Merge pull request #280 from boutproject/polygon-plots

Polygonal 2D poloidal plots

xbout/boutdataarray.py

@@ -1072,6 +1072,12 @@ def pcolormesh(self, ax=None, **kwargs):
         """
         return plotfuncs.plot2d_wrapper(self.data, xr.plot.pcolormesh, ax=ax, **kwargs)
 
+    def polygon(self, ax=None, **kwargs):
+        """
+        Colour-plot of a radial-poloidal slice on the R-Z plane using polygons
+        """
+        return plotfuncs.plot2d_polygon(self.data, ax=ax, **kwargs)
+
     def plot_regions(self, ax=None, **kwargs):
         """
         Plot the regions into which xBOUT splits radial-poloidal arrays to handle

xbout/geometries.py

@@ -381,6 +381,14 @@ def add_toroidal_geometry_coords(ds, *, coordinates=None, grid=None):
             "total_poloidal_distance",
             "zShift",
             "zShift_ylow",
+            "Rxy_corners",  # Lower left corners
+            "Rxy_lower_right_corners",
+            "Rxy_upper_left_corners",
+            "Rxy_upper_right_corners",
+            "Zxy_corners",  # Lower left corners
+            "Zxy_lower_right_corners",
+            "Zxy_upper_left_corners",
+            "Zxy_upper_right_corners",
         ],
     )
 
@@ -420,6 +428,24 @@ def add_toroidal_geometry_coords(ds, *, coordinates=None, grid=None):
     else:
         ds = ds.set_coords(("Rxy", "Zxy"))
 
+    # Add cell corners as coordinates for polygon plotting
+    if "Rxy_lower_right_corners" in ds:
+        ds = ds.rename(
+            Rxy_corners="Rxy_lower_left_corners", Zxy_corners="Zxy_lower_left_corners"
+        )
+        ds = ds.set_coords(
+            (
+                "Rxy_lower_left_corners",
+                "Rxy_lower_right_corners",
+                "Rxy_upper_left_corners",
+                "Rxy_upper_right_corners",
+                "Zxy_lower_left_corners",
+                "Zxy_lower_right_corners",
+                "Zxy_upper_left_corners",
+                "Zxy_upper_right_corners",
+            )
+        )
+
     # Rename zShift_ylow if it was added from grid file, to be consistent with name if
     # it was added from dump file
     if "zShift_CELL_YLOW" in ds and "zShift_ylow" in ds:

xbout/plotting/animate.py

@@ -97,6 +97,7 @@ def animate_poloidal(
     cax=None,
     animate_over=None,
     separatrix=True,
+    separatrix_kwargs=dict(),
     targets=True,
     add_limiter_hatching=True,
     cmap=None,
@@ -130,6 +131,8 @@ def animate_poloidal(
         Dimension over which to animate, defaults to the time dimension
     separatrix : bool, optional
         Add dashed lines showing separatrices
+    separatrix_kwargs : dict, optional
+        Options to pass to the separatrix plotter (e.g. line color)
     targets : bool, optional
         Draw solid lines at the target surfaces
     add_limiter_hatching : bool, optional
@@ -277,7 +280,7 @@ def animate_poloidal(
         targets = False
 
     if separatrix:
-        plot_separatrices(da_regions, ax, x=x, y=y)
+        plot_separatrices(da_regions, ax, x=x, y=y, **separatrix_kwargs)
 
     if targets:
         plot_targets(da_regions, ax, x=x, y=y, hatching=add_limiter_hatching)

xbout/plotting/plotfuncs.py

@@ -1,6 +1,7 @@
 from collections.abc import Sequence
 import matplotlib
 import matplotlib.pyplot as plt
+from mpl_toolkits.axes_grid1 import make_axes_locatable
 import numpy as np
 from pathlib import Path
 from tempfile import TemporaryDirectory
@@ -752,9 +753,9 @@ def create_or_update_plot(plot_objects=None, tind=None, this_save_as=None):
                                 X, Y, Z, scalars=data, vmin=vmin, vmax=vmax, **kwargs
                             )
                         else:
-                            plot_objects[
-                                region_name + str(i)
-                            ].mlab_source.scalars = data
+                            plot_objects[region_name + str(i)].mlab_source.scalars = (
+                                data
+                            )
 
                 if mayavi_view is not None:
                     mlab.view(*mayavi_view)
@@ -849,3 +850,181 @@ def animation_func():
         plt.show()
     else:
         raise ValueError(f"Unrecognised plot3d() 'engine' argument: {engine}")
+
+
+def plot2d_polygon(
+    da,
+    ax=None,
+    cax=None,
+    cmap="viridis",
+    norm=None,
+    logscale=False,
+    antialias=False,
+    vmin=None,
+    vmax=None,
+    extend="neither",
+    add_colorbar=True,
+    colorbar_label=None,
+    separatrix=True,
+    separatrix_kwargs={"color": "white", "linestyle": "-", "linewidth": 2},
+    targets=False,
+    add_limiter_hatching=False,
+    grid_only=False,
+    linewidth=0,
+    linecolor="black",
+):
+    """
+    Nice looking 2D plots which have no visual artifacts around the X-point.
+
+    Parameters
+    ----------
+    da : xarray.DataArray
+        A 2D (x,y) DataArray of data to plot
+    ax :  Axes, optional
+        Axes to plot on. If not provided, will make its own.
+    cax : Axes, optional
+        Axes to plot colorbar on. If not provided, will plot on the same axes as the plot.
+    cmap : str or matplotlib.colors.Colormap, default "viridis"
+        Colormap to use for the plot
+    norm : matplotlib.colors.Normalize, optional
+        Normalization to use for the color scale
+    logscale : bool, default False
+        If True, use a symlog color scale
+    antialias : bool, default False
+        Enables antialiasing. Note: this also shows mesh cell edges - it's unclear how to disable this.
+    vmin : float, optional
+        Minimum value for the color scale
+    vmax : float, optional
+        Maximum value for the color scale
+    extend : str, optional, default "neither"
+        Extend the colorbar. Options are "neither", "both", "min", "max"
+    add_colorbar : bool, default True
+        Enable colorbar in figure?
+    colorbar_label : str, optional
+        Label for the colorbar
+    separatrix : bool, default True
+        Add lines showing separatrices
+    separatrix_kwargs : dict
+        Keyword arguments to pass custom style to the separatrices plot
+    targets : bool, default True
+        Draw solid lines at the target surfaces
+    add_limiter_hatching : bool, default True
+        Draw hatched areas at the targets
+    grid_only : bool, default False
+        Only plot the grid, not the data. This sets all the polygons to have a white face.
+    linewidth : float, default 0
+        Width of the gridlines on cell edges
+    linecolor : str, default "black"
+        Color of the gridlines on cell edges
+    """
+
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(3, 6), dpi=120)
+    else:
+        fig = ax.get_figure()
+
+    if cax is None:
+        cax = ax
+
+    if vmin is None:
+        vmin = np.nanmin(da.values)
+
+    if vmax is None:
+        vmax = np.nanmax(da.max().values)
+
+    if colorbar_label == None:
+        if "short_name" in da.attrs:
+            colorbar_label = da.attrs["short_name"]
+        elif da.name != None:
+            colorbar_label = da.name
+        else:
+            colorbar_label = ""
+
+    if "units" in da.attrs:
+        colorbar_label += f" [{da.attrs['units']}]"
+
+    if "Rxy_lower_right_corners" in da.coords:
+        r_nodes = [
+            "R",
+            "Rxy_lower_left_corners",
+            "Rxy_lower_right_corners",
+            "Rxy_upper_left_corners",
+            "Rxy_upper_right_corners",
+        ]
+        z_nodes = [
+            "Z",
+            "Zxy_lower_left_corners",
+            "Zxy_lower_right_corners",
+            "Zxy_upper_left_corners",
+            "Zxy_upper_right_corners",
+        ]
+        cell_r = np.concatenate(
+            [np.expand_dims(da[x], axis=2) for x in r_nodes], axis=2
+        )
+        cell_z = np.concatenate(
+            [np.expand_dims(da[x], axis=2) for x in z_nodes], axis=2
+        )
+    else:
+        raise Exception("Cell corners not present in mesh, cannot do polygon plot")
+
+    Nx = len(cell_r)
+    Ny = len(cell_r[0])
+    patches = []
+
+    # https://matplotlib.org/2.0.2/examples/api/patch_collection.html
+
+    idx = [np.array([1, 2, 4, 3, 1])]
+    patches = []
+    for i in range(Nx):
+        for j in range(Ny):
+            p = matplotlib.patches.Polygon(
+                np.concatenate((cell_r[i][j][tuple(idx)], cell_z[i][j][tuple(idx)]))
+                .reshape(2, 5)
+                .T,
+                fill=False,
+                closed=True,
+                facecolor=None,
+            )
+            patches.append(p)
+
+    norm = _create_norm(logscale, norm, vmin, vmax)
+
+    if grid_only is True:
+        cmap = matplotlib.colors.ListedColormap(["white"])
+    colors = da.data.flatten()
+    polys = matplotlib.collections.PatchCollection(
+        patches,
+        alpha=1,
+        norm=norm,
+        cmap=cmap,
+        antialiaseds=antialias,
+        edgecolors=linecolor,
+        linewidths=linewidth,
+        joinstyle="bevel",
+    )
+
+    polys.set_array(colors)
+
+    if add_colorbar:
+        # This produces a "foolproof" colorbar which
+        # is always the height of the plot
+        # From https://joseph-long.com/writing/colorbars/
+        divider = make_axes_locatable(ax)
+        cax = divider.append_axes("right", size="5%", pad=0.05)
+        fig.colorbar(polys, cax=cax, label=colorbar_label, extend=extend)
+        cax.grid(which="both", visible=False)
+
+    ax.add_collection(polys)
+
+    ax.set_aspect("equal", adjustable="box")
+    ax.set_xlabel("R [m]")
+    ax.set_ylabel("Z [m]")
+    ax.set_ylim(cell_z.min(), cell_z.max())
+    ax.set_xlim(cell_r.min(), cell_r.max())
+    ax.set_title(da.name)
+
+    if separatrix:
+        plot_separatrices(da, ax, x="R", y="Z", **separatrix_kwargs)
+
+    if targets:
+        plot_targets(da, ax, x="R", y="Z", hatching=add_limiter_hatching)

xbout/plotting/utils.py

@@ -78,8 +78,10 @@ def _is_core_only(da):
     return ix1 >= nx and ix2 >= nx
 
 
-def plot_separatrices(da, ax, *, x="R", y="Z"):
-    """Plot separatrices"""
+def plot_separatrices(da, ax, *, x="R", y="Z", **kwargs):
+    """
+    Plot separatrices. Kwargs are passed to ax.plot().
+    """
 
     if not isinstance(da, dict):
         da_regions = _decompose_regions(da)
@@ -116,7 +118,13 @@ def plot_separatrices(da, ax, *, x="R", y="Z"):
             y_sep = 0.5 * (
                 da_region[y].isel(**{xcoord: 0}) + da_inner[y].isel(**{xcoord: -1})
             )
-            ax.plot(x_sep, y_sep, "k--")
+            default_style = {"color": "black", "linestyle": "--"}
+            if any(x for x in kwargs if x in ["c", "ls"]):
+                raise ValueError(
+                    "When passing separatrix plot style kwargs, use 'color' and 'linestyle' instead lf 'c' and 'ls'"
+                )
+            style = {**default_style, **kwargs}
+            ax.plot(x_sep, y_sep, **style)
 
 
 def plot_targets(da, ax, *, x="R", y="Z", hatching=True):

xbout/tests/test_against_collect.py

@@ -220,5 +220,4 @@ def test_new_collect_indexing_slice(self, tmp_path_factory):
 
 
 @pytest.mark.skip
-class test_speed_against_old_collect:
-    ...
+class test_speed_against_old_collect: ...

xbout/tests/test_load.py

@@ -472,8 +472,7 @@ def test_combine_along_y(self, tmp_path_factory, bout_xyt_example_files):
         xrt.assert_identical(actual, fake)
 
     @pytest.mark.skip
-    def test_combine_along_t(self):
-        ...
+    def test_combine_along_t(self): ...
 
     @pytest.mark.parametrize(
         "bout_v5,metric_3D", [(False, False), (True, False), (True, True)]
@@ -623,8 +622,7 @@ def test_drop_vars(self, tmp_path_factory, bout_xyt_example_files):
         assert "n" in ds.keys()
 
     @pytest.mark.skip
-    def test_combine_along_tx(self):
-        ...
+    def test_combine_along_tx(self): ...
 
     def test_restarts(self):
         datapath = Path(__file__).parent.joinpath(

xbout/utils.py

@@ -167,12 +167,16 @@ def _1d_coord_from_spacing(spacing, dim, ds=None, *, origin_at=None):
             )
 
         point_to_use = {
-            spacing.metadata["bout_xdim"]: spacing.metadata.get("MXG", 0)
-            if spacing.metadata["keep_xboundaries"]
-            else 0,
-            spacing.metadata["bout_ydim"]: spacing.metadata.get("MYG", 0)
-            if spacing.metadata["keep_yboundaries"]
-            else 0,
+            spacing.metadata["bout_xdim"]: (
+                spacing.metadata.get("MXG", 0)
+                if spacing.metadata["keep_xboundaries"]
+                else 0
+            ),
+            spacing.metadata["bout_ydim"]: (
+                spacing.metadata.get("MYG", 0)
+                if spacing.metadata["keep_yboundaries"]
+                else 0
+            ),
             spacing.metadata["bout_zdim"]: spacing.metadata.get("MZG", 0),
         }