netcdf_to_cvm

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netcdf_to_cvm#

Overview#

The netcdf_to_cvm tool is a utility tool for converting an existing netCDF CVM file to the corresponding CVM-compliant netCDF file. This tool will add any missing CVM attributes based on the provided metadata files.

In this tutorial, we will demonstrate how to run netcdf_to_cvm on a CVM netCDF file Cascadia-ANT+RF-test-missing.nc that is missing some CVM metadata attributes.

Steps#

  1. Navigate to the model directory

    Change your directory to the location of the model file:

    cd sample-files/Cascadia-ANT+RF-Delph2018

  2. Update the parameter files

    To create a netCDF file with some missing attributes, edit the global file and comment out the data_layout attribute in Cascadia-ANT+RF_global_meta.txt file:

    # data_layout = vertex

    also edit the variables parameter file Cascadia-ANT+RF_meta.txt and comment out the data_source attribute:

    #  data_source = data-derived

  3. Create a netCDF file with missing attributes

    We create Cascadia-ANT+RF-test-missing.nc the same way we created Cascadia-ANT+RF-test in our cvm_writer tutorial. The only difference is that each parameter file has a missing attribute and we want to output the file to Cascadia-ANT+RF-test-missing.nc

    
python ../../src/cvm_writer.py -m Cascadia-ANT+RF_meta.txt -g Cascadia-ANT+RF_global_meta.txt -o Cascadia-ANT+RF-test-missing -d Cascadia-ANT+RF_data.txt -t netcdf

    Check and verify that Cascadia-ANT+RF-test-missing.nc is created.

  4. Run the netcdf_to_cvm tool

    Before we run the netcdf_to_cvm tool to detect and correct the missing parameters, we need to update the Cascadia-ANT+RF_global_meta.txt and Cascadia-ANT+RF_meta.txt and uncomment the parameters we commented in step 2 above:

    
data_source = data-derived
data_layout = vertex

    Now, use the netcdf_to_cvm tool to update the Cascadia-ANT+RF-test-missing.nc file and add the missing parameters to it and save the updated model as Cascadia-ANT+RF-test-updated:

    
../../src/netcdf_to_cvm.py -d Cascadia-ANT+RF-test-missing.nc -g Cascadia-ANT+RF_global_meta.txt -m Cascadia-ANT+RF_meta.txt -o Cascadia-ANT+RF-test-updated

    Command breakdown

    • -d Cascadia-ANT+RF-test-missing.nc: Specifies the name of the input file to check.

    • -g Cascadia-ANT+RF_global_meta.txt: Specifies the global metadata file.

    • -m Cascadia-ANT+RF_meta.txt: Specifies the variables metadata file.

    • -o Cascadia-ANT+RF-test-updated.nc: Specifies the name of the output file (do not include a file extension).

    The netcdf_to_cvm output, as shown below, informs us of what it needed to update/add in the file:

    
[INFO] Cascadia-ANT+RF-test-missing.nc is a netCDF file
[INFO] nc_format: '{'format': 'NETCDF4_CLASSIC', 'encoding': {'zlib': True, 'complevel': 9}}'
[INFO] Added the missing global attribute data_layout: 'vertex'
[INFO] Added the missing vs attribute data_source: 'data-derived'
[Elapsed time: 3.14s] Model netCDF file: Cascadia-ANT+RF-test-updated.nc

  5. Verification

    Use the netCDF_summary_info utility tool to verify that the listed updates have taken place.

    
../../src/netcdf_summary_info.py
Enter the path to the netCDF file:

    For example:

    From Cascadia-ANT+RF-test-missing.nc summary output:

    
Global Attributes:

- title: 3D vertical shear-wave velocity model of the Cascadian forearc from the joint inversion of ambient noise dispersion and receiver functions
- institution: Rice University
- source: Cascadia-ANT+RF-Delph2018
- history: Created on 2023-05-01
- references: Delph, J.R., Levander, A., Niu, F. (2018)
- conventions: CF-1.6

Dimensions:

- depth: 84
- latitude: 46
- longitude: 25

Variables:

- depth (dimensions: ('depth',), shape: (84,))
  - units: km
  - long_name: Depth below sea level
    Range: -3.00 to 80.00
- latitude (dimensions: ('latitude',), shape: (46,))
  - units: degrees_north
  - long_name: Latitude
    Range: 40.00 to 49.00
- longitude (dimensions: ('longitude',), shape: (25,))
  - units: degrees_east
  - long_name: Longitude
    Range: -124.80 to -120.00
- vs (dimensions: ('depth', 'latitude', 'longitude'), shape: (84, 46, 25))
  - units: km/s
  - long_name: Shear-wave velocity
    Range: 2.50 to 4.50

    From Cascadia-ANT+RF-test-updated.nc summary output:

    
Global Attributes:

- title: 3D vertical shear-wave velocity model of the Cascadian forearc from the joint inversion of ambient noise dispersion and receiver functions
- institution: Rice University
- source: Cascadia-ANT+RF-Delph2018
- history: Created on 2023-05-01
- references: Delph, J.R., Levander, A., Niu, F. (2018)
- conventions: CF-1.6
- data_layout: vertex

Dimensions:

- depth: 84
- latitude: 46
- longitude: 25

Variables:

- depth (dimensions: ('depth',), shape: (84,))
  - units: km
  - long_name: Depth below sea level
    Range: -3.00 to 80.00
- latitude (dimensions: ('latitude',), shape: (46,))
  - units: degrees_north
  - long_name: Latitude
    Range: 40.00 to 49.00
- longitude (dimensions: ('longitude',), shape: (25,))
  - units: degrees_east
  - long_name: Longitude
    Range: -124.80 to -120.00
- vs (dimensions: ('depth', 'latitude', 'longitude'), shape: (84, 46, 25))
  - units: km/s
  - long_name: Shear-wave velocity
  - data_source: data-derived
    Range: 2.50 to 4.50
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