Global Root-zone moisture Analysis & Forecasting System (GRAFS)

Both datasets are external to the Digital Earth Africa platform.

Keywords: data used; ERA5, datasets; ERA5, data used; GRAFS, datasets; GRAFS, soil moisture, precipitation

Background

Soil moisture is a measure of water stored in the soil zone that is accessible to plant roots, making it a major contributing factor to plant health and crop yield.

The Global Root-zone moisture Analysis & Forecasting System (GRAFS) is produced by the ANU Centre for Water and Landscape Dynamics. The model estimates the surface (0-5 cm) and root-zone (0-1 m) soil moisture at 10 km spatial resolution globally, using the precipitation measured by the Global Precipitation Measurement (GPM) mission and through assimilation of the soil moisture product from the Soil Moisture Active/Passive (SMAP) mission.

This product is regularly updated and made available through National Computational Infrastructure’s open access THREDDS data server.

For more information on this product, contact Luigi Renzullo and Siyuan Tian.

Description

This notebook demonstrates the following steps: 1. Retrieval of surface and root-zone wetness through NCI’s THREDDS OPeNDAP service 2. Compare soil moisture to precipitation data from ERA5


Getting started

To run this analysis, run all the cells in the notebook, starting with the “Load packages” cell.

Load packages

Import Python packages that are used for the analysis.

[1]:
%matplotlib inline
from matplotlib import pyplot as plt
import xarray as xr
import numpy as np
import datacube

from deafrica_tools.load_era5 import load_era5

Analysis parameters

Define location and time period of interest. The time period is chosen to be less than a year to limit ERA5 data download.

[2]:
# Define the analysis region (Lat-Lon box)

# Il Ngwesi region of Kenya - Rhino Project
lat = (0.412, 0.266)
lon = (37.32, 37.40)

# High Energy Stereoscopic System site near Windhoek Namibia
#lat = (-23.28, -23.26)
#lon = (16.49, 16.51)

# Define the time window
time = '2018-07-01', '2019-05-31'

Retrieval of surface and root-zone wetness

Surface wetness is measured relative to wettest condition recorded for a location.

Rootzone Soil Water Index is derived from surface relative wetness

[3]:
# function to load soil moisture data

def load_soil_moisture(lat, lon, time, product = 'surface', grid = 'nearest'):
    product_baseurl = 'http://dapds00.nci.org.au/thredds/dodsC/ub8/global/GRAFS/'
    assert product in ['surface', 'rootzone'], 'product parameter must be surface or root-zone'
    # lat, lon grid
    if grid == 'nearest':
        # select lat/lon range from data; snap to nearest grid
        lat_range, lon_range = None, None
    else:
        # define a grid that covers the entire area of interest
        lat_range = np.arange(np.max(np.ceil(np.array(lat)*10.+0.5)/10.-0.05), np.min(np.floor(np.array(lat)*10.-0.5)/10.+0.05)-0.05, -0.1)
        lon_range = np.arange(np.min(np.floor(np.array(lon)*10.-0.5)/10.+0.05), np.max(np.ceil(np.array(lon)*10.+0.5)/10.-0.05)+0.05, 0.1)
    # split time window into years
    day_range = np.array(time).astype("M8[D]")
    year_range = np.array(time).astype("M8[Y]")
    if product == 'surface':
        product_name = 'GRAFS_TopSoilRelativeWetness_'
    else: product_name = 'GRAFS_RootzoneSoilWaterIndex_'
    datasets = []
    for year in np.arange(year_range[0], year_range[1]+1, np.timedelta64(1, 'Y')):
        start = np.max([day_range[0], year.astype("M8[D]")])
        end = np.min([day_range[1], (year+1).astype("M8[D]")-1])
        product_url = product_baseurl + product_name +'%s.nc'%str(year)
        print(product_url)
        # data is loaded lazily through OPeNDAP
        ds = xr.open_dataset(product_url)
        if lat_range is None:
            # select lat/lon range from data if not specified; snap to nearest grid
            test = ds.sel(lat=lat, lon=lon, method='nearest')
            lat_range = slice(test.lat.values[0], test.lat.values[1])
            lon_range = slice(test.lon.values[0], test.lon.values[1])
        # slice before return
        ds = ds.sel(lat=lat_range, lon=lon_range, time=slice(start, end)).compute()
        datasets.append(ds)
    return xr.merge(datasets)
[4]:
# Retrieve surface soil moisture using query parameters
surface_wetness = load_soil_moisture(lat, lon, time, grid='nearest')
http://dapds00.nci.org.au/thredds/dodsC/ub8/global/GRAFS/GRAFS_TopSoilRelativeWetness_2018.nc
http://dapds00.nci.org.au/thredds/dodsC/ub8/global/GRAFS/GRAFS_TopSoilRelativeWetness_2019.nc
[5]:
# retrieve rootzone soil moisture using query parameters
rootzone_wetness = load_soil_moisture(lat, lon, time, product='rootzone', grid='nearest')
http://dapds00.nci.org.au/thredds/dodsC/ub8/global/GRAFS/GRAFS_RootzoneSoilWaterIndex_2018.nc
http://dapds00.nci.org.au/thredds/dodsC/ub8/global/GRAFS/GRAFS_RootzoneSoilWaterIndex_2019.nc

Plot surface and root-zone wetness over time

[6]:
surface_wetness.relative_wetness.mean(['lat','lon']).plot(figsize=(16,8), label='surface');
rootzone_wetness.soil_water_index.mean(['lat','lon']).plot(label='root-zone');
plt.legend()
[6]:
<matplotlib.legend.Legend at 0x7f769fcf2e48>
../../../_images/sandbox_notebooks_Datasets_Soil_Moisture_14_1.png

Compare soil moisture to precipitation data from ERA5

The first cell will load the precipitation parameter, precipitation_amount_1hour_Accumulation, from ERA5. Depending on the size of your query, this step can take a few minutes to complete. Data will be stored in the folder era5.

[7]:
# load precipitation data from ERA5
var_precipitation = 'precipitation_amount_1hour_Accumulation'
precipitation = load_era5(var_precipitation, lat, lon, time, reduce_func=np.sum)

# Convert from Meters (m) to Millimeters (mm)
precipitation[var_precipitation]=precipitation[var_precipitation]*1000

Plot soil moisture with precipitation

[8]:
# plot soil moisture with precipitation

fig, ax1 = plt.subplots(figsize=(16,8))
ax2 = ax1.twinx()
surface_wetness.relative_wetness.mean(['lat','lon']).plot(ax = ax1, label = 'surface wetness', color = 'blue');
rootzone_wetness.soil_water_index.mean(['lat','lon']).plot(ax = ax1, label = 'root-zone wetness', color = 'black');
precipitation[var_precipitation].mean(['lat','lon']).plot(ax = ax2, label = 'precipitation (mm)', color = 'orange');
ax1.legend()
ax2.legend()
[8]:
<matplotlib.legend.Legend at 0x7f7696788f28>
../../../_images/sandbox_notebooks_Datasets_Soil_Moisture_18_1.png

Additional information

License: The code in this notebook is licensed under the Apache License, Version 2.0. Digital Earth Africa data is licensed under the Creative Commons by Attribution 4.0 license.

Contact: If you need assistance, please post a question on the Open Data Cube Slack channel or on the GIS Stack Exchange using the open-data-cube tag (you can view previously asked questions here). If you would like to report an issue with this notebook, you can file one on Github.

Compatible datacube version:

[9]:
print(datacube.__version__)
1.8.4.dev52+g07bc51a5

Last Tested:

[10]:
from datetime import datetime
datetime.today().strftime('%Y-%m-%d')
[10]:
'2021-05-20'