same lengthiicSs||jo ||jS(N((tx1ty1tx2ty2tstep((sc:\py\lib\flib.pyt are_similarscSsdS(N((RtnewvalR-((sc:\py\lib\flib.pyt average_arrayscSs!||jot|||jS(N(tabs(RRRRR((sc:\py\lib\flib.pyRscSs"||d||d|d6s(tslice(RtNwindowttruncatetextend_last_bin((sc:\py\lib\flib.pytaverage1scCs4t|d|||t|d|||fS(s  divide the original 'array' into bins 'Nwindow' elements wide and return arrays containing the means and standard deviations over the bins. 'truncate' and 'extend_last_bin' govern the treatment of the very end of the supplied array if its size is not a multiple of 'Nwindow': If 'truncate' is True, the last up to 'Nwindow-1' elements are truncated. Otherwise they are treated as a separate bin if 'extend_last_bin' is False or added to the preceeding 'Nwindow' elements if 'extend_last_bin' is True. cSs|iddS(Ri(R(R((sc:\py\lib\flib.pyRRscSs|iddS(Ri(tstd(R((sc:\py\lib\flib.pyRSs(R(RRRR((sc:\py\lib\flib.pytslice_mean_and_stdFs cCs2ti|}|i}t|id|}|i||f|id||}| o|i||jo|o\|idjoL|||d}|idt|f|id}|||d)q.|||}|idt|f|id}ti |||g}n|S(s divide the original 'array' into bins 'Nwindow' elements wide along the first axis. and do similar processing of the bins. 'function' is called on the reshaped array of MxNwindow and bins are along the axis=1 (second dimension). 'truncate' and 'extend_last_bin' govern the treatment of the very end of the supplied array if its size is not a multiple of 'Nwindow': If 'truncate' is True, the last up to 'Nwindow-1' elements (rows) are truncated. Otherwise they are treated as a separate bin if 'extend_last_bin' is False or added to the preceeding 'Nwindow' elements if 'extend_last_bin' is True. iii( RR=tcopytintR~tresizetsizetreshapeR0RJ(RtfunctionRRRtdtNR((sc:\py\lib\flib.pyRs  &&cCsKti|oti|i|in"titi|ti|S(sa Return Argument (phase in radians) of complex number or an array of complex numbers (RRtmathtatan2timagRptarctan2(R((sc:\py\lib\flib.pytphasestPeriodcBs#eZdZdZdZRS(cKsnt||_t||_xI|iD];}||ijotd|n|||i|t__dict__R](tthisRRtvargsR+((sc:\py\lib\flib.pyt__init__s cCsit|to||}}ny*t|}|i|j||ij@SWntj o tSnXdS(s] Comparision. True if 'b' is a moment of time that belongs to the period 'a' N(RRRRRt ExceptiontFalse(RRR((sc:\py\lib\flib.pyt__eq__s cCs dt|it|ifS(Ns Period(%s-%s)(RRR(R((sc:\py\lib\flib.pyt__repr__s(t__name__t __module__RRR(((sc:\py\lib\flib.pyRs  cCsqti|}x[tdt|D]D}||dd||||d||||d||sb              # 7 z  lMP A