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Edit File: colorbar.py

""" Colorbar toolkit with two classes and a function: :class:`ColorbarBase` the base class with full colorbar drawing functionality. It can be used as-is to make a colorbar for a given colormap; a mappable object (e.g., image) is not needed. :class:`Colorbar` the derived class for use with images or contour plots. :func:`make_axes` a function for resizing an axes and adding a second axes suitable for a colorbar The :meth:`~matplotlib.figure.Figure.colorbar` method uses :func:`make_axes` and :class:`Colorbar`; the :func:`~matplotlib.pyplot.colorbar` function is a thin wrapper over :meth:`~matplotlib.figure.Figure.colorbar`. """ import numpy as np import matplotlib as mpl import matplotlib.colors as colors import matplotlib.cm as cm from matplotlib import docstring import matplotlib.ticker as ticker import matplotlib.collections as collections import matplotlib.contour as contour from matplotlib.path import Path from matplotlib.patches import PathPatch from matplotlib.transforms import Bbox make_axes_kw_doc = ''' ============= ==================================================== Property Description ============= ==================================================== *orientation* vertical or horizontal *fraction* 0.15; fraction of original axes to use for colorbar *pad* 0.05 if vertical, 0.15 if horizontal; fraction of original axes between colorbar and new image axes *shrink* 1.0; fraction by which to shrink the colorbar *aspect* 20; ratio of long to short dimensions ============= ==================================================== ''' colormap_kw_doc = ''' =========== ==================================================== Property Description =========== ==================================================== *extend* [ 'neither' | 'both' | 'min' | 'max' ] If not 'neither', make pointed end(s) for out-of- range values. These are set for a given colormap using the colormap set_under and set_over methods. *spacing* [ 'uniform' | 'proportional' ] Uniform spacing gives each discrete color the same space; proportional makes the space proportional to the data interval. *ticks* [ None | list of ticks | Locator object ] If None, ticks are determined automatically from the input. *format* [ None | format string | Formatter object ] If None, the :class:`~matplotlib.ticker.ScalarFormatter` is used. If a format string is given, e.g., '%.3f', that is used. An alternative :class:`~matplotlib.ticker.Formatter` object may be given instead. *drawedges* bool Whether to draw lines at color boundaries. =========== ==================================================== The following will probably be useful only in the context of indexed colors (that is, when the mappable has norm=NoNorm()), or other unusual circumstances. ============ =================================================== Property Description ============ =================================================== *boundaries* None or a sequence *values* None or a sequence which must be of length 1 less than the sequence of *boundaries*. For each region delimited by adjacent entries in *boundaries*, the color mapped to the corresponding value in values will be used. ============ =================================================== ''' colorbar_doc = ''' Add a colorbar to a plot. Function signatures for the :mod:`~matplotlib.pyplot` interface; all but the first are also method signatures for the :meth:`~matplotlib.figure.Figure.colorbar` method:: colorbar(**kwargs) colorbar(mappable, **kwargs) colorbar(mappable, cax=cax, **kwargs) colorbar(mappable, ax=ax, **kwargs) arguments: *mappable* the :class:`~matplotlib.image.Image`, :class:`~matplotlib.contour.ContourSet`, etc. to which the colorbar applies; this argument is mandatory for the :meth:`~matplotlib.figure.Figure.colorbar` method but optional for the :func:`~matplotlib.pyplot.colorbar` function, which sets the default to the current image. keyword arguments: *cax* None | axes object into which the colorbar will be drawn *ax* None | parent axes object from which space for a new colorbar axes will be stolen Additional keyword arguments are of two kinds: axes properties: %s colorbar properties: %s If *mappable* is a :class:`~matplotlib.contours.ContourSet`, its *extend* kwarg is included automatically. Note that the *shrink* kwarg provides a simple way to keep a vertical colorbar, for example, from being taller than the axes of the mappable to which the colorbar is attached; but it is a manual method requiring some trial and error. If the colorbar is too tall (or a horizontal colorbar is too wide) use a smaller value of *shrink*. For more precise control, you can manually specify the positions of the axes objects in which the mappable and the colorbar are drawn. In this case, do not use any of the axes properties kwargs. It is known that some vector graphics viewer (svg and pdf) renders white gaps between segments of the colorbar. This is due to bugs in the viewers not matplotlib. As a workaround the colorbar can be rendered with overlapping segments:: cbar = colorbar() cbar.solids.set_edgecolor("face") draw() However this has negative consequences in other circumstances. Particularly with semi transparent images (alpha < 1) and colorbar extensions and is not enabled by default see (issue #1188). returns: :class:`~matplotlib.colorbar.Colorbar` instance; see also its base class, :class:`~matplotlib.colorbar.ColorbarBase`. Call the :meth:`~matplotlib.colorbar.ColorbarBase.set_label` method to label the colorbar. The transData of the *cax* is adjusted so that the limits in the longest axis actually corresponds to the limits in colorbar range. On the other hand, the shortest axis has a data limits of [1,2], whose unconventional value is to prevent underflow when log scale is used. ''' % (make_axes_kw_doc, colormap_kw_doc) #docstring.interpd.update(colorbar_doc=colorbar_doc) class CbarAxesLocator(object): """ CbarAxesLocator is a axes_locator for colorbar axes. It adjust the position of the axes to make a room for extended ends, i.e., the extended ends are located outside the axes area. """ def __init__(self, locator=None, extend="neither", orientation="vertical"): """ *locator* : the bbox returned from the locator is used as a initial axes location. If None, axes.bbox is used. *extend* : same as in ColorbarBase *orientation* : same as in ColorbarBase """ self._locator = locator self.extesion_fraction = 0.05 self.extend = extend self.orientation = orientation def get_original_position(self, axes, renderer): """ get the original position of the axes. """ if self._locator is None: bbox = axes.get_position(original=True) else: bbox = self._locator(axes, renderer) return bbox def get_end_vertices(self): """ return a tuple of two vertices for the colorbar extended ends. The first vertices is for the minimum end, and the second is for the maximum end. """ # Note that concatenating two vertices needs to make a # vertices for the frame. extesion_fraction = self.extesion_fraction corx = extesion_fraction*2. cory = 1./(1. - corx) x1, y1, w, h = 0, 0, 1, 1 x2, y2 = x1 + w, y1 + h dw, dh = w*extesion_fraction, h*extesion_fraction*cory if self.extend in ["min", "both"]: bottom = [(x1, y1), (x1+w/2., y1-dh), (x2, y1)] else: bottom = [(x1, y1), (x2, y1)] if self.extend in ["max", "both"]: top = [(x2, y2), (x1+w/2., y2+dh), (x1, y2)] else: top = [(x2, y2), (x1, y2)] if self.orientation == "horizontal": bottom = [(y, x) for (x, y) in bottom] top = [(y, x) for (x, y) in top] return bottom, top def get_path_patch(self): """ get the path for axes patch """ end1, end2 = self.get_end_vertices() verts = [] + end1 + end2 + end1[:1] return Path(verts) def get_path_ends(self): """ get the paths for extended ends """ end1, end2 = self.get_end_vertices() return Path(end1), Path(end2) def __call__(self, axes, renderer): """ Return the adjusted position of the axes """ bbox0 = self.get_original_position(axes, renderer) bbox = bbox0 x1, y1, w, h = bbox.bounds extesion_fraction = self.extesion_fraction dw, dh = w*extesion_fraction, h*extesion_fraction if self.extend in ["min", "both"]: if self.orientation == "horizontal": x1 = x1 + dw else: y1 = y1+dh if self.extend in ["max", "both"]: if self.orientation == "horizontal": w = w-2*dw else: h = h-2*dh return Bbox.from_bounds(x1, y1, w, h) class ColorbarBase(cm.ScalarMappable): ''' Draw a colorbar in an existing axes. This is a base class for the :class:`Colorbar` class, which is the basis for the :func:`~matplotlib.pyplot.colorbar` method and pyplot function. It is also useful by itself for showing a colormap. If the *cmap* kwarg is given but *boundaries* and *values* are left as None, then the colormap will be displayed on a 0-1 scale. To show the under- and over-value colors, specify the *norm* as:: colors.Normalize(clip=False) To show the colors versus index instead of on the 0-1 scale, use:: norm=colors.NoNorm. Useful attributes: :attr:`ax` the Axes instance in which the colorbar is drawn :attr:`lines` a LineCollection if lines were drawn, otherwise None :attr:`dividers` a LineCollection if *drawedges* is True, otherwise None Useful public methods are :meth:`set_label` and :meth:`add_lines`. ''' def __init__(self, ax, cmap=None, norm=None, alpha=1.0, values=None, boundaries=None, orientation='vertical', extend='neither', spacing='uniform', # uniform or proportional ticks=None, format=None, drawedges=False, filled=True, ): self.ax = ax if cmap is None: cmap = cm.get_cmap() if norm is None: norm = colors.Normalize() self.alpha = alpha cm.ScalarMappable.__init__(self, cmap=cmap, norm=norm) self.values = values self.boundaries = boundaries self.extend = extend self.spacing = spacing self.orientation = orientation self.drawedges = drawedges self.filled = filled # artists self.solids = None self.lines = None self.dividers = None self.extension_patch1 = None self.extension_patch2 = None if orientation == "vertical": self.cbar_axis = self.ax.yaxis else: self.cbar_axis = self.ax.xaxis if format is None: if isinstance(self.norm, colors.LogNorm): # change both axis for proper aspect self.ax.set_xscale("log") self.ax.set_yscale("log") self.cbar_axis.set_minor_locator(ticker.NullLocator()) formatter = ticker.LogFormatter() else: formatter = None elif isinstance(format, str): formatter = ticker.FormatStrFormatter(format) else: formatter = format # Assume it is a Formatter if formatter is None: formatter = self.cbar_axis.get_major_formatter() else: self.cbar_axis.set_major_formatter(formatter) if np.iterable(ticks): self.cbar_axis.set_ticks(ticks) elif ticks is not None: self.cbar_axis.set_major_locator(ticks) else: self._select_locator(formatter) self._config_axes() self.update_artists() self.set_label_text('') def _get_colorbar_limits(self): """ initial limits for colorbar range. The returned min, max values will be used to create colorbar solid(?) and etc. """ if self.boundaries is not None: C = self.boundaries if self.extend in ["min", "both"]: C = C[1:] if self.extend in ["max", "both"]: C = C[:-1] return min(C), max(C) else: return self.get_clim() def _config_axes(self): ''' Adjust the properties of the axes to be adequate for colorbar display. ''' ax = self.ax axes_locator = CbarAxesLocator(ax.get_axes_locator(), extend=self.extend, orientation=self.orientation) ax.set_axes_locator(axes_locator) # override the get_data_ratio for the aspect works. def _f(): return 1. ax.get_data_ratio = _f ax.get_data_ratio_log = _f ax.set_frame_on(True) ax.set_navigate(False) self.ax.set_autoscalex_on(False) self.ax.set_autoscaley_on(False) if self.orientation == 'horizontal': ax.xaxis.set_label_position('bottom') ax.set_yticks([]) else: ax.set_xticks([]) ax.yaxis.set_label_position('right') ax.yaxis.set_ticks_position('right') def update_artists(self): """ Update the colorbar associated artists, *filled* and *ends*. Note that *lines* are not updated. This needs to be called whenever clim of associated image changes. """ self._process_values() self._add_ends() X, Y = self._mesh() if self.filled: C = self._values[:, np.newaxis] self._add_solids(X, Y, C) ax = self.ax vmin, vmax = self._get_colorbar_limits() if self.orientation == 'horizontal': ax.set_ylim(1, 2) ax.set_xlim(vmin, vmax) else: ax.set_xlim(1, 2) ax.set_ylim(vmin, vmax) def _add_ends(self): """ Create patches from extended ends and add them to the axes. """ del self.extension_patch1 del self.extension_patch2 path1, path2 = self.ax.get_axes_locator().get_path_ends() fc=mpl.rcParams['axes.facecolor'] ec=mpl.rcParams['axes.edgecolor'] linewidths=0.5*mpl.rcParams['axes.linewidth'] self.extension_patch1 = PathPatch(path1, fc=fc, ec=ec, lw=linewidths, zorder=2., transform=self.ax.transAxes, clip_on=False) self.extension_patch2 = PathPatch(path2, fc=fc, ec=ec, lw=linewidths, zorder=2., transform=self.ax.transAxes, clip_on=False) self.ax.add_artist(self.extension_patch1) self.ax.add_artist(self.extension_patch2) def _set_label_text(self): """ set label. """ self.cbar_axis.set_label_text(self._label, **self._labelkw) def set_label_text(self, label, **kw): ''' Label the long axis of the colorbar ''' self._label = label self._labelkw = kw self._set_label_text() def _edges(self, X, Y): ''' Return the separator line segments; helper for _add_solids. ''' N = X.shape[0] # Using the non-array form of these line segments is much # simpler than making them into arrays. if self.orientation == 'vertical': return [list(zip(X[i], Y[i])) for i in range(1, N-1)] else: return [list(zip(Y[i], X[i])) for i in range(1, N-1)] def _add_solids(self, X, Y, C): ''' Draw the colors using :meth:`~matplotlib.axes.Axes.pcolormesh`; optionally add separators. ''' ## Change to pcolorfast after fixing bugs in some backends... if self.extend in ["min", "both"]: cc = self.to_rgba([C[0][0]]) self.extension_patch1.set_facecolor(cc[0]) X, Y, C = X[1:], Y[1:], C[1:] if self.extend in ["max", "both"]: cc = self.to_rgba([C[-1][0]]) self.extension_patch2.set_facecolor(cc[0]) X, Y, C = X[:-1], Y[:-1], C[:-1] if self.orientation == 'vertical': args = (X, Y, C) else: args = (np.transpose(Y), np.transpose(X), np.transpose(C)) del self.solids del self.dividers col = self.ax.pcolormesh( *args, cmap=self.cmap, norm=self.norm, shading='flat', alpha=self.alpha) self.solids = col if self.drawedges: self.dividers = collections.LineCollection( self._edges(X, Y), colors=(mpl.rcParams['axes.edgecolor'],), linewidths=(0.5*mpl.rcParams['axes.linewidth'],), ) self.ax.add_collection(self.dividers) else: self.dividers = None def add_lines(self, levels, colors, linewidths): ''' Draw lines on the colorbar. It deletes preexisting lines. ''' X, Y = np.meshgrid([1, 2], levels) if self.orientation == 'vertical': xy = np.stack([X, Y], axis=-1) else: xy = np.stack([Y, X], axis=-1) col = collections.LineCollection(xy, linewidths=linewidths) self.lines = col col.set_color(colors) self.ax.add_collection(col) def _select_locator(self, formatter): ''' select a suitable locator ''' if self.boundaries is None: if isinstance(self.norm, colors.NoNorm): nv = len(self._values) base = 1 + int(nv/10) locator = ticker.IndexLocator(base=base, offset=0) elif isinstance(self.norm, colors.BoundaryNorm): b = self.norm.boundaries locator = ticker.FixedLocator(b, nbins=10) elif isinstance(self.norm, colors.LogNorm): locator = ticker.LogLocator() else: locator = ticker.MaxNLocator(nbins=5) else: b = self._boundaries[self._inside] locator = ticker.FixedLocator(b) self.cbar_axis.set_major_locator(locator) def _process_values(self, b=None): ''' Set the :attr:`_boundaries` and :attr:`_values` attributes based on the input boundaries and values. Input boundaries can be *self.boundaries* or the argument *b*. ''' if b is None: b = self.boundaries if b is not None: self._boundaries = np.asarray(b, dtype=float) if self.values is None: self._values = (self._boundaries[:-1] + self._boundaries[1:]) / 2 if isinstance(self.norm, colors.NoNorm): self._values = (self._values + 0.00001).astype(np.int16) return self._values = np.array(self.values) return if self.values is not None: self._values = np.array(self.values) if self.boundaries is None: b = np.zeros(len(self.values) + 1) b[1:-1] = 0.5*(self._values[:-1] - self._values[1:]) b[0] = 2.0*b[1] - b[2] b[-1] = 2.0*b[-2] - b[-3] self._boundaries = b return self._boundaries = np.array(self.boundaries) return # Neither boundaries nor values are specified; # make reasonable ones based on cmap and norm. if isinstance(self.norm, colors.NoNorm): self._boundaries = ( self._uniform_y(self.cmap.N + 1) * self.cmap.N - 0.5) self._values = np.arange(self.cmap.N, dtype=np.int16) return elif isinstance(self.norm, colors.BoundaryNorm): self._boundaries = np.array(self.norm.boundaries) self._values = (self._boundaries[:-1] + self._boundaries[1:]) / 2 return else: b = self._uniform_y(self.cmap.N + 1) self._process_values(b) def _uniform_y(self, N): ''' Return colorbar data coordinates for *N* uniformly spaced boundaries. ''' vmin, vmax = self._get_colorbar_limits() if isinstance(self.norm, colors.LogNorm): y = np.logspace(np.log10(vmin), np.log10(vmax), N) else: y = np.linspace(vmin, vmax, N) return y def _mesh(self): ''' Return X,Y, the coordinate arrays for the colorbar pcolormesh. These are suitable for a vertical colorbar; swapping and transposition for a horizontal colorbar are done outside this function. ''' x = np.array([1.0, 2.0]) if self.spacing == 'uniform': y = self._uniform_y(len(self._boundaries)) else: y = self._boundaries self._y = y X, Y = np.meshgrid(x, y) return X, Y def set_alpha(self, alpha): """ set alpha value. """ self.alpha = alpha class Colorbar(ColorbarBase): def __init__(self, ax, mappable, **kw): # Ensure mappable.norm.vmin, vmax are set when colorbar is called, even # if mappable.draw has not yet been called. This will not change vmin, # vmax if they are already set. mappable.autoscale_None() self.mappable = mappable kw['cmap'] = mappable.cmap kw['norm'] = mappable.norm kw['alpha'] = mappable.get_alpha() if isinstance(mappable, contour.ContourSet): CS = mappable kw['boundaries'] = CS._levels kw['values'] = CS.cvalues kw['extend'] = CS.extend #kw['ticks'] = CS._levels kw.setdefault('ticks', ticker.FixedLocator(CS.levels, nbins=10)) kw['filled'] = CS.filled ColorbarBase.__init__(self, ax, **kw) if not CS.filled: self.add_lines(CS) else: ColorbarBase.__init__(self, ax, **kw) def add_lines(self, CS): ''' Add the lines from a non-filled :class:`~matplotlib.contour.ContourSet` to the colorbar. ''' if not isinstance(CS, contour.ContourSet) or CS.filled: raise ValueError('add_lines is only for a ContourSet of lines') tcolors = [c[0] for c in CS.tcolors] tlinewidths = [t[0] for t in CS.tlinewidths] # The following was an attempt to get the colorbar lines # to follow subsequent changes in the contour lines, # but more work is needed: specifically, a careful # look at event sequences, and at how # to make one object track another automatically. #tcolors = [col.get_colors()[0] for col in CS.collections] #tlinewidths = [col.get_linewidth()[0] for lw in CS.collections] ColorbarBase.add_lines(self, CS.levels, tcolors, tlinewidths) def update_bruteforce(self, mappable): """ Update the colorbar artists to reflect the change of the associated mappable. """ self.update_artists() if isinstance(mappable, contour.ContourSet): if not mappable.filled: self.add_lines(mappable) @docstring.Substitution(make_axes_kw_doc) def make_axes(parent, *, fraction=0.15, shrink=1.0, aspect=20, **kw): ''' Resize and reposition a parent axes, and return a child axes suitable for a colorbar :: cax, kw = make_axes(parent, **kw) Keyword arguments may include the following (with defaults): *orientation* 'vertical' or 'horizontal' %s All but the first of these are stripped from the input kw set. Returns (cax, kw), the child axes and the reduced kw dictionary. ''' orientation = kw.setdefault('orientation', 'vertical') #pb = transforms.PBox(parent.get_position()) pb = parent.get_position(original=True).frozen() if orientation == 'vertical': pad = kw.pop('pad', 0.05) x1 = 1.0-fraction pb1, pbx, pbcb = pb.splitx(x1-pad, x1) pbcb = pbcb.shrunk(1.0, shrink).anchored('C', pbcb) anchor = (0.0, 0.5) panchor = (1.0, 0.5) else: pad = kw.pop('pad', 0.15) pbcb, pbx, pb1 = pb.splity(fraction, fraction+pad) pbcb = pbcb.shrunk(shrink, 1.0).anchored('C', pbcb) aspect = 1.0/aspect anchor = (0.5, 1.0) panchor = (0.5, 0.0) parent.set_position(pb1) parent.set_anchor(panchor) fig = parent.get_figure() cax = fig.add_axes(pbcb) cax.set_aspect(aspect, anchor=anchor, adjustable='box') return cax, kw @docstring.Substitution(colorbar_doc) def colorbar(mappable, cax=None, ax=None, **kw): """ Create a colorbar for a ScalarMappable instance. Documentation for the pyplot thin wrapper: %s """ import matplotlib.pyplot as plt if ax is None: ax = plt.gca() if cax is None: cax, kw = make_axes(ax, **kw) cb = Colorbar(cax, mappable, **kw) def on_changed(m): cb.set_cmap(m.get_cmap()) cb.set_clim(m.get_clim()) cb.update_bruteforce(m) cbid = mappable.callbacksSM.connect('changed', on_changed) mappable.colorbar = cb ax.figure.sca(ax) return cb