Extend poloidal_plot option in animate_list() to support polygon plotting.

[mrhardman]

Mike Kryjak improved the poloidal plotting in #280, by introducing a function

xBOUT/xbout/plotting/plotfuncs.py

Lines 852 to 872 in 64408ea

	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",
	):

, so that unphysical artefacts of plotting do not appear. This feature has not been extended to support animate_list, used in examples in Hermes-3, e.g.,

ds.bout.animate_list(
    ["Nd"],
    poloidal_plot=True,
    show=True,
    save_as="hermes_animation",
)

This appears to affect nonorthogonal grids particularly badly. The figures below are generated from two simulations of neutral diffusion on orthogonal and nonorthogonal grids for the same physics case.

Orthogonal output:

Nonorthogonal output showing fictitious artefacts:

[mrhardman]

Further notes:

It looks like the function that requires upgrading is

xBOUT/xbout/plotting/animate.py

Line 93 in 64408ea

def animate_poloidal(

, with changes to lines

xBOUT/xbout/plotting/animate.py

Lines 263 to 271 in 64408ea

	amp.blocks.Pcolormesh(
	da_region.coords[x].values,
	da_region.coords[y].values,
	da_region.values,
	ax=ax,
	cmap=cmap,
	norm=norm,
	**kwargs,
	)

needed to replace Pcolormesh.

Unfortunately it looks like animatplot does not support a plot option like plot2d_polygon, i.e., it is not clear if we can supply a list of frames make by a homemade plotting function to the animator. https://animatplot.readthedocs.io/en/stable/api.html.