Simplifying swash tutorial code

Author: erikvansebille

docs/user_guide/examples/tutorial_swash.ipynb

@@ -5,7 +5,7 @@
    "id": "0",
    "metadata": {},
    "source": [
-    "# Tutorial for using SWASH data in Parcels"
+    "# 🖥️ SWASH tutorial"
    ]
   },
   {
@@ -15,13 +15,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import glob\n",
-    "\n",
     "import matplotlib.pyplot as plt\n",
-    "import matplotlib.tri as mtri\n",
     "import numpy as np\n",
-    "import uxarray as ux\n",
-    "import xarray as xr\n",
     "\n",
     "import parcels\n",
     "import parcels.tutorial"
@@ -34,8 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "grid_file = parcels.tutorial.open_dataset(\"SWASH_data/data\", download_only=True)\n",
-    "print(grid_file)"
+    "swash_files = parcels.tutorial.open_dataset(\"SWASH_data/data\", download_only=True)"
    ]
   },
   {
@@ -45,12 +39,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# grid_file = \"/Users/YanTo001/Documents/GitHub/parcels-data/data-matlab/F1GRD.mat\"#\"/Users/YanTo001/Library/Caches/parcels/data-matlab/F1GRD.mat\"\n",
-    "# result_file = \"/Users/YanTo001/Documents/GitHub/parcels-data/data-matlab/F1ALL.mat\"#\"/Users/YanTo001/Library/Caches/parcels/data-matlab/F1ALL.mat\"\n",
-    "# ds = parcels.convert.swash_to_sgrid(grid_file, result_file, total_depth=8.0)\n",
-    "ds = parcels.convert.swash_to_sgrid(grid_file[1], grid_file[0], total_depth=8.0)\n",
-    "\n",
-    "fieldset = parcels.FieldSet.from_sgrid_conventions(ds)"
+    "ds = parcels.convert.swash_to_sgrid(\n",
+    "    data_file=swash_files[0], coord_file=swash_files[1], total_depth=8.0\n",
+    ")\n",
+    "fieldset = parcels.FieldSet.from_sgrid_conventions(ds)\n",
+    "fieldset.describe()"
    ]
   },
   {
@@ -60,26 +53,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "npart = 150  # number of particles to be released\n",
-    "# release particles in a line along a meridian\n",
-    "lat = np.linspace(1, 16, npart)  ## y\n",
-    "lon = np.repeat(15, npart)  ## x\n",
-    "time = np.repeat(ds.time.values[0], npart)\n",
+    "npart = 10  # number of particles to be released\n",
+    "y = np.linspace(1, 16, npart)\n",
+    "x = np.repeat(15, npart)\n",
+    "\n",
     "layerI = 0  # at which water depth, the particles are released\n",
     "z = np.repeat(ds.depth.values[layerI], npart)\n",
-    "pset = parcels.ParticleSet(\n",
-    "    fieldset=fieldset, pclass=parcels.Particle, t=time, x=lon, y=lat, z=z\n",
-    ")\n",
-    "kernels = [parcels.kernels.AdvectionRK2]\n",
+    "pset = parcels.ParticleSet(fieldset, x=x, y=y, z=z)\n",
     "\n",
     "output_file = parcels.ParticleFile(\n",
-    "    \"output-quickstart.parquet\", outputdt=np.timedelta64(5, \"s\"), mode=\"w\"\n",
-    ")  #\n",
+    "    \"output-swash.parquet\", outputdt=np.timedelta64(5, \"s\"), mode=\"w\"\n",
+    ")\n",
     "pset.execute(\n",
-    "    kernels,\n",
+    "    parcels.kernels.AdvectionRK2,\n",
     "    runtime=np.timedelta64(20, \"s\"),\n",
-    "    dt=np.timedelta64(5, \"s\"),\n",
+    "    dt=np.timedelta64(1, \"s\"),\n",
     "    output_file=output_file,\n",
+    "    verbose_progress=False,\n",
     ")"
    ]
   },
@@ -90,12 +80,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df = parcels.read_particlefile(\"output-quickstart.parquet\")\n",
-    "waterlevel = ds.isel(time=2).watlev.plot(cmap=\"magma\")\n",
-    "scatter = plt.scatter(df[\"x\"], df[\"y\"], c=df[\"t\"], s=10)\n",
-    "plt.scatter(\n",
-    "    df[\"x\"][:npart], df[\"y\"][:npart], facecolors=\"none\", edgecolors=\"r\", s=10\n",
-    ")  # starting positions"
+    "df = parcels.read_particlefile(\"output-swash.parquet\")\n",
+    "\n",
+    "fig, ax = plt.subplots(figsize=(8, 4))\n",
+    "waterlevel = ds.isel(time=2).watlev.plot(cmap=\"magma\", ax=ax)\n",
+    "for traj in df.partition_by(\"particle_id\"):\n",
+    "    ax.plot(traj[\"x\"][0], traj[\"y\"][0], \"wo\", markersize=5)\n",
+    "    ax.plot(traj[\"x\"], traj[\"y\"], color=\"k\")\n",
+    "ax.set_xlim([14, 16])\n",
+    "plt.show()"
    ]
   },
   {
@@ -107,7 +100,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Parcels:default (3.14.6)",
+   "display_name": "Parcels:docs (3.14.6)",
    "language": "python",
    "name": "python3"
   },

docs/user_guide/index.md

@@ -40,6 +40,7 @@ examples/explanation_grids.md
 examples/tutorial_nemo.ipynb
 examples/tutorial_croco_3D.ipynb
 examples/tutorial_mitgcm.ipynb
+examples/tutorial_swash.ipynb
 examples/tutorial_fesom.ipynb
 examples/tutorial_schism.ipynb
 examples/tutorial_velocityconversion.ipynb