openghg_inversions

OpenGHG inversions.

• openghg_inversions.basis
  • basis_functions_wrapper()
  • bucketbasisfunction()
  • fixed_outer_regions_basis()
  • quadtreebasisfunction()
  • openghg_inversions.basis.algorithms
    • quadtree_algorithm()
    • weighted_algorithm()
  • openghg_inversions.basis.basis_functions
    • BasisFunctions
    • FluxWeightedBasis
      • FluxWeightedBasis.flux
      • FluxWeightedBasis.from_basis_flat()
      • FluxWeightedBasis.from_datatree()
      • FluxWeightedBasis.from_multi_source_basis_flat()
      • FluxWeightedBasis.interpolate()
      • FluxWeightedBasis.operator
      • FluxWeightedBasis.plot()
      • FluxWeightedBasis.sensitivity()
      • FluxWeightedBasis.to_datatree()
  • openghg_inversions.basis.operators
    • Design goals
    • How to use
    • BasisMeta
      • BasisMeta.grid_dims
      • BasisMeta.state_dim
    • BasisOperator
      • BasisOperator.basis_matrix
      • BasisOperator.decode_datatree()
      • BasisOperator.from_datatree()
      • BasisOperator.interpolate()
      • BasisOperator.kind
      • BasisOperator.meta
      • BasisOperator.schema
      • BasisOperator.schema_version
      • BasisOperator.sensitivity()
      • BasisOperator.to_datatree()
    • BucketBasisOperator
      • BucketBasisOperator.basis_matrix
      • BucketBasisOperator.from_datatree()
      • BucketBasisOperator.kind
      • BucketBasisOperator.meta
      • BucketBasisOperator.to_datatree()
    • MultiSourceBucketBasisOperator
      • MultiSourceBucketBasisOperator.basis_matrix
      • MultiSourceBucketBasisOperator.from_datatree()
      • MultiSourceBucketBasisOperator.interpolate()
      • MultiSourceBucketBasisOperator.kind
      • MultiSourceBucketBasisOperator.meta
      • MultiSourceBucketBasisOperator.sensitivity()
      • MultiSourceBucketBasisOperator.to_datatree()
    • drop_singleton_time()
    • get_basis_operator_class()
    • register_basis_operator()
• openghg_inversions.config
  • openghg_inversions.config.config
    • all_param()
    • all_parameters_in_param_type()
    • convert()
    • eval_check()
    • extract_params()
    • find_param_key()
    • generate_from_template()
    • generate_param_dict()
    • get_value()
    • list_check()
    • open_config()
    • str_check()
  • openghg_inversions.config.paths
    • Paths
      • Paths.openghginv
  • openghg_inversions.config.version
    • code_version()
• openghg_inversions.hbmcmc
  • openghg_inversions.hbmcmc.components
    • make_offset()
  • openghg_inversions.hbmcmc.hbmcmc
    • fixedbasisMCMC()
    • rerun_output()
    • update_log_normal_prior()
  • openghg_inversions.hbmcmc.hbmcmc_output
    • check_and_create_folder()
    • copy_config_file()
    • define_output_filename()
  • openghg_inversions.hbmcmc.hbmcmc_post_process
    • Functions
    • calculate_DIC()
    • check_missing_dates()
    • check_platform()
    • country_emissions()
    • country_emissions_mult()
    • define_stations()
    • extract_hbmcmc_files()
    • open_ds()
    • plot_abs_map()
    • plot_country_timeseries()
    • plot_diff_map()
    • plot_map()
    • plot_map_mult()
    • plot_multi_country_timeseries()
    • plot_scale_map()
    • plot_timeseries()
    • set_clevels()
    • subplot_fmt()
    • unbiasedDivergingCmap()
  • openghg_inversions.hbmcmc.inversion_pymc
    • build_inferpymc_model()
    • extend_inferencedata_predictive()
    • inferpymc()
    • inferpymc_postprocessouts()
    • sample()
  • openghg_inversions.hbmcmc.inversionsetup
    • create_bc_sensitivity()
    • monthly_bcs()
    • sigma_freq_indicies()
  • openghg_inversions.hbmcmc.post_process_inputs
  • openghg_inversions.hbmcmc.run_hbmcmc
    • define_mcmc_function()
    • extract_mcmc_type()
    • fixed_basis_expected_param()
    • hbmcmc_extract_param()
• openghg_inversions.inversion_data
  • data_processing_surface_notracer()
  • load_merged_data()
  • openghg_inversions.inversion_data.get_data
    • add_obs_error()
    • convert_to_list()
    • data_processing_surface_notracer()
  • openghg_inversions.inversion_data.getters
    • adjust_flux_start_date()
    • get_flux_data()
    • get_footprint_data()
    • get_footprint_to_match()
    • get_fp_indexer()
    • get_obs_data()
  • openghg_inversions.inversion_data.scenario
    • merged_scenario_data()
  • openghg_inversions.inversion_data.serialise
    • clear_datatree_encoding()
    • clear_datatree_time_attrs()
    • combine_scenario_attrs()
    • dataset_to_bc_data()
    • dataset_to_flux_data()
    • datatree_compression_encoding()
    • datatree_to_flux_dict()
    • datatree_to_fp_all()
    • flux_dict_to_datatree()
    • fp_all_from_dataset()
    • fp_all_to_datatree()
    • load_merged_data()
    • make_combined_scenario()
    • openghg_data_to_dataset()
• openghg_inversions.models
  • CoordRegistry
    • CoordRegistry.add()
    • CoordRegistry.auxiliary_coords
    • CoordRegistry.original_coords
    • CoordRegistry.pymc_coords
  • LinearComponentResult
    • LinearComponentResult.data
    • LinearComponentResult.latent
    • LinearComponentResult.output
  • add_coords()
  • add_inferpymc_likelihood_component()
  • add_linear_component()
  • add_model_data()
  • add_offset_component()
  • add_sigma_component()
  • attach_coord_registry()
  • get_coord_registry()
  • parse_prior()
  • restore_inferencedata_coords()
  • openghg_inversions.models.components
    • LinearComponentResult
      • LinearComponentResult.data
      • LinearComponentResult.latent
      • LinearComponentResult.output
    • add_inferpymc_likelihood_component()
    • add_linear_component()
    • add_model_data()
    • add_offset_component()
    • add_sigma_component()
    • get_model_latent()
    • resolve_model_variable()
  • openghg_inversions.models.coords
    • CoordRegistry
      • CoordRegistry.add()
      • CoordRegistry.auxiliary_coords
      • CoordRegistry.original_coords
      • CoordRegistry.pymc_coords
    • add_coords()
    • attach_coord_registry()
    • get_coord_registry()
    • restore_inferencedata_coords()
    • sanitize_coords_for_pymc()
  • openghg_inversions.models.priors
    • lognormal_mu_sigma()
    • parse_prior()
  • openghg_inversions.models.rhime
    • build_rhime_model()
    • build_rhime_multisector_model()
    • safe_pymc_name()
• openghg_inversions.postprocessing
  • openghg_inversions.postprocessing.countries
    • Countries
      • Countries.from_file()
      • Countries.get_country_trace()
      • Countries.get_x_to_country_mat()
      • Countries.merge()
    • CountryRegions
      • CountryRegions.align()
      • CountryRegions.all_region_countries_present_in()
      • CountryRegions.from_file()
      • CountryRegions.region_countries_missing_from()
      • CountryRegions.region_names
      • CountryRegions.to_dict()
    • get_area_grid()
  • openghg_inversions.postprocessing.diagnostics
    • Diagnostic
      • Diagnostic.func
      • Diagnostic.params
    • bayes_r2_by_site()
    • bayes_r2_by_site_resample()
    • register_diagnostic()
    • summary()
  • openghg_inversions.postprocessing.inversion_output
    • InversionOutput
      • InversionOutput.basis
      • InversionOutput.domain
      • InversionOutput.end_date
      • InversionOutput.end_time
      • InversionOutput.flux
      • InversionOutput.from_datatree()
      • InversionOutput.get_flat_basis()
      • InversionOutput.get_model_data()
      • InversionOutput.get_model_err()
      • InversionOutput.get_obs_and_errors()
      • InversionOutput.get_total_err()
      • InversionOutput.get_trace_dataset()
      • InversionOutput.load()
      • InversionOutput.nmeasure_to_site_time()
      • InversionOutput.obs
      • InversionOutput.obs_err
      • InversionOutput.obs_prior_factor
      • InversionOutput.obs_prior_upper_level_factor
      • InversionOutput.obs_repeatability
      • InversionOutput.obs_variability
      • InversionOutput.period_midpoint
      • InversionOutput.save()
      • InversionOutput.site_indicators
      • InversionOutput.site_names
      • InversionOutput.species
      • InversionOutput.start_date
      • InversionOutput.start_time
      • InversionOutput.times
      • InversionOutput.to_datatree()
      • InversionOutput.trace
    • convert_idata_to_dataset()
    • filter_data_vars_by_prefix()
    • make_inv_out_for_fixed_basis_mcmc()
    • make_inv_out_from_rhime_outputs()
  • openghg_inversions.postprocessing.legacy_outputs
    • make_legacy_hbmcmc_output()
  • openghg_inversions.postprocessing.make_outputs
    • basic_output()
    • convert_suffixes_to_dim()
    • flatten_post_prior()
    • make_concentration_outputs()
    • make_country_outputs()
    • make_flux_outputs()
    • sort_data_vars()
  • openghg_inversions.postprocessing.make_paris_outputs
    • add_variable_attrs()
    • convert_time_to_unix_epoch()
    • get_data_var_attrs()
    • infer_flux_frequency()
    • make_global_attrs()
    • make_paris_flux_outputs_from_rhime()
    • make_paris_outputs()
    • paris_concentration_outputs()
    • paris_flux_output()
    • shift_measurement_time_to_midpoint()
  • openghg_inversions.postprocessing.stats
    • StatsFunction
      • StatsFunction.func
      • StatsFunction.name
      • StatsFunction.params
    • calculate_stats()
    • hdi()
    • mean()
    • median()
    • mode()
    • mode_kde()
    • quantiles()
    • register_stat()
    • stdev()
  • openghg_inversions.postprocessing.utils
    • add_suffix()
    • get_parameters()
    • make_replace_names_dict()
    • rename_by_replacement()
    • update_attrs()

• openghg_inversions.array_ops
  • Functions
  • Coordinate Alignment Policy
  • align_sparse_lat_lon()
  • align_to_multi_index_level_values()
  • concat_data_arrays()
  • concat_gather_data_arrays()
  • concat_gather_datasets()
  • concat_gather_datatree()
  • force_align()
  • get_xr_dummies()
  • sparse_xr_dot()
  • to_dense()
• openghg_inversions.cli
  • build_parser()
  • main()
• openghg_inversions.convert
  • convert_to_hours()
  • mol2g()
  • prefix()
• openghg_inversions.filters
  • daily_median()
  • daytime()
  • daytime9to5()
  • filtering()
  • list_filters()
  • local_influence()
  • nighttime()
  • noon()
  • pblh()
  • pblh_inlet_diff()
  • pblh_min()
  • register_filter()
  • six_hr_mean()
• openghg_inversions.inversion_inputs
  • add_min_error()
  • add_site_indicator()
  • make_freq_indicator()
  • make_inv_inputs()
  • make_sigma_freq()
  • make_site_indicator()
  • make_site_names()
  • transform_bc()
  • xr_factorize()
  • xr_unique_inv()
• openghg_inversions.model_error
  • percentile_error_method()
  • residual_error_method()
  • setup_min_error()
  • xr_setup_min_error()
• openghg_inversions.rhime
  • RhimeModelSpec
    • RhimeModelSpec.add_offset
    • RhimeModelSpec.domain
    • RhimeModelSpec.no_model_error
    • RhimeModelSpec.pollution_events_from_obs
    • RhimeModelSpec.power
    • RhimeModelSpec.sectors
    • RhimeModelSpec.sigma_per_site
    • RhimeModelSpec.species
    • RhimeModelSpec.use_bc
  • RhimeOutputSpec
    • RhimeOutputSpec.country_file
    • RhimeOutputSpec.output_format
    • RhimeOutputSpec.output_name
    • RhimeOutputSpec.output_path
    • RhimeOutputSpec.paris_postprocessing_kwargs
    • RhimeOutputSpec.save_inversion_output
    • RhimeOutputSpec.save_trace
  • RhimeResult
    • RhimeResult.idata
    • RhimeResult.inv_inputs
    • RhimeResult.inv_out
    • RhimeResult.model
    • RhimeResult.model_spec
    • RhimeResult.output_metadata
    • RhimeResult.output_spec
    • RhimeResult.outputs
    • RhimeResult.run_spec
  • RhimeRunSpec
    • RhimeRunSpec.averaging_period
    • RhimeRunSpec.end_date
    • RhimeRunSpec.model
    • RhimeRunSpec.output
    • RhimeRunSpec.sites
    • RhimeRunSpec.split_by_sectors
    • RhimeRunSpec.start_date
  • SectorSpec
    • SectorSpec.flux_source
    • SectorSpec.name
    • SectorSpec.variable_suffix
    • SectorSpec.x_prior
  • make_multisector_flux_diagnostics()
  • params_from_config()
  • resolve_flux_sources()
  • run_rhime()
  • run_rhime_multisector()
• openghg_inversions.utils
  • areagrid()
  • combine_datasets()
  • datatree_ncdf_encoding()
  • get_country()
  • get_country_file_path()
  • ncdf_encoding()
  • open_ds()
  • read_netcdfs()