AQUA
  • Introduction
    • Overview of AQUA
    • Purpose
    • Key Features
    • Contributing
  • Installation
    • Prerequisites
    • Installation with Miniforge
    • Update of the environment
    • HPC Installation
      • Installation on LUMI HPC
      • Installation on Levante HPC at DKRZ
      • Installation on MareNostrum 5 (MN5) HPC at BSC
      • Installation on ECMWF HPC2020
    • Installation and use of the AQUA container
  • Getting Started
    • Basic Concepts
    • Python installation
    • Catalog installation
      • Set up the configuration folder
      • Add a catalog
    • Set up Jupyter kernel
  • Example use case
  • The Reader class
    • The Reader
    • Input and Output formats
    • Catalog exploration
    • Reader basic usage
    • Dask and streaming capabilities
  • The AQUA console
    • What is the AQUA console?
    • aqua install
    • aqua avail
    • aqua add <catalog>
    • aqua remove <catalog>
    • aqua set <catalog>
    • aqua uninstall
    • aqua list
    • aqua update
    • aqua fixes {add,remove} <fixes-file>
    • aqua grids {add,remove} <grid-file>
    • aqua grids set <path>
    • aqua grids build
    • aqua drop -c <config_file> <drop-options>
    • aqua analysis <analysis-options>
  • Regrid and interpolation capabilities
    • Basic usage within the Reader()
    • Basic usage of the Regridder()
    • Concept
    • Available target grids
    • Oceanic grid files naming scheme
      • Elements Description
      • Examples
    • Vertical interpolation
  • Fixer functionalities
    • Concept
    • Convention file structure
    • Fixer file structure
    • AQUA variables convention
    • Metadata Correction
      • Merge of convention and fixer
      • Variables block structure
    • Data Model and Coordinates/Dimensions Correction
    • Develop your own fix
  • Graphic tools
    • Plot styles
    • Single map
    • Single map with differences
    • Projections and custom maps
    • Vertical profiles
    • Vertical lines
    • Time series
    • Seasonal cycle
    • Multiple maps
    • Multiple maps with differences
  • Other core functionalities
    • Time Statistics
    • Detrend
    • Spatial Selection
    • Spatial Statistics
    • Histogram
    • Time selection
    • Level selection
    • Streaming of data
      • Basic usage
    • Accessors
      • Basic usage
      • Usage with multiple Reader instances
    • Parallel Processing
    • Data provenance
  • Container
    • Download the container image
    • Load the container
      • Load container script
    • Generate a Personal Access Token (PAT)
    • Advanced Topics
      • Running Jupyter Notebook
      • Running Jupyter Notebook within VSCode
      • Temporary Upgrade of Any Package
  • State of the art diagnostics
    • List of diagnostics
      • Boxplots Diagnostic
        • Description
        • Classes
        • File structure
        • Input variables and datasets
        • Basic usage
        • CLI usage
        • Output
        • Example plots
        • Available demo notebooks
        • Detailed API
      • Global Biases Diagnostic
        • Description
        • Classes
        • File structure
        • Input variables and datasets
        • Basic usage
        • CLI usage
        • Config file structure
        • Output
        • Observations
        • Example Plots
        • Available demo notebooks
        • Authors and contributors
        • Detailed API
      • ECmean4 Performance Metrics
        • Description
        • Structure
        • Input variables
        • Output
        • Methods and functions used
        • Observations
        • References
        • Example Plot(s)
        • Available demo notebooks
      • Timeseries
        • Description
        • Classes
        • File structure
        • Input variables and datasets
        • CLI usage
        • Config file structure
        • Output
        • Observations
        • Example Plots
        • Available demo notebooks
        • Authors and contributors
        • Detailed API
      • Ocean3D
        • Description
        • Structure
        • Input variables example
        • Output
        • CLI (Command Line Interface)
        • Prepare the o3d request
        • Functions used
        • Methods used
        • Observations
        • References
        • Example Plot(s)
        • Available demo notebooks
        • Detailed API
      • Sea ice
        • Description
        • Classes
        • File structure
        • Input variables and datasets
        • Basic usage
        • CLI usage
        • Config file structure
        • CLI processing
        • Outputs
        • Example Plot(s)
        • Observations (Reference data)
        • Available demo notebooks
        • Authors and contributors
        • Detailed API
      • Teleconnections
        • Description
        • Classes
        • File structure
        • Input variables and datasets
        • CLI usage
        • Config file structure
        • Output
        • Example Plots
        • Available demo notebooks
        • Authors and contributors
        • Detailed API
      • Ensemble Statistics
        • Description
        • Structure
        • Input variables
        • Ensemble computation
        • Ensemble Plotting
        • Basic usage
        • Example Plots
        • Detailed API
    • Diagnostics configuration files
    • Diagnostics CLI arguments
    • Running the monitoring diagnostics
      • Minimum Data Requirements
  • Frontier diagnostics
    • SSH variability
      • Description
      • Structure
      • Input variables
      • Output
      • Observations
      • Available demo notebooks
      • References
      • Example Plot(s)
      • Detailed API
    • Tropical Cyclones detection, tracking and zoom in diagnostic
      • Description
      • Structure
      • Input variables
      • Output
      • Methods used
      • Functions used
      • Observations
      • References
      • Example Plot(s)
      • Available demo notebooks
      • Detailed API
    • Tropical rainfall diagnostic
      • Description
      • Structure
      • Input variables
      • Output
      • Examples
        • The histogram calculation
        • List of histograms
        • The histogram plots
        • Seasonal Mean Values
        • Bias between model and observations
      • Available demo notebooks
      • Detailed API
  • Creating Custom Diagnostics
    • Core Diagnostic: Diagnostic
    • Diagnostic Classes
    • Comparison and Plot Classes
    • Command-Line Interface (CLI)
    • Configuration file
    • Configuration Files and AQUA console
    • Automatic Standardized File Naming
      • Class Overview
      • Attributes
      • Example Usage
        • Initializing the OutputSaver Class
        • Generating a Filename
        • Generating a Filename with Extra Keys
        • Saving a NetCDF File with Metadata
        • Saving a PDF or PNG Plot with Metadata
        • Opening a PDF File and Displaying Metadata
        • Generating a Filename for Multimodel or Multireference Comparisons
        • Creating a catalog entry
    • Core Functions
      • Diagnostic
        • Diagnostic.retrieve()
        • Diagnostic.save_netcdf()
        • Diagnostic.select_region()
      • OutputSaver
        • OutputSaver.create_metadata()
        • OutputSaver.generate_folder()
        • OutputSaver.generate_name()
        • OutputSaver.generate_path()
        • OutputSaver.save_figure()
        • OutputSaver.save_netcdf()
        • OutputSaver.save_pdf()
        • OutputSaver.save_png()
        • OutputSaver.unpack_list()
      • close_cluster()
      • get_diagnostic_configpath()
      • load_diagnostic_config()
      • merge_config_args()
      • open_cluster()
      • round_enddate()
      • round_startdate()
      • start_end_dates()
      • template_parse_arguments()
  • Adding new data
    • File-based sources
    • FDB-based sources
    • Experiment metadata
    • Regridding capabilities
    • Grid definitions
    • Compact catalogs with YAML override
    • Intake capabilities and kwargs data access
    • DE_340 source syntax convention
      • Models (model key)
      • Experiments (exp key)
      • Sources (source key)
  • Catalog Generator
    • aqua catgen -c <config_file> -p <portfolio>
      • Basic usage
    • Configuration file
  • DROP - Data Reduction OPerator
    • What is DROP?
    • DROP Capabilities
    • The Low Resolution Archive (LRA) Context
    • Source Naming Convention
    • Accessing DROP-generated data
    • Using DROP to process data
      • Usage
      • Parallel DROP tool
  • AQUA analysis wrapper
    • Basic usage
    • Additional options
    • Configuration file
      • Job
      • Cluster
      • Diagnostics
  • Dashboard
    • General description and main components
    • Automatic uploading of figures and documentation to aqua-web
      • Basic usage
      • Additional options
      • Returns
      • Grouping configuration file
      • AWS credentials file
    • Pushing to LUMI-O or another S3 bucket
      • Basic usage
      • Options
      • Returns
    • Multiple experiment analysis submitter
      • Basic usage
      • Options
  • Examples and Tutorials
    • Jupyter Notebooks for Various Use Cases
  • Command Line Interface tools
    • Benchmarker
    • Grids management
      • Grids downloader
      • Checksum verifications for obs and grids
      • Generation of grid from data
      • Grids synchronization
      • Grids uploader
      • ORCA grid generator
    • HPC container utilities
    • LUMI conda installation
    • Weights generator
    • Orography generator
  • Advanced Topics
    • Set up the configuration file
    • Adding a new catalog
      • Creation of the catalog folder
      • Populating the catalog
      • Adding the catalog to the AQUA package
      • Access to aqua-dvc data for developers
      • Download of grids
    • Dask access to FDB or GSV
    • Polytope access to Destination Earth data
    • Level selection and regridding
    • Reader prepocessing option
    • Enable regrid capabilities in a new machine
      • Set the machine in the catalog machine file
      • Download the grids
    • Developer notes
      • Set up environment variables
      • Add new catalogs as developer
    • ecCodes
      • ecCodes fixer
  • API Reference
    • Drop
      • Drop.append_history()
      • Drop.check_integrity()
      • Drop.create_catalog_entry()
      • Drop.create_zarr_entry()
      • Drop.dask
      • Drop.drop_generator()
      • Drop.get_filename()
      • Drop.retrieve()
      • Drop.write_chunk()
    • Fixer
      • Fixer.find_fixes()
      • Fixer.fixer()
      • Fixer.get_fixer_varname()
    • FldStat
      • FldStat.AVAILABLE_FLDSTATS
      • FldStat.align_area_coordinates()
      • FldStat.align_area_dimensions()
      • FldStat.fldstat()
      • FldStat.integrate_over_area()
      • FldStat.select_area()
      • FldStat.sum_area()
    • GridBuilder
      • GridBuilder.GRIDTYPE_REGISTRY
      • GridBuilder.build()
    • Reader
      • Reader.detrend()
      • Reader.fldarea()
      • Reader.fldintg()
      • Reader.fldmax()
      • Reader.fldmean()
      • Reader.fldmin()
      • Reader.fldstat()
      • Reader.fldstd()
      • Reader.fldsum()
      • Reader.histogram()
      • Reader.instance
      • Reader.reader_esm()
      • Reader.reader_fdb()
      • Reader.reader_intake()
      • Reader.regrid()
      • Reader.retrieve()
      • Reader.select_area()
      • Reader.set_default()
      • Reader.timhist()
      • Reader.timmax()
      • Reader.timmean()
      • Reader.timmin()
      • Reader.timstat()
      • Reader.timstd()
      • Reader.timsum()
      • Reader.vertinterp()
    • Regridder
      • Regridder.loglevel
      • Regridder.logger
      • Regridder.cfg_grid_dict
      • Regridder.src_grid_name
      • Regridder.handler
      • Regridder.src_grid_dict
      • Regridder.src_horizontal_dims
      • Regridder.src_vertical_dim
      • Regridder.tgt_horizontal_dims
      • Regridder.error
      • Regridder.cdo
      • Regridder.smmregridder
      • Regridder.src_grid_area
      • Regridder.tgt_grid_area
      • Regridder.masked_attrs
      • Regridder.masked_vars
      • Regridder.extra_dims
      • Regridder.areas()
      • Regridder.configure_masked_fields()
      • Regridder.regrid()
      • Regridder.weights()
    • Streaming
      • Streaming.reset()
      • Streaming.stream()
      • Streaming.stream_chunk()
    • catalog()
    • histogram()
    • inspect_catalog()
    • plot_hovmoller()
    • plot_lat_lon_profiles()
    • plot_maps()
    • plot_seasonal_lat_lon_profiles()
    • plot_single_map()
    • plot_single_map_diff()
    • plot_timeseries()
  • Troubleshooting and FAQ
    • I am getting an error when trying to install AQUA on LUMI
      • Resource is busy
      • Pip dependency resolution
      • Permission denied
    • I am getting an error MissingGridDefinitionPathError
    • I am getting TypeError: ‘GeometryCollection’ object is not subscriptable when using plot_single_map function
    • How do I cite AQUA in my research or publications?
  • Contributing to AQUA
    • Reporting Bugs
    • Suggesting Features
    • Contributing Code
    • Documentation and Tutorials
    • Testing
      • Running Tests Locally
      • Writing Tests
  • References and Acknowledgments
    • Citing AQUA
    • Acknowledgments
AQUA
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