solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.0__py3-none-any.whl

solarwindpy/plotting/spiral.py

@@ -0,0 +1,980 @@
+#!/usr/bin/env python
+r"""Spiral mesh plots and associated binning utilities."""
+
+import pdb  # noqa: F401
+import logging
+
+import numpy as np
+import pandas as pd
+import matplotlib as mpl
+
+from datetime import datetime
+from numbers import Number
+from collections import namedtuple
+from numba import njit, prange
+
+from matplotlib import pyplot as plt
+
+from . import base
+from . import labels as labels_module
+
+InitialSpiralEdges = namedtuple("InitialSpiralEdges", "x,y")
+# SpiralMeshData = namedtuple("SpiralMeshData", "x,y")
+SpiralMeshBinID = namedtuple("SpiralMeshBinID", "id,fill,visited")
+SpiralFilterThresholds = namedtuple(
+    "SpiralFilterThresholds", "density,size", defaults=(False,)
+)
+
+
+@njit(parallel=True)
+def get_counts_per_bin(bins, x, y):
+    nbins = bins.shape[0]
+    cell_count = np.full(nbins, 0, dtype=np.int64)
+
+    for i in prange(nbins):
+        x0, x1, y0, y1 = bins[i]
+        left = x >= x0
+        right = x < x1
+        bottom = y >= y0
+        top = y < y1
+        chk_cell = left & right & bottom & top
+        cell_count[i] = chk_cell.sum()
+
+    return cell_count
+
+
+@njit(parallel=True)
+def calculate_bin_number_with_numba(mesh, x, y):
+    fill = -9999
+    zbin = np.full(x.size, fill, dtype=np.int64)
+
+    nbins = mesh.shape[0]
+    bin_visited = np.zeros(nbins, dtype=np.int64)
+    for i in prange(nbins):
+        x0, x1, y0, y1 = mesh[i]
+
+        # Assume that largest x- and y-edges are extended by larger of 1% and 0.01
+        # so that we can just naively use < instead of a special case of <=.
+        # At time of writing (20200418), `SpiralPlot.initialize_mesh` did this.
+        tk = (x >= x0) & (x < x1) & (y >= y0) & (y < y1)
+
+        zbin[tk] = i
+        bin_visited[i] += 1
+
+    return zbin, fill, bin_visited
+
+
+class SpiralMesh(object):
+    def __init__(self, x, y, initial_xedges, initial_yedges, min_per_bin=250):
+        self.set_data(x, y)
+        self.set_min_per_bin(min_per_bin)
+        self.set_initial_edges(initial_xedges, initial_yedges)
+        self._cell_filter_thresholds = SpiralFilterThresholds(density=False, size=False)
+
+    @property
+    def bin_id(self):
+        return self._bin_id
+
+    @property
+    def cat(self):
+        r""":py:class:`pd.Categorical` version of `bin_id`, with fill bin removed."""
+        return self._cat
+
+    @property
+    def data(self):
+        return self._data
+
+    @property
+    def initial_edges(self):
+        return self._initial_edges
+
+    @property
+    def mesh(self):
+        return self._mesh
+
+    @property
+    def min_per_bin(self):
+        return self._min_per_bin
+
+    @property
+    def cell_filter_thresholds(self):
+        return self._cell_filter_thresholds
+
+    @property
+    def cell_filter(self):
+        r"""Boolean :py:class:`Series` identifying properly filled mesh cells.
+
+        Series selects mesh cells that meet density and area criteria specified
+        by :py:meth:`mesh_cell_filter_thresholds`.
+
+        Notes
+        ----
+        Neither `density` nor `size` convert log-scale edges into linear scale.
+        Doing so would overweight the area of mesh cells at larger values on a
+        given axis.
+        """
+        density = self.cell_filter_thresholds.density
+        size = self.cell_filter_thresholds.size
+
+        x = self.mesh[:, [0, 1]]
+        y = self.mesh[:, [2, 3]]
+
+        dx = x[:, 1] - x[:, 0]
+        dy = y[:, 1] - y[:, 0]
+        dA = dx * dy
+
+        tk = np.full_like(dx, True, dtype=bool)
+        if size:
+            size_quantile = np.quantile(dA, size)
+            tk_size = dA < size_quantile
+            tk = tk & (tk_size)
+        if density:
+            cnt = np.bincount(self.bin_id.id, minlength=self.mesh.shape[0])
+            assert cnt.shape == tk.shape
+            cell_density = cnt / dA
+            density_quantile = np.quantile(cell_density, density)
+            tk_density = cell_density > density_quantile
+            tk = tk & tk_density
+
+        return tk
+
+    def set_cell_filter_thresholds(self, **kwargs):
+        r"""Set or update the :py:meth:`mesh_cell_filter_thresholds`.
+
+        Parameters
+        ----------
+        density: scalar
+            The density quantile above which we want to select bins, e.g.
+            above the 0.01 quantile. This ensures that each bin meets some
+            sufficient fill factor.
+        size: scalar
+            The size quantile below which we want to select bins, e.g.
+            below the 0.99 quantile. This ensures that the bin isn't so large
+            that it will appear as an outlier.
+        """
+        density = kwargs.pop("density", False)
+        size = kwargs.pop("size", False)
+        if len(kwargs.keys()):
+            extra = "\n".join(["{}: {}".format(k, v) for k, v in kwargs.items()])
+            raise KeyError("Unexpected kwarg\n{}".format(extra))
+
+        self._cell_filter_thresholds = SpiralFilterThresholds(
+            density=density, size=size
+        )
+
+    def set_initial_edges(self, xedges, yedges):
+        self._initial_edges = InitialSpiralEdges(xedges, yedges)
+
+    def set_data(self, x, y):
+        data = pd.concat({"x": x, "y": y}, axis=1)
+        self._data = data  # SpiralMeshData(x, y)
+
+    def set_min_per_bin(self, new):
+        self._min_per_bin = int(new)
+
+    def initialize_bins(self):
+        # Leaves initial edges altered when we change maximum edge.
+        xbins = self.initial_edges.x
+        ybins = self.initial_edges.y
+
+        #         # Account for highest bin = 0 already done in `SpiralPlot2D.initialize_mesh`.
+        #         xbins[-1] = np.max([0.01, 1.01 * xbins[-1]])
+        #         ybins[-1] = np.max([0.01, 1.01 * ybins[-1]])
+
+        left = xbins[:-1]
+        right = xbins[1:]
+        bottom = ybins[:-1]
+        top = ybins[1:]
+
+        nx = left.size
+        ny = bottom.size
+
+        mesh = np.full((nx * ny, 4), np.nan, dtype=np.float64)
+        for x0, x1, i in zip(left, right, range(nx)):
+            for y0, y1, j in zip(bottom, top, range(ny)):
+                # NOTE: i*ny+j means go to i'th row, which has
+                #       nrow * number of bins passed. Then go
+                #       to j'th bin because we have to traverse
+                #       to the j'th y-bin too.
+                mesh[(i * ny) + j] = [x0, x1, y0, y1]
+
+        mesh = np.array(mesh)
+
+        #         pdb.set_trace()
+
+        self.initial_mesh = np.array(mesh)
+        return mesh
+
+    @staticmethod
+    def process_one_spiral_step(bins, x, y, min_per_bin):
+        #         print("Processing spiral step", flush=True)
+        #         start0 = datetime.now()
+        cell_count = get_counts_per_bin(bins, x, y)
+
+        bins_to_replace = cell_count > min_per_bin
+        nbins_to_replace = bins_to_replace.sum()
+
+        if not nbins_to_replace:
+            return None, 0
+
+        xhyh = 0.5 * (bins[:, [0, 2]] + bins[:, [1, 3]])
+
+        def split_this_cell(idx):
+            x0, x1, y0, y1 = bins[idx]
+            xh, yh = xhyh[idx]
+
+            # Reduce calls to `np.array`.
+            # Just return a list here.
+            split_cell = [
+                [x0, xh, y0, yh],
+                [xh, x1, y0, yh],
+                [xh, x1, yh, y1],
+                [x0, xh, yh, y1],
+            ]
+
+            return split_cell
+
+        new_cells = bins_to_replace.sum() * [None]
+        for i, idx in enumerate(np.where(bins_to_replace)[0]):
+            new_cells[i] = split_this_cell(idx)
+
+        new_cells = np.vstack(new_cells)
+
+        bins[bins_to_replace] = np.nan
+
+        #         stop = datetime.now()
+        #         print(f"Done Building replacement grid cells (dt={stop-start1})", flush=True)
+        #         print(f"Done Processing spiral step (dt={stop-start0})", flush=True)
+
+        return new_cells, nbins_to_replace
+
+    @staticmethod
+    def _visualize_logged_stats(stats_str):
+        from matplotlib import pyplot as plt
+
+        stats = [[y.strip() for y in x.split("  ") if y] for x in stats_str.split("\n")]
+        stats.pop(1)  # Remove column underline row
+        stats = np.array(stats)
+        index = pd.Index(stats[1:, 0].astype(int), name="Step")
+        n_replaced = stats[1:, 1].astype(int)
+
+        dt = pd.to_timedelta(stats[1:, 2]).total_seconds()
+        dt_unit = "s"
+        if dt.max() > 60:
+            dt /= 60
+            dt_unit = "m"
+        if dt.max() > 60:
+            dt /= 60
+            dt_unit = "H"
+        if dt.max() > 24:
+            dt /= 24
+            dt_unit = "D"
+
+        dt_key = f"Elapsed [{dt_unit}]"
+        stats = pd.DataFrame({dt_key: dt, "N Divisions": n_replaced}, index=index)
+
+        #         stats = pd.Series(stats[1:, 1].astype(int), index=stats[1:, 0].astype(int), name=stats[0, 1])
+        #         stats.index.name = stats[0, 0]
+
+        fig, ax = plt.subplots()
+        tax = ax.twinx()
+
+        x = stats.index
+        k = f"Elapsed [{dt_unit}]"
+        ax.plot(x, stats.loc[:, k], label=k, marker="+", ms=8)
+
+        k = "N Divisions"
+        tax.plot(x, stats.loc[:, k], label=k, c="C1", ls="--", marker="x", ms=8)
+
+        tax.grid(False)
+        ax.set_xlabel("Step Number")
+        ax.set_ylabel(dt_key)
+        tax.set_ylabel("N Divisions")
+
+        h0, l0 = ax.get_legend_handles_labels()
+        h1, l1 = tax.get_legend_handles_labels()
+
+        ax.legend(
+            h0 + h1,
+            l0 + l1,
+            title=rf"$\Delta t = {stats.loc[:, dt_key].sum():.0f} \, {dt_unit}$",
+        )
+
+        ax.set_yscale("log")
+        tax.set_yscale("log")
+
+        return ax, tax, stats
+
+    def generate_mesh(self):
+        logger = logging.getLogger("__main__")
+        start = datetime.now()
+        logger.warning(f"Generating {self.__class__.__name__} at {start}")
+
+        x = self.data.x.values
+        y = self.data.y.values
+
+        min_per_bin = self.min_per_bin
+        #         max_bins = int(1e5)
+
+        initial_bins = self.initialize_bins()
+
+        # To reduce memory needs, only process data in mesh.
+        x0 = initial_bins[:, 0].min()
+        x1 = initial_bins[:, 1].max()
+        y0 = initial_bins[:, 2].min()
+        y1 = initial_bins[:, 3].max()
+        tk_data_in_mesh = (
+            (x0 <= x)
+            & (x <= x1)
+            & (y0 <= y)
+            & (y <= y1)
+            & np.isfinite(x)
+            & np.isfinite(y)
+        )
+        x = x[tk_data_in_mesh]
+        y = y[tk_data_in_mesh]
+
+        initial_cell_count = get_counts_per_bin(initial_bins, x, y)
+        #         initial_cell_count = self.get_counts_per_bin_loop(initial_bins, x, y)
+        bins_to_replace = initial_cell_count > min_per_bin
+        nbins_to_replace = bins_to_replace.sum()
+
+        #         raise ValueError
+
+        list_of_bins = [initial_bins]
+        active_bins = initial_bins
+
+        logger.warning(
+            """
+ Step      N      Elapsed Time
+======  =======  =============="""
+        )
+        step_start = datetime.now()
+        step = 0
+        while nbins_to_replace > 0:
+            active_bins, nbins_to_replace = self.process_one_spiral_step(
+                active_bins, x, y, min_per_bin
+            )
+            now = datetime.now()
+            #             if not(step % 10):
+            logger.warning(f"{step:>6}  {nbins_to_replace:>7}  {(now - step_start)}")
+            list_of_bins.append(active_bins)
+            step += 1
+            step_start = now
+
+        list_of_bins = [b for b in list_of_bins if b is not None]
+        final_bins = np.vstack(list_of_bins)
+        valid_bins = np.isfinite(final_bins).all(axis=1)
+        final_bins = final_bins[valid_bins]
+
+        stop = datetime.now()
+        #         logger.warning(f"Complete at {stop}")
+        logger.warning(f"\nCompleted {self.__class__.__name__} at {stop}")
+        logger.warning(f"Elasped time {stop - start}")
+        logger.warning(f"Split bin threshold {min_per_bin}")
+        logger.warning(
+            f"Generated {final_bins.shape[0]} bins for {x.size} spectra (~{x.size / final_bins.shape[0]:.3f} spectra per bin)\n"
+        )
+
+        self._mesh = final_bins
+
+    #         return final_bins
+
+    def calculate_bin_number(self):
+        logger = logging.getLogger(__name__)
+        logger.warning(
+            f"Calculating {self.__class__.__name__} bin_number at {datetime.now()}"
+        )
+        x = self.data.loc[:, "x"].values
+        y = self.data.loc[:, "y"].values
+        mesh = self.mesh
+        nbins = mesh.shape[0]
+
+        start = datetime.now()
+        zbin, fill, bin_visited = calculate_bin_number_with_numba(mesh, x, y)
+        stop = datetime.now()
+
+        logger.warning(f"Elapsed time {stop - start}")
+
+        #         return calculate_bin_number_with_numba_broadcast(mesh, x, y, fill)
+
+        #             if ( verbose > 0 and
+        #                  (i % verbose == 0) ):
+        #                     print(i+1, end=", ")
+
+        if (zbin == fill).any():
+            #         if (zbin < 0).any():
+            #             pdb.set_trace()
+            logger.warning(
+                f"""`zbin` contains {(zbin == fill).sum()} ({100 * (zbin == fill).mean():.1f}%) fill values that are outside of mesh.
+They will be replaced by NaNs and excluded from the aggregation.
+"""
+            )
+            # raise ValueError(msg % (zbin == fill).sum())
+
+        # Set fill bin to zero
+        is_fill = zbin == fill
+        #         zbin[~is_fill] += 1
+        #         zbin[is_fill] = -1
+        #         print(zbin.min())
+        #         zbin += 1
+        #         print(zbin.min())
+        # `minlength=nbins` forces us to include empty bins at the end of the array.
+        bin_frequency = np.bincount(zbin[~is_fill], minlength=nbins)
+        n_empty = (bin_frequency == 0).sum()
+        logger.warning(
+            f"""Largest bin population is {bin_frequency.max()}
+{n_empty} of {nbins} bins ({100 * n_empty / nbins:.1f}%) are empty
+"""
+        )
+
+        if not bin_visited.all():
+            logger.warning(f"{(~bin_visited).sum()} bins went unvisited.")
+        if (bin_visited > 1).any():
+            logger.warning(f"({(bin_visited > 1).sum()} bins visted more than once.")
+
+        if nbins - bin_frequency.shape[0] != 0:
+            raise ValueError(
+                f"{nbins - bin_frequency.shape[0]} mesh cells do not have an associated z-value"
+            )
+
+        # zbin = _pd.Series(zbin, index=self.data.index, name="zbin")
+        # # Pandas groupby will treat NaN as not belonging to a bin.
+        # zbin.replace(fill, _np.nan, inplace=True)
+        bin_id = SpiralMeshBinID(zbin, fill, bin_visited)
+        self._bin_id = bin_id
+        return bin_id
+
+    def place_spectra_in_mesh(self):
+        self.generate_mesh()
+        bin_id = self.calculate_bin_number()
+        return bin_id
+
+    def build_cat(self):
+        bin_id = self.bin_id.id
+        fill = self.bin_id.fill
+
+        # Integer number corresponds to the order over
+        # which the mesh was traversed.
+        cat = pd.Categorical(bin_id, ordered=False)
+        if fill in bin_id:
+            cat.remove_categories(fill, inplace=True)
+
+        self._cat = cat
+
+
+class SpiralPlot2D(base.PlotWithZdata, base.CbarMaker):
+    r"""2D spiral plotting with adaptive mesh refinement.
+
+    Examples
+    --------
+    splot = SpiralPlot2D(...)
+    splot.initialize_mesh()
+    """
+
+    def __init__(
+        self, x, y, z=None, logx=False, logy=False, initial_bins=5, clip_data=False
+    ):
+        super().__init__()
+        self.set_log(x=logx, y=logy)
+        self.set_data(x, y, z, clip_data)
+        self.set_labels(x="x", y="y", z=labels_module.Count() if z is None else "z")
+        self.calc_initial_bins(initial_bins)
+        self.set_clim(None, None)
+
+    @property
+    def clim(self):
+        return self._clim
+
+    @property
+    def initial_bins(self):
+        return dict(self._initial_bins)
+
+    @property
+    def grouped(self):
+        return self._grouped
+
+    @property
+    def mesh(self):
+        return self._mesh
+
+    def agg(self, fcn=None):
+        r"""Aggregate the z-values into their bins."""
+        self.logger.debug("aggregating z-data")
+
+        #         start = datetime.now()
+        #         self.logger.warning(f"Start {start}")
+
+        if fcn is None:
+            if self.data.loc[:, "z"].unique().size == 1:
+                fcn = "count"
+            else:
+                fcn = "mean"
+
+        gb = self.grouped
+        agg = gb.agg(fcn)
+
+        c0, c1 = self.clim
+        if c0 is not None or c1 is not None:
+            cnt = gb.agg("count")
+            tk = pd.Series(True, index=agg.index)
+
+            if c0 is not None:
+                tk = tk & (cnt >= c0)
+            if c1 is not None:
+                tk = tk & (cnt <= c1)
+
+            agg = agg.where(tk)
+
+        # reindex to ensure we have a z-value for every bin.
+        reindex = pd.RangeIndex(start=0, stop=self.mesh.mesh.shape[0], step=1)
+        agg = agg.reindex(reindex)
+
+        cell_filter = self.mesh.cell_filter
+        if agg.shape != cell_filter.shape:
+            raise ValueError(
+                f"""Unable to algin `agg` and `cell_filter.
+agg    : {agg.shape}
+filter : {cell_filter.shape}"""
+            )
+        #         pdb.set_trace()
+        agg = agg.where(cell_filter, axis=0)
+
+        #         stop = datetime.now()
+        #         self.logger.warning(f"Stop {stop}")
+        #         self.logger.warning(f"Elapsed {stop - start}")
+
+        return agg
+
+    def build_grouped(self):
+        cat = self.mesh.cat
+        z = self.data.loc[:, "z"]
+
+        if not (cat.size == z.size):
+            raise ValueError(
+                f"""`cat` must have same size as data's first dimesion
+cat  : {cat.size}
+data : {z.size}
+"""
+            )
+
+        gb = z.groupby(cat)
+        self._grouped = gb
+
+    def calc_initial_bins(self, nbins):
+        data = self.data
+        keys = ("x", "y")
+        bins = {}
+
+        if isinstance(nbins, int):
+            # Single paramter for `nbins`.
+            nbins = {k: nbins for k in keys}
+
+        elif len(nbins) == len(keys):
+            # Passed one bin spec per axis
+            nbins = {k: v for k, v in zip(keys, nbins)}
+
+        else:
+            msg = f"Unrecognized `nbins`\ntype: {type(nbins)}\n bins:{nbins}"
+            raise ValueError(msg)
+
+        for k, b in nbins.items():
+            # Numpy and Astropy don't like NaNs when calculating bins.
+            # Infinities in bins (typically from log10(0)) also create problems.
+            d = data.loc[:, k].replace([-np.inf, np.inf], np.nan).dropna()
+
+            if not isinstance(b, (int, np.ndarray)):
+                raise TypeError("Only want in integer or np.ndarrays for initial edges")
+
+            if isinstance(b, int):
+                # Lets calculate the following quantiles.
+                b = np.quantile(
+                    d, np.linspace(0, 1, b + 1)
+                )  # Need N + 1 edges to make N bins.
+
+            # Extend the right most bin by the larger of 1% or 0.01 (in the case of zero)
+            # So that y < y1 inludes data at real data edge.
+            b[-1] = np.max([0.01, 1.01 * b.max()])
+
+            assert not np.isnan(b).any()
+
+            bins[k] = b
+
+        bins = tuple(bins.items())
+        self._initial_bins = bins
+        return bins
+
+    def initialize_mesh(self, **kwargs):
+        x = self.data.loc[:, "x"]
+        y = self.data.loc[:, "y"]
+
+        #         if self.log.x:
+        #             x = x.apply(np.log10)
+        #         if self.log.y:
+        #             y = y.apply(np.log10)
+
+        xbins = self.initial_bins["x"]
+        ybins = self.initial_bins["y"]
+
+        mesh = SpiralMesh(x, y, xbins, ybins, **kwargs)
+        # Attach mesh before anything else.
+        # Makes debugging easier.
+        self._mesh = mesh
+
+        mesh.place_spectra_in_mesh()
+        mesh.build_cat()
+
+    def set_clim(self, lower=None, upper=None):
+        """Set the min (lower) and max (upper) counts per bin.
+
+        This limit is applied after the :py:meth:`groupby.agg` is run."""
+        assert isinstance(lower, Number) or lower is None
+        assert isinstance(upper, Number) or upper is None
+        self._clim = base.RangeLimits(lower, upper)
+
+    def set_data(self, x, y, z, clip):
+        super().set_data(x, y, z, clip)
+        data = self.data
+        if self.log.x:
+            data.loc[:, "x"] = np.log10(np.abs(data.loc[:, "x"]))
+        if self.log.y:
+            data.loc[:, "y"] = np.log10(np.abs(data.loc[:, "y"]))
+        self._data = data
+
+    def _limit_color_norm(self, norm):
+        pct = self.data.loc[:, "z"].quantile([0.01, 0.99])
+        v0 = pct.loc[0.01]
+        v1 = pct.loc[0.99]
+        if norm.vmin is None:
+            norm.vmin = v0
+        if norm.vmax is None:
+            norm.vmax = v1
+        norm.clip = True
+
+    def make_plot(
+        self,
+        ax=None,
+        cbar=True,
+        limit_color_norm=False,
+        cbar_kwargs=None,
+        fcn=None,
+        alpha_fcn=None,
+        **kwargs,
+    ):
+
+        #         start = datetime.now()
+        #         self.logger.warning("Making plot")
+        #         self.logger.warning(f"Start {start}")
+
+        if ax is None:
+            fig, ax = plt.subplots()
+
+        C = self.agg(fcn=fcn)
+        C = np.ma.masked_invalid(C.values)
+        assert isinstance(C, np.ndarray)
+        assert C.ndim == 1
+        if C.shape[0] != self.mesh.mesh.shape[0]:
+            raise ValueError(
+                f"""{self.mesh.mesh.shape[0] - C.shape[0]} mesh cells do not have a z-value associated with them. The z-values and mesh are not properly aligned."""
+            )
+
+        xmesh = self.mesh.mesh[:, [0, 1]]
+        ymesh = self.mesh.mesh[:, [2, 3]]
+
+        if self.log.x:
+            xmesh = 10.0**xmesh
+        if self.log.y:
+            ymesh = 10.0**ymesh
+
+        # (x,y) of bin's lower left corner.
+        xy = zip(xmesh[:, 0], ymesh[:, 0])
+        dx = xmesh[:, 1] - xmesh[:, 0]
+        dy = ymesh[:, 1] - ymesh[:, 0]
+
+        start1 = datetime.now()
+        self.logger.warning("Making patches")
+        self.logger.warning(f"Start {start1}")
+
+        patches = [
+            mpl.patches.Rectangle(this_xy, this_dx, this_dy)
+            for this_xy, this_dx, this_dy in zip(xy, dx, dy)
+        ]
+
+        stop1 = datetime.now()
+        self.logger.warning(f"Stop {stop1}")
+        self.logger.warning(f"Elapsed {stop1 - start1}")
+
+        # TODO: `match_original=False` if calculate alpha for each patch.
+        edgecolors = "none"
+        linewidth = 0.0
+        collection = mpl.collections.PatchCollection(
+            patches, linewidth=linewidth, edgecolors=edgecolors
+        )
+
+        collection.set_array(C)
+
+        cmap = kwargs.pop("cmap", None)
+        norm = kwargs.pop("norm", None)
+        if len(kwargs):
+            raise ValueError(f"Unexpected kwargs {kwargs.keys()}")
+        #         assert not kwargs
+
+        if limit_color_norm and norm is not None:
+            self._limit_color_norm(norm)
+
+        collection.set_alpha(None)
+        collection.set_cmap(cmap)
+        collection.set_norm(norm)
+        collection.autoscale_None()
+
+        ax.add_collection(collection, autolim=False)
+
+        minx = xmesh[:, 0].min()
+        miny = ymesh[:, 0].min()
+        maxx = xmesh[:, 1].max()
+        maxy = ymesh[:, 1].max()
+        collection.sticky_edges.x[:] = [minx, maxx]
+        collection.sticky_edges.y[:] = [miny, maxy]
+        corners = (minx, miny), (maxx, maxy)
+        ax.update_datalim(corners)
+        ax.autoscale_view()
+
+        cbar_or_mappable = collection
+        if cbar:
+            if cbar_kwargs is None:
+                cbar_kwargs = dict()
+
+            if "cax" not in cbar_kwargs.keys() and "ax" not in cbar_kwargs.keys():
+                cbar_kwargs["ax"] = ax
+
+            cbar = self._make_cbar(collection, norm=norm, **cbar_kwargs)
+            cbar_or_mappable = cbar
+
+        self._format_axis(ax)
+
+        if alpha_fcn is not None:
+            alpha_agg = np.ma.masked_invalid(self.agg(fcn=alpha_fcn).values)
+            # Feature scale then invert so smallest STD
+            # is most opaque.
+            alpha_agg = mpl.colors.Normalize()(alpha_agg)
+            alpha = 1 - alpha_agg
+            self.logger.warning("Scaling alpha filter as alpha**0.25")
+            alpha = alpha**0.25
+
+            # Set masked values to zero. Otherwise, masked
+            # values are rendered as black.
+            alpha = alpha.filled(0)
+
+            # Must draw to initialize `facecolor`s
+            plt.draw()
+            colors = collection.get_facecolors()
+            colors[:, 3] = alpha
+            collection.set_facecolor(colors)
+
+        #         stop = datetime.now()
+        #         self.logger.warning(f"Stop {stop}")
+        #         self.logger.warning(f"Elapsed {stop - start}")
+
+        return ax, cbar_or_mappable
+
+    def _verify_contour_passthrough_kwargs(
+        self, ax, clabel_kwargs, edges_kwargs, cbar_kwargs
+    ):
+        if clabel_kwargs is None:
+            clabel_kwargs = dict()
+        if edges_kwargs is None:
+            edges_kwargs = dict()
+        if cbar_kwargs is None:
+            cbar_kwargs = dict()
+        if "cax" not in cbar_kwargs.keys() and "ax" not in cbar_kwargs.keys():
+            cbar_kwargs["ax"] = ax
+
+        return clabel_kwargs, edges_kwargs, cbar_kwargs
+
+    def plot_contours(
+        self,
+        ax=None,
+        label_levels=True,
+        cbar=True,
+        limit_color_norm=False,
+        cbar_kwargs=None,
+        fcn=None,
+        plot_edges=False,
+        edges_kwargs=None,
+        clabel_kwargs=None,
+        skip_max_clbl=True,
+        use_contourf=False,
+        #         gaussian_filter_std=0,
+        #         gaussian_filter_kwargs=None,
+        **kwargs,
+    ):
+        """Make a contour plot on `ax` using `ax.contour`.
+
+        Parameters
+        ----------
+        ax: mpl.axes.Axes, None
+            If None, create an `Axes` instance from `plt.subplots`.
+        label_levels: bool
+            If True, add labels to contours with `ax.clabel`.
+        cbar: bool
+            If True, create color bar with `labels.z`.
+        limit_color_norm: bool
+            If True, limit the color range to 0.001 and 0.999 percentile range
+            of the z-value, count or otherwise.
+        cbar_kwargs: dict, None
+            If not None, kwargs passed to `self._make_cbar`.
+        fcn: FunctionType, None
+            Aggregation function. If None, automatically select in :py:meth:`agg`.
+        plot_edges: bool
+            If True, plot the smoothed, extreme edges of the 2D histogram.
+        clabel_kwargs: None, dict
+            If not None, dictionary of kwargs passed to `ax.clabel`.
+        skip_max_clbl: bool
+            If True, don't label the maximum contour. Primarily used when the maximum
+            contour is, effectively, a point.
+        maximum_color:
+            The color for the maximum of the PDF.
+        use_contourf: bool
+            If True, use `ax.contourf`. Else use `ax.contour`.
+        gaussian_filter_std: int
+            If > 0, apply `scipy.ndimage.gaussian_filter` to the z-values using the
+            standard deviation specified by `gaussian_filter_std`.
+        gaussian_filter_kwargs: None, dict
+            If not None and gaussian_filter_std > 0, passed to :py:meth:`scipy.ndimage.gaussian_filter`
+        kwargs:
+            Passed to :py:meth:`ax.pcolormesh`.
+            If row or column normalized data, `norm` defaults to `mpl.colors.Normalize(0, 1)`.
+        """
+        levels = kwargs.pop("levels", None)
+        cmap = kwargs.pop("cmap", None)
+        norm = kwargs.pop(
+            "norm",
+            None,
+            #             mpl.colors.BoundaryNorm(np.linspace(0, 1, 11), 256, clip=True)
+            #             if self.axnorm in ("c", "r")
+            #             else None,
+        )
+        linestyles = kwargs.pop(
+            "linestyles",
+            [
+                "-",
+                ":",
+                "--",
+                (0, (7, 3, 1, 3, 1, 3, 1, 3, 1, 3)),
+                "--",
+                ":",
+                "-",
+                (0, (7, 3, 1, 3, 1, 3)),
+            ],
+        )
+
+        if ax is None:
+            fig, ax = plt.subplots()
+
+        (
+            clabel_kwargs,
+            edges_kwargs,
+            cbar_kwargs,
+        ) = self._verify_contour_passthrough_kwargs(
+            ax, clabel_kwargs, edges_kwargs, cbar_kwargs
+        )
+
+        inline = clabel_kwargs.pop("inline", True)
+        inline_spacing = clabel_kwargs.pop("inline_spacing", -3)
+        fmt = clabel_kwargs.pop("fmt", "%s")
+
+        if ax is None:
+            fig, ax = plt.subplots()
+
+        C = self.agg(fcn=fcn).values
+        assert isinstance(C, np.ndarray)
+        assert C.ndim == 1
+        if C.shape[0] != self.mesh.mesh.shape[0]:
+            raise ValueError(
+                f"""{self.mesh.mesh.shape[0] - C.shape[0]} mesh cells do not have a z-value associated with them. The z-values and mesh are not properly aligned."""
+            )
+
+        x = self.mesh.mesh[:, [0, 1]].mean(axis=1)
+        y = self.mesh.mesh[:, [2, 3]].mean(axis=1)
+
+        if self.log.x:
+            x = 10.0**x
+        if self.log.y:
+            y = 10.0**y
+
+        tk_finite = np.isfinite(C)
+        x = x[tk_finite]
+        y = y[tk_finite]
+        C = C[tk_finite]
+
+        contour_fcn = ax.tricontour
+        if use_contourf:
+            contour_fcn = ax.tricontourf
+
+        if levels is None:
+            args = [x, y, C]
+        else:
+            args = [x, y, C, levels]
+
+        qset = contour_fcn(*args, linestyles=linestyles, cmap=cmap, norm=norm, **kwargs)
+
+        try:
+            args = (qset, levels[:-1] if skip_max_clbl else levels)
+        except TypeError:
+            # None can't be subscripted.
+            args = (qset,)
+
+        class nf(float):
+            # Source: https://matplotlib.org/3.1.0/gallery/images_contours_and_fields/contour_label_demo.html
+            # Define a class that forces representation of float to look a certain way
+            # This remove trailing zero so '1.0' becomes '1'
+            def __repr__(self):
+                return str(self).rstrip("0")
+
+        lbls = None
+        if label_levels:
+            qset.levels = [nf(level) for level in qset.levels]
+            lbls = ax.clabel(
+                *args,
+                inline=inline,
+                inline_spacing=inline_spacing,
+                fmt=fmt,
+                **clabel_kwargs,
+            )
+
+        cbar_or_mappable = qset
+        if cbar:
+            # Pass `norm` to `self._make_cbar` so that we can choose the ticks to use.
+            cbar = self._make_cbar(qset, norm=norm, **cbar_kwargs)
+            cbar_or_mappable = cbar
+
+        self._format_axis(ax)
+
+        return ax, lbls, cbar_or_mappable, qset
+
+
+#    def plot_surface(self):
+#
+#        from scipy.interpolate import griddata
+#
+#        z = self.agg()
+#        x = self.mesh.mesh[:, [0, 1]].mean(axis=1)
+#        y = self.mesh.mesh[:, [2, 3]].mean(axis=1)
+#
+#        is_finite = np.isfinite(z)
+#        z = z[is_finite]
+#        x = x[is_finite]
+#        y = y[is_finite]
+#
+#        xi = np.linspace(x.min(), x.max(), 100)
+#        yi = np.linspace(y.min(), y.max(), 100)
+#        # VERY IMPORTANT, to tell matplotlib how is your data organized
+#        zi = griddata((x, y), y, (xi[None, :], yi[:, None]), method="cubic")
+#
+#        if ax is None:
+#            fig = plt.figure(figsize=(8, 8))
+#            ax = fig.add_subplot(projection="3d")
+#
+#        xig, yig = np.meshgrid(xi, yi)
+#
+#        ax.plot_surface(xx, yy, zz, cmap="Spectral_r", norm=chavp.norms.vsw)