solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.1__py3-none-any.whl

solarwindpy/instabilities/verscharen2016.py

@@ -0,0 +1,631 @@
+#!/usr/bin/env python
+"""Instability thresholds from Verscharen et al. (2016).
+
+The empirical fits of :cite:`Verscharen2016a` are implemented to
+evaluate when a plasma becomes unstable in the ``(beta, R)`` plane.
+
+References
+----------
+.. [1] Verscharen, D., Chandran, B. D. G., Klein, K. G., & Quataert, E.
+   *Collisionless Isotropization of the Solar-Wind Protons By Compressive
+   Fluctuations and Plasma Instabilities*, Astrophys. J., **831**, 128
+   (2016).
+"""
+
+import pdb  # noqa: F401
+import logging
+
+import numpy as np
+import pandas as pd
+import matplotlib as mpl
+
+from collections import namedtuple
+from matplotlib import pyplot as plt
+
+_inst_type_idx = pd.Index(["AIC", "FMW", "MM", "OFI"], name="Intability")
+_param_idx = pd.Index(["a", "b", "c"], name="Fit Parameter")
+
+_inst_type_idx = pd.Index(["AIC", "FMW", "MM", "OFI"], name="Intability")
+_param_idx = pd.Index(["a", "b", "c"], name="Fit Parameter")
+
+insta_params = pd.concat(
+    {
+        -4: pd.DataFrame(
+            [
+                [0.367, 0.364, 0.011],
+                [-0.408, 0.529, 0.41],
+                [0.702, 0.674, -0.009],
+                [-1.454, 1.023, -0.178],
+            ],
+            index=_inst_type_idx,
+            columns=_param_idx,
+        ),
+        -3: pd.DataFrame(
+            [
+                [0.437, 0.428, -0.003],
+                [-0.497, 0.566, 0.543],
+                [0.801, 0.763, -0.063],
+                [-1.39, 1.005, -0.111],
+            ],
+            index=_inst_type_idx,
+            columns=_param_idx,
+        ),
+        -2: pd.DataFrame(
+            [
+                [0.649, 0.4, 0.0],
+                [-0.647, 0.583, 0.713],
+                [1.04, 0.633, -0.012],
+                [-1.447, 1.0, -0.148],
+            ],
+            index=_inst_type_idx,
+            columns=_param_idx,
+        ),
+    },
+    axis=1,
+    names=["Growth Rate"],
+).stack("Growth Rate")
+
+_plot_contour_kwargs = pd.DataFrame(
+    [
+        ["#ffcb05", "--", "X"],
+        ["#00B2A9", "--", "d"],
+        ["#00274c", "--", "o"],
+        ["#D86018", "--", "P"],
+        ["#ffcb05", ":", "X"],
+        ["#00B2A9", ":", "d"],
+        ["#00274c", ":", "o"],
+        ["#D86018", ":", "P"],
+        ["#ffcb05", "-.", "X"],
+        ["#00B2A9", "-.", "d"],
+        ["#00274c", "-.", "o"],
+        ["#D86018", "-.", "P"],
+    ],
+    index=pd.MultiIndex.from_tuples(
+        [
+            (-4, "AIC"),
+            (-4, "FMW"),
+            (-4, "MM"),
+            (-4, "OFI"),
+            (-3, "AIC"),
+            (-3, "FMW"),
+            (-3, "MM"),
+            (-3, "OFI"),
+            (-2, "AIC"),
+            (-2, "FMW"),
+            (-2, "MM"),
+            (-2, "OFI"),
+        ],
+        names=["Growth Rate", "Instability"],
+    ),
+    columns=["color", "linestyle", "marker"],
+)
+
+_instability_tests = namedtuple("InstabilityTests", "AIC,MM,FMW,OFI")(
+    np.greater, np.greater, np.less, np.less
+)
+
+
+def beta_ani_inst(beta, a=None, b=None, c=None):
+    r"""Return the anisotropy threshold for a given beta.
+
+    Implements Eq. (5) of :cite:`Verscharen2016a`:
+
+    .. math::
+
+       R_p = 1 + \frac{a}{(\beta_{\parallel,p} - c)^b}
+
+    where $p$ is defined assuming only a single proton population is fit.
+
+    Parameters
+    ----------
+    beta : array-like
+        Parallel proton beta.
+    a, b, c : float
+        Fit parameters from Verscharen et al. (2016).
+
+    Returns
+    -------
+    numpy.ndarray
+        Threshold anisotropy values.
+
+    Examples
+    --------
+    >>> beta = np.logspace(-2, 2, 5)
+    >>> beta_ani_inst(beta, a=0.367, b=-0.408, c=0.011)  # doctest: +ELLIPSIS
+    array([       nan, 1.1367783..., 1.36534751..., 1.93857946..., 3.40240693...])
+    """
+    # Effectively, type checking.
+    a = float(a)
+    b = float(b)
+    c = float(c)
+    return 1 + (a / ((beta - c) ** b))
+
+
+class StabilityCondition(object):
+    """Evaluate plasma stability using the Verscharen et al. fits.
+
+    Parameters
+    ----------
+    growth_rate : int
+        Index of the growth-rate table to use (``-2``, ``-3`` or ``-4``).
+    beta : pandas.Series
+        Parallel proton beta.
+    anisotropy : pandas.Series
+        Temperature anisotropy.
+
+    Attributes
+    ----------
+    instability_thresholds : pandas.DataFrame
+        Threshold anisotropies for each instability.
+    is_unstable : pandas.DataFrame
+        Boolean mask indicating unstable modes.
+    stability_bin : pandas.Series
+        Integer label describing the dominant instability.
+    """
+
+    def __init__(self, growth_rate, beta, anisotropy):
+        """Initialize the object.
+
+        Parameters
+        ----------
+        growth_rate : int
+            Growth rate index (``-2``, ``-3`` or ``-4``).
+        beta, anisotropy : pandas.Series
+            Arrays of parallel beta and temperature anisotropy.
+        """
+        self._init_logger()
+        self.set_instability_parameters(growth_rate)
+        self.set_beta_ani(beta, anisotropy)
+        self.calculate_stability_criteria()
+
+    def __str__(self):
+        """Return the class name."""
+
+        return self.__class__.__name__
+
+    def _init_logger(self):
+        """Initialize a logger namespaced to the class."""
+
+        logger = logging.getLogger("{}.{}".format(__name__, self.__class__.__name__))
+        self._logger = logger
+
+    @property
+    def fill(self):
+        r"""Used to build data containers and check all entries are visited."""
+        return -9999.0
+
+    @property
+    def instability_parameters(self):
+        """The Pandas DataFrame of instability parameters."""
+
+        return self._instability_parameters
+
+    @property
+    def data(self):
+        """DataFrame with beta and anisotropy measurements."""
+
+        return self._data
+
+    @property
+    def beta(self):
+        """The beta values of the object."""
+
+        return self.data.loc[:, "beta"]
+
+    @property
+    def anisotropy(self):
+        """The anisotropy values of the object."""
+
+        return self.data.loc[:, "anisotropy"]
+
+    @property
+    def stability_map(self):
+        """The map of ints to strings identifying the instabilities."""
+
+        return {
+            4: "MM",
+            3: "Between\nAIC &\nMM",
+            2: "Stable",
+            1: "Between\nFMW &\nOFI",
+            0: "OFI",
+        }
+
+    @property
+    def stability_map_inverse(self):
+        """The inverse of ``stability_map``."""
+
+        return {v: k for k, v in self.stability_map.items()}
+
+    @property
+    def instability_thresholds(self):
+        """The value of the anisotropy for which the plasma goes unstable."""
+
+        return self._instability_thresholds
+
+    @property
+    def instability_tests(self):
+        """The tests used for each instability threshold.
+
+        The keys are ``"AIC"``, ``"MM"``, ``"FMW"``, and ``"OFI"`` for
+        Alfven/Ion-Cyclotron, Mirror Mode, Fast Magnetosonic / Whistler, and
+        Oblique Firehose. The values are NumPy ufuncs.
+        """
+
+        return _instability_tests._asdict()
+
+    @property
+    def is_unstable(self):
+        """Boolean DataFrame indicating instability to a given instability."""
+
+        return self._is_unstable
+
+    @property
+    def stability_bin(self):
+        """The integer corresponding to the (in)stability condition."""
+
+        return self._stability_bin
+
+    @property
+    def cmap(self):
+        """A linearly segmented colormap for the (in)stability condition."""
+
+        return plt.cm.get_cmap("Paired", len(self.stability_map))
+
+    @property
+    # TODO: rename to `color_norm` for consistancy w/ plotting code.
+    def norm(self):
+        """The normalization instance used for plotting the stability bin."""
+
+        # Change the normalization slightly so that the tick marks are
+        # centered in their respective regions.
+
+        # TODO: What about using a BoundaryNorm instead and setting
+        # the boundaries at the mid points (avgs) between the stability_map
+        # keys? (20161112_1505)
+        min_norm = min(self.stability_map) - 0.5
+        max_norm = max(self.stability_map) + 0.5
+
+        return mpl.colors.Normalize(min_norm, max_norm)
+
+    @property
+    def cbar_kwargs(self):
+        """Keyword arguments for drawing a colorbar."""
+
+        cbar_formatter = mpl.pyplot.FuncFormatter(
+            lambda val, loc: self.stability_map[val]
+        )
+        ticks = sorted(self.stability_map.keys())
+
+        format_dict = dict(
+            format=cbar_formatter,
+            ticks=ticks,
+            extend="neither",
+            cmap=self.cmap,
+            norm=self.norm,
+        )
+
+        return format_dict
+
+    def set_instability_parameters(self, growth_rate):
+        """Take the instability parameters corresponding to ``growth_rate``.
+
+        Parameters
+        ----------
+        growth_rate : int
+            Growth-rate index (``-2``, ``-3`` or ``-4``).
+        """
+
+        growth_rate = int(growth_rate)
+        temp = insta_params.xs(growth_rate, axis=0, level="Growth Rate")
+        self._instability_parameters = temp
+
+    def set_beta_ani(self, beta, anisotropy):
+        """Set the beta and anisotropy values."""
+
+        assert beta.shape == anisotropy.shape
+        data = pd.concat({"beta": beta, "anisotropy": anisotropy}, axis=1)
+        self._data = data
+
+    def _calc_instability_thresholds(self):
+        r"""Calculate the instability thresholds.
+
+        This is a private method that should not be called. See
+        :meth:`calculate_stability_criteria`.
+        """
+        instability_thresholds = {
+            k: beta_ani_inst(self.beta, **v)
+            for k, v in self.instability_parameters.iterrows()
+        }
+        instability_thresholds = pd.DataFrame.from_dict(instability_thresholds)
+        instability_thresholds = instability_thresholds.sort_index(axis=1)
+        self._instability_thresholds = instability_thresholds
+
+    def _calc_is_unstable(self):
+        r"""Determine if a measurement is unstable to each instability.
+
+        This is a private method that should not be called. See
+        :meth:`calculate_stability_criteria`.
+        """
+        is_unstable = {
+            k: self.instability_tests[k](self.anisotropy, v)
+            for k, v in self.instability_thresholds.iteritems()
+        }
+        is_unstable = pd.concat(is_unstable, axis=1).sort_index(axis=1)
+
+        # If the value is NaN in `instability_thresholds`, the comparison
+        # returns False. We want to propagate it so that we can check the
+        # other instabilities.
+        is_unstable.mask(self.instability_thresholds.isnull(), inplace=True)
+
+        # When an instability is NaN, we have to check the other instabilities.
+        for key, column in is_unstable.iteritems():
+
+            # Temporarily replace the NaNs here with False because NaNs don"t
+            # qualify as unstable on their own. We make the replacement here
+            # and not earlier because we are relying on those NaNs to indicate
+            # the spectra we must actually check against the other
+            # instabilities.
+            others = is_unstable.drop(key, axis=1)
+            others = others.replace(np.nan, False).all(axis=1)
+            column = column.mask(column.isnull(), others).astype(bool)
+
+            is_unstable.loc[:, key] = column
+
+        if is_unstable.isnull().any().any():
+            msg = "Did you visit every data point? " "It looks like you missed %s."
+            msg = msg % (not is_unstable.isnull()).sum()
+            raise ValueError(msg)
+
+        self._is_unstable = is_unstable
+
+    def _calc_stability_bin(self):
+        r"""Identify which instability (if any) each measurement is unstable to.
+
+        This is a private method that should not be called. See
+        :meth:`calculate_stability_criteria`.
+        """
+        unstable = self.is_unstable
+        between_AIC_MM = unstable.AIC & unstable.MM.pipe(np.logical_not)
+        between_FMW_OFI = unstable.FMW & unstable.OFI.pipe(np.logical_not)
+        stable = unstable.pipe(np.logical_not).all(axis=1)
+
+        # Here, we use integer identifiers b/c they are more
+        # computationally efficient to process.
+        stability_bin = pd.Series(self.fill, index=unstable.index, name="Stability")
+
+        map_inverse = self.stability_map_inverse
+        stability_bin.mask(stable, map_inverse["Stable"], inplace=True)
+        stability_bin.mask(
+            between_AIC_MM, map_inverse["Between\nAIC &\nMM"], inplace=True
+        )
+        stability_bin.mask(unstable.MM, map_inverse["MM"], inplace=True)
+        stability_bin.mask(
+            between_FMW_OFI, map_inverse["Between\nFMW &\nOFI"], inplace=True
+        )
+        stability_bin.mask(unstable.OFI, map_inverse["OFI"], inplace=True)
+
+        if (stability_bin == self.fill).any():
+            msg = "Did you visit every data point? " "It looks like you missed %s."
+            msg = msg % (stability_bin == self.fill).sum()
+            raise ValueError(msg)
+
+        self._stability_bin = stability_bin
+
+    def calculate_stability_criteria(self):
+        r"""Run the full instability calculation.
+
+        This method calls :meth:`_calc_instability_thresholds`,
+        :meth:`_calc_is_unstable`, and :meth:`_calc_stability_bin` in that
+        order. Use this method over calling the private methods individually.
+        """
+        self._calc_instability_thresholds()
+        self._calc_is_unstable()
+        self._calc_stability_bin()
+
+
+class StabilityContours(object):
+    """Precompute and plot instability contours.
+
+    Parameters
+    ----------
+    beta : numpy.ndarray
+        Parallel proton beta values used for the contours.
+    """
+
+    def __init__(self, beta):
+        self.set_beta(beta)
+        self._calc_instability_contours()
+
+    @property
+    def beta(self):
+        r"""Proton core parallel beta."""
+        return self._beta
+
+    def set_beta(self, new):
+        assert isinstance(new, np.ndarray)
+        self._beta = new
+
+    def _calc_instability_contours(self):
+        r"""Calculate instability contours.
+
+        Because we can call the contours many times, but only need to calculate them
+        once, move the calculation to a separate method.
+        """
+        contours = {
+            k: beta_ani_inst(self.beta, **v) for k, v in insta_params.iterrows()
+        }
+        contours = pd.Series(contours).unstack(level=0)
+
+        assert isinstance(contours, pd.DataFrame)
+        self._contours = contours
+
+    @property
+    def contours(self):
+        return self._contours
+
+    def plot_contours(
+        self, ax, fix_scale=True, plot_gamma=None, tk_kind=None, **kwargs
+    ):
+        r"""Add the instability contours to the plot.
+
+        Parameters
+        ----------
+        ax: mpl.axis
+        fix_scale: bool
+            If True, make x- and y-axes log scaled.
+        plot_gamma: None, -2, -3, -4
+            If not None, the instability parameter to plot.
+        tk_kind: None, str, list-like of str
+            Contours to plot. Valid options are "MM", "AIC", "FMW", "OFI",
+            and any combination thereof.
+        """
+        assert isinstance(ax, mpl.axes.Axes)
+
+        images_for_table_legend = pd.DataFrame(
+            index=self.contours.index, columns=self.contours.columns
+        )
+
+        kwargs = mpl.cbook.normalize_kwargs(kwargs, mpl.lines.Line2D._alias_map)
+        ms = kwargs.pop("markersize", 10)
+        mew = kwargs.pop("markeredgewidth", 0.5)
+        mec = kwargs.pop("markeredgecolor", "k")
+        markevery = kwargs.pop("markevery", 10)
+
+        if tk_kind is not None:
+            if isinstance(tk_kind, str):
+                tk_kind = [tk_kind]
+            if not np.all([isinstance(x, str) for x in tk_kind]):
+                raise TypeError(f"""Unexpected types for `tk_kind` ({tk_kind})""")
+
+            tk_kind = [x.upper() for x in tk_kind]
+            if not np.all([x in self.contours.columns for x in tk_kind]):
+                raise ValueError(f"""Unexpected values for `tk_kind` ({tk_kind})""")
+
+        target_contours = self.contours
+        if tk_kind is not None:
+            target_contours = target_contours.loc[:, tk_kind]
+        target_contours = target_contours.stack()
+
+        for k, v in target_contours.iteritems():
+            gamma, itype = k
+
+            if plot_gamma is not None:
+                plot_gamma = int(plot_gamma)
+                assert plot_gamma in [-2, -3, -4], "Unrecognized gamma: %s" % plot_gamma
+                if gamma != plot_gamma:
+                    # Don't plot this gamma.
+                    continue
+
+            plot_kwargs = _plot_contour_kwargs.loc[gamma, itype]
+            if gamma is not None:
+                plot_kwargs["label"] = itype
+            im = ax.plot(
+                self.beta,
+                v,
+                # label=k,
+                markevery=markevery,
+                ms=ms,
+                mew=mew,
+                mec=mec,
+                **plot_kwargs,
+                **kwargs,
+            )
+            # only want line object, not list of them. so im[0].
+            images_for_table_legend.loc[gamma, itype] = im[0]
+
+        if fix_scale:
+            ax.set_xscale("log")
+            ax.set_yscale("log")
+
+        if plot_gamma is None:
+            # Only need legend table if plotting all contours.
+            self._add_table_legend(ax, images_for_table_legend)
+        else:
+            ax.legend(
+                loc=1,
+                title=r"$\gamma/\Omega_{p} = 10^{%s}$" % plot_gamma,
+                framealpha=0,
+                ncol=2,
+            )
+
+    @staticmethod
+    def _add_table_legend(ax, images):
+        r"""Create a compact legend in table format identifying the contours.
+
+        Modified from stackoverflow.
+        Source: https://stackoverflow.com/a/25995730/1200989
+        """
+        assert isinstance(images, pd.DataFrame)
+        #         assert images.shape == _plot_contour_kwargs.shape
+
+        # create blank rectangle
+        extra = mpl.patches.Rectangle(
+            (0, 0), 1, 1, fc="w", fill=False, edgecolor="none", linewidth=0
+        )
+
+        # Create organized list containing all handles for table.
+        # Extra represent empty space
+        legend_handles = [
+            extra,
+            extra,
+            extra,
+            extra,
+            extra,
+            extra,
+            images.loc[-2, "MM"],
+            images.loc[-2, "AIC"],
+            images.loc[-2, "FMW"],
+            images.loc[-2, "OFI"],
+            extra,
+            images.loc[-3, "MM"],
+            images.loc[-3, "AIC"],
+            images.loc[-3, "FMW"],
+            images.loc[-3, "OFI"],
+            extra,
+            images.loc[-4, "MM"],
+            images.loc[-4, "AIC"],
+            images.loc[-4, "FMW"],
+            images.loc[-4, "OFI"],
+        ]
+
+        # Define the labels
+        label_rows = [
+            r"",
+            r"$\mathrm{AIC}$",
+            r"$\mathrm{FMW}$",
+            r"$\mathrm{MM}$",
+            r"$\mathrm{OFI}$",
+        ]
+        label_col_0 = [r"$-2$"]
+        label_col_1 = [r"$-3$"]
+        label_col_2 = [r"$-4$"]
+        label_empty = [""]
+
+        # organize labels for table construction
+        legend_labels = (
+            label_rows
+            + label_col_0
+            + label_empty * 4
+            + label_col_1
+            + label_empty * 4
+            + label_col_2
+            + label_empty * 4
+        )
+
+        # Create legend
+        ax.legend(
+            legend_handles,
+            legend_labels,
+            loc=1,
+            ncol=4,
+            shadow=True,
+            handletextpad=-2,
+            framealpha=0.75,
+        )
+
+        # plt.show()
+
+
+# if __name__ == "__main__":
+#     import unittest
+#     unittest.runner

solarwindpy/plotting/__init__.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+r"""High level plotting API for :mod:`solarwindpy`.
+
+This subpackage exposes a collection of plotters and helper functions that simplify
+producing publication quality figures.
+"""
+
+__all__ = [
+    "labels",
+    "histograms",
+    "scatter",
+    "spiral",
+    "orbits",
+    "tools",
+    "subplots",
+    "save",
+    "select_data_from_figure",
+]
+
+from . import (
+    labels,
+    histograms,
+    scatter,
+    spiral,
+    orbits,
+    tools,
+    select_data_from_figure,
+)
+
+subplots = tools.subplots
+
+subplots = tools.subplots
+save = tools.save