diff --git a/GPy/plotting/matplot_dep/base_plots.py b/GPy/plotting/matplot_dep/base_plots.py new file mode 100644 index 00000000..d9910f59 --- /dev/null +++ b/GPy/plotting/matplot_dep/base_plots.py @@ -0,0 +1,265 @@ +# #Copyright (c) 2012, GPy authors (see AUTHORS.txt). +# Licensed under the BSD 3-clause license (see LICENSE.txt) +from matplotlib import pyplot as plt +import numpy as np + +def ax_default(fignum, ax): + if ax is None: + fig = plt.figure(fignum) + ax = fig.add_subplot(111) + else: + fig = ax.figure + return fig, ax + +def meanplot(x, mu, color='#3300FF', ax=None, fignum=None, linewidth=2,**kw): + _, axes = ax_default(fignum, ax) + return axes.plot(x,mu,color=color,linewidth=linewidth,**kw) + +def gpplot(x, mu, lower, upper, edgecol='#3300FF', fillcol='#33CCFF', ax=None, fignum=None, **kwargs): + _, axes = ax_default(fignum, ax) + + mu = mu.flatten() + x = x.flatten() + lower = lower.flatten() + upper = upper.flatten() + + plots = [] + + #here's the mean + plots.append(meanplot(x, mu, edgecol, axes)) + + #here's the box + kwargs['linewidth']=0.5 + if not 'alpha' in kwargs.keys(): + kwargs['alpha'] = 0.3 + plots.append(axes.fill(np.hstack((x,x[::-1])),np.hstack((upper,lower[::-1])),color=fillcol,**kwargs)) + + #this is the edge: + plots.append(meanplot(x, upper,color=edgecol, linewidth=0.2, ax=axes)) + plots.append(meanplot(x, lower,color=edgecol, linewidth=0.2, ax=axes)) + + return plots + +def gradient_fill(x, percentiles, ax=None, fignum=None, **kwargs): + _, ax = ax_default(fignum, ax) + + plots = [] + + #here's the box + if 'linewidth' not in kwargs: + kwargs['linewidth'] = 0.5 + if not 'alpha' in kwargs.keys(): + kwargs['alpha'] = 1./(len(percentiles)) + + # pop where from kwargs + where = kwargs.pop('where') if 'where' in kwargs else None + # pop interpolate, which we actually do not do here! + if 'interpolate' in kwargs: kwargs.pop('interpolate') + + def pairwise(inlist): + l = len(inlist) + for i in range(int(np.ceil(l/2.))): + yield inlist[:][i], inlist[:][(l-1)-i] + + polycol = [] + for y1, y2 in pairwise(percentiles): + import matplotlib.mlab as mlab + # Handle united data, such as dates + ax._process_unit_info(xdata=x, ydata=y1) + ax._process_unit_info(ydata=y2) + + # Convert the arrays so we can work with them + from numpy import ma + x = ma.masked_invalid(ax.convert_xunits(x)) + y1 = ma.masked_invalid(ax.convert_yunits(y1)) + y2 = ma.masked_invalid(ax.convert_yunits(y2)) + + if y1.ndim == 0: + y1 = np.ones_like(x) * y1 + if y2.ndim == 0: + y2 = np.ones_like(x) * y2 + + if where is None: + where = np.ones(len(x), np.bool) + else: + where = np.asarray(where, np.bool) + + if not (x.shape == y1.shape == y2.shape == where.shape): + raise ValueError("Argument dimensions are incompatible") + + mask = reduce(ma.mask_or, [ma.getmask(a) for a in (x, y1, y2)]) + if mask is not ma.nomask: + where &= ~mask + + polys = [] + for ind0, ind1 in mlab.contiguous_regions(where): + xslice = x[ind0:ind1] + y1slice = y1[ind0:ind1] + y2slice = y2[ind0:ind1] + + if not len(xslice): + continue + + N = len(xslice) + X = np.zeros((2 * N + 2, 2), np.float) + + # the purpose of the next two lines is for when y2 is a + # scalar like 0 and we want the fill to go all the way + # down to 0 even if none of the y1 sample points do + start = xslice[0], y2slice[0] + end = xslice[-1], y2slice[-1] + + X[0] = start + X[N + 1] = end + + X[1:N + 1, 0] = xslice + X[1:N + 1, 1] = y1slice + X[N + 2:, 0] = xslice[::-1] + X[N + 2:, 1] = y2slice[::-1] + + polys.append(X) + polycol.extend(polys) + from matplotlib.collections import PolyCollection + plots.append(PolyCollection(polycol, **kwargs)) + ax.add_collection(plots[-1], autolim=True) + ax.autoscale_view() + return plots + +def gperrors(x, mu, lower, upper, edgecol=None, ax=None, fignum=None, **kwargs): + _, axes = ax_default(fignum, ax) + + mu = mu.flatten() + x = x.flatten() + lower = lower.flatten() + upper = upper.flatten() + + plots = [] + + if edgecol is None: + edgecol='#3300FF' + + if not 'alpha' in kwargs.keys(): + kwargs['alpha'] = 1. + + + if not 'lw' in kwargs.keys(): + kwargs['lw'] = 1. + + + plots.append(axes.errorbar(x,mu,yerr=np.vstack([mu-lower,upper-mu]),color=edgecol,**kwargs)) + plots[-1][0].remove() + return plots + + +def removeRightTicks(ax=None): + ax = ax or plt.gca() + for i, line in enumerate(ax.get_yticklines()): + if i%2 == 1: # odd indices + line.set_visible(False) + +def removeUpperTicks(ax=None): + ax = ax or plt.gca() + for i, line in enumerate(ax.get_xticklines()): + if i%2 == 1: # odd indices + line.set_visible(False) + +def fewerXticks(ax=None,divideby=2): + ax = ax or plt.gca() + ax.set_xticks(ax.get_xticks()[::divideby]) + +def align_subplots(N,M,xlim=None, ylim=None): + """make all of the subplots have the same limits, turn off unnecessary ticks""" + #find sensible xlim,ylim + if xlim is None: + xlim = [np.inf,-np.inf] + for i in range(N*M): + plt.subplot(N,M,i+1) + xlim[0] = min(xlim[0],plt.xlim()[0]) + xlim[1] = max(xlim[1],plt.xlim()[1]) + if ylim is None: + ylim = [np.inf,-np.inf] + for i in range(N*M): + plt.subplot(N,M,i+1) + ylim[0] = min(ylim[0],plt.ylim()[0]) + ylim[1] = max(ylim[1],plt.ylim()[1]) + + for i in range(N*M): + plt.subplot(N,M,i+1) + plt.xlim(xlim) + plt.ylim(ylim) + if (i)%M: + plt.yticks([]) + else: + removeRightTicks() + if i<(M*(N-1)): + plt.xticks([]) + else: + removeUpperTicks() + +def align_subplot_array(axes,xlim=None, ylim=None): + """ + Make all of the axes in the array hae the same limits, turn off unnecessary ticks + use plt.subplots() to get an array of axes + """ + #find sensible xlim,ylim + if xlim is None: + xlim = [np.inf,-np.inf] + for ax in axes.flatten(): + xlim[0] = min(xlim[0],ax.get_xlim()[0]) + xlim[1] = max(xlim[1],ax.get_xlim()[1]) + if ylim is None: + ylim = [np.inf,-np.inf] + for ax in axes.flatten(): + ylim[0] = min(ylim[0],ax.get_ylim()[0]) + ylim[1] = max(ylim[1],ax.get_ylim()[1]) + + N,M = axes.shape + for i,ax in enumerate(axes.flatten()): + ax.set_xlim(xlim) + ax.set_ylim(ylim) + if (i)%M: + ax.set_yticks([]) + else: + removeRightTicks(ax) + if i<(M*(N-1)): + ax.set_xticks([]) + else: + removeUpperTicks(ax) + +def x_frame1D(X,plot_limits=None,resolution=None): + """ + Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits + """ + assert X.shape[1] ==1, "x_frame1D is defined for one-dimensional inputs" + if plot_limits is None: + from ...core.parameterization.variational import VariationalPosterior + if isinstance(X, VariationalPosterior): + xmin,xmax = X.mean.min(0),X.mean.max(0) + else: + xmin,xmax = X.min(0),X.max(0) + xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin) + elif len(plot_limits)==2: + xmin, xmax = plot_limits + else: + raise ValueError("Bad limits for plotting") + + Xnew = np.linspace(xmin,xmax,resolution or 200)[:,None] + return Xnew, xmin, xmax + +def x_frame2D(X,plot_limits=None,resolution=None): + """ + Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits + """ + assert X.shape[1] ==2, "x_frame2D is defined for two-dimensional inputs" + if plot_limits is None: + xmin,xmax = X.min(0),X.max(0) + xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin) + elif len(plot_limits)==2: + xmin, xmax = plot_limits + else: + raise ValueError("Bad limits for plotting") + + resolution = resolution or 50 + xx,yy = np.mgrid[xmin[0]:xmax[0]:1j*resolution,xmin[1]:xmax[1]:1j*resolution] + Xnew = np.vstack((xx.flatten(),yy.flatten())).T + return Xnew, xx, yy, xmin, xmax