Automatic Standardized File Naming

Class Overview

Warning

A refactor of the OutputSaver class is currently in progress. The class will be moved in the aqua.diagnostics.core package.

The OutputSaver class is designed to manage output file naming conventions for scientific data. It supports generating filenames for various types of file (e.g., NetCDF, PDF, PNG) with metadata integration to enhance data management and traceability. The class ensures consistent and descriptive filenames, facilitating better data management and reproducibility.

Attributes

diagnostic (str): Name of the diagnostic.
model (str): Model used in the diagnostic.
exp (str): Experiment identifier.
diagnostic_product (str, optional): Product of the diagnostic analysis.
catalog (str, optional): Catalog where to search for the triplet. By default, the catalog is the catalog name at the top of the list in .aqua/config-aqua.yaml. For more information on how to set the default catalog, read the section aqua set <catalog>.
loglevel (str, optional): Log level for the class’s logger. Default is ‘WARNING’.
default_path (str, optional): Default path where files will be saved. Default is ‘.’.
rebuild (bool, optional): Flag indicating whether to rebuild existing files. If set to True, existing files with the same name will be overwritten. Default is True.

Note

The OutputSaver class automatically includes the current date and time when saving files as metadata date_saved. This ensures each file has a timestamp indicating when it was generated.

Default Catalog Setup

The OutputSaver class includes a catalog attribute to specify the catalog used for generating filenames. By default, the catalog is the catalog name at the top of the list in .aqua/config-aqua.yaml. For more information on how to set the default catalog, read the section aqua set <catalog>.

This setup ensures that if multiple model, exp are found in multiple catalogs, the first one found in the selected default catalog will be used.

If a different catalog is needed, it can be specified during the initialization of the OutputSaver class. For example, to use a different catalog, you can pass it as an argument during initialization.

Example Usage

Initializing the OutputSaver Class

The following example demonstrates how to initialize the OutputSaver class:

from aqua.util import OutputSaver

# Initializing with the system-defined default catalog
names = OutputSaver(diagnostic='tropical_rainfall', model='MSWEP', exp='past',
                    loglevel='DEBUG', default_path='.')

# Initializing with a specified catalog 'lumi-phase2'
names_with_catalog = OutputSaver(diagnostic='tropical_rainfall', model='MSWEP', exp='past',
                                 catalog='lumi-phase2', loglevel='DEBUG', default_path='.')

Generating a Filename for a NetCDF File

This example shows how to generate a filename for a NetCDF file with the ‘mean’ diagnostic product for the previously initialized class. This and the following methods return the generated filename as a string, to be used with the incorporated methods or with other functions.

netcdf_filename = names.generate_name(diagnostic_product='mean', suffix='nc')
# Output: 'tropical_rainfall.mean.MSWEP.past.<default_catalog>.nc'

netcdf_filename_with_catalog = names_with_catalog.generate_name(diagnostic_product='mean', suffix='nc')
# Output: 'tropical_rainfall.mean.MSWEP.past.lumi-phase2.nc'

Generating a Filename with Flexible Date Inputs

This example demonstrates generating a filename with flexible date inputs and the ‘ym’ time precision, including a second dataset with a different catalog:

filename = names.generate_name(var='mtpr', model_2='ERA5', exp_2='era5',
                               time_start='1990-01-01', time_end='1990-02-28',
                               time_precision='ym', area='indian_ocean', catalog_2='lumi-phase3')
# Output: 'tropical_rainfall.<diagnostic_product>.mtpr.MSWEP.past.<default_catalog>.ERA5.era5.lumi-phase3.indian_ocean.199001-199002.nc'

Saving a NetCDF File with Metadata

Here is an example of saving a NetCDF file with metadata. The metadata includes the title, author, and description of the file.

import xarray as xr

# Example dataset
dataset = xr.Dataset()

# Define metadata for the NetCDF file
metadata = {
    'title': 'Testing the saving of NetCDF files',
    'author': 'OutputSaver',
    'description': 'Demonstrating netCDF Metadata Addition'
}

# Save the NetCDF to the specified path with the metadata
saved_file_path = names.save_netcdf(dataset, path='.', diagnostic_product='histogram',
                                    metadata=metadata)

Note

If the history metadata field is provided, the OutputSaver class will append the current message to the existing history.

Saving a PDF Plot with Metadata

This example demonstrates saving a PDF plot with metadata. The metadata includes the title, author, subject, and keywords of the PDF.

import matplotlib.pyplot as plt

# Create a sample figure
fig, ax = plt.subplots()
ax.plot([0, 1], [0, 1])

# Define metadata for the PDF file
metadata = {
    '/Title': 'Sample PDF',
    '/Author': 'OutputSaver',
    '/Subject': 'Demonstrating PDF Metadata Addition',
    '/Keywords': 'PDF, OutputSaver, Metadata'
}

# Save the PDF with metadata
pdf_path = names.save_pdf(fig, diagnostic_product='histogram', metadata=metadata, dpi=300)

Note

We suggest at the moment to use the metadata /Caption field to store the plot description. This is used at the moment by the AQUA dashboard to generate the plot description.

Opening a PDF File and Displaying Metadata

To open a PDF file and display its metadata:

from aqua.util import open_image

open_image("/path/to/my/file/tropical_rainfall.histogram.IFS-NEMO.historical-1990.pdf")