Merge pull request #244 from ArtesiaWater/plotting-in-notebooks

improve plotting in notebooks #224
gwmod · Aug 25, 2023 · 8ecca8a · 8ecca8a
2 parents 021fc6a + 4fa08c8
commit 8ecca8a
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Showing 26 changed files with 229 additions and 158 deletions.
diff --git a/docs/examples/00_model_from_scratch.ipynb b/docs/examples/00_model_from_scratch.ipynb
@@ -270,20 +270,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, ax = plt.subplots(1, 1, figsize=(10, 8))\n",
-    "\n",
-    "pc = nlmod.plot.data_array(\n",
+    "# using nlmod plotting methods\n",
+    "ax = nlmod.plot.map_array(\n",
     "    head.sel(layer=0).isel(time=0),\n",
-    "    ds=ds,\n",
+    "    ds,\n",
     "    cmap=\"RdYlBu\",\n",
-    "    ax=ax,\n",
-    ")\n",
-    "nlmod.plot.modelgrid(ds, ax=ax, alpha=0.5, lw=0.5)\n",
-    "ax.axis(extent)\n",
-    "cbar = ax.figure.colorbar(pc, shrink=1.0)\n",
-    "cbar.set_label(\"head [m NAP]\")\n",
-    "ax.set_title(\"head first layer\")\n",
-    "fig.tight_layout()"
+    "    colorbar_label=\"head [m NAP]\",\n",
+    "    xlabel=\"x [km]\",\n",
+    "    ylabel=\"y [km]\",\n",
+    "    title=\"head first layer\",\n",
+    "    plot_grid=True,\n",
+    ")"
    ]
   },
   {
@@ -300,13 +297,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# using xarray plotting methods\n",
     "fg = head.plot(\n",
     "    x=\"x\",\n",
     "    y=\"y\",\n",
     "    col=\"layer\",\n",
     "    col_wrap=3,\n",
     "    cmap=\"RdYlBu\",\n",
     "    subplot_kws={\"aspect\": \"equal\"},\n",
+    "    cbar_kwargs={\"label\": \"head [m NAP]\"},\n",
     ")\n",
     "\n",
     "for iax in fg.axs.flat:\n",
@@ -322,8 +321,14 @@
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "artesia",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/01_basic_model.ipynb b/docs/examples/01_basic_model.ipynb
@@ -262,30 +262,36 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(14, 11))\n",
+    "fig, axes = nlmod.plot.get_map(ds.extent, nrows=2, ncols=2, figsize=14)\n",
     "ds[\"ahn\"].plot(ax=axes[0][0])\n",
     "ds[\"botm\"][0].plot(ax=axes[0][1])\n",
     "ds[\"idomain\"][0].plot(ax=axes[1][0])\n",
     "ds[\"edge_mask\"][0].plot(ax=axes[1][1])\n",
-    "for axes1 in axes:\n",
-    "    for ax in axes1:\n",
-    "        ax.axis(\"scaled\")\n",
     "\n",
-    "fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(14, 11))\n",
+    "fig, axes = nlmod.plot.get_map(ds.extent, nrows=2, ncols=2, figsize=14)\n",
     "ds[\"bathymetry\"].plot(ax=axes[0][0])\n",
     "ds[\"northsea\"].plot(ax=axes[0][1])\n",
     "ds[\"kh\"][1].plot(ax=axes[1][0])\n",
-    "ds[\"recharge\"].plot(ax=axes[1][1])\n",
-    "\n",
-    "for axes1 in axes:\n",
-    "    for ax in axes1:\n",
-    "        ax.axis(\"scaled\")\n"
+    "ds[\"recharge\"].plot(ax=axes[1][1]);"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "artesia",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/02_surface_water.ipynb b/docs/examples/02_surface_water.ipynb
@@ -293,14 +293,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, ax = plt.subplots(1, 1, figsize=(10, 8))\n",
-    "ax.set_aspect(\"equal\", adjustable=\"box\")\n",
-    "sfw.plot(ax=ax, column=\"stage\", legend=True)\n",
-    "ax.grid(True)\n",
-    "ax.set_xlabel(\"X (m RD)\")\n",
-    "ax.set_ylabel(\"Y (m RD)\")\n",
-    "plt.yticks(rotation=90, va=\"center\")\n",
-    "fig.tight_layout()"
+    "fig, ax = nlmod.plot.get_map(extent)\n",
+    "sfw.plot(ax=ax, column=\"stage\", legend=True)"
    ]
   },
   {
@@ -446,14 +440,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, ax = plt.subplots(1, 1, figsize=(10, 8))\n",
-    "ax.set_aspect(\"equal\", adjustable=\"box\")\n",
+    "fig, ax = nlmod.plot.get_map(extent)\n",
     "sfw_grid.plot(ax=ax, column=\"cellid\")\n",
-    "gwf.modelgrid.plot(ax=ax, linewidth=0.5, color=\"k\")\n",
-    "xmin, xmax, ymin, ymax = extent\n",
-    "offset = 100\n",
-    "ax.set_xlim(xmin - offset, xmax + offset)\n",
-    "ax.set_ylim(ymin - offset, ymax + offset)\n"
+    "nlmod.plot.modelgrid(ds, ax=ax, lw=0.2)"
    ]
   },
   {
@@ -494,7 +483,10 @@
    "source": [
     "fig, ax = plt.subplots(1, 1, figsize=(10, 8))\n",
     "sfw_grid.loc[mask].plot(\n",
-    "    column=\"identificatie\", legend=True, ax=ax, legend_kwds={\"loc\": \"upper left\"}\n",
+    "    column=\"identificatie\",\n",
+    "    legend=True,\n",
+    "    ax=ax,\n",
+    "    legend_kwds={\"loc\": \"lower left\", \"ncol\": 2, \"fontsize\": \"x-small\"},\n",
     ")\n",
     "xlim = ax.get_xlim()\n",
     "ylim = ax.get_ylim()\n",
@@ -691,6 +683,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# use flopy plotting methods\n",
     "fig, ax = plt.subplots(1, 1, figsize=(10, 8), constrained_layout=True)\n",
     "mv = flopy.plot.PlotMapView(model=gwf, ax=ax, layer=0)\n",
     "mv.plot_bc(\"RIV\")"
@@ -751,13 +744,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ilay = 0\n",
-    "fig, ax = plt.subplots(1, 1, figsize=(10, 8), constrained_layout=True)\n",
-    "mv = flopy.plot.PlotMapView(model=gwf, ax=ax, layer=ilay)\n",
-    "qm = mv.plot_array(head[-1], cmap=\"RdBu\")  # last timestep\n",
-    "mv.plot_ibound()  # plot inactive cells in red\n",
-    "fig.colorbar(qm, shrink=1.0)\n",
-    "ax.set_title(f\"Heads top-view, layer {ilay}\")\n"
+    "# using nlmod plotting methods\n",
+    "ax = nlmod.plot.map_array(\n",
+    "    head,\n",
+    "    ds,\n",
+    "    ilay=0,\n",
+    "    iper=0,\n",
+    "    plot_grid=True,\n",
+    "    title=\"Heads top-view\",\n",
+    "    cmap=\"RdBu\",\n",
+    "    colorbar_label=\"head [m NAP]\",\n",
+    ")"
    ]
   },
   {
@@ -775,21 +772,40 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, ax = plt.subplots(1, 1, figsize=(10, 3), constrained_layout=True)\n",
-    "xs = flopy.plot.PlotCrossSection(\n",
-    "    model=gwf, ax=ax, line={\"column\": gwf.modelgrid.ncol // 2}\n",
-    ")\n",
+    "# using flopy plotting methods\n",
+    "col = gwf.modelgrid.ncol // 2\n",
+    "\n",
+    "fig, ax = plt.subplots(1, 1, figsize=(10, 3))\n",
+    "xs = flopy.plot.PlotCrossSection(model=gwf, ax=ax, line={\"column\": col})\n",
     "qm = xs.plot_array(head[-1], cmap=\"RdBu\")  # last timestep\n",
     "xs.plot_ibound()  # plot inactive cells in red\n",
-    "fig.colorbar(qm, shrink=1.0)\n",
-    "col = gwf.modelgrid.ncol // 2\n",
-    "ax.set_title(f\"Cross-section along column {col}\")\n"
+    "xs.plot_grid(lw=0.25, color=\"k\")\n",
+    "ax.set_ylim(bottom=-150)\n",
+    "ax.set_ylabel(\"elevation [m NAP]\")\n",
+    "ax.set_xlabel(\"distance along cross-section [m]\")\n",
+    "ax.set_title(f\"Cross-section along column {col}\")\n",
+    "cbar = fig.colorbar(qm, shrink=1.0)\n",
+    "cbar.set_label(\"head [m NAP]\")"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6e5833d6",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "artesia",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/03_local_grid_refinement.ipynb b/docs/examples/03_local_grid_refinement.ipynb
@@ -315,7 +315,7 @@
     "nlmod.plot.data_array(ds[\"bathymetry\"], ds, ax=axes[0][0])\n",
     "nlmod.plot.data_array(ds[\"northsea\"], ds, ax=axes[0][1])\n",
     "nlmod.plot.data_array(ds[\"kh\"][1], ds, ax=axes[1][0])\n",
-    "nlmod.plot.data_array(ds[\"recharge\"][0], ds, ax=axes[1][1])"
+    "nlmod.plot.data_array(ds[\"recharge\"][0], ds, ax=axes[1][1]);"
    ]
   },
   {

diff --git a/docs/examples/06_gridding_vector_data.ipynb b/docs/examples/06_gridding_vector_data.ipynb
@@ -183,12 +183,11 @@
     "sim = nlmod.sim.sim(ds)\n",
     "gwf = nlmod.gwf.gwf(ds, sim)\n",
     "dis = nlmod.gwf.dis(ds, gwf)\n",
-    "da1 = nlmod.grid.gdf_to_da(\n",
-    "    point_gdf, ds, column=\"values\", agg_method=\"nearest\"\n",
-    ")\n",
+    "da1 = nlmod.grid.gdf_to_da(point_gdf, ds, column=\"values\", agg_method=\"nearest\")\n",
     "da2 = xr.DataArray(np.nan, dims=(\"y\", \"x\"), coords={\"y\": ds.y, \"x\": ds.x})\n",
-    "da2.values = nlmod.grid.interpolate_gdf_to_array(point_gdf, gwf, field='values', \n",
-    "method='linear')\n",
+    "da2.values = nlmod.grid.interpolate_gdf_to_array(\n",
+    "    point_gdf, gwf, field=\"values\", method=\"linear\"\n",
+    ")\n",
     "\n",
     "vmin = min(da1.min(), da2.min())\n",
     "vmax = max(da1.max(), da2.max())\n",
@@ -575,22 +574,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "nlmod",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.4"
+   "name": "python"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/07_resampling.ipynb b/docs/examples/07_resampling.ipynb
@@ -224,7 +224,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Rectangular Bivariate Spline (not yet included in nlmod)"
+    "### Rectangular Bivariate Spline\n",
+    "\n",
+    "*Note: not yet included as a method in nlmod*"
    ]
   },
   {
@@ -251,7 +253,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Rectangular Bivariate Spline with nans (not yet included in nlmod)"
+    "### Rectangular Bivariate Spline with nans\n",
+    "\n",
+    "*Note: not yet included as a method in nlmod*"
    ]
   },
   {

diff --git a/docs/examples/08_gis.ipynb b/docs/examples/08_gis.ipynb
@@ -217,7 +217,7 @@
    "source": [
     "## Export griddata\n",
     "\n",
-    "The model data can be exported to a netcdf file that can be visualised in Qgis. For a structured model the standard model dataset (xarray.Dataset) can be exported to a netdf file. For a vertex model you have to convert the model dataset to a certain format before you can write it to a netcdf and read it with Qgis. With the code below we export the vertex model dataset to a netcdf file ('model_qgis.nc') that can be read using Qgis. For more background, see this discussion https://github.com/ArtesiaWater/nlmod/issues/14. "
+    "The model data can be exported to a netcdf file that can be visualised in Qgis. For a structured model the standard model dataset (xarray.Dataset) can be exported to a netdf file. For a vertex model you have to convert the model dataset to a certain format before you can write it to a netcdf and read it with Qgis. With the code below we export the vertex model dataset to a netcdf file ('model_qgis.nc') that can be read using Qgis."
    ]
   },
   {