netcdf_to_h5

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netcdf_to_h5#

Overview#

The netcdf_to_h5 tool is a utility tool for converting an existing CVM-compliant netCDF file to CVM-compliant HDF5 format.

In this tutorial, we will demonstrate how to run netcdf_to_h5 on the CVM netCDF file Cascadia-ANT+RF-Delph2018.r0.1.nc to convert it to HDF5 format.

Steps#

  1. Navigate to the model directory

    Change your directory to the location of the model file:

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

    and make sure the input netCDF file, Cascadia-ANT+RF-Delph2018.r0.1.nc, exists.

  2. Run the netcdf_to_h5 tool

    Use the netcdf_to_h5 tool to convert the Cascadia-ANT+RF-Delph2018.r0.1.nc file HDF5 format and save it as Cascadia-ANT+RF-test.h5:

    ../../src/netcdf_to_h5.py -i Cascadia-ANT+RF-Delph2018.r0.1.nc -g MODEL -s VELOCITY -o Cascadia-ANT+RF-test

    Note: The HDF5 files have “.h5” extension. The converter script will add it if it is missing from your -o file name.

    Command breakdown

    • -i Cascadia-ANT+RF-Delph2018.r0.1.nc: Specifies the name of the netcdf input file.

    • -g MODEL: informs the tool that the name of the main HDF5 group for this data is MODEL.

    • -s VELOCITY: is an optional argument and informs the tool that the name of the subgroup under the main group is MODEL. As a result, the netCDF dataset in the HDF5 will be stored under /MODEL/VELOCITY.

    • -o Cascadia-ANT+RF-test: Specifies the name of the output file (the file extension of .h5 is optional).

    The netcdf_to_h5 output, as shown below, informs us of how the conversion is going.

    [INFO] Cascadia-ANT+RF-Delph2018.r0.1.nc is a netCDF file
[WARN] Variable 'depth' already exists in the subgroup 'VELOCITY'. Skipping.
[WARN] Variable 'latitude' already exists in the subgroup 'VELOCITY'. Skipping.
[WARN] Variable 'longitude' already exists in the subgroup 'VELOCITY'. Skipping.
[INFO] Conversion from Cascadia-ANT+RF-Delph2018.r0.1.nc to Cascadia-ANT+RF-test.h5 under '/MODEL/VELOCITY' completed successfully.

    We can run the show_file_structure toll and the the data structure of the output file:

../../src/show_file_structure.py Enter the path to the input file (HDF5 or netCDF): Cascadia-ANT+RF-test.h5

File Name: Cascadia-ANT+RF-test.h5
File Size: 421678 bytes
File Type: HDF5

HDF5 File Structure:
├── MODEL
│ ├── VELOCITY
│ │ ├── depth
│ │ ├── easting
│ │ ├── latitude
│ │ ├── longitude
│ │ ├── northing
│ │ ├── vs
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