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.


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 Datasets in native format.

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 in the appropriate of these three folders.

For each additional dataset, an entry needs to be made to the file datasets.yml. The dataset entry should contain:

  • the correct tier information;

  • the source of the raw data;

  • the last_access date;

  • the info that explain how to download the data.

Note that these fields should be identical to the content of the header of the cmorizing script (see Section 4. Create a cmorizer for the dataset).

3.1 Downloader script (optional)#

A Python script can be written to download raw observations from source and store the data in the appropriate tier subdirectory of the folder RAWOBS automatically. There are many downloading scripts available in /esmvaltool/cmorizers/data/downloaders/datasets/ where several data download mechanisms are provided:

  • A wget get based downloader for http(s) downloads, with a specific derivation for NASA datasets.

  • A ftp downloader with a specific derivation for ESACCI datasets available from CEDA.

  • A Climate Data Store downloader based on cdsapi.

Note that the name of this downloading script has to be identical to the name of the dataset.

Depending on the source server, the downloading script needs to contain paths to raw observations, filename patterns and various necessary fields to retrieve the data. Default start_date and end_date can be provided in cases where raw data are stored in daily, monthly, and yearly files.

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

esmvaltool data download --config_file <config-user.yml>  <dataset-name>

The options --start and --end can be added to the command above to restrict the download of raw data to a time range. They will be ignored if a specific dataset does not support it (i.e. because it is provided as a single file). Valid formats are YYYY, YYYYMM and YYYYMMDD. By default, already downloaded data are not overwritten unless the option --overwrite=True is used.

4. Create a cmorizer for the dataset#

There are many cmorizing scripts available in /esmvaltool/cmorizers/data/formatters/datasets/ where solutions to many kinds of format issues with observational data are addressed. These scripts are either written in Python or in NCL.


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: 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/data/cmor_config/. Note that both the name of this configuration file and the cmorizing script have to be identical to the name of your dataset. 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 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, cfg_user, start_date, end_date):

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, cfg to the dataset-specific configuration file, cfg_user to the user configuration file, start_date to the start of the period to format, and end_date to the end of the period to format. If not needed, the last three arguments can be ignored using underscores. 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 esmvaltool.cmorizers.data 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: 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 are imported by default into your CMORizer. 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:

esmvaltool data format --config_file <config-user.yml> <dataset-name>

The options --start and --end can be added to the command above to restrict the formatting of raw data to a time range. They will be ignored if a specific dataset does not support it (i.e. because it is provided as a single file). Valid formats are YYYY, YYYYMM and YYYYMMDD.


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 dataset. In this folder the cmorized data set will be stored as a NetCDF file. The cmorized dataset will be automatically moved to the correct tier subfolder of your OBS or OBS6 directory if the option --install=True is used in the command above and no such directory was already created.

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

If a downloading script is available for the dataset, the downloading and the cmorizing scripts can be run in a single command with:

esmvaltool data prepare --config_file <config-user.yml> <dataset-name>

Note that options from the `esmvaltool data download and esmvaltool data format commands can be passed to the above command.

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:


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


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;

  • 200301-201812: Is the period the dataset spans with 200301 being the start year and month, and 201812 being the end year and month;


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.