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q = arr(where(left*(q==q), 1-q, q)) | q = arr(where(left+q-q, 1-q, q)) | def weibullppf(q, shape, left=0, loc=0.0, scale=1.0): a, b, loc, q, left = map(arr,(shape, scale, loc, q, left)) cond1 = (a>0) & (b>0) & (0<=q) & (q<=1) q = arr(where(left*(q==q), 1-q, q)) vals = pow(arr(log(1.0/arr(1-q))),1.0/a) return select([1-cond1,left==0], [scipy.nan, b*vals+loc], -b*vals+loc) |
if (N%2 != 0): raise ValueError, "Length of sequence must be even." xtilde = 0.0*x | even = (N%2 == 0) | def dct(x,axis=-1): n = len(x.shape) N = x.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." xtilde = 0.0*x slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) for k in range(4): slices[k] = tuple(slices[k]) xtilde[slices[0]] = x[slices[1]] xtilde[slices[2]] = x[slices[3]] Xt = scipy.fft(xtilde,axis=axis) pk = exp(-1j*pi*arange(N)/(2*N)) newshape = ones(n) newshape[axis] = N pk.shape = newshape return squeeze(real(Xt*pk)) |
slices[k].append(slice(None)) slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) | slices[k].append(slice(None)) if even: xtilde = 0.0*x slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) else: newshape = list(x.shape) newshape[axis] = 2*N xtilde = sb.empty(newshape,sb.Float) slices[0][axis] = slice(None,N) slices[2][axis] = slice(N,None) slices[3][axis] = slice(None,None,-1) | def dct(x,axis=-1): n = len(x.shape) N = x.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." xtilde = 0.0*x slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) for k in range(4): slices[k] = tuple(slices[k]) xtilde[slices[0]] = x[slices[1]] xtilde[slices[2]] = x[slices[3]] Xt = scipy.fft(xtilde,axis=axis) pk = exp(-1j*pi*arange(N)/(2*N)) newshape = ones(n) newshape[axis] = N pk.shape = newshape return squeeze(real(Xt*pk)) |
pk = exp(-1j*pi*arange(N)/(2*N)) newshape = ones(n) | pk = sb.exp(-1j*pi*sb.arange(N)/(2*N)) newshape = sb.ones(n) | def dct(x,axis=-1): n = len(x.shape) N = x.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." xtilde = 0.0*x slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) for k in range(4): slices[k] = tuple(slices[k]) xtilde[slices[0]] = x[slices[1]] xtilde[slices[2]] = x[slices[3]] Xt = scipy.fft(xtilde,axis=axis) pk = exp(-1j*pi*arange(N)/(2*N)) newshape = ones(n) newshape[axis] = N pk.shape = newshape return squeeze(real(Xt*pk)) |
return squeeze(real(Xt*pk)) | if not even: pk /= 2; Xt = Xt[slices[0]] return sb.real(Xt*pk) | def dct(x,axis=-1): n = len(x.shape) N = x.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." xtilde = 0.0*x slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,N/2) slices[1][axis] = slice(None,None,2) slices[2][axis] = slice(N/2,None) slices[3][axis] = slice(N,None,-2) for k in range(4): slices[k] = tuple(slices[k]) xtilde[slices[0]] = x[slices[1]] xtilde[slices[2]] = x[slices[3]] Xt = scipy.fft(xtilde,axis=axis) pk = exp(-1j*pi*arange(N)/(2*N)) newshape = ones(n) newshape[axis] = N pk.shape = newshape return squeeze(real(Xt*pk)) |
N = v.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." k = arange(N) ak = sb.r_[1.0,[2]*(N-1)]*exp(1j*pi*k/(2*N)) newshape = ones(n) newshape[axis] = N ak.shape = newshape xhat = real(scipy.ifft(v*ak,axis=axis)) x = 0.0*v | N = v.shape[axis] even = (N%2 == 0) | def idct(v,axis=-1): n = len(v.shape) N = v.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." k = arange(N) ak = sb.r_[1.0,[2]*(N-1)]*exp(1j*pi*k/(2*N)) newshape = ones(n) newshape[axis] = N ak.shape = newshape xhat = real(scipy.ifft(v*ak,axis=axis)) x = 0.0*v slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,None,2) slices[1][axis] = slice(None,N/2) slices[2][axis] = slice(N,None,-2) slices[3][axis] = slice(N/2,None) for k in range(4): slices[k] = tuple(slices[k]) x[slices[0]] = xhat[slices[1]] x[slices[2]] = xhat[slices[3]] return x |
slices[k].append(slice(None)) slices[0][axis] = slice(None,None,2) slices[1][axis] = slice(None,N/2) slices[2][axis] = slice(N,None,-2) slices[3][axis] = slice(N/2,None) for k in range(4): slices[k] = tuple(slices[k]) x[slices[0]] = xhat[slices[1]] x[slices[2]] = xhat[slices[3]] return x | slices[k].append(slice(None)) k = arange(N) if even: ak = sb.r_[1.0,[2]*(N-1)]*exp(1j*pi*k/(2*N)) newshape = ones(n) newshape[axis] = N ak.shape = newshape xhat = real(scipy.ifft(v*ak,axis=axis)) x = 0.0*v slices[0][axis] = slice(None,None,2) slices[1][axis] = slice(None,N/2) slices[2][axis] = slice(N,None,-2) slices[3][axis] = slice(N/2,None) for k in range(4): slices[k] = tuple(slices[k]) x[slices[0]] = xhat[slices[1]] x[slices[2]] = xhat[slices[3]] return x else: ak = 2*sb.exp(1j*pi*k/(2*N)) newshape = ones(n) newshape[axis] = N ak.shape = newshape newshape = list(v.shape) newshape[axis] = 2*N Y = zeros(newshape,sb.Complex) slices[0][axis] = slice(None,N) slices[1][axis] = slice(None,None) slices[2][axis] = slice(N+1,None) slices[3][axis] = slice((N-1),0,-1) Y[slices[0]] = ak*v Y[slices[2]] = conj(Y[slices[3]]) x = real(scipy.ifft(Y,axis=axis))[slices[0]] return x | def idct(v,axis=-1): n = len(v.shape) N = v.shape[axis] if (N%2 != 0): raise ValueError, "Length of sequence must be even." k = arange(N) ak = sb.r_[1.0,[2]*(N-1)]*exp(1j*pi*k/(2*N)) newshape = ones(n) newshape[axis] = N ak.shape = newshape xhat = real(scipy.ifft(v*ak,axis=axis)) x = 0.0*v slices = [None]*4 for k in range(4): slices[k] = [] for j in range(n): slices[k].append(slice(None)) slices[0][axis] = slice(None,None,2) slices[1][axis] = slice(None,N/2) slices[2][axis] = slice(N,None,-2) slices[3][axis] = slice(N/2,None) for k in range(4): slices[k] = tuple(slices[k]) x[slices[0]] = xhat[slices[1]] x[slices[2]] = xhat[slices[3]] return x |
def yield(): | def Yield(): | def yield(): if not threaded(): # forces the event handlers to finish their work. # this also forces deletion of windows. wxYield() else: time.sleep(0.05) # sync threads |
yield() | Yield() | def check_wx_class(self): "Checking a wxFrame proxied class" for i in range(5): f = gui_thread.register(TestFrame) a = f(None) p = weakref.ref(a) a.Close(1) del a yield() # this checks for memory leaks self.assertEqual(is_alive(p), 0) |
yield() | Yield() | def check_exception(self): "Checking exception handling" f = gui_thread.register(TestFrame) a = f(None) p = weakref.ref(a) self.assertRaises(TypeError, a.Close, 1, 2, 3) a.Close() del a yield() # this checks for memory leaks self.assertEqual(is_alive(p), 0) |
y = x | y = scipy.squeeze(x) | def plot(x,*args,**keywds): """Plot curves. Description: Plot one or more curves on the same graph. Inputs: There can be a variable number of inputs which consist of pairs or triples. The second variable is plotted against the first using the linetype specified by the optional third variable in the triple. If only two plots are being compared, the x-axis does not have to be repeated. """ try: override = 1 savesys = gist.plsys(2) gist.plsys(savesys) except: override = 0 global _hold try: _hold=keywds['hold'] except KeyError: pass try: linewidth=float(keywds['width']) except KeyError: linewidth=1.0 if _hold or override: pass else: gist.fma() gist.animate(0) savesys = gist.plsys() winnum = gist.window() if winnum < 0: gist.window(0) gist.plsys(savesys) nargs = len(args) if nargs == 0: y = x x = Numeric.arange(0,len(y)) if scipy.iscomplexobj(y): print "Warning: complex data plotting real part." y = y.real y = where(scipy.isfinite(y),y,0) gist.plg(y,x,type='solid',color='blue',marks=0,width=linewidth) return y = args[0] argpos = 1 nowplotting = 0 clear_global_linetype() while 1: try: thearg = args[argpos] except IndexError: thearg = 0 thetype,thecolor,themarker,tomark = _parse_type_arg(thearg,nowplotting) if themarker == 'Z': # args[argpos] was data or non-existent. pass append_global_linetype(_rtypes[thetype]+_rcolors[thecolor]) else: # args[argpos] was a string argpos = argpos + 1 if tomark: append_global_linetype(_rtypes[thetype]+_rcolors[thecolor]+_rmarkers[themarker]) else: append_global_linetype(_rtypes[thetype]+_rcolors[thecolor]) if scipy.iscomplexobj(x) or scipy.iscomplexobj(y): print "Warning: complex data provided, using only real part." x = scipy.real(x) y = scipy.real(y) y = where(scipy.isfinite(y),y,0) y = scipy.squeeze(y) x = scipy.squeeze(x) gist.plg(y,x,type=thetype,color=thecolor,marker=themarker,marks=tomark,width=linewidth) nowplotting = nowplotting + 1 ## Argpos is pointing to the next potential triple of data. ## Now one of four things can happen: ## ## 1: argpos points to data, argpos+1 is a string ## 2: argpos points to data, end ## 3: argpos points to data, argpos+1 is data ## 4: argpos points to data, argpos+1 is data, argpos+2 is a string if argpos >= nargs: break # no more data if argpos == nargs-1: # this is a single data value. x = x y = args[argpos] argpos = argpos+1 elif type(args[argpos+1]) is types.StringType: x = x y = args[argpos] argpos = argpos+1 else: # 3 x = args[argpos] y = args[argpos+1] argpos = argpos+2 return |
z = norm(size=self._size) | z = norm.rvs(size=self._size) | def _rvs(self, c): z = norm(size=self._size) U = random(size=self._size) fac = 2 + c*c*z*z det = sqrt(fac*fac - 4) t1 = fac + det t2 = fac - det return t1*(U>0.5) + t2*(U<0.5) |
return abs(norm(mu=c,size=self._size)) | return abs(norm.rvs(mu=c,size=self._size)) | def _rvs(self, c): return abs(norm(mu=c,size=self._size)) |
return abs(norm(size=self._size)) | return abs(norm.rvs(size=self._size)) | def _rvs(self): return abs(norm(size=self._size)) |
return exp(s * norm(size=self._size)) | return exp(s * norm.rvs(size=self._size)) | def _rvs(self, s): return exp(s * norm(size=self._size)) |
M,rest = divmod(header[0],1000) | M,rest = divmod(int(header[0]),1000) | def loadmat(name, dict=None, appendmat=1, basename='raw'): """Load the MATLAB(tm) mat file. If name is a full path name load it in. Otherwise search for the file on the sys.path list and load the first one found (the current directory is searched first). Both v4 (Level 1.0) and v6 matfiles are supported. Version 7.0 files are not yet supported. Inputs: name -- name of the mat file (don't need .mat extension if appendmat=1) dict -- the dictionary to insert into. If none the variables will be returned in a dictionary. appendmat -- non-zero to append the .mat extension to the end of the given filename. basename -- for MATLAB(tm) v5 matfiles raw data will have this basename. Outputs: If dict is None, then a dictionary of names and objects representing the stored arrays is returned. """ if appendmat and name[-4:] == ".mat": name = name[:-4] if os.sep in name: full_name = name if appendmat: full_name = name + ".mat" else: full_name = None junk,name = os.path.split(name) for path in sys.path: test_name = os.path.join(path,name) if appendmat: test_name += ".mat" try: fid = open(test_name,'rb') fid.close() full_name = test_name break except IOError: pass if full_name is None: raise IOError, "%s not found on the path." % name fid = fopen(full_name,'rb') test_vals = fid.fread(4,'byte') if not (0 in test_vals): # MATLAB version 5 format fid.rewind() thisdict = _loadv5(fid,basename) if dict is not None: dict.update(thisdict) return else: return thisdict testtype = struct.unpack('i',test_vals.tostring()) # Check to see if the number is positive and less than 5000. if testtype[0] < 0 or testtype[0] > 4999: # wrong byte-order if LittleEndian: format = 'ieee-be' else: format = 'ieee-le' else: # otherwise we are O.K. if LittleEndian: format = 'ieee-le' else: format = 'ieee-be' fid.setformat(format) length = fid.size() fid.rewind() # back to the begining defnames = [] thisdict = {} while 1: if (fid.tell() == length): break header = fid.fread(5,'int') if len(header) != 5: fid.close() print "Warning: Read error in file." break M,rest = divmod(header[0],1000) O,rest = divmod(rest,100) P,rest = divmod(rest,10) T = rest if (M > 1): fid.close() raise ValueError, "Unsupported binary format." if (O != 0): fid.close() raise ValuError, "Hundreds digit of first integer should be zero." if (T not in [0,1]): fid.close() raise ValueError, "Cannot handle sparse matrices, yet." storage = {0:'d',1:'f',2:'i',3:'h',4:'H',5:'B'}[P] varname = fid.fread(header[-1],'char')[:-1] varname = varname.tostring() defnames.append(varname) numels = header[1]*header[2] if T == 0: # Text data data = atleast_1d(fid.fread(numels,storage)) if header[3]: # imaginary data data2 = fid.fread(numels,storage) new = zeros(data.shape,data.dtype.char.capitalize()) new.real = data new.imag = data2 data = new del(new) del(data2) if len(data) > 1: data=data.reshape((header[2], header[1]) ) thisdict[varname] = transpose(squeeze(data)) else: thisdict[varname] = data else: data = atleast_1d(fid.fread(numels,storage,'char')) if len(data) > 1: data=data.reshape((header[2], header[1])) thisdict[varname] = transpose(squeeze(data)) else: thisdict[varname] = data fid.close() if dict is not None: print "Names defined = ", defnames dict.update(thisdict) else: return thisdict |
if cfcn = None: | if cfcn is None: | def collapse (a,keepcols,collapsecols,stderr=0,ns=0,cfcn=None): """Averages data in collapsecol, keeping all unique items in keepcols (using unique, which keeps unique LISTS of column numbers), retaining the unique sets of values in keepcols, the mean for each. If the sterr or N of the mean are desired, set either or both parameters to 1. Returns: unique 'conditions' specified by the contents of columns specified by keepcols, abutted with the mean(s) of column(s) specified by collapsecols """ if cfcn = None: cfcn = stats.mean a = asarray(a) if keepcols == []: avgcol = colex(a,collapsecols) means = cfcn(avgcol) return means else: if type(keepcols) not in [ListType,TupleType,N.ArrayType]: keepcols = [keepcols] values = colex(a,keepcols) # so that "item" can be appended (below) uniques = unique(values) # get a LIST, so .sort keeps rows intact uniques.sort() newlist = [] for item in uniques: if type(item) not in [ListType,TupleType,N.ArrayType]: item =[item] tmprows = linexand(a,keepcols,item) for col in collapsecols: avgcol = colex(tmprows,col) item.append(cfcn(avgcol)) if sterr: if len(avgcol)>1: item.append(stats.sterr(avgcol)) else: item.append('N/A') if ns: item.append(len(avgcol)) newlist.append(item) try: new_a = N.array(newlist) except TypeError: new_a = N.array(newlist,'O') return new_a |
def figure(n=None, style='/tmp/currstyle.gs', color=-2, frame=0, labelsize=14, labelfont='helvetica',aspect=1.618,dpi=75): | def setdpi(num): """ Set the dpi for new windows """ if num in [75,100]: _dpi = num gist.set_default_dpi(_dpi) else: raise ValueError, "DPI must be 75 or 100" def figure(n=None,style='/tmp/currstyle.gs', color=-2, frame=0, labelsize=14, labelfont='helvetica',aspect=1.618): global _figures | def figure(n=None, style='/tmp/currstyle.gs', color=-2, frame=0, labelsize=14, labelfont='helvetica',aspect=1.618,dpi=75): if (aspect < 0.1) or (aspect > 10): aspect = 1.618 if isinstance(color, types.StringType): color = _colornum[color] fid = open(style,'w') syst = write_style.getsys(color=color,frame=frame, labelsize=labelsize,font=labelfont) cntr = (5.5*inches,4.25*inches) # horizontal, vertical height = 4.25*inches width = aspect*height syst['viewport'] = [cntr[0]-width/2.0,cntr[0]+width/2.0,cntr[1]-height/2.0,cntr[1]+height/2.0] fid.write(write_style.style2string(syst,landscape=1)) fid.close() if n is None: gist.window(style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) else: gist.window(n,style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) _current_style = style return |
gist.window(style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) else: gist.window(n,style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) _current_style = style | winnum = gist.window(style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi)) if winnum < 0: gist.window(style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi)) else: gist.window(n,style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi)) _current_style = style | def figure(n=None, style='/tmp/currstyle.gs', color=-2, frame=0, labelsize=14, labelfont='helvetica',aspect=1.618,dpi=75): if (aspect < 0.1) or (aspect > 10): aspect = 1.618 if isinstance(color, types.StringType): color = _colornum[color] fid = open(style,'w') syst = write_style.getsys(color=color,frame=frame, labelsize=labelsize,font=labelfont) cntr = (5.5*inches,4.25*inches) # horizontal, vertical height = 4.25*inches width = aspect*height syst['viewport'] = [cntr[0]-width/2.0,cntr[0]+width/2.0,cntr[1]-height/2.0,cntr[1]+height/2.0] fid.write(write_style.style2string(syst,landscape=1)) fid.close() if n is None: gist.window(style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) else: gist.window(n,style=style,width=int(width*1.25/inches*dpi),height=int(height*1.4/inches*dpi),dpi=dpi) _current_style = style return |
def full_page(win,dpi=75): gist.window(win,style=_current_style,width=int(dpi*8.5),height=dpi*11,dpi=dpi) | def full_page(win): gist.window(win,style=_current_style,width=int(_dpi*8.5),height=_dpi*11) | def full_page(win,dpi=75): gist.window(win,style=_current_style,width=int(dpi*8.5),height=dpi*11,dpi=dpi) |
def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,ticks=1): | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
if dpi != 100: dpi = 75 | if _dpi != 100: | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
conv = inches *1.0 / dpi | conv = inches *1.0 / _dpi | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): | maxw = 11*_dpi maxh = 8.5*_dpi if ph > (8.5*_dpi) and pw < (8.5*_dpi): | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
maxh = 11*dpi maxw = 8.5*dpi | maxh = 11*_dpi maxw = 8.5*_dpi | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
cntr = array([5.5,4.25])*dpi else: cntr = array([4.25,6.75])*dpi | cntr = array([5.5,4.25])*_dpi else: cntr = array([4.25,6.75])*_dpi | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) | gist.window(win,style=_current_style,width=int(pw),height=int(ph)) | def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,dpi=100,ticks=1): # Use gist.plsys to change coordinate systems # all inputs (except fontsize) given as pixels, gist wants # things in normalized device # coordinate. Window is brought up with center of window at # center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25) # or at position (4.25,6.75) for portrait mode msg = 1 if pw is None: pw = Numx*300 msg = 0 if ph is None: ph = Numy*300 msg = 0 maxwidth=int(os.environ.get('XPLT_MAXWIDTH')) maxheight=int(os.environ.get('XPLT_MAXHEIGHT')) printit = 0 if ph > maxheight: ph = maxheight printit = 1 if pw > maxwidth: pw = maxwidth printit = 1 if dpi != 100: dpi = 75 fontsize = 12 conv = inches *1.0 / dpi # multiply by this factor to convert pixels to # NDC # Use landscape mode unless requested height is large land = 1 maxw = 11*dpi maxh = 8.5*dpi if ph > (8.5*dpi) and pw < (8.5*dpi): land = 0 maxh = 11*dpi maxw = 8.5*dpi if ph > maxh: ph = maxh printit=1 if pw > maxw: pw = maxw printit=1 if printit and msg: message = "Warning: Requested height and width too large.\n" message +="Changing to %d x %d" % (pw,ph) print message # Now we've got a suitable height and width if land: cntr = array([5.5,4.25])*dpi # landscape else: cntr = array([4.25,6.75])*dpi # portrait Yspace = ph/float(Numy)*conv Xspace = pw/float(Numx)*conv hsep = hsep * conv vsep = vsep * conv ytop = (cntr[1]+ph/2.0)*conv xleft = (cntr[0]-pw/2.0)*conv if type(color) is types.StringType: color = _colornum[color] systems=[] ind = -1 for nY in range(Numy): ystart = ytop - (nY+1)*Yspace for nX in range(Numx): xstart = xleft + nX*Xspace systems.append({}) systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0] if font is not None or fontsize is not None: _chng_font(systems[-1],font,fontsize) if color != -3 or frame != 0: _add_color(systems[-1],color,frame=frame) if ticks != 1: _remove_ticks(systems[-1]) _current_style='/tmp/subplot%s.gs' % win fid = open(_current_style,'w') fid.write(write_style.style2string(systems,landscape=land)) fid.close() gist.winkill(win) gist.window(win,style=_current_style,width=int(pw),height=int(ph),dpi=100) |
q=scipy.split(a,len(self.workers)) herd.cluster.loop_code(name+'=_q_','_q_',inputs={'_q_':q},returns=(),global_vars=(name,)) def row_rather(self,name): | import scipy q=scipy.split(sequence,len(self.workers)) self.loop_code(name+'=_q_','_q_',inputs={'_q_':q},returns=(),global_vars=(name,)) def row_gather(self,name): | def row_split(self,name,sequence): """experimental""" q=scipy.split(a,len(self.workers)) herd.cluster.loop_code(name+'=_q_','_q_',inputs={'_q_':q},returns=(),global_vars=(name,)) |
concatenate(herd.cluster.[name]) | from Numeric import concatenate return concatenate(self[name]) | def row_rather(self,name): """experimental""" concatenate(herd.cluster.[name]) |
elif p<81: | elif p<35: | def daub(p): """The coefficients for the FIR low-pass filter producing Daubechies wavelets. p>=1 gives the order of the zero at f=1/2. There are 2p filter coefficients. """ sqrt = sb.sqrt assert(p>=1) if p==1: c = 1/sqrt(2) return sb.array([c,c]) elif p==2: f = sqrt(2)/8 c = sqrt(3) return f*sb.array([1+c,3+c,3-c,1-c]) elif p==3: tmp = 12*sqrt(10) z1 = 1.5 + sqrt(15+tmp)/6 - 1j*(sqrt(15)+sqrt(tmp-15))/6 z1c = sb.conj(z1) f = sqrt(2)/8 d0 = sb.real((1-z1)*(1-z1c)) a0 = sb.real(z1*z1c) a1 = 2*sb.real(z1) return f/d0*sb.array([a0, 3*a0-a1, 3*a0-3*a1+1, a0-3*a1+3, 3-a1, 1]) elif p<81: # construct polynomial and factor it if p<35: P = [s.comb(p-1+k,k,exact=1) for k in range(p)][::-1] yj = sb.roots(P) else: raise ValueError, "Cannot factor such large polynomial well." k = sb.r_[0:p] P = s.comb(p-1+k,k)/4.0**k yj = sb.roots(P) / 4 # for each root, compute two z roots, select the one with |z|>1 # Build up final polynomial c = sb.poly1d([1,1])**p q = sb.poly1d([1]) for k in range(p-1): yval = yj[k] part = 2*sqrt(yval*(yval-1)) const = 1-2*yval z1 = const + part if (abs(z1)) < 1: z1 = const - part q = q * [1,-z1] q = sb.real(q) * c # Normalize result q = q / sb.sum(q) * sqrt(2) return q.c[::-1] else: raise ValueError, "Polynomial factorization does not work "\ "well for p too large." |
else: raise ValueError, "Cannot factor such large polynomial well." k = sb.r_[0:p] P = s.comb(p-1+k,k)/4.0**k | else: P = [s.comb(p-1+k,k,exact=1)/4.0**k for k in range(p)][::-1] | def daub(p): """The coefficients for the FIR low-pass filter producing Daubechies wavelets. p>=1 gives the order of the zero at f=1/2. There are 2p filter coefficients. """ sqrt = sb.sqrt assert(p>=1) if p==1: c = 1/sqrt(2) return sb.array([c,c]) elif p==2: f = sqrt(2)/8 c = sqrt(3) return f*sb.array([1+c,3+c,3-c,1-c]) elif p==3: tmp = 12*sqrt(10) z1 = 1.5 + sqrt(15+tmp)/6 - 1j*(sqrt(15)+sqrt(tmp-15))/6 z1c = sb.conj(z1) f = sqrt(2)/8 d0 = sb.real((1-z1)*(1-z1c)) a0 = sb.real(z1*z1c) a1 = 2*sb.real(z1) return f/d0*sb.array([a0, 3*a0-a1, 3*a0-3*a1+1, a0-3*a1+3, 3-a1, 1]) elif p<81: # construct polynomial and factor it if p<35: P = [s.comb(p-1+k,k,exact=1) for k in range(p)][::-1] yj = sb.roots(P) else: raise ValueError, "Cannot factor such large polynomial well." k = sb.r_[0:p] P = s.comb(p-1+k,k)/4.0**k yj = sb.roots(P) / 4 # for each root, compute two z roots, select the one with |z|>1 # Build up final polynomial c = sb.poly1d([1,1])**p q = sb.poly1d([1]) for k in range(p-1): yval = yj[k] part = 2*sqrt(yval*(yval-1)) const = 1-2*yval z1 = const + part if (abs(z1)) < 1: z1 = const - part q = q * [1,-z1] q = sb.real(q) * c # Normalize result q = q / sb.sum(q) * sqrt(2) return q.c[::-1] else: raise ValueError, "Polynomial factorization does not work "\ "well for p too large." |
ext_args['macros'] = [('ATLAS_INFO',atlas_version)] | ext_args['define_macros'] = [('ATLAS_INFO',atlas_version)] | def configuration(parent_package=''): from scipy_distutils.core import Extension from scipy_distutils.misc_util import fortran_library_item, dot_join,\ SourceGenerator, get_path, default_config_dict, get_build_temp from scipy_distutils.system_info import get_info,dict_append,\ AtlasNotFoundError,LapackNotFoundError,BlasNotFoundError,\ LapackSrcNotFoundError,BlasSrcNotFoundError package = 'linalg' from interface_gen import generate_interface config = default_config_dict(package,parent_package) local_path = get_path(__name__) atlas_info = get_info('atlas') #atlas_info = {} # uncomment if ATLAS is available but want to use # Fortran LAPACK/BLAS; useful for testing f_libs = [] atlas_version = None temp_path = os.path.join(get_build_temp(),'linalg','atlas_version') dir_util.mkpath(temp_path,verbose=1) atlas_version_file = os.path.join(temp_path,'atlas_version') if atlas_info: if os.path.isfile(atlas_version_file): atlas_version = open(atlas_version_file).read() print 'ATLAS version',atlas_version if atlas_info and atlas_version is None: # Try to determine ATLAS version shutil.copy(os.path.join(local_path,'atlas_version.c'),temp_path) cur_dir = os.getcwd() os.chdir(temp_path) cmd = '%s %s build_ext --inplace --force'%\ (sys.executable, os.path.join(local_path,'setup_atlas_version.py')) print cmd s,o=run_command(cmd) if not s: cmd = sys.executable+' -c "import atlas_version"' print cmd s,o=run_command(cmd) if not s: m = re.match(r'ATLAS version (?P<version>\d+[.]\d+[.]\d+)',o) if m: atlas_version = m.group('version') print 'ATLAS version',atlas_version if atlas_version is None: if re.search(r'undefined symbol: ATL_buildinfo',o,re.M): atlas_version = '3.2.1_pre3.3.6' print 'ATLAS version',atlas_version else: print o else: print o os.chdir(cur_dir) if atlas_version is None: print 'Failed to determine ATLAS version' else: f = open(atlas_version_file,'w') f.write(atlas_version) f.close() if atlas_info: if ('ATLAS_WITHOUT_LAPACK',None) in atlas_info.get('define_macros',[]): lapack_info = get_info('lapack') if not lapack_info: warnings.warn(LapackNotFoundError.__doc__) lapack_src_info = get_info('lapack_src') if not lapack_src_info: raise LapackSrcNotFoundError,LapackSrcNotFoundError.__doc__ dict_append(lapack_info,libraries=['lapack_src']) f_libs.append(fortran_library_item(\ 'lapack_src',lapack_src_info['sources'], )) dict_append(lapack_info,**atlas_info) atlas_info = lapack_info blas_info,lapack_info = {},{} if not atlas_info: warnings.warn(AtlasNotFoundError.__doc__) blas_info = get_info('blas') #blas_info = {} # test building BLAS from sources. if not blas_info: warnings.warn(BlasNotFoundError.__doc__) blas_src_info = get_info('blas_src') if not blas_src_info: raise BlasSrcNotFoundError,BlasSrcNotFoundError.__doc__ dict_append(blas_info,libraries=['blas_src']) f_libs.append(fortran_library_item(\ 'blas_src',blas_src_info['sources'] + \ [os.path.join(local_path,'src','fblaswrap.f')], )) lapack_info = get_info('lapack') #lapack_info = {} # test building LAPACK from sources. if not lapack_info: warnings.warn(LapackNotFoundError.__doc__) lapack_src_info = get_info('lapack_src') if not lapack_src_info: raise LapackSrcNotFoundError,LapackSrcNotFoundError.__doc__ dict_append(lapack_info,libraries=['lapack_src']) f_libs.append(fortran_library_item(\ 'lapack_src',lapack_src_info['sources'], )) dict_append(atlas_info,**lapack_info) dict_append(atlas_info,**blas_info) target_dir = '' skip_names = {'clapack':[],'flapack':[],'cblas':[],'fblas':[]} if skip_single_routines: target_dir = 'dbl' skip_names['clapack'].extend(\ 'sgesv cgesv sgetrf cgetrf sgetrs cgetrs sgetri cgetri'\ ' sposv cposv spotrf cpotrf spotrs cpotrs spotri cpotri'\ ' slauum clauum strtri ctrtri'.split()) skip_names['flapack'].extend(skip_names['clapack']) skip_names['flapack'].extend(\ 'sgesdd cgesdd sgelss cgelss sgeqrf cgeqrf sgeev cgeev'\ ' sgegv cgegv ssyev cheev slaswp claswp sgees cgees' ' sggev cggev'.split()) skip_names['cblas'].extend('saxpy caxpy'.split()) skip_names['fblas'].extend(skip_names['cblas']) skip_names['fblas'].extend(\ 'srotg crotg srotmg srot csrot srotm sswap cswap sscal cscal'\ ' csscal scopy ccopy sdot cdotu cdotc snrm2 scnrm2 sasum scasum'\ ' isamax icamax sgemv cgemv chemv ssymv strmv ctrmv'\ ' sgemm cgemm'.split()) if using_lapack_blas: target_dir = os.path.join(target_dir,'blas') skip_names['fblas'].extend(\ 'drotmg srotmg drotm srotm'.split()) if atlas_version=='3.2.1_pre3.3.6': target_dir = os.path.join(target_dir,'atlas321') skip_names['clapack'].extend(\ 'sgetri dgetri cgetri zgetri spotri dpotri cpotri zpotri'\ ' slauum dlauum clauum zlauum strtri dtrtri ctrtri ztrtri'.split()) # atlas_version: ext_args = {'name':dot_join(parent_package,package,'atlas_version'), 'sources':[os.path.join(local_path,'atlas_version.c')]} if atlas_info: ext_args['libraries'] = [atlas_info['libraries'][-1]] ext_args['library_dirs'] = atlas_info['library_dirs'][:] ext_args['macros'] = [('ATLAS_INFO',atlas_version)] else: ext_args['macros'] = [('NO_ATLAS_INFO',1)] ext = Extension(**ext_args) config['ext_modules'].append(ext) # In case any of atlas|lapack|blas libraries are not available def generate_empty_pyf(target,sources,generator,skips): name = os.path.basename(target)[:-4] f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() # fblas: def generate_fblas_pyf(target,sources,generator,skips): generator('fblas',sources[0],target,skips) if not (blas_info or atlas_info): generate_fblas_pyf = generate_empty_pyf sources = ['generic_fblas.pyf', 'generic_fblas1.pyf', 'generic_fblas2.pyf', 'generic_fblas3.pyf', os.path.join('src','fblaswrap.f')] sources = [os.path.join(local_path,s) for s in sources] fblas_pyf = SourceGenerator(generate_fblas_pyf, os.path.join(target_dir,'fblas.pyf'), sources,generate_interface, skip_names['fblas']) ext_args = {'name':dot_join(parent_package,package,'fblas'), 'sources':[fblas_pyf,sources[-1]]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # cblas: def generate_cblas_pyf(target,sources,generator,skips): generator('cblas',sources[0],target,skips) if not atlas_info: generate_cblas_pyf = generate_empty_pyf sources = ['generic_cblas.pyf', 'generic_cblas1.pyf'] sources = [os.path.join(local_path,s) for s in sources] cblas_pyf = SourceGenerator(generate_cblas_pyf, os.path.join(target_dir,'cblas.pyf'), sources,generate_interface, skip_names['cblas']) ext_args = {'name':dot_join(parent_package,package,'cblas'), 'sources':[cblas_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # flapack: def generate_flapack_pyf(target,sources,generator,skips): generator('flapack',sources[0],target,skips) if not (lapack_info or atlas_info): generate_flapack_pyf = generate_empty_pyf sources = ['generic_flapack.pyf','flapack_user_routines.pyf'] sources = [os.path.join(local_path,s) for s in sources] flapack_pyf = SourceGenerator(generate_flapack_pyf, os.path.join(target_dir,'flapack.pyf'), sources,generate_interface, skip_names['flapack']) ext_args = {'name':dot_join(parent_package,package,'flapack'), 'sources':[flapack_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # clapack: def generate_clapack_pyf(target,sources,generator,skips): generator('clapack',sources[0],target,skips) if not atlas_info: generate_cblas_pyf = generate_empty_pyf sources = ['generic_clapack.pyf'] sources = [os.path.join(local_path,s) for s in sources] clapack_pyf = SourceGenerator(generate_clapack_pyf, os.path.join(target_dir,'clapack.pyf'), sources,generate_interface, skip_names['clapack']) ext_args = {'name':dot_join(parent_package,package,'clapack'), 'sources':[clapack_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # _flinalg: flinalg = [] for f in ['det.f','lu.f', #'wrappers.c','inv.f', ]: flinalg.append(os.path.join(local_path,'src',f)) ext_args = {'name':dot_join(parent_package,package,'_flinalg'), 'sources':flinalg} dict_append(ext_args,**atlas_info) config['ext_modules'].append(Extension(**ext_args)) # calc_lwork: ext_args = {'name':dot_join(parent_package,package,'calc_lwork'), 'sources':[os.path.join(local_path,'src','calc_lwork.f')], } dict_append(ext_args,**atlas_info) config['ext_modules'].append(Extension(**ext_args)) config['fortran_libraries'].extend(f_libs) return config |
ext_args['macros'] = [('NO_ATLAS_INFO',1)] | ext_args['define_macros'] = [('NO_ATLAS_INFO',1)] | def configuration(parent_package=''): from scipy_distutils.core import Extension from scipy_distutils.misc_util import fortran_library_item, dot_join,\ SourceGenerator, get_path, default_config_dict, get_build_temp from scipy_distutils.system_info import get_info,dict_append,\ AtlasNotFoundError,LapackNotFoundError,BlasNotFoundError,\ LapackSrcNotFoundError,BlasSrcNotFoundError package = 'linalg' from interface_gen import generate_interface config = default_config_dict(package,parent_package) local_path = get_path(__name__) atlas_info = get_info('atlas') #atlas_info = {} # uncomment if ATLAS is available but want to use # Fortran LAPACK/BLAS; useful for testing f_libs = [] atlas_version = None temp_path = os.path.join(get_build_temp(),'linalg','atlas_version') dir_util.mkpath(temp_path,verbose=1) atlas_version_file = os.path.join(temp_path,'atlas_version') if atlas_info: if os.path.isfile(atlas_version_file): atlas_version = open(atlas_version_file).read() print 'ATLAS version',atlas_version if atlas_info and atlas_version is None: # Try to determine ATLAS version shutil.copy(os.path.join(local_path,'atlas_version.c'),temp_path) cur_dir = os.getcwd() os.chdir(temp_path) cmd = '%s %s build_ext --inplace --force'%\ (sys.executable, os.path.join(local_path,'setup_atlas_version.py')) print cmd s,o=run_command(cmd) if not s: cmd = sys.executable+' -c "import atlas_version"' print cmd s,o=run_command(cmd) if not s: m = re.match(r'ATLAS version (?P<version>\d+[.]\d+[.]\d+)',o) if m: atlas_version = m.group('version') print 'ATLAS version',atlas_version if atlas_version is None: if re.search(r'undefined symbol: ATL_buildinfo',o,re.M): atlas_version = '3.2.1_pre3.3.6' print 'ATLAS version',atlas_version else: print o else: print o os.chdir(cur_dir) if atlas_version is None: print 'Failed to determine ATLAS version' else: f = open(atlas_version_file,'w') f.write(atlas_version) f.close() if atlas_info: if ('ATLAS_WITHOUT_LAPACK',None) in atlas_info.get('define_macros',[]): lapack_info = get_info('lapack') if not lapack_info: warnings.warn(LapackNotFoundError.__doc__) lapack_src_info = get_info('lapack_src') if not lapack_src_info: raise LapackSrcNotFoundError,LapackSrcNotFoundError.__doc__ dict_append(lapack_info,libraries=['lapack_src']) f_libs.append(fortran_library_item(\ 'lapack_src',lapack_src_info['sources'], )) dict_append(lapack_info,**atlas_info) atlas_info = lapack_info blas_info,lapack_info = {},{} if not atlas_info: warnings.warn(AtlasNotFoundError.__doc__) blas_info = get_info('blas') #blas_info = {} # test building BLAS from sources. if not blas_info: warnings.warn(BlasNotFoundError.__doc__) blas_src_info = get_info('blas_src') if not blas_src_info: raise BlasSrcNotFoundError,BlasSrcNotFoundError.__doc__ dict_append(blas_info,libraries=['blas_src']) f_libs.append(fortran_library_item(\ 'blas_src',blas_src_info['sources'] + \ [os.path.join(local_path,'src','fblaswrap.f')], )) lapack_info = get_info('lapack') #lapack_info = {} # test building LAPACK from sources. if not lapack_info: warnings.warn(LapackNotFoundError.__doc__) lapack_src_info = get_info('lapack_src') if not lapack_src_info: raise LapackSrcNotFoundError,LapackSrcNotFoundError.__doc__ dict_append(lapack_info,libraries=['lapack_src']) f_libs.append(fortran_library_item(\ 'lapack_src',lapack_src_info['sources'], )) dict_append(atlas_info,**lapack_info) dict_append(atlas_info,**blas_info) target_dir = '' skip_names = {'clapack':[],'flapack':[],'cblas':[],'fblas':[]} if skip_single_routines: target_dir = 'dbl' skip_names['clapack'].extend(\ 'sgesv cgesv sgetrf cgetrf sgetrs cgetrs sgetri cgetri'\ ' sposv cposv spotrf cpotrf spotrs cpotrs spotri cpotri'\ ' slauum clauum strtri ctrtri'.split()) skip_names['flapack'].extend(skip_names['clapack']) skip_names['flapack'].extend(\ 'sgesdd cgesdd sgelss cgelss sgeqrf cgeqrf sgeev cgeev'\ ' sgegv cgegv ssyev cheev slaswp claswp sgees cgees' ' sggev cggev'.split()) skip_names['cblas'].extend('saxpy caxpy'.split()) skip_names['fblas'].extend(skip_names['cblas']) skip_names['fblas'].extend(\ 'srotg crotg srotmg srot csrot srotm sswap cswap sscal cscal'\ ' csscal scopy ccopy sdot cdotu cdotc snrm2 scnrm2 sasum scasum'\ ' isamax icamax sgemv cgemv chemv ssymv strmv ctrmv'\ ' sgemm cgemm'.split()) if using_lapack_blas: target_dir = os.path.join(target_dir,'blas') skip_names['fblas'].extend(\ 'drotmg srotmg drotm srotm'.split()) if atlas_version=='3.2.1_pre3.3.6': target_dir = os.path.join(target_dir,'atlas321') skip_names['clapack'].extend(\ 'sgetri dgetri cgetri zgetri spotri dpotri cpotri zpotri'\ ' slauum dlauum clauum zlauum strtri dtrtri ctrtri ztrtri'.split()) # atlas_version: ext_args = {'name':dot_join(parent_package,package,'atlas_version'), 'sources':[os.path.join(local_path,'atlas_version.c')]} if atlas_info: ext_args['libraries'] = [atlas_info['libraries'][-1]] ext_args['library_dirs'] = atlas_info['library_dirs'][:] ext_args['macros'] = [('ATLAS_INFO',atlas_version)] else: ext_args['macros'] = [('NO_ATLAS_INFO',1)] ext = Extension(**ext_args) config['ext_modules'].append(ext) # In case any of atlas|lapack|blas libraries are not available def generate_empty_pyf(target,sources,generator,skips): name = os.path.basename(target)[:-4] f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() # fblas: def generate_fblas_pyf(target,sources,generator,skips): generator('fblas',sources[0],target,skips) if not (blas_info or atlas_info): generate_fblas_pyf = generate_empty_pyf sources = ['generic_fblas.pyf', 'generic_fblas1.pyf', 'generic_fblas2.pyf', 'generic_fblas3.pyf', os.path.join('src','fblaswrap.f')] sources = [os.path.join(local_path,s) for s in sources] fblas_pyf = SourceGenerator(generate_fblas_pyf, os.path.join(target_dir,'fblas.pyf'), sources,generate_interface, skip_names['fblas']) ext_args = {'name':dot_join(parent_package,package,'fblas'), 'sources':[fblas_pyf,sources[-1]]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # cblas: def generate_cblas_pyf(target,sources,generator,skips): generator('cblas',sources[0],target,skips) if not atlas_info: generate_cblas_pyf = generate_empty_pyf sources = ['generic_cblas.pyf', 'generic_cblas1.pyf'] sources = [os.path.join(local_path,s) for s in sources] cblas_pyf = SourceGenerator(generate_cblas_pyf, os.path.join(target_dir,'cblas.pyf'), sources,generate_interface, skip_names['cblas']) ext_args = {'name':dot_join(parent_package,package,'cblas'), 'sources':[cblas_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # flapack: def generate_flapack_pyf(target,sources,generator,skips): generator('flapack',sources[0],target,skips) if not (lapack_info or atlas_info): generate_flapack_pyf = generate_empty_pyf sources = ['generic_flapack.pyf','flapack_user_routines.pyf'] sources = [os.path.join(local_path,s) for s in sources] flapack_pyf = SourceGenerator(generate_flapack_pyf, os.path.join(target_dir,'flapack.pyf'), sources,generate_interface, skip_names['flapack']) ext_args = {'name':dot_join(parent_package,package,'flapack'), 'sources':[flapack_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # clapack: def generate_clapack_pyf(target,sources,generator,skips): generator('clapack',sources[0],target,skips) if not atlas_info: generate_cblas_pyf = generate_empty_pyf sources = ['generic_clapack.pyf'] sources = [os.path.join(local_path,s) for s in sources] clapack_pyf = SourceGenerator(generate_clapack_pyf, os.path.join(target_dir,'clapack.pyf'), sources,generate_interface, skip_names['clapack']) ext_args = {'name':dot_join(parent_package,package,'clapack'), 'sources':[clapack_pyf]} dict_append(ext_args,**atlas_info) ext = Extension(**ext_args) ext.need_fcompiler_opts = 1 config['ext_modules'].append(ext) # _flinalg: flinalg = [] for f in ['det.f','lu.f', #'wrappers.c','inv.f', ]: flinalg.append(os.path.join(local_path,'src',f)) ext_args = {'name':dot_join(parent_package,package,'_flinalg'), 'sources':flinalg} dict_append(ext_args,**atlas_info) config['ext_modules'].append(Extension(**ext_args)) # calc_lwork: ext_args = {'name':dot_join(parent_package,package,'calc_lwork'), 'sources':[os.path.join(local_path,'src','calc_lwork.f')], } dict_append(ext_args,**atlas_info) config['ext_modules'].append(Extension(**ext_args)) config['fortran_libraries'].extend(f_libs) return config |
f.write('\ndef get_info(name): return globals().get(name,{})\n') | f.write('\ndef get_info(name): g=globals(); return g.get(name,g.get(name+"_info",{}))\n') | f.write('\ndef get_info(name): return globals().get(name,{})\n') |
self.obj = scipy.ppresolve(obj) | self.obj = obj | def __init__(self, parent, obj, **kw): self.parent = parent self.obj = scipy.ppresolve(obj) self.name = kw.pop('name',None) if self.name is None: self.name = self.obj.__name__ self.canedit = kw.pop('canedit',1) rend.Page.__init__(self, **kw) |
if name not in self.all: | if name not in self.all and not hasattr(self.obj,name): | def childFactory(self, context, name): if name not in self.all: print "Err 1: ", name, self.all return None child = getattr(self.obj,name,None) |
basic_inv = linalg.inverse | basic_inv = linalg.inv | def bench_random(self,level=5): import numpy.linalg as linalg basic_inv = linalg.inverse print print ' Finding matrix inverse' print ' ==================================' print ' | contiguous | non-contiguous ' print '----------------------------------------------' print ' size | scipy | basic | scipy | basic' |
if 'X11BASE' in os.environ: X11BASE=os.environ['X11BASE'] else: X11BASE="/no/suggested/x11dir" | X11BASE=os.environ.get('X11BASE','/no/suggested/x11dir') | def config_x11(self): print print " ============= begin play/x11 configuration ==============" print from string import replace self.fatality=0 |
libraries = ['X11'] | libraries = x11_info.get('libraries','X11') | def getallparams(gistpath,local): if windows: extra_compile_args = ['-DGISTPATH="\\"' + gistpath + '\\""' ] else: extra_compile_args = ['-DGISTPATH="' + gistpath + '"' ] extra_link_args = [] if windows or cygwin: extra_compile_args.append("-DWINDOWS") extra_compile_args.append("-mwindows") extra_link_args.append("-mwindows") if cygwin: extra_compile_args.append("-DCYGWIN") include_dirs = [ 'src/gist', 'src/play', 'src/play/unix' ] if windows or cygwin: libraries = [] else: libraries = ['X11'] library_dirs = [os.path.join(local,x) for x in ['.','src']] library_dirs.extend(get_special_dirs(sys.platform)) include_dirs = [os.path.join(local,x) for x in include_dirs] if not run_config: inputfile = open(os.path.join(local,"pygist","Make.cfg")) lines = inputfile.readlines() inputfile.close() for line in lines: if line[:8]=="MATHLIB=": mathlib = line[8:-1] #removing the \n # remove the -l mathlib = mathlib[2:] libraries.append(mathlib) if line[:9]=="NO_EXP10=": no_exp10 = line[9:-1] # removing \n if no_exp10: extra_compile_args.append(no_exp10) if line[:5]=="XINC=": xinc = line[5:-1] # removing \n if xinc and not (windows or cygwin): # remove the -I xinc = xinc[2:] if xinc: include_dirs.append(xinc) if line[:5]=="XLIB=": xlib = line[5:-1] # removing \n if xlib and not (windows or cygwin): # remove the -L xlib = xlib[2:] library_dirs.append(xlib) return include_dirs, library_dirs, libraries, \ extra_compile_args, extra_link_args |
try: import scipy_distutils except ImportError: extra_packages.append('scipy_distutils') sys.argv.insert(0,'scipy_core') | sys.path.insert(0,'scipy_core') | def get_package_config(name): sys.path.insert(0,os.path.join('scipy_core',name)) try: mod = __import__('setup_'+name) config = mod.configuration() finally: del sys.path[0] return config |
def ramp(x, y): | def xramp(x, y): | def ramp(x, y): return x |
ramp.title = 'Ramp' | xramp.title = 'X Ramp' def yramp(x, y): return y yramp.title = 'Y Ramp' | def ramp(x, y): return x |
self.inputs = B.shape[-1] self.outputs = C.shape[0] | self.inputs = self.B.shape[-1] self.outputs = self.C.shape[0] | def __init__(self,*args,**kwords): """Initialize the LTI system using either: (numerator, denominator) (zeros, poles, gain) (A, B, C, D) -- state-space. """ N = len(args) if N == 2: # Numerator denominator transfer function input self.__dict__['num'], self.__dict__['den'] = normalize(*args) self.__dict__['zeros'], self.__dict__['poles'], \ self.__dict__['gain'] = tf2zpk(*args) self.__dict__['A'], self.__dict__['B'], \ self.__dict__['C'], \ self.__dict__['D'] = tf2ss(*args) self.inputs = 1 if len(self.num.shape) > 1: self.outputs = self.num.shape[0] else: self.outputs = 1 elif N == 3: # Zero-pole-gain form self.__dict__['zeros'], self.__dict__['poles'], \ self.__dict__['gain'] = args self.__dict__['num'], self.__dict__['den'] = zpk2tf(*args) self.__dict__['A'], self.__dict__['B'], \ self.__dict__['C'], \ self.__dict__['D'] = zpk2ss(*args) self.inputs = 1 if len(self.zeros.shape) > 1: self.outputs = self.zeros.shape[0] else: self.outputs = 1 elif N == 4: # State-space form self.__dict__['A'], self.__dict__['B'], \ self.__dict__['C'], \ self.__dict__['D'] = abcd_normalize(*args) self.__dict__['zeros'], self.__dict__['poles'], \ self.__dict__['gain'] = ss2zpk(*args) self.__dict__['num'], self.__dict__['den'] = ss2tf(*args) self.inputs = B.shape[-1] self.outputs = C.shape[0] else: raise ValueError, "Needs 2, 3, or 4 arguments." |
fact = (1-exp(-lamba_)) | fact = (1-exp(-lambda_)) | def _pmf(self, k, lambda_): fact = (1-exp(-lamba_)) return fact*exp(-lambda_(k)) |
y = scipy.stats.stdev(X) | y = scipy.stats.std(X) | def check_stdX(self): y = scipy.stats.stdev(X) assert_almost_equal(y,2.738612788) |
y = scipy.stats.stdev(ZERO) | y = scipy.stats.std(ZERO) | def check_stdZERO(self): y = scipy.stats.stdev(ZERO) assert_almost_equal(y,0.0) |
y = scipy.stats.stdev(BIG) | y = scipy.stats.std(BIG) | def check_stdBIG(self): y = scipy.stats.stdev(BIG) assert_almost_equal(y,2.738612788) |
y = scipy.stats.stdev(LITTLE) | y = scipy.stats.std(LITTLE) | def check_stdLITTLE(self): y = scipy.stats.stdev(LITTLE) assert_approx_equal(y,2.738612788e-8) |
y = scipy.stats.stdev(HUGE) | y = scipy.stats.std(HUGE) | def check_stdHUGE(self): y = scipy.stats.stdev(HUGE) assert_approx_equal(y,2.738612788e12) |
y = scipy.stats.stdev(TINY) | y = scipy.stats.std(TINY) | def check_stdTINY(self): y = scipy.stats.stdev(TINY) assert_almost_equal(y,0.0) |
y = scipy.stats.stdev(ROUND) | y = scipy.stats.std(ROUND) | def check_stdROUND(self): y = scipy.stats.stdev(ROUND) assert_approx_equal(y,2.738612788) |
import fnmatch from fnmatch | from fnmatch import fnmatch | def rmdir(dir,depth=0): import os path = os.path.abspath(dir) all_files = os.listdir(path) indent = ' ' * depth for i in all_files: if not i == 'CVS': print indent, i if os.path.isdir(os.path.join(path,i)): rmdir(os.path.join(path,i),depth+1) else: cmd = 'cd ' + path + ';rm -r ' + i + ';cvs rm ' + i + ';cd ..' print cmd os.system(cmd) |
19391512145,2404879675441, 370371188237525,69348874393137901, 15514534163557086905] | 19391512145l,2404879675441l, 370371188237525l,69348874393137901l, 15514534163557086905l] | def check_euler(self): eu0 = euler(0) eu1 = euler(1) eu2 = euler(2) # just checking segfaults assert_almost_equal(eu0[0],1,8) assert_almost_equal(eu2[2],-1,8) eu24 = euler(24) mathworld = [1,1,5,61,1385,50521,2702765,199360981, 19391512145,2404879675441, 370371188237525,69348874393137901, 15514534163557086905] correct = zeros((25,),'d') for k in range(0,13): if (k % 2): correct[2*k] = -float(mathworld[k]) else: correct[2*k] = float(mathworld[k]) err = nan_to_num((eu24-correct)/correct) errmax = max(err) assert_almost_equal(errmax, 0.0, 14) |
self.vecfunc = new.instancemethod(sgf(self._ppf_single_call), self, rv_continuous) | self.vecfunc = sgf(self._ppf_single_call) self.vecentropy = sgf(self._entropy) | def __init__(self, momtype=1, a=None, b=None, xa=-10.0, xb=10.0, xtol=1e-14, badvalue=None, name=None, longname=None, shapes=None, extradoc=None): if badvalue is None: badvalue = nan self.badvalue = badvalue self.name = name self.a = a self.b = b if a is None: self.a = -scipy.inf if b is None: self.b = scipy.inf self.xa = xa self.xb = xb self.xtol = xtol self._size = 1 self.m = 0.0 self.moment_type = momtype self.vecfunc = new.instancemethod(sgf(self._ppf_single_call), self, rv_continuous) self.expandarr = 1 if momtype == 0: self.generic_moment = new.instancemethod(sgf(self._mom0_sc), self, rv_continuous) else: self.generic_moment = new.instancemethod(sgf(self._mom1_sc), self, rv_continuous) cdf_signature = inspect.getargspec(self._cdf.im_func) numargs1 = len(cdf_signature[0]) - 2 pdf_signature = inspect.getargspec(self._pdf.im_func) numargs2 = len(pdf_signature[0]) - 2 self.numargs = max(numargs1, numargs2) |
self.generic_moment = new.instancemethod(sgf(self._mom0_sc), self, rv_continuous) | self.generic_moment = sgf(self._mom0_sc) | def __init__(self, momtype=1, a=None, b=None, xa=-10.0, xb=10.0, xtol=1e-14, badvalue=None, name=None, longname=None, shapes=None, extradoc=None): if badvalue is None: badvalue = nan self.badvalue = badvalue self.name = name self.a = a self.b = b if a is None: self.a = -scipy.inf if b is None: self.b = scipy.inf self.xa = xa self.xb = xb self.xtol = xtol self._size = 1 self.m = 0.0 self.moment_type = momtype self.vecfunc = new.instancemethod(sgf(self._ppf_single_call), self, rv_continuous) self.expandarr = 1 if momtype == 0: self.generic_moment = new.instancemethod(sgf(self._mom0_sc), self, rv_continuous) else: self.generic_moment = new.instancemethod(sgf(self._mom1_sc), self, rv_continuous) cdf_signature = inspect.getargspec(self._cdf.im_func) numargs1 = len(cdf_signature[0]) - 2 pdf_signature = inspect.getargspec(self._pdf.im_func) numargs2 = len(pdf_signature[0]) - 2 self.numargs = max(numargs1, numargs2) |
self.generic_moment = new.instancemethod(sgf(self._mom1_sc), self, rv_continuous) | self.generic_moment = sgf(self._mom1_sc) | def __init__(self, momtype=1, a=None, b=None, xa=-10.0, xb=10.0, xtol=1e-14, badvalue=None, name=None, longname=None, shapes=None, extradoc=None): if badvalue is None: badvalue = nan self.badvalue = badvalue self.name = name self.a = a self.b = b if a is None: self.a = -scipy.inf if b is None: self.b = scipy.inf self.xa = xa self.xb = xb self.xtol = xtol self._size = 1 self.m = 0.0 self.moment_type = momtype self.vecfunc = new.instancemethod(sgf(self._ppf_single_call), self, rv_continuous) self.expandarr = 1 if momtype == 0: self.generic_moment = new.instancemethod(sgf(self._mom0_sc), self, rv_continuous) else: self.generic_moment = new.instancemethod(sgf(self._mom1_sc), self, rv_continuous) cdf_signature = inspect.getargspec(self._cdf.im_func) numargs1 = len(cdf_signature[0]) - 2 pdf_signature = inspect.getargspec(self._pdf.im_func) numargs2 = len(pdf_signature[0]) - 2 self.numargs = max(numargs1, numargs2) |
def _ppf_tosolve(self, x, q, *args): return apply(self.cdf, (x, )+args) - q | def _ppf_tosolve(self, x, q, *args): return apply(self.cdf, (x, )+args) - q |
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return scipy.optimize.brentq(self._ppf_tosolve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol) | return scipy.optimize.brentq(self._ppf_to_solve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol) | def _ppf_single_call(self, q, *args): return scipy.optimize.brentq(self._ppf_tosolve, self.xa, self.xb, args=(q,)+args, xtol=self.xtol) |
kstwobign = kstwobign_gen(a=0.0,name='kstwobign', longname='Kolmogorov-Smirnov two-sided large N statistic', extradoc=""" Kolmogorov-Smirnov two-sided large N stiatistics | kstwobign = kstwobign_gen(a=0.0,name='kstwobign', longname='Kolmogorov-Smirnov two-sided (for large N)', extradoc=""" Kolmogorov-Smirnov two-sided test for large N | def _ppf(self,q): return special.kolmogi(1.0-q) |
def _entropy(self, c): k = log(1+c) return k/2.0 - log(c/k) | def _stats(self, c, moments='mv'): k = log(1.0+c) mu = (c-k)/(c*k) mu2 = ((c+2.0)*k-2.0*c)/(2*c*k*k) g1 = None g2 = None if 's' in moments: g1 = sqrt(2)*(12*c*c-9*c*k*(c+2)+2*k*k*(c*(c+3)+3)) g1 /= sqrt(c*(c*(k-2)+2*k))*(3*c*(k-2)+6*k) if 'k' in moments: g2 = c**3*(k-3)*(k*(3*k-16)+24)+12*k*c*c*(k-4)*(k-3) \ + 6*c*k*k*(3*k-14) + 12*k**3 g2 /= 3*c*(c*(k-2)+2*k)**2 return mu, mu2, g1, g2 |
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def _stats(self, x, c): return burr_gen._stats(self, x, c, 1.0) | def _stats(self, c): return burr_gen._stats(self, c, 1.0) def _entropy(self, c): return 2 - log(c) | def _stats(self, x, c): return burr_gen._stats(self, x, c, 1.0) |
def _isf(self, q, dfn, dfd): return special.fdtri(dfn, dfd, q) | def _isf(self, q, dfn, dfd): return special.fdtri(dfn, dfd, q) |
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return self._isf(1.0-q, dfn, dfd) | return special.fdtri(dfn, dfd, q) | def _ppf(self, q, dfn, dfd): return self._isf(1.0-q, dfn, dfd) |
self.a = where(c > 0, 0.0, -scipy.inf) | def _argcheck(self, c): c = arr(c) self.b = where(c < 0, 1.0/abs(c), scipy.inf) self.a = where(c > 0, 0.0, -scipy.inf) return where(c==0, 0, 1) |
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genpareto = genpareto_gen(name='genpareto', | def _entropy(self, c): if (c > 0): return 1+c else: self.b = -1.0 / c return rv_continuous._entropy(self, c) genpareto = genpareto_gen(a=0.0,name='genpareto', | def _munp(self, n, c): k = arange(0,n+1) val = (-1.0/c)**n * sum(scipy.comb(n,k)*(-1)**k / (1.0-c*k)) return where(c*n < 1, val, scipy.inf) |
invweibull = invweibull_gen(name='invweibull', | def _entropy(self, c): return 1+_EULER + _EULER / c - log(c) invweibull = invweibull_gen(a=0,name='invweibull', | def _ppf(self, q, c): return pow(-log(q),arr(-1.0/c)) |
return 0, pi*pi/3.0, 0, 6.0/5.0 | return 0, pi*pi/3.0, 0, 6.0/5.0 def _entropy(self): return 1.0 | def _stats(self): return 0, pi*pi/3.0, 0, 6.0/5.0 |
def _stats(self, x): | def _stats(self): | def _stats(self, x): return 0, 0.25, 0, -1.0 |
return 0, None, 0, None | mu2 = 2*gam(lam+1.5)-lam*pow(4,-lam)*sqrt(pi)*gam(lam)*(1-2*lam) mu2 /= lam*lam*(1+2*lam)*gam(1+1.5) mu4 = 3*gam(lam)*gam(lam+0.5)*pow(2,-2*lam) / lam**3 / gam(2*lam+1.5) mu4 += 2.0/lam**4 / (1+4*lam) mu4 -= 2*sqrt(3)*gam(lam)*pow(2,-6*lam)*pow(3,3*lam) * \ gam(lam+1.0/3)*gam(lam+2.0/3) / (lam**3.0 * gam(2*lam+1.5) * \ gam(lam+0.5)) g2 = mu4 / mu2 / mu2 - 3.0 return 0, mu2, 0, g2 def _entropy(self, lam): def integ(p): return log(pow(p,lam-1)+pow(1-p,lam-1)) return scipy.integrate.quad(integ,0,1)[0] | def _stats(self, lam): return 0, None, 0, None |
xp = extract( x<pi,x) xn = extract( x>=pi,x) | c1 = x<pi c2 = 1-c1 xp = extract( c1,x) valp = extract(c1,val) xn = extract( c2,x) valn = extract(c2,val) | def _cdf(self, x, c): output = 0.0*x val = (1.0+c)/(1.0-c) xp = extract( x<pi,x) xn = extract( x>=pi,x) if (any(xn)): xn = 2*pi - xn yn = tan(xn/2.0) on = 1.0-1.0/pi*arctan(val*yn) insert(output, x>=pi, on) if (any(xp)): yp = tan(xp/2.0) op = 1.0/pi*arctan(val*yp) insert(output, x<pi, op) return output |
on = 1.0-1.0/pi*arctan(val*yn) insert(output, x>=pi, on) | on = 1.0-1.0/pi*arctan(valn*yn) insert(output, c2, on) | def _cdf(self, x, c): output = 0.0*x val = (1.0+c)/(1.0-c) xp = extract( x<pi,x) xn = extract( x>=pi,x) if (any(xn)): xn = 2*pi - xn yn = tan(xn/2.0) on = 1.0-1.0/pi*arctan(val*yn) insert(output, x>=pi, on) if (any(xp)): yp = tan(xp/2.0) op = 1.0/pi*arctan(val*yp) insert(output, x<pi, op) return output |
op = 1.0/pi*arctan(val*yp) insert(output, x<pi, op) return output | op = 1.0/pi*arctan(valp*yp) insert(output, c1, op) return output def _ppf(self, q, c): val = (1.0-c)/(1.0+c) rcq = 2*arctan(val*tan(pi*q)) rcmq = 2*pi-2*arctan(val*tan(pi*(1-q))) return where(q < 1.0/2, rcq, rcmq) def _entropy(self, c): return log(2*pi*(1-c*c)) | def _cdf(self, x, c): output = 0.0*x val = (1.0+c)/(1.0-c) xp = extract( x<pi,x) xn = extract( x>=pi,x) if (any(xn)): xn = 2*pi - xn yn = tan(xn/2.0) on = 1.0-1.0/pi*arctan(val*yn) insert(output, x>=pi, on) if (any(xp)): yp = tan(xp/2.0) op = 1.0/pi*arctan(val*yp) insert(output, x<pi, op) return output |
raise ValueError | def __call__(self, *args, **kwds): raise ValueError return self.freeze(*args,**kwds) |
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binom = binom_gen(a=0,name='binom',shapes="n,pr",extradoc=""" | def _entropy(self, n, pr): k = r_[0:n+1] vals = self._pmf(k,n,pr) lvals = where(vals==0,0.0,log(vals)) return -sum(vals*lvals) binom = binom_gen(name='binom',shapes="n,pr",extradoc=""" | def _stats(self, n, pr): q = 1.0-pr mu = n * pr var = n * pr * q g1 = (q-pr) / sqrt(n*pr*q) g2 = (1.0-6*pr*q)/(n*pr*q) return mu, var, g1, g2 |
bernoulli = bernoulli_gen(a=0,b=1,name='bernoulli',shapes="pr",extradoc=""" | def _entropy(self, pr): return -pr*log(pr)-(1-pr)*log(1-pr) bernoulli = bernoulli_gen(b=1,name='bernoulli',shapes="pr",extradoc=""" | def _stats(self, pr): return binom_gen._stats(self, 1, pr) |
self.a = n | def _argcheck(self, n, pr): self.a = n return (n >= 0) & (pr >= 0) & (pr <= 1) |
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poisson = poisson_gen(a=0,name="poisson", longname='A Poisson', | poisson = poisson_gen(name="poisson", longname='A Poisson', | def _stats(self, mu): var = mu g1 = 1.0/arr(sqrt(mu)) g2 = 1.0 / arr(mu) return mu, var, g1, g2 |
dlaplace = dlaplace_gen(a=1,name='dlaplace', longname='A discrete Laplacian', | def _entropy(self, a): return a / sinh(a) - log(tanh(a/2.0)) dlaplace = dlaplace_gen(a=-scipy.inf, name='dlaplace', longname='A discrete Laplacian', | def _stats(self, a): ea = exp(-a) e2a = exp(-2*a) e3a = exp(-3*a) e4a = exp(-4*a) mu2 = 2* (e2a + ea) / (1-ea)**3.0 mu4 = 2* (e4a + 11*e3a + 11*e2a + ea) / (1-ea)**5.0 return 0.0, mu2, 0.0, mu4 / mu2**2.0 - 3 |
A = ones((Npts,2),'d') A[:,0] = arange(1,Npts+1)*1.0/Npts | A = ones((Npts,2),dtype) A[:,0] = cast[dtype](arange(1,Npts+1)*1.0/Npts) | def detrend(data, axis=-1, type='linear', bp=0): """Remove linear trend along axis from data. If type is 'constant' then remove mean only. If bp is given, then it is a sequence of points at which to break a piecewise-linear fit to the data. """ if type not in ['linear','l','constant','c']: raise ValueError, "Trend type must be linear or constant" data = asarray(data) if type in ['constant','c']: ret = data - expand_dims(mean(data,axis),axis) return ret else: dshape = data.shape N = dshape[axis] bp = sort(unique(r_[0,bp,N])) if any(bp > N): raise ValueError, "Breakpoints must be less than length of data along given axis." Nreg = len(bp) - 1 # Restructure data so that axis is along first dimension and # all other dimensions are collapsed into second dimension rnk = len(dshape) if axis < 0: axis = axis + rnk newdims = r_[axis,0:axis,axis+1:rnk] newdata = reshape(transpose(data,tuple(newdims)),(N,prod(dshape)/N)) newdata = newdata.copy() # make sure we have a copy # Find leastsq fit and remove it for each piece for m in range(Nreg): Npts = bp[m+1] - bp[m] A = ones((Npts,2),'d') A[:,0] = arange(1,Npts+1)*1.0/Npts sl = slice(bp[m],bp[m+1]) coef,resids,rank,s = linalg.lstsq(A,newdata[sl]) newdata[sl] = newdata[sl] - dot(A,coef) # Put data back in original shape. tdshape = take(dshape,newdims) ret = reshape(newdata,tdshape) vals = range(1,rnk) olddims = vals[:axis] + [0] + vals[axis:] ret = transpose(ret,tuple(olddims)) return ret |
" .astype(), or set sparse.useUmfpack = False" | " .astype(), or set linsolve.useUmfpack = False" | def spsolve(A, b, permc_spec=2): if not hasattr(A, 'tocsr') and not hasattr(A, 'tocsc'): raise ValueError, "sparse matrix must be able to return CSC format--"\ "A.tocsc()--or CSR format--A.tocsr()" if not hasattr(A, 'shape'): raise ValueError, "sparse matrix must be able to return shape" \ " (rows, cols) = A.shape" M, N = A.shape if (M != N): raise ValueError, "matrix must be square" if isUmfpack and useUmfpack: mat = _toCS_umfpack( A ) if mat.dtype.char not in 'dD': raise ValueError, "convert matrix data to double, please, using"\ " .astype(), or set sparse.useUmfpack = False" family = {'d' : 'di', 'D' : 'zi'} umf = umfpack.UmfpackContext( family[mat.dtype.char] ) return umf.linsolve( umfpack.UMFPACK_A, mat, b, autoTranspose = True ) else: mat, csc = _toCS_superLU( A ) ftype, lastel, data, index0, index1 = \ mat.ftype, mat.nnz, mat.data, mat.rowind, mat.indptr gssv = eval('_superlu.' + ftype + 'gssv') print "data-ftype: %s compared to data %s" % (ftype, data.dtype.char) print "Calling _superlu.%sgssv" % ftype return gssv(N, lastel, data, index0, index1, b, csc, permc_spec)[0] |
eps = scipy.limits.epsilon('d') | eps = scipy_base.limits.double_epsilon | def _stats(self): return 0.5, 1.0/12, 0, -1.2 |
def configuration(parent_package='', parent_path=None): local_path = get_path(__name__) config = Configuration('delaunay', parent_package, parent_path) | def configuration(parent_package='', top_path=None): config = Configuration('delaunay', parent_package, top_path) | def configuration(parent_package='', parent_path=None): local_path = get_path(__name__) config = Configuration('delaunay', parent_package, parent_path) config.add_extension("_delaunay", sources=["_delaunay.cpp", "VoronoiDiagramGenerator.cpp", "delaunay_utils.cpp", "natneighbors.cpp"], include_dirs=[local_path], ) return config |
include_dirs=[local_path], | include_dirs=['.'], | def configuration(parent_package='', parent_path=None): local_path = get_path(__name__) config = Configuration('delaunay', parent_package, parent_path) config.add_extension("_delaunay", sources=["_delaunay.cpp", "VoronoiDiagramGenerator.cpp", "delaunay_utils.cpp", "natneighbors.cpp"], include_dirs=[local_path], ) return config |
svsp = m.spacesaver() | svsp = getattr(m,'spacesaver',lambda:0)() | def tril(m, k=0): """ returns the elements on and below the k-th diagonal of m. k=0 is the main diagonal, k > 0 is above and k < 0 is below the main diagonal. """ svsp = m.spacesaver() m = asarray(m,savespace=1) out = tri(m.shape[0], m.shape[1], k=k, typecode=m.typecode())*m out.savespace(svsp) return out |
svsp = m.spacesaver() | svsp = getattr(m,'spacesaver',lambda:0)() | def triu(m, k=0): """ returns the elements on and above the k-th diagonal of m. k=0 is the main diagonal, k > 0 is above and k < 0 is below the main diagonal. """ svsp = m.spacesaver() m = asarray(m,savespace=1) out = (1-tri(m.shape[0], m.shape[1], k-1, m.typecode()))*m out.savespace(svsp) return out |
func -- a Python function or method to integrate. | func -- a Python function or method to integrate (must accept vector inputs) | def fixed_quad(func,a,b,args=(),n=5): """Compute a definite integral using fixed-order Gaussian quadrature. Description: Integrate func from a to b using Gaussian quadrature of order n. Inputs: func -- a Python function or method to integrate. a -- lower limit of integration b -- upper limit of integration args -- extra arguments to pass to function. n -- order of quadrature integration. Outputs: (val, None) val -- Gaussian quadrature approximation to the integral. """ [x,w] = p_roots(n) ainf, binf = map(scipy.isinf,(a,b)) if ainf or binf: raise ValueError, "Gaussian quadrature is only available for finite limits." y = (b-a)*(x+1)/2.0 + a return (b-a)/2.0*sum(w*func(y,*args)), None |
newval = fixed_quad(func,a,b,args,n)[0] | newval = fixed_quad(vec_func,a,b,(func,)+args,n)[0] | def quadrature(func,a,b,args=(),tol=1.49e-8,maxiter=50): """Compute a definite integral using fixed-tolerance Gaussian quadrature. Description: Integrate func from a to b using Gaussian quadrature with absolute tolerance tol. Inputs: func -- a Python function or method to integrate. a -- lower limit of integration. b -- upper limit of integration. args -- extra arguments to pass to function. tol -- iteration stops when error between last two iterates is less than tolerance. maxiter -- maximum number of iterations. Outputs: (val, err) val -- Gaussian quadrature approximation (within tolerance) to integral. err -- Difference between last two estimates of the integral. """ err = 100.0 val = err n = 1 while (err > tol) and (n < maxiter): newval = fixed_quad(func,a,b,args,n)[0] err = abs(newval-val) val = newval n = n + 1 if (n==maxiter): print "maxiter (%d) exceeded. Latest difference = %e" % (n,err) else: print "Took %d points." % n return val, err |
from scipy_distutils.misc_util import fortran_library_item, dot_join,\ SourceGenerator, get_path, default_config_dict, get_build_temp from scipy_distutils.system_info import get_info,dict_append,\ AtlasNotFoundError,LapackNotFoundError,BlasNotFoundError,\ LapackSrcNotFoundError,BlasSrcNotFoundError,NotFoundError | from scipy_distutils.misc_util import dot_join, get_path, default_config_dict from scipy_distutils.system_info import get_info, dict_append, NotFoundError | def configuration(parent_package='',parent_path=None): from scipy_distutils.core import Extension from scipy_distutils.misc_util import fortran_library_item, dot_join,\ SourceGenerator, get_path, default_config_dict, get_build_temp from scipy_distutils.system_info import get_info,dict_append,\ AtlasNotFoundError,LapackNotFoundError,BlasNotFoundError,\ LapackSrcNotFoundError,BlasSrcNotFoundError,NotFoundError package = 'linalg' from interface_gen import generate_interface config = default_config_dict(package,parent_package) local_path = get_path(__name__,parent_path) def local_join(*paths): return os.path.join(*((local_path,)+paths)) abs_local_path = os.path.abspath(local_path) no_atlas = 0 lapack_opt = get_info('lapack_opt') if not lapack_opt: raise NotFoundError,'no lapack/blas resources found' atlas_version = ([v[3:-3] for k,v in lapack_opt.get('define_macros',[]) \ if k=='ATLAS_INFO']+[None])[0] if atlas_version: print 'ATLAS version',atlas_version target_dir = '' skip_names = {'clapack':[],'flapack':[],'cblas':[],'fblas':[]} if skip_single_routines: target_dir = 'dbl' skip_names['clapack'].extend(\ 'sgesv cgesv sgetrf cgetrf sgetrs cgetrs sgetri cgetri'\ ' sposv cposv spotrf cpotrf spotrs cpotrs spotri cpotri'\ ' slauum clauum strtri ctrtri'.split()) skip_names['flapack'].extend(skip_names['clapack']) skip_names['flapack'].extend(\ 'sgesdd cgesdd sgelss cgelss sgeqrf cgeqrf sgeev cgeev'\ ' sgegv cgegv ssyev cheev slaswp claswp sgees cgees' ' sggev cggev'.split()) skip_names['cblas'].extend('saxpy caxpy'.split()) skip_names['fblas'].extend(skip_names['cblas']) skip_names['fblas'].extend(\ 'srotg crotg srotmg srot csrot srotm sswap cswap sscal cscal'\ ' csscal scopy ccopy sdot cdotu cdotc snrm2 scnrm2 sasum scasum'\ ' isamax icamax sgemv cgemv chemv ssymv strmv ctrmv'\ ' sgemm cgemm'.split()) if using_lapack_blas: target_dir = join(target_dir,'blas') skip_names['fblas'].extend(\ 'drotmg srotmg drotm srotm'.split()) if atlas_version=='3.2.1_pre3.3.6': target_dir = join(target_dir,'atlas321') skip_names['clapack'].extend(\ 'sgetri dgetri cgetri zgetri spotri dpotri cpotri zpotri'\ ' slauum dlauum clauum zlauum strtri dtrtri ctrtri ztrtri'.split()) elif atlas_version>'3.4.0' and atlas_version<='3.5.12': skip_names['clapack'].extend('cpotrf zpotrf'.split()) def generate_pyf(extension, build_dir): name = extension.name.split('.')[-1] target = join(build_dir,target_dir,name+'.pyf') if name[0]=='c' and atlas_version is None and newer(__file__,target): f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() return target if newer_group(extension.depends,target): generate_interface(name, extension.depends[0], target, skip_names[name]) return target # fblas: ext_args = {'name': dot_join(parent_package,package,'fblas'), 'sources': [generate_pyf, local_join('src','fblaswrap.f')], 'depends': map(local_join,['generic_fblas.pyf', 'generic_fblas1.pyf', 'generic_fblas2.pyf', 'generic_fblas3.pyf']) } dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) config['ext_modules'].append(ext) # cblas: ext_args = {'name': dot_join(parent_package,package,'cblas'), 'sources': [generate_pyf], 'depends': map(local_join,['generic_cblas.pyf', 'generic_cblas1.pyf']) } dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) config['ext_modules'].append(ext) # flapack: ext_args = {'name': dot_join(parent_package,package,'flapack'), 'sources': [generate_pyf], 'depends': map(local_join,['generic_flapack.pyf', 'flapack_user_routines.pyf']) } dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) config['ext_modules'].append(ext) # clapack: ext_args = {'name': dot_join(parent_package,package,'clapack'), 'sources': [generate_pyf], 'depends': map(local_join,['generic_clapack.pyf']) } dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) config['ext_modules'].append(ext) # _flinalg: ext_args = {'name':dot_join(parent_package,package,'_flinalg'), 'sources':[local_join('src','det.f'), local_join('src','lu.f')] } dict_append(ext_args,**lapack_opt) config['ext_modules'].append(Extension(**ext_args)) # calc_lwork: ext_args = {'name':dot_join(parent_package,package,'calc_lwork'), 'sources':[local_join('src','calc_lwork.f')], } dict_append(ext_args,**lapack_opt) config['ext_modules'].append(Extension(**ext_args)) # atlas_version: ext_args = {'name':dot_join(parent_package,package,'atlas_version'), 'sources':[os.path.join(local_path,'atlas_version.c')]} dict_append(ext_args,**lapack_opt) ext = Extension(**ext_args) config['ext_modules'].append(ext) return config |
'generic_fblas3.pyf']) | 'generic_fblas3.pyf', 'interface_gen.py']) | def generate_pyf(extension, build_dir): name = extension.name.split('.')[-1] target = join(build_dir,target_dir,name+'.pyf') if name[0]=='c' and atlas_version is None and newer(__file__,target): f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() return target if newer_group(extension.depends,target): generate_interface(name, extension.depends[0], target, skip_names[name]) return target |
'generic_cblas1.pyf']) | 'generic_cblas1.pyf', 'interface_gen.py']) | def generate_pyf(extension, build_dir): name = extension.name.split('.')[-1] target = join(build_dir,target_dir,name+'.pyf') if name[0]=='c' and atlas_version is None and newer(__file__,target): f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() return target if newer_group(extension.depends,target): generate_interface(name, extension.depends[0], target, skip_names[name]) return target |
'flapack_user_routines.pyf']) | 'flapack_user_routines.pyf', 'interface_gen.py']) | def generate_pyf(extension, build_dir): name = extension.name.split('.')[-1] target = join(build_dir,target_dir,name+'.pyf') if name[0]=='c' and atlas_version is None and newer(__file__,target): f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() return target if newer_group(extension.depends,target): generate_interface(name, extension.depends[0], target, skip_names[name]) return target |
'depends': map(local_join,['generic_clapack.pyf']) | 'depends': map(local_join,['generic_clapack.pyf', 'interface_gen.py']) | def generate_pyf(extension, build_dir): name = extension.name.split('.')[-1] target = join(build_dir,target_dir,name+'.pyf') if name[0]=='c' and atlas_version is None and newer(__file__,target): f = open(target,'w') f.write('python module '+name+'\n') f.write('usercode void empty_module(void) {}\n') f.write('interface\n') f.write('subroutine empty_module()\n') f.write('intent(c) empty_module\n') f.write('end subroutine empty_module\n') f.write('end interface\nend python module'+name+'\n') f.close() return target if newer_group(extension.depends,target): generate_interface(name, extension.depends[0], target, skip_names[name]) return target |
elif mtype in ['f','float','float32','real*4']: | elif mtype in ['f','float','float32','real*4', 'real']: | def getsize_type(mtype): if mtype in ['b','uchar','byte','unsigned char','integer*1', 'int8']: mtype = 'b' elif mtype in ['c', 'char','char*1']: mtype = 'c' elif mtype in ['1','schar', 'signed char']: mtype = '1' elif mtype in ['s','short','int16','integer*2']: mtype = 's' elif mtype in ['i','int']: mtype = 'i' elif mtype in ['l','long','int32','integer*4']: mtype = 'l' elif mtype in ['f','float','float32','real*4']: mtype = 'f' elif mtype in ['d','double','float64','real*8']: mtype = 'd' elif mtype in ['F','complex float','complex*8','complex64']: mtype = 'F' elif mtype in ['D','complex*16','complex128','complex','complex double']: mtype = 'D' else: raise TypeError, 'Bad datatype -- ' + mtype argout = (array(0,mtype).itemsize(),mtype) return argout |
elif mtype in ['d','double','float64','real*8']: | elif mtype in ['d','double','float64','real*8', 'double precision']: | def getsize_type(mtype): if mtype in ['b','uchar','byte','unsigned char','integer*1', 'int8']: mtype = 'b' elif mtype in ['c', 'char','char*1']: mtype = 'c' elif mtype in ['1','schar', 'signed char']: mtype = '1' elif mtype in ['s','short','int16','integer*2']: mtype = 's' elif mtype in ['i','int']: mtype = 'i' elif mtype in ['l','long','int32','integer*4']: mtype = 'l' elif mtype in ['f','float','float32','real*4']: mtype = 'f' elif mtype in ['d','double','float64','real*8']: mtype = 'd' elif mtype in ['F','complex float','complex*8','complex64']: mtype = 'F' elif mtype in ['D','complex*16','complex128','complex','complex double']: mtype = 'D' else: raise TypeError, 'Bad datatype -- ' + mtype argout = (array(0,mtype).itemsize(),mtype) return argout |
sz,mtype = getsize_type(args[0]) | if len(args) > 0: sz,mtype = getsize_type(args[0]) else: sz,mtype = getsize_type(fmt.typecode()) | def fort_write(self,fmt,*args): """Write a Fortran binary record. |
name = ''.join(asarray(_get_element(fid)[0]).astype('c')) | name = asarray(_get_element(fid)[0]).tostring() | def _parse_mimatrix(fid,bytes): dclass, cmplx, nzmax =_parse_array_flags(fid) dims = _get_element(fid)[0] name = ''.join(asarray(_get_element(fid)[0]).astype('c')) tupdims = tuple(dims[::-1]) if dclass in mxArrays: result, unused =_get_element(fid) if type == mxCHAR_CLASS: result = ''.join(asarray(result).astype('c')) else: if cmplx: imag, unused =_get_element(fid) try: result = result + _unit_imag[imag.typecode()] * imag except KeyError: result = result + 1j*imag result = squeeze(transpose(reshape(result,tupdims))) elif dclass == mxCELL_CLASS: length = product(dims) result = zeros(length, PyObject) for i in range(length): sa, unused = _get_element(fid) result[i]= sa result = squeeze(transpose(reshape(result,tupdims))) if rank(result)==0: result = result.toscalar() elif dclass == mxSTRUCT_CLASS: length = product(dims) result = zeros(length, PyObject) namelength = _get_element(fid)[0] # get field names names = _get_element(fid)[0] splitnames = [names[i:i+namelength] for i in \ xrange(0,len(names),namelength)] fieldnames = [''.join(asarray(x).astype('c')).strip('\x00') for x in splitnames] for i in range(length): result[i] = mat_struct() for element in fieldnames: val,unused = _get_element(fid) result[i].__dict__[element] = val result = squeeze(transpose(reshape(result,tupdims))) if rank(result)==0: result = result.toscalar() # object is like a structure with but with a class name elif dclass == mxOBJECT_CLASS: class_name = ''.join(asarray(_get_element(fid)[0]).astype('c')) length = product(dims) result = zeros(length, PyObject) namelength = _get_element(fid)[0] # get field names names = _get_element(fid)[0] splitnames = [names[i:i+namelength] for i in \ xrange(0,len(names),namelength)] fieldnames = [''.join(asarray(x).astype('c')).strip('\x00') for x in splitnames] for i in range(length): result[i] = mat_obj() result[i]._classname = class_name for element in fieldnames: val,unused = _get_element(fid) result[i].__dict__[element] = val result = squeeze(transpose(reshape(result,tupdims))) if rank(result)==0: result = result.toscalar() elif dclass == mxSPARSE_CLASS: rowind, unused = _get_element(fid) colind, unused = _get_element(fid) res, unused = _get_element(fid) if cmplx: imag, unused = _get_element(fid) try: res = res + _unit_imag[imag.typecode()] * imag except KeyError: res = res + 1j*imag if have_sparse: spmat = scipy.sparse.csc_matrix(res, (rowind[:len(res)], colind), M=dims[0],N=dims[1]) result = spmat else: result = (dims, rowind, colind, res) return result, name |
except AtrributeError: | except AttributeError: | def getnzmax(self): try: nzmax = self.nzmax except AttributeError: try: nzmax = self.nnz except AtrributeError: nzmax = 0 return nzmax |
tcode = s.typecode func = getattr(sparsetools,tcode+'transp') | func = getattr(sparsetools,s.ftype+'transp') | def __init__(self,s,ij=None,M=None,N=None,nzmax=100,typecode=Float,copy=0): spmatrix.__init__(self, 'csc') if isinstance(s,spmatrix): if isinstance(s, csc_matrix): # do nothing but copy information self.shape = s.shape if copy: self.data = s.data.copy() self.rowind = s.rowind.copy() self.indptr = s.indptr.copy() else: self.data = s.data self.rowind = s.rowind self.indptr = s.indptr elif isinstance(s, csr_matrix): self.shape = s.shape tcode = s.typecode func = getattr(sparsetools,tcode+'transp') self.data, self.rowind, self.indptr = \ func(s.data, s.colind, s.indptr) else: temp = s.tocsc() self.data = temp.data self.rowind = temp.rowind self.indptr = temp.indptr self.shape = temp.shape elif isinstance(s,type(3)): M=s N=ij self.data = zeros((nzmax,),typecode) self.rowind = zeros((nzmax,),'i') self.indptr = zeros((N+1,),'i') self.shape = (M,N) elif (isinstance(s,ArrayType) or \ isinstance(s,type([]))): s = asarray(s) if (rank(s) == 2): # converting from a full array M, N = s.shape s = asarray(s) if s.typecode() not in 'fdFD': s = s*1.0 typecode = s.typecode() func = getattr(sparsetools,_transtabl[typecode]+'fulltocsc') ierr = irow = jcol = 0 nnz = sum(ravel(s != 0.0)) a = zeros((nnz,),typecode) rowa = zeros((nnz,),'i') ptra = zeros((N+1,),'i') while 1: a, rowa, ptra, irow, jcol, ierr = \ func(s, a, rowa, ptra, irow, jcol, ierr) if (ierr == 0): break nnz = nnz + ALLOCSIZE a = resize1d(a, nnz) rowa = resize1d(rowa, nnz) |
func(s.data, s.colind, s.indptr) | func(s.shape[1], s.data, s.colind, s.indptr) | def __init__(self,s,ij=None,M=None,N=None,nzmax=100,typecode=Float,copy=0): spmatrix.__init__(self, 'csc') if isinstance(s,spmatrix): if isinstance(s, csc_matrix): # do nothing but copy information self.shape = s.shape if copy: self.data = s.data.copy() self.rowind = s.rowind.copy() self.indptr = s.indptr.copy() else: self.data = s.data self.rowind = s.rowind self.indptr = s.indptr elif isinstance(s, csr_matrix): self.shape = s.shape tcode = s.typecode func = getattr(sparsetools,tcode+'transp') self.data, self.rowind, self.indptr = \ func(s.data, s.colind, s.indptr) else: temp = s.tocsc() self.data = temp.data self.rowind = temp.rowind self.indptr = temp.indptr self.shape = temp.shape elif isinstance(s,type(3)): M=s N=ij self.data = zeros((nzmax,),typecode) self.rowind = zeros((nzmax,),'i') self.indptr = zeros((N+1,),'i') self.shape = (M,N) elif (isinstance(s,ArrayType) or \ isinstance(s,type([]))): s = asarray(s) if (rank(s) == 2): # converting from a full array M, N = s.shape s = asarray(s) if s.typecode() not in 'fdFD': s = s*1.0 typecode = s.typecode() func = getattr(sparsetools,_transtabl[typecode]+'fulltocsc') ierr = irow = jcol = 0 nnz = sum(ravel(s != 0.0)) a = zeros((nnz,),typecode) rowa = zeros((nnz,),'i') ptra = zeros((N+1,),'i') while 1: a, rowa, ptra, irow, jcol, ierr = \ func(s, a, rowa, ptra, irow, jcol, ierr) if (ierr == 0): break nnz = nnz + ALLOCSIZE a = resize1d(a, nnz) rowa = resize1d(rowa, nnz) |
data1, data2 = _convert_data(self.data[:nnz1], other.data[:nnz2], typecode) | data1, data2 = _convert_data(self.data[:nnz1], ocs.data[:nnz2], typecode) | def __add__(self, other): ocs = csc_matrix(other) if (ocs.shape != self.shape): raise ValueError, "Inconsistent shapes." typecode = _coerce_rules[(self.typecode,other.typecode)] nnz1, nnz2 = self.nnz, other.nnz data1, data2 = _convert_data(self.data[:nnz1], other.data[:nnz2], typecode) func = getattr(sparsetools,_transtabl[typecode]+'cscadd') c,rowc,ptrc,ierr = func(data1,self.rowind[:nnz1],self.indptr,data2,other.rowind[:nnz2],other.indptr) if ierr: raise ValueError, "Ran out of space (but shouldn't have happened)." M, N = self.shape return csc_matrix(c,(rowc,ptrc),M=M,N=N) |
Subsets and Splits