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mnfienen merged 4 commits into from
Aug 5, 2026
+36,301 −39,475
Merged

Updates for FloPy notebooks 04 and 05 #200

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62ee45c
Update pandas notebook solution
jlarsen-usgs Aug 4, 2026
cd4518b
update notebook 04_Modelgrid_and_intersection.ipynb for new "waterdat…
jlarsen-usgs Aug 4, 2026
1de0f10
Updates for notebook 05. Update nwis to waterdata support.
jlarsen-usgs Aug 4, 2026
6987ddf
revert environment.yml changes
jlarsen-usgs Aug 4, 2026
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239 changes: 35 additions & 204 deletions notebooks/part0_python_intro/08_pandas.ipynb
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1,068 changes: 624 additions & 444 deletions notebooks/part0_python_intro/solutions/08_pandas.ipynb
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78 changes: 32 additions & 46 deletions notebooks/part1_flopy/04_Modelgrid_and_intersection.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"source": [
"# Modelgrid and intersection\n",
"\n",
"The first part of this notebook is focused on the `flopy.discretization.Grid` (modelgrid) object(s). The modelgrid object(s) are a relatively new addition to FloPy's capabilities and are the backbone of plotting, exporting, and GIS data processing within FloPy. These objects are automatically created when a model is loaded. Alternatively they can also be created as a stand alone object. \n",
"The first part of this notebook is focused on the `flopy.discretization.Grid` (modelgrid) object(s). The modelgrid object(s) are core to FloPy's capabilities and are the backbone of plotting, exporting, and GIS data processing within FloPy. These objects are automatically created when a model is loaded. Alternatively they can also be created as a stand alone object. \n",
"\n",
"There are three types of modelgrids:\n",
"\n",
Expand Down Expand Up @@ -426,26 +426,6 @@
"shape"
]
},
{
"cell_type": "markdown",
"id": "49458e73",
"metadata": {},
"source": [
"## Class Exercise 2: \n",
"\n",
"Find and plot all of the nearest neighbors at node 79 on the vertex modelgrid.\n",
"\n",
"**Hint**: Use `flopy.plot.PlotMapView` for your plotting, and plot a boolean (1, 0) array with the cells that are not neighbors masked out.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fad34d11",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"id": "0426f4ab",
Expand Down Expand Up @@ -479,24 +459,6 @@
"ugrid.plot();"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5575ecf9",
"metadata": {},
"outputs": [],
"source": [
"neighbors = ugrid.neighbors(79)\n",
"arr = np.zeros(ugrid.shape, dtype=int)\n",
"arr[neighbors] = 1\n",
"\n",
"fig, ax = plt.subplots(figsize=(8, 8))\n",
"\n",
"pmv = flopy.plot.PlotMapView(ax=ax, modelgrid=ugrid)\n",
"pmv.plot_grid()\n",
"pmv.plot_array(arr, masked_values=[0,]);"
]
},
{
"cell_type": "markdown",
"id": "32fb78b6",
Expand Down Expand Up @@ -677,7 +639,7 @@
"source": [
"gx = GridIntersect(modelgrid)\n",
"\n",
"result = gx.intersect(basin.loc[station_id, \"geometry\"])\n",
"result = gx.intersect(basin.loc[station_id, \"geometry\"], geo_dataframe=False)\n",
"result.cellids"
]
},
Expand Down Expand Up @@ -979,7 +941,7 @@
"outputs": [],
"source": [
"arr = np.genfromtxt(data_path / \"pet.txt\")\n",
"arr.shape = (12, modelgrid.nrow, modelgrid.ncol)\n",
"arr = arr.reshape(12, modelgrid.nrow, modelgrid.ncol)\n",
"pet_monthly = {i: a for i, a in enumerate(arr)}\n",
"pet_monthly"
]
Expand Down Expand Up @@ -1269,10 +1231,14 @@
"metadata": {},
"outputs": [],
"source": [
"import dataretrieval.nwis as nwis\n",
"from dataretrieval import waterdata\n",
"try:\n",
" gage = nwis.get_record(sites=station_id, service='iv', start=\"2024-01-01\", end=\"2024-12-31\", parameterCd=\"00065\")\n",
" gage.reset_index(inplace=True)\n",
" import dataretrieval.nwis as nwis\n",
" gage, metadata = waterdata.get_continuous(\n",
" f\"USGS-{station_id}\",\n",
" parameter_code=\"00065\",\n",
" time=\"2024-01-01/2024-12-31\"\n",
" )\n",
" gage.to_csv(data_path / \"sagehen_gage_data.csv\")\n",
"except (ValueError, ConnectionError, NameError):\n",
" gage = pd.read_csv(data_path / \"sagehen_gage_data.csv\")\n",
Expand All @@ -1287,10 +1253,10 @@
"metadata": {},
"outputs": [],
"source": [
"gage[\"datetime\"] = pd.to_datetime(gage[\"datetime\"])\n",
"gage[\"datetime\"] = pd.to_datetime(gage[\"time\"])\n",
"gage = gage.set_index(\"datetime\")\n",
"\n",
"gage.rename(columns={\"00065\": \"stage\"}, inplace=True)\n",
"gage.rename(columns={\"value\": \"stage\"}, inplace=True)\n",
"gage.stage *= 0.3284\n",
"ax = gage.stage.plot()\n",
"ax.set_ylabel(\"stage, in feet\")\n",
Expand Down Expand Up @@ -1488,13 +1454,33 @@
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "3f9dadaa-53e6-45c2-a3ff-130b1305c8f5",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.14.6"
}
},
"nbformat": 4,
Expand Down
72 changes: 42 additions & 30 deletions notebooks/part1_flopy/05_Unstructured_Grid_generation.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
"import numpy as np\n",
"import pandas as pd\n",
"import contextily as ctx\n",
"from dataretrieval import nldi, nwis\n",
"from dataretrieval import nldi, waterdata\n",
"from flopy.discretization import StructuredGrid, VertexGrid\n",
"from flopy.plot import PlotMapView\n",
"from flopy.utils.gridgen import Gridgen\n",
Expand Down Expand Up @@ -120,8 +120,7 @@
"metadata": {},
"outputs": [],
"source": [
"# live code modelgrid creation\n",
"cellsize = 200\n"
"# live code modelgrid creation\n"
]
},
{
Expand Down Expand Up @@ -257,14 +256,16 @@
"griddf = sgrid.geo_dataframe.set_crs(epsg=26911)\n",
"grid_wgs = griddf.to_crs(epsg=4326)\n",
"\n",
"wxmin, wxmax, wymin, wymax = grid_wgs.total_bounds\n",
"wxmin, wymin, wxmax, wymax = grid_wgs.total_bounds\n",
"wgs_bounds = [wxmin, wymin, wxmax, wymax]\n",
"\n",
"try:\n",
" info, metadata = nwis.get_info(bBox=[f\"{i :.2f}\" for i in wgs_bounds])\n",
" info, metadata = waterdata.get_monitoring_locations(bbox=wgs_bounds)\n",
" # info.to_file(geospatial_ws / \"gage_info.geojson\", driver=\"GeoJSON\")\n",
"except (ValueError, ConnectionError, NameError):\n",
" info = gpd.read_file(geospatial_ws / \"gage_info.shp\")\n",
"\n",
" info = gpd.read_file(geospatial_ws / \"gage_info.geojson\")\n",
" \n",
"info = info.set_crs(grid_wgs.crs)\n",
"info.head()"
]
},
Expand Down Expand Up @@ -305,7 +306,7 @@
"\n",
"rstr.plot(ax=ax)\n",
"info.plot(\n",
" column=\"site_no\",\n",
" column=\"monitoring_location_number\",\n",
" ax=ax,\n",
" cmap=\"tab20\",\n",
" legend=True,\n",
Expand All @@ -328,7 +329,7 @@
"metadata": {},
"outputs": [],
"source": [
"sitedf = info.loc[info.site_no == \"10343500\"]\n",
"sitedf = info.loc[info.monitoring_location_number == \"10343500\"]\n",
"sitedf"
]
},
Expand All @@ -350,7 +351,7 @@
"try:\n",
" basindf = nldi.get_basin(\n",
" feature_source=\"nwissite\",\n",
" feature_id=f\"USGS-{sitedf.site_no.values[0]}\",\n",
" feature_id=sitedf.monitoring_location_id.values[0],\n",
" )\n",
" basindf = basindf.to_crs(epsg=epsg)\n",
"except (ValueError, ConnectionError, NameError):\n",
Expand All @@ -376,7 +377,7 @@
"rstr.plot(ax=ax)\n",
"basindf.plot(ax=ax, facecolor=\"None\", edgecolor=\"k\", lw=1.5)\n",
"info.plot(\n",
" column=\"site_no\",\n",
" column=\"monitoring_location_number\",\n",
" ax=ax,\n",
" cmap=\"tab20\",\n",
" legend=True,\n",
Expand Down Expand Up @@ -488,7 +489,7 @@
"\n",
"basindf.plot(ax=ax, facecolor=\"None\", edgecolor=\"r\", lw=1.5)\n",
"sitedf.plot(\n",
" column=\"site_no\",\n",
" column=\"monitoring_location_number\",\n",
" ax=ax,\n",
" cmap=\"tab20\",\n",
" legend=True,\n",
Expand Down Expand Up @@ -525,7 +526,7 @@
" navigation_mode=\"UT\",\n",
" distance=999,\n",
" feature_source=\"nwissite\",\n",
" feature_id=f\"USGS-{sitedf.site_no.values[0]}\",\n",
" feature_id=sitedf.monitoring_location_id.values[0],\n",
" )\n",
" nhddf = nhddf.to_crs(epsg=epsg)\n",
"except (ValueError, ConnectionError, NameError):\n",
Expand Down Expand Up @@ -732,7 +733,7 @@
"\n",
"basindf.plot(ax=ax, facecolor=\"None\", edgecolor=\"r\", lw=1.5)\n",
"sitedf.plot(\n",
" column=\"site_no\",\n",
" column=\"monitoring_location_number\",\n",
" ax=ax,\n",
" cmap=\"tab20\",\n",
" legend=True,\n",
Expand Down Expand Up @@ -1677,11 +1678,11 @@
"source": [
"## Activity (If time permits); Build a Voronoi mesh/Vertex Grid:\n",
"\n",
"Define a voronoi grid for the basin upstream of the Black Earth Creek streamgauge near Cross Plains, WI. The upstream basin information is supplied by NLDI and has been saved to the class repo in case of internet connectivity or NLDI service issues.\n",
"Define a voronoi grid for the basin upstream of the Little Sandy River streamgauge near Bull Run, OR. The upstream basin information is supplied by NLDI and has been saved to the class repo in case of internet connectivity or NLDI service issues.\n",
"\n",
"Some of the previous code can be re-used to create a voronoi mesh and subsequent `VertexGrid` representation of the basin. See the Triangular and Voronoi grid sections of the notebook.\n",
"\n",
"**Optional**, use the Upstream Main segment of Black Earth Creek to refine the voronoi mesh around the stream location. Refinement control points have been pre-defined below."
"**Optional**, use the Upstream Main segment of the Little Sandy River to refine the voronoi mesh around the stream location. Refinement control points have been pre-defined below."
]
},
{
Expand All @@ -1692,16 +1693,15 @@
"outputs": [],
"source": [
"epsg = 5070 # NAD83 CONUS Albers\n",
"# try:\n",
" # todo: update this for black earth creek near cross plains WI site-no 05406479\n",
"be_cr_nr_cp = \"05406479\"\n",
"basindf = nldi.get_basin(\n",
" feature_source=\"nwissite\", feature_id=f\"USGS-{be_cr_nr_cp}\"\n",
")\n",
"basindf = basindf.to_crs(epsg=epsg)\n",
"basindf.to_file(geospatial_ws / \"black_earth_basin.shp\")\n",
"# except (ValueError, ConnectionError, NameError):\n",
"# basindf = gpd.read_file(geospatial_ws / \"black_earth_basin.shp\")"
"try:\n",
" lsr_gauge_id = \"USGS-14141500\"\n",
" basindf = nldi.get_basin(\n",
" feature_source=\"nwissite\", feature_id=lsr_gauge_id\n",
" )\n",
" basindf = basindf.to_crs(epsg=epsg)\n",
" basindf.to_file(geospatial_ws / \"little_sandy_basin.shp\")\n",
"except (ValueError, ConnectionError, NameError):\n",
" basindf = gpd.read_file(geospatial_ws / \"little_sandy_basin.shp\")"
]
},
{
Expand All @@ -1716,12 +1716,12 @@
" navigation_mode=\"UM\",\n",
" distance=9999,\n",
" feature_source=\"nwissite\",\n",
" feature_id=f\"USGS-{be_cr_nr_cp}\",\n",
" feature_id=lsr_gauge_id,\n",
" )\n",
" nhddf = nhddf.to_crs(epsg=epsg)\n",
" nhddf.to_file(geospatial_ws / \"black_earth_creek_main.shp\")\n",
" nhddf.to_file(geospatial_ws / \"little_sandy_river_main.shp\")\n",
"except (ValueError, ConnectionError, NameError):\n",
" nhddf = gpd.read_file(geospatial_ws / \"black_earth_creek_main.shp\")"
" nhddf = gpd.read_file(geospatial_ws / \"little_sandy_river_main.shp\")"
]
},
{
Expand Down Expand Up @@ -1766,7 +1766,7 @@
"outputs": [],
"source": [
"wsloc = basindf.centroid.values[0]\n",
"stloc = list(zip(*nhddf.geometry.values[10].xy))[0]"
"stloc = list(zip(*nhddf.geometry.values[5].xy))[0]"
]
},
{
Expand Down Expand Up @@ -1799,6 +1799,18 @@
"display_name": "Python 3 (ipykernel)",
"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": "3.14.6"
}
},
"nbformat": 4,
Expand Down
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