Writing a CMORizer script for an additional dataset

ESMValTool is designed to work with CF compliant data and follows the CMOR tables from the CMIP data request, therefore the observational datasets need to be CMORized for usage in ESMValTool. The following steps are necessary to prepare an observational data set for the use in ESMValTool.

Note

CMORization as a fix. As of early 2020, we’ve started implementing cmorization as fixes. As compared to the workflow described below, this has the advantage that the user does not need to store a duplicate (CMORized) copy of the data. Instead, the CMORization is performed ‘on the fly’ when running a recipe. ERA5 is the first dataset for which this ‘CMORization on the fly’ is supported. For more information, see: CMORization as a fix.

1. Check if your variable is CMOR standard

Most variables are defined in the CMIP data request and can be found in the CMOR tables in the folder /esmvalcore/cmor/tables/cmip6/Tables/, differentiated according to the MIP they belong to. The tables are a copy of the PCMDI guidelines. If you find the variable in one of these tables, you can proceed to the next section.

If your variable is not available in the standard CMOR tables, you need to write a custom CMOR table entry for the variable as outlined below and add it to /esmvalcore/cmor/tables/custom/.

To create a new custom CMOR table you need to follow these guidelines:

  • Provide the variable_entry;

  • Provide the modeling_realm;

  • Provide the variable attributes, but leave standard_name blank. Necessary variable attributes are: units, cell_methods, cell_measures, long_name, comment.

  • Provide some additional variable attributes. Necessary additional variable attributes are: dimensions, out_name, type. There are also additional variable attributes that can be defined here (see the already available cmorizers).

It is recommended to use an existing custom table as a template, to edit the content and save it as CMOR_<short_name>.dat.

2. Edit your configuration file

Make sure that beside the paths to the model simulations and observations, also the path to raw observational data to be cmorized (RAWOBS) is present in your configuration file.

3. Store your dataset in the right place

The folder RAWOBS needs the subdirectories Tier1, Tier2 and Tier3. The different tiers describe the different levels of restrictions for downloading (e.g. providing contact information, licence agreements) and using the observations. The unformatted (raw) observations should then be stored then in the appropriate of these three folders.

4. Create a cmorizer for the dataset

There are many cmorizing scripts available in /esmvaltool/cmorizers/obs/ where solutions to many kinds of format issues with observational data are addressed. Most of these scripts are written in NCL at the moment, but more and more examples for Python-based cmorizing scripts become available.

Note

NCL support will terminate soon, so new cmorizer scripts should preferably be written in Python.

How much cmorizing an observational data set needs is strongly dependent on the original NetCDF file and how close the original formatting already is to the strict CMOR standard.

In the following two subsections two cmorizing scripts, one written in Python and one written in NCL, are explained in more detail.

4.1 Cmorizer script written in python

Find here an example of a cmorizing script, written for the MTE dataset that is available at the MPI for Biogeochemistry in Jena: cmorize_obs_mte.py.

All the necessary information about the dataset to write the filename correctly, and which variable is of interest, is stored in a separate configuration file: MTE.yml in the directory ESMValTool/esmvaltool/cmorizers/obs/cmor_config/. Note that the name of this configuration file has to be identical to the name of your data set. It is recommended that you set project to OBS6 in the configuration file. That way, the variables defined in the CMIP6 CMOR table, augmented with the custom variables described above, are available to your script.

The first part of this configuration file defines the filename of the raw observations file. The second part defines the common global attributes for the cmorizer output, e.g. information that is needed to piece together the final observations file name in the correct structure (see Section 6. Naming convention of the observational data files). Another global attribute is reference which includes a doi related to the dataset. Please see the section adding references on how to add reference tags to the reference section in the configuration file. If a single dataset has more than one reference, it is possible to add tags as a list e.g. reference: ['tag1', 'tag2']. The third part in the configuration file defines the variables that are supposed to be cmorized.

The actual cmorizing script cmorize_obs_mte.py consists of a header with information on where and how to download the data, and noting the last access of the data webpage.

The main body of the CMORizer script must contain a function called

def cmorization(in_dir, out_dir, cfg, config_user):

with this exact call signature. Here, in_dir corresponds to the input directory of the raw files, out_dir to the output directory of final reformatted data set and cfg to the configuration dictionary given by the .yml configuration file. The return value of this function is ignored. All the work, i.e. loading of the raw files, processing them and saving the final output, has to be performed inside its body. To simplify this process, ESMValTool provides a set of predefined utilities.py, which can be imported into your CMORizer by

from . import utilities as utils

Apart from a function to easily save data, this module contains different kinds of small fixes to the data attributes, coordinates, and metadata which are necessary for the data field to be CMOR-compliant.

Note that this specific CMORizer script contains several subroutines in order to make the code clearer and more readable (we strongly recommend to follow that code style). For example, the function _get_filepath converts the raw filepath to the correct one and the function _extract_variable extracts and saves a single variable from the raw data.

4.2 Cmorizer script written in NCL

Find here an example of a cmorizing script, written for the ESACCI XCH4 dataset that is available on the Copernicus Climate Data Store: cmorize_obs_cds_xch4.ncl.

The first part of the script collects all the information about the dataset that are necessary to write the filename correctly and to understand which variable is of interest here. Please make sure to provide the correct information for following key words: DIAG_SCRIPT, VAR, NAME, MIP, FREQ, CMOR_TABLE.

  • Note: the fields VAR, NAME, MIP and FREQ all ask for one or more entries. If more than one entry is provided, make sure that the order of the entries is the same for all four fields! (for example, that the first entry in all four fields describe the variable xch4 that you would like to extract);

  • Note: some functions in the script are NCL-specific and are available through the loading of the script interface.ncl. There are similar functions available for python scripts.

In the second part of the script each variable defined in VAR is separately extracted from the original data file and processed. Most parts of the code are commented, and therefore it should be easy to follow. ESMValTool provides a set of predefined utilities.ncl, which can be imported into your CMORizer by

loadscript(getenv("esmvaltool_root") + "/esmvaltool/cmorizers/obs/utilities.ncl")

This module contains different kinds of small fixes to the data attributes, coordinates, and metadata which are necessary for the data field to be CMOR-compliant.

5. Run the cmorizing script

The cmorizing script for the given dataset can be run with:

cmorize_obs -c <config-user.yml> -o <dataset-name>

Note

The output path given in the configuration file is the path where your cmorized dataset will be stored. The ESMValTool will create a folder with the correct tier information (see Section 2. Edit your configuration file) if that tier folder is not already available, and then a folder named after the data set. In this folder the cmorized data set will be stored as a netCDF file.

If your run was successful, one or more NetCDF files are produced in your output directory.

6. Naming convention of the observational data files

For the ESMValTool to be able to read the observations from the NetCDF file, the file name needs a very specific structure and order of information parts (very similar to the naming convention for observations in ESMValTool v1.0). The file name will be automatically correctly created if a cmorizing script has been used to create the netCDF file.

The correct structure of an observational data set is defined in config-developer.yml, and looks like the following:

OBS_[dataset]_[type]_[version]_[mip]_[short_name]_YYYYMM-YYYYMM.nc

For the example of the CDS-XCH4 data set, the correct structure of the file name looks then like this:

OBS_CDS-XCH4_sat_L3_Amon_xch4_200301-201612.nc

The different parts of the name are explained in more detail here:

  • OBS: describes what kind of data can be expected in the file, in this case observations;

  • CDS-XCH4: that is the name of the dataset. It has been named this way for illustration purposes (so that everybody understands it is the xch4 dataset downloaded from the CDS), but a better name would indeed be ESACCI-XCH4 since it is a ESA-CCI dataset;

  • sat: describes the source of the data, here we are looking at satellite data (therefore sat), could also be reanaly for reanalyses;

  • L3: describes the version of the dataset:

  • Amon: is the information in which mip the variable is to be expected, and what kind of temporal resolution it has; here we expect xch4 to be part of the atmosphere (A) and we have the dataset in a monthly resolution (mon);

  • xch4: Is the name of the variable. Each observational data file is supposed to only include one variable per file;

  • 200301-201612: Is the period the dataset spans with 200301 being the start year and month, and 201612 being the end year and month;

Note

There is a different naming convention for obs4mips data (see the exact specifications for the obs4mips data file naming convention in the config-developer.yml file).

7. Test the cmorized dataset

To verify that the cmorized data file is indeed correctly formatted, you can run a dedicated test recipe, that does not include any diagnostic, but only reads in the data file and has it processed in the preprocessor. Such a recipe is called recipes/examples/recipe_check_obs.yml. You just need to add a diagnostic for your dataset following the existing entries. Only the diagnostic of interest needs to be run, the others should be commented out for testing.