pymatgen.vis.plotters — pymatgen 2020.7.3 documentation

# Source code for pymatgen.vis.plotters

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    This module defines generic plotters.
    """

    import collections
    import importlib
    from pymatgen.util.plotting import pretty_plot

    class SpectrumPlotter:
        """
        Class for plotting Spectrum objects and subclasses. Note that the interface
        is extremely flexible given that there are many different ways in which
        people want to view spectra. The typical usage is::

            # Initializes plotter with some optional args. Defaults are usually
            # fine,
            plotter = SpectrumPlotter()

            # Adds a DOS (A kind of spectra) with a label.
            plotter.add_spectrum("Total DOS", dos)

            # Alternatively, you can add a dict of DOSs. This is the typical
            # form returned by CompleteDos.get_spd/element/others_dos().
            plotter.add_spectra({"dos1": dos1, "dos2": dos2})
        """

        def __init__(self, xshift=0.0, yshift=0.0, stack=False,
                     color_cycle=("qualitative", "Set1_9")):
            """
            Args:
                xshift (float): A shift that is applied to the x values. This is
                    commonly used to shift to an arbitrary zero. E.g., zeroing at the
                    Fermi energy in DOS, or at the absorption edge in XAS spectra. The
                    same xshift is applied to all spectra.
                yshift (float): A shift that is applied to the y values. This is
                    commonly used to displace spectra for easier visualization.
                    Successive spectra are applied successive shifts.
                stack (bool): Whether to stack plots rather than simply plot them.
                    For example, DOS plot can usually be stacked to look at the
                    contribution of each orbital.
                color_cycle (str): Default color cycle to use. Note that this can be
                    overridden
            """
            self.xshift = xshift
            self.yshift = yshift
            self.stack = stack

            mod = importlib.import_module("palettable.colorbrewer.%s" %
                                          color_cycle[0])
            self.colors_cycle = getattr(mod, color_cycle[1]).mpl_colors
            self.colors = []
            self._spectra = collections.OrderedDict()

        def add_spectrum(self, label, spectrum, color=None):
            """
            Adds a Spectrum for plotting.

            Args:
                label (str): Label for the Spectrum. Must be unique.
                spectrum: Spectrum object
                color (str): This is passed on to matplotlib. E.g., "k--" indicates
                    a dashed black line. If None, a color will be chosen based on
                    the default color cycle.
            """
            self._spectra[label] = spectrum
            self.colors.append(
                color or
                self.colors_cycle[len(self._spectra) % len(self.colors_cycle)])

        def add_spectra(self, spectra_dict, key_sort_func=None):
            """
            Add a dictionary of doses, with an optional sorting function for the
            keys.

            Args:
                dos_dict: dict of {label: Dos}
                key_sort_func: function used to sort the dos_dict keys.
            """
            if key_sort_func:
                keys = sorted(spectra_dict.keys(), key=key_sort_func)
            else:
                keys = spectra_dict.keys()
            for label in keys:
                self.add_spectra(label, spectra_dict[label])

        def get_plot(self, xlim=None, ylim=None):
            """
            Get a matplotlib plot showing the DOS.

            Args:
                xlim: Specifies the x-axis limits. Set to None for automatic
                    determination.
                ylim: Specifies the y-axis limits.
            """

            plt = pretty_plot(12, 8)
            base = 0.0
            i = 0
            for key, sp in self._spectra.items():
                if not self.stack:
                    plt.plot(sp.x, sp.y + self.yshift * i, color=self.colors[i],
                             label=str(key), linewidth=3)
                else:
                    plt.fill_between(sp.x, base, sp.y + self.yshift * i,
                                     color=self.colors[i],
                                     label=str(key), linewidth=3)
                    base = sp.y + base
                plt.xlabel(sp.XLABEL)
                plt.ylabel(sp.YLABEL)
                i += 1

            if xlim:
                plt.xlim(xlim)
            if ylim:
                plt.ylim(ylim)

            plt.legend()
            leg = plt.gca().get_legend()
            ltext = leg.get_texts()  # all the text.Text instance in the legend
            plt.setp(ltext, fontsize=30)
            plt.tight_layout()
            return plt

        def save_plot(self, filename, img_format="eps", **kwargs):
            """
            Save matplotlib plot to a file.

            Args:
                filename: Filename to write to.
                img_format: Image format to use. Defaults to EPS.
            """
            plt = self.get_plot(**kwargs)
            plt.savefig(filename, format=img_format)

        def show(self, **kwargs):
            """
            Show the plot using matplotlib.
            """
            plt = self.get_plot(**kwargs)
            plt.show()