def probplot(x, sparams=(), dist='norm', fit=1, plot=None): """Return (osm, osr){,(scale,loc,r)} where (osm, osr) are order statistic medians and ordered response data respectively so that plot(osm, osr) is a probability plot. If fit==1, then do a regression fit and compute the slope (scale), intercept (loc), and correlation coefficient (r), of the best straight line through the points. If fit==0, only (osm, osr) is returned. sparams is a tuple of shape parameter arguments for the distribution. """ N = len(x) Ui = zeros(N)*1.0 Ui[-1] = 0.5**(1.0/N) Ui[0] = 1-Ui[-1] i = arange(2,N) Ui[1:-1] = (i-0.3175)/(N+0.365) try: ppf_func = eval('distributions.%s.ppf'%dist) except AttributError: raise dist, "is not a valid distribution with a ppf." if sparams is None: sparams = () if isscalar(sparams): sparams = (sparams,) if not isinstance(sparams,types.TupleType): sparams = tuple(sparams) res = inspect.getargspec(ppf_func) if not ('loc' == res[0][-2] and 'scale' == res[0][-1] and \ 0.0==res[-1][-2] and 1.0==res[-1][-1]): raise ValueError, "Function has does not have default location", \ "and scale parameters\n that are 0.0 and 1.0 respectively." if (len(sparams) < len(res[0])-len(res[-1])-1) or \ (len(sparams) > len(res[0])-3): raise ValueError, "Incorrect number of shape parameters." osm = ppf_func(Ui,*sparams) osr = sort(x) if fit or (plot is not None): # perform a linear fit. slope, intercept, r, prob, sterrest = stats.linregress(osm,osr) if plot is not None: try: import scipy.xplt as xplt xplt.limits() except: pass plot.plot(osm, osr, 'o', osm, slope*osm + intercept) plot.title('Probability Plot') plot.xlabel('Order Statistic Medians') plot.ylabel('Ordered Values') try: plot.expand_limits(5) except: pass xmin,xmax= amin(osm),amax(osm) ymin,ymax= amin(x),amax(x) pos = xmin+0.70*(xmax-xmin), ymin+0.01*(ymax-ymin) try: plot.addtext("r^2^=%1.4f" % r, xy=pos,tosys=1) except: pass if fit: return (osm, osr), (slope, intercept, r) else: return osm, osr
def norm(x, ord=2): """ norm(x, ord=2) -> n Matrix and vector norm. Inputs: x -- a rank-1 (vector) or rank-2 (matrix) array ord -- the order of norm. Comments: For vectors ord can be any real number including Inf or -Inf. ord = Inf, computes the maximum of the magnitudes ord = -Inf, computes minimum of the magnitudes ord is finite, computes sum(abs(x)**ord)**(1.0/ord) For matrices ord can only be + or - 1, 2, Inf. ord = 2 computes the largest singular value ord = -2 computes the smallest singular value ord = 1 computes the largest column sum of absolute values ord = -1 computes the smallest column sum of absolute values ord = Inf computes the largest row sum of absolute values ord = -Inf computes the smallest row sum of absolute values ord = 'fro' computes the frobenius norm sqrt(sum(diag(X.H * X))) """ x = asarray_chkfinite(x) nd = len(x.shape) Inf = scipy_base.Inf if nd == 1: if ord == Inf: return scipy_base.amax(abs(x)) elif ord == -Inf: return scipy_base.amin(abs(x)) else: return scipy_base.sum(abs(x)**ord)**(1.0/ord) elif nd == 2: if ord == 2: return scipy_base.amax(decomp.svd(x,compute_uv=0)) elif ord == -2: return scipy_base.amin(decomp.svd(x,compute_uv=0)) elif ord == 1: return scipy_base.amax(scipy_base.sum(abs(x))) elif ord == Inf: return scipy_base.amax(scipy_base.sum(abs(x),axis=1)) elif ord == -1: return scipy_base.amin(scipy_base.sum(abs(x))) elif ord == -Inf: return scipy_base.amin(scipy_base.sum(abs(x),axis=1)) elif ord in ['fro','f']: val = real((conjugate(x)*x).flat) return sqrt(add.reduce(val)) else: raise ValueError, "Invalid norm order for matrices." else: raise ValueError, "Improper number of dimensions to norm."
def orth(A): """Return an orthonormal basis for the range of A using svd""" u,s,vh = svd(A) M,N = A.shape tol = max(M,N)*scipy_base.amax(s)*eps num = scipy_base.sum(s > tol) Q = u[:,:num] return Q
def bytescale(data, cmin=None, cmax=None, high=255, low=0): if data.typecode == _UInt8: return data high = high - low if cmin is None: cmin = amin(ravel(data)) if cmax is None: cmax = amax(ravel(data)) scale = high *1.0 / (cmax-cmin or 1) bytedata = ((data*1.0-cmin)*scale + 0.4999).astype(_UInt8) return bytedata + cast[_UInt8](low)
def toimage(arr,high=255,low=0,cmin=None,cmax=None,pal=None, mode=None,channel_axis=None): """Takes a Numeric array and returns a PIL image. The mode of the PIL image depends on the array shape, the pal keyword, and the mode keyword. For 2-D arrays, if pal is a valid (N,3) byte-array giving the RGB values (from 0 to 255) then mode='P', otherwise mode='L', unless mode is given as 'F' or 'I' in which case a float and/or integer array is made For 3-D arrays, the channel_axis argument tells which dimension of the array holds the channel data. For 3-D arrays if one of the dimensions is 3, the mode is 'RGB' by default or 'YCbCr' if selected. if the The Numeric array must be either 2 dimensional or 3 dimensional. """ data = asarray(arr) if iscomplexobj(data): raise ValueError, "Cannot convert a complex-valued array." shape = list(data.shape) valid = len(shape)==2 or ((len(shape)==3) and \ ((3 in shape) or (4 in shape))) assert valid, "Not a suitable array shape for any mode." if len(shape) == 2: shape = (shape[1],shape[0]) # columns show up first if mode == 'F': image = Image.fromstring(mode,shape,data.astype('f').tostring()) return image if mode in [None, 'L', 'P']: bytedata = bytescale(data,high=high,low=low,cmin=cmin,cmax=cmax) image = Image.fromstring('L',shape,bytedata.tostring()) if pal is not None: image.putpalette(asarray(pal,typecode=_UInt8).tostring()) # Becomes a mode='P' automagically. elif mode == 'P': # default gray-scale pal = arange(0,256,1,typecode='b')[:,NewAxis] * \ ones((3,),typecode='b')[NewAxis,:] image.putpalette(asarray(pal,typecode=_UInt8).tostring()) return image if mode == '1': # high input gives threshold for 1 bytedata = ((data > high)*255).astype('b') image = Image.fromstring('L',shape,bytedata.tostring()) image = image.convert(mode='1') return image if cmin is None: cmin = amin(ravel(data)) if cmax is None: cmax = amax(ravel(data)) data = (data*1.0 - cmin)*(high-low)/(cmax-cmin) + low if mode == 'I': image = Image.fromstring(mode,shape,data.astype('i').tostring()) else: raise ValueError, _errstr return image # if here then 3-d array with a 3 or a 4 in the shape length. # Check for 3 in datacube shape --- 'RGB' or 'YCbCr' if channel_axis is None: if (3 in shape): ca = Numeric.nonzero(asarray(shape) == 3)[0] else: ca = Numeric.nonzero(asarray(shape) == 4) if len(ca): ca = ca[0] else: raise ValueError, "Could not find channel dimension." else: ca = channel_axis numch = shape[ca] if numch not in [3,4]: raise ValueError, "Channel axis dimension is not valid." bytedata = bytescale(data,high=high,low=low,cmin=cmin,cmax=cmax) if ca == 2: strdata = bytedata.tostring() shape = (shape[1],shape[0]) elif ca == 1: strdata = transpose(bytedata,(0,2,1)).tostring() shape = (shape[2],shape[0]) elif ca == 0: strdata = transpose(bytedata,(1,2,0)).tostring() shape = (shape[2],shape[1]) if mode is None: if numch == 3: mode = 'RGB' else: mode = 'RGBA' if mode not in ['RGB','RGBA','YCbCr','CMYK']: raise ValueError, _errstr if mode in ['RGB', 'YCbCr']: assert numch == 3, "Invalid array shape for mode." if mode in ['RGBA', 'CMYK']: assert numch == 4, "Invalid array shape for mode." # Here we know data and mode is coorect image = Image.fromstring(mode, shape, strdata) return image