diff --git a/example/plot_Efield.py b/example/plot_Efield.py index bc6563d..21444b6 100644 --- a/example/plot_Efield.py +++ b/example/plot_Efield.py @@ -19,7 +19,7 @@ def plotVmaxx1it(ax: mpl.axes.Axes, V: xarray.DataArray) -> None: ax.set_ylabel("Potential [V]") ax.set_xlabel("mag. latitude [deg.]") elif V.ndim == 2: - hi = ax.pcolormesh(dat["mlon"], dat["mlat"], V, cmap="bwr") + hi = ax.pcolormesh(dat["mlon"], dat["mlat"], V, cmap="bwr", shading="nearest") ax.set_xlabel("mag. longitude [deg.]") ax.set_ylabel("mag. latitude [deg.]") ax.figure.colorbar(hi, ax=ax).set_label("potential [V]") diff --git a/example/plotdata.py b/example/plotdata.py index 548bd9c..92489dc 100644 --- a/example/plotdata.py +++ b/example/plotdata.py @@ -14,7 +14,7 @@ def plotplasma(dat: xarray.Dataset): continue ax = figure().gca() - ax.pcolormesh(v.squeeze()) + ax.pcolormesh(v.squeeze(), shading="nearest") ax.set_title(f"{k} {t}") diff --git a/scripts/plot_neutral.py b/scripts/plot_neutral.py index cfe4626..80240de 100644 --- a/scripts/plot_neutral.py +++ b/scripts/plot_neutral.py @@ -22,6 +22,6 @@ ax = fg.gca() ax.set_title(k) - ax.pcolormesh(f[k][:].T) + ax.pcolormesh(f[k][:].transpose(), shading="nearest") plt.show() diff --git a/src/gemini3d/compare/plot.py b/src/gemini3d/compare/plot.py index 62b99b2..eb44ca9 100644 --- a/src/gemini3d/compare/plot.py +++ b/src/gemini3d/compare/plot.py @@ -132,16 +132,16 @@ def diff2d(A, B, name: str, fg, axs): bmin = min(A.min(), B.min()) bmax = max(A.max(), B.max()) - hi = axs[0].pcolormesh(A, cmap=cmap, vmin=bmin, vmax=bmax) + hi = axs[0].pcolormesh(A, cmap=cmap, vmin=bmin, vmax=bmax, shading="nearest") fg.colorbar(hi, ax=axs[0]) - hi = axs[1].pcolormesh(B, cmap=cmap, vmin=bmin, vmax=bmax) + hi = axs[1].pcolormesh(B, cmap=cmap, vmin=bmin, vmax=bmax, shading="nearest") fg.colorbar(hi, ax=axs[1]) dAB = A - B b = max(abs(dAB.min()), abs(dAB.max())) - hi = axs[2].pcolormesh(A - B, cmap="bwr", vmin=-b, vmax=b) + hi = axs[2].pcolormesh(A - B, cmap="bwr", vmin=-b, vmax=b, shading="nearest") fg.colorbar(hi, ax=axs[2]) return abs(dAB).max().data diff --git a/src/gemini3d/efield/__init__.py b/src/gemini3d/efield/__init__.py index 66671b3..513d16b 100644 --- a/src/gemini3d/efield/__init__.py +++ b/src/gemini3d/efield/__init__.py @@ -196,7 +196,7 @@ def Efield_BCs(cfg: dict[str, T.Any], xg: dict[str, T.Any]) -> xarray.Dataset: # LEAVE THE SPATIAL AND TEMPORAL INTERPOLATION TO THE # FORTRAN CODE IN CASE DIFFERENT GRIDS NEED TO BE TRIED. # THE EFIELD DATA DO NOT TYPICALLY NEED TO BE SMOOTHED. - print("Size used for Efield input: ",llon,llat); + print("Size used for Efield input: ", llon, llat) write.Efield(E, cfg["E0dir"]) return E diff --git a/src/gemini3d/grid/tilted_dipole.py b/src/gemini3d/grid/tilted_dipole.py index c3d15a6..9b4b84b 100644 --- a/src/gemini3d/grid/tilted_dipole.py +++ b/src/gemini3d/grid/tilted_dipole.py @@ -500,7 +500,7 @@ def tilted_dipole3d_NUx2(cfg: dict[str, T.Any]) -> dict[str, T.Any]: ########################################################################### print(" Uniform grid lat lims: ", xg["glat"].min(), xg["glat"].max()) - + print(" Generating non-uniform grid...") # Determine a target differential spacing based on user extents and number of # grid points. @@ -540,8 +540,7 @@ def tilted_dipole3d_NUx2(cfg: dict[str, T.Any]) -> dict[str, T.Any]: """ xg = generate_tilted_dipole3d(q, pnew, phi) - - print(" Shifting end L-shell by: ", pnew[-3]-p[-3], pnew[-3], p[-3]) + print(" Shifting end L-shell by: ", pnew[-3] - p[-3], pnew[-3], p[-3]) print(" Non-uniform grid lat lims: ", xg["glat"].min(), xg["glat"].max()) - + return xg diff --git a/src/gemini3d/magtools.py b/src/gemini3d/magtools.py index deed732..c73a82d 100644 --- a/src/gemini3d/magtools.py +++ b/src/gemini3d/magtools.py @@ -95,7 +95,7 @@ def makegrid_full( write_grid: bool = False, ) -> dict[str, T.Any]: """ - Make a field point to cover the entire mlat/mlon range for a given simulation grid + Make a field point to cover the entire mlat/mlon range for a given simulation grid """ direc = Path(direc).expanduser() @@ -119,10 +119,10 @@ def makegrid_full( # TABULATE THE SOURCE OR GRID CENTER LOCATION if "sourcemlon" not in cfg.keys(): - thdist = xg["theta"].mean() + # thdist = xg["theta"].mean() phidist = xg["phi"].mean() else: - thdist = np.pi / 2 - np.radians(cfg["sourcemlat"]) + # thdist = np.pi / 2 - np.radians(cfg["sourcemlat"]) # zenith angle of source location phidist = np.radians(cfg["sourcemlon"]) @@ -134,14 +134,14 @@ def makegrid_full( # Computer a buffer region around the grid thmin = xg["theta"].min() thmax = xg["theta"].max() - dtheta=thmax-thmin - thmin=thmin-dtheta/5 - thmax=thmax+dtheta/5 + dtheta = thmax - thmin + thmin = thmin - dtheta / 5 + thmax = thmax + dtheta / 5 phimin = xg["phi"].min() phimax = xg["phi"].max() - dphi=phimax-phimin - phimin=phimin-dphi/5 - phimax=phimax+dtheta/5 + dphi = phimax - phimin + phimin = phimin - dphi / 5 + phimax = phimax + dtheta / 5 theta = np.linspace(thmin, thmax, ltheta) phi = phidist if flag2D else np.linspace(phimin, phimax, lphi) @@ -169,7 +169,6 @@ def makegrid_full( return mag - def magframe( filename: str | Path, *, @@ -260,8 +259,8 @@ def magframe( with h5py.File(filename, "r") as f: for k in {"Br", "Btheta", "Bphi"}: if flatlist: - dat[k] = f[f"/magfields/{k}"][:] + dat[k] = f[f"/magfields/{k}"][:] else: dat[k] = f[f"/magfields/{k}"][:].reshape((lr, ltheta, lphi)) - + return dat diff --git a/src/gemini3d/model.py b/src/gemini3d/model.py index bca1db5..cb440bf 100644 --- a/src/gemini3d/model.py +++ b/src/gemini3d/model.py @@ -164,7 +164,7 @@ def equilibrium(cfg: dict[str, T.Any]): # %% Equilibrium input generation dat = equilibrium_state(cfg, xg) - + write.state(cfg["indat_file"], dat) diff --git a/src/gemini3d/particles/__init__.py b/src/gemini3d/particles/__init__.py index 7b1d7d5..316229d 100644 --- a/src/gemini3d/particles/__init__.py +++ b/src/gemini3d/particles/__init__.py @@ -50,10 +50,10 @@ def particles_BCs(cfg: dict[str, T.Any], xg: dict[str, T.Any]): else: Qfunc = str2func("gemini3d.particles.gaussian2d") - Qtmp=Qfunc(pg, cfg["Qprecip"], cfg["Qprecip_background"]) + Qtmp = Qfunc(pg, cfg["Qprecip"], cfg["Qprecip_background"]) for i in range(i_on, i_off): - pg["Q"][i, :, :] = Qtmp[i,:,:] + pg["Q"][i, :, :] = Qtmp[i, :, :] pg["E0"][i, :, :] = cfg["E0precip"] assert np.isfinite(pg["Q"]).all(), "Q flux must be finite" diff --git a/src/gemini3d/patch/plot.py b/src/gemini3d/patch/plot.py index db7402b..24ea267 100644 --- a/src/gemini3d/patch/plot.py +++ b/src/gemini3d/patch/plot.py @@ -92,6 +92,7 @@ def patch(indir: Path, var: set[str]) -> None: dat[k][ix1, :, :].transpose(), vmin=clim[k][0], vmax=clim[k][1], + shading="nearest", ) ax.text( x2[x2.size // 2], diff --git a/src/gemini3d/plot/cartesian.py b/src/gemini3d/plot/cartesian.py index 15da603..e65d2a4 100644 --- a/src/gemini3d/plot/cartesian.py +++ b/src/gemini3d/plot/cartesian.py @@ -171,7 +171,7 @@ def plot_interp( # hack for pcolormesh to put labels in center of pixel wl = kwargs["wavelength"] + [""] hi = ax.pcolormesh( - np.arange(len(wl)), yp / 1e3, f(yp)[:, i].T, shading="nearest" + np.arange(len(wl)), yp / 1e3, f(yp)[:, i].transpose(), shading="nearest" ) ax.set_xticks(np.arange(len(wl)) + 0.5) ax.set_xticklabels(wl)