Exporting data to NetCDF files

  • Compatability: Notebook currently compatible with both the NCI and DEA Sandbox environments

  • Products used: ls8_nbart_geomedian_annual

Background

NetCDF is a file format for storing multidimensional scientific data. This file format supports datasets containing multiple observation dates, as well as multiple bands. It is a native format for storing the xarray datasets that are produced by Open Data Cube, i.e. by dc.load commands.

NetCDF files should follow Climate and Forecast (CF) metadata conventions for the description of Earth sciences data. By providing metadata such as geospatial coordinates and sensor information in the same file as the data, CF conventions allow NetCDF files to be “self-describing”. This makes CF-compliant NetCDFs a useful way to save multidimensional data loaded from Digital Earth Australia, as the data can later be loaded with all the information required for further analysis.

The xarray library which underlies the Open Data Cube (and hence Digital Earth Australia) was specifically designed for representing NetCDF files in Python. However, some geospatial metadata is represented quite differently between the NetCDF-CF conventions versus the GDAL (or proj4) model that is common to most geospatial software (including ODC, e.g. for reprojecting raster data when necessary). The main difference between to_netcdf (in xarray natively) and write_dataset_to_netcdf (provided by datacube) is that the latter is able to appropriately serialise the coordinate reference system object which is associated to the dataset.

Description

In this notebook we will load some data from Digital Earth Australia and then write it to a (CF-compliant) NetCDF file using the write_dataset_to_netcdf function provided by datacube. We will then verify the file was saved correctly, and (optionally) clean up.


Getting started

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

Load packages

[1]:
%matplotlib inline

import datacube
import xarray as xr
from datacube.drivers.netcdf import write_dataset_to_netcdf

Connect to the datacube

[2]:
dc = datacube.Datacube(app='Exporting_NetCDFs')

Load data from the datacube

Here we load a sample dataset from the DEA Landsat-8 Annual Geomedian product (ls8_nbart_geomedian_annual). The loaded data is multidimensional, and contains two time-steps (2015, 2016) and six satellite bands (blue, green, red, nir, swir1, swir2).

[3]:
lat, lon = -35.282052, 149.128667  # City Hill, Canberra
radius = 0.01  # Approx. 1km

# Load data from the datacube
ds = dc.load(product='ls8_nbart_geomedian_annual',
             lat=(lat - radius, lat + radius),
             lon=(lon - radius, lon + radius),
             time=('2015', '2016'))

# Print output data
print(ds)
<xarray.Dataset>
Dimensions:  (time: 2, x: 85, y: 98)
Coordinates:
  * time     (time) datetime64[ns] 2015-01-01 2016-01-01
  * y        (y) float64 -3.956e+06 -3.956e+06 ... -3.959e+06 -3.959e+06
  * x        (x) float64 1.549e+06 1.549e+06 1.549e+06 ... 1.551e+06 1.551e+06
Data variables:
    blue     (time, y, x) int16 569 849 852 854 709 632 ... 494 521 594 575 479
    green    (time, y, x) int16 707 1093 1105 1187 1004 ... 755 799 864 870 719
    red      (time, y, x) int16 782 1260 1255 1377 1235 ... 798 839 923 897 735
    nir      (time, y, x) int16 1951 1935 1941 1954 2294 ... 2626 2733 2894 2634
    swir1    (time, y, x) int16 1699 2335 2314 2353 2464 ... 2028 2026 2202 1876
    swir2    (time, y, x) int16 1291 1971 1989 2158 2049 ... 1279 1343 1396 1142
Attributes:
    crs:      EPSG:3577

Export to a NetCDF file

To export a CF-compliant NetCDF file, we use the write_dataset_to_netcdf function:

[4]:
write_dataset_to_netcdf(ds, 'output_netcdf.nc')

That’s all. The file has now been produced, and stored in the current working directory.

Reading back from saved NetCDF

Let’s start just by confirming the file now exists. We can use the special ! command to run command line tools directly within a Jupyter notebook. In the example below, ! ls *.nc runs the ls shell command, which will give us a list of any files in the NetCDF file format (i.e. with file names ending with .nc).

For an introduction to using shell commands in Jupyter, see the guide here.

[5]:
! ls *.nc
output_netcdf.nc

We could inspect this file using external utilities such as gdalinfo or ncdump, or open it for visualisation e.g. in QGIS.

We can also load the file back into Python using xarray:

[6]:
# Load the NetCDF from file
reloaded_ds = xr.open_dataset('output_netcdf.nc')

# Print loaded data
print(reloaded_ds)
<xarray.Dataset>
Dimensions:  (time: 2, x: 85, y: 98)
Coordinates:
  * time     (time) datetime64[ns] 2015-01-01 2016-01-01
  * y        (y) float64 -3.956e+06 -3.956e+06 ... -3.959e+06 -3.959e+06
  * x        (x) float64 1.549e+06 1.549e+06 1.549e+06 ... 1.551e+06 1.551e+06
Data variables:
    crs      int32 ...
    blue     (time, y, x) float32 ...
    green    (time, y, x) float32 ...
    red      (time, y, x) float32 ...
    nir      (time, y, x) float32 ...
    swir1    (time, y, x) float32 ...
    swir2    (time, y, x) float32 ...
Attributes:
    date_created:           2019-12-06T10:31:41.636127
    Conventions:            CF-1.6, ACDD-1.3
    history:                NetCDF-CF file created by datacube version '1.7+1...
    geospatial_bounds:      POLYGON ((149.115177462794 -35.2723871652199,149....
    geospatial_bounds_crs:  EPSG:4326
    geospatial_lat_min:     -35.29422745465402
    geospatial_lat_max:     -35.26983245892383
    geospatial_lat_units:   degrees_north
    geospatial_lon_min:     149.11517746279415
    geospatial_lon_max:     149.14198087534984
    geospatial_lon_units:   degrees_east

We can now use this reloaded dataset just like the original dataset, for example by plotting one of its colour bands:

[7]:
reloaded_ds.red.plot(col='time')
[7]:
<xarray.plot.facetgrid.FacetGrid at 0x7faf6dc19240>
../../_images/notebooks_Frequently_used_code_Exporting_NetCDFs_17_1.png

Clean-up

To remove the saved NetCDF file that we created, run the cell below. This is optional.

[10]:
! rm output_netcdf.nc

Additional information

License: The code in this notebook is licensed under the Apache License, Version 2.0. Digital Earth Australia 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.

Last modified: December 2019

Compatible datacube version:

[9]:
print(datacube.__version__)
1.7+142.g7f8581cf

Tags

Browse all available tags on the DEA User Guide’s Tags Index

Tags: sandbox compatible, NCI compatible, annual geomedian, NetCDF, write_dataset_to_netcdf, exporting data, metadata, shell commands