3. Extract data within a shapefile using ERDDAP

This tutorial will teach you how to extract and display SST values for a particular time period or average SST over the whole time-series available within a shapefile. The shapefile for the NOAA Marine National Monument and sanctuaries boundaries can be downloaded here: http://sanctuaries.noaa.gov/library/imast_gis.html.

We are going to extract SST data for the Papahanaumokuakea Marine National Monument (PMNM) in Hawaii. However, because the Monument boundaries cross the dateline, the shapefile provided on the website is tricky to work with. We'll work with a cleaned up version, available here: https://oceanwatch.pifsc.noaa.gov/files/PMNM_bounds.csv

This tutorial is also available as a Jupyter notebook.

Load packages

import pandas as pd import numpy as np import urllib.request import xarray as xr import netCDF4 as nc from matplotlib import pyplot as plt from matplotlib.colors import LinearSegmentedColormap from shapely.geometry import Point, Polygon import geopandas as gpd np.warnings.filterwarnings('ignore')

Load the Monument boundary

df=pd.read_csv('PMNM_bounds.csv')

Transform the boundary to a Polygon

geometry = [Point(xy) for xy in zip(df.lon, df.lat)] poly = Polygon([(p.x, p.y) for p in geometry])

poly

Data extraction

The example below extracts monthly 5km CoralTemp SST data within the monument boundary.

• We are going to download data from ERDDAP for the smallest bounding box that contains our polygon

xcoord1 = (np.min(df.lon), np.max(df.lon)) ycoord1 = (np.min(df.lat), np.max(df.lat))

• let's select a date range:

tcoord = ("2019-01-15", "2019-12-15")

• and let's build our ERDDAP URL:

url='https://oceanwatch.pifsc.noaa.gov/erddap/griddap/CRW_sst_v1_0_monthly.nc?analysed_sst[('+ tcoord[0] +'):1:('+ tcoord[1] +')][('+ str(ycoord1[0]) +'):1:('+ str(ycoord1[1]) +')][(' + str(xcoord1[0]) +'):1:('+ str(xcoord1[1]) +')]'

url

'https://oceanwatch.pifsc.noaa.gov/erddap/griddap/CRW_sst_v1_0_monthly.nc?analysed_sst[(2019-01-15):1:(2019-12-15)][(19.2345832):1:(31.79786423)][(177.84422):1:(198.9827)]'

• now we can download the data:

urllib.request.urlretrieve(url, "sst.nc")

• and load it as an xarray dataset:

ds = xr.open_dataset('sst.nc',decode_cf=False)

ds.analysed_sst.shape

(12, 252, 424)

We now have data for a box around our polygon, for 12 monthly time steps (= 1 year).

Masking the data outside the Monument boundary

The .within() function from the shapelypackage checks if a point is within a polygon. We are using it to create a mask which will take the value 1 within the polygon boundary, and NaN outside.

(This takes about 1min or less to run).

mask=np.empty((len(ds.latitude.values),len(ds.longitude.values))) mask[:]=np.NaN for i in range(len(ds.latitude.values)): for j in range(len(ds.longitude.values)): p=Point(ds.longitude.values[j],ds.latitude.values[i],) if int(p.within(poly))==1: mask[i,j]=int(p.within(poly))

plt.contourf(ds.longitude,ds.latitude,mask)

We now multiply the SST data we downloaded by the mask values:

SST=ds.analysed_sst*mask

Plotting the data

The extracted data contains several time steps (months) of sst data in the monument boundaries. Let's make a plot of the 4th time step for example.

• setting up the colormap

np.min(SST),np.max(SST)

array(16.863333), array(28.78)

levs = np.arange(16, 29, 0.05) jet=["blue", "#007FFF", "cyan","#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"] cm = LinearSegmentedColormap.from_list('my_jet', jet, N=len(levs))

• loading data to plot the coastline. The file can be downloaded here, and was provided by https://eric.clst.org/tech/usgeojson/. Download the file and save it to your computer.

country = gpd.read_file("gz_2010_us_outline_20m.json")

• plot:

country.plot(figsize=(12,8),color='black') plt.xlim(-183,-153) plt.ylim(18,32) cs=plt.contourf(ds.longitude-360,ds.latitude,SST[3,:,:],levs,cmap=cm) cbar=plt.colorbar(fraction=0.022) cbar.ax.tick_params(labelsize=12) cs.ax.tick_params(labelsize=12) plt.title('SST - April 2019', fontsize=20)