openghg_inversions

• openghg_inversions
  • openghg_inversions.basis
    • basis_functions_wrapper()
    • basis_weights_from_fp_all()
    • bucket_basis_from_weights()
    • bucket_basis_function()
    • bucketbasisfunction()
    • fixed_outer_regions_basis()
    • load_basis_functions()
    • make_basis_functions()
    • quadtree_basis_from_weights()
    • quadtree_basis_function()
    • quadtreebasisfunction()
    • region_constrained_basis_from_weights()
    • region_constrained_basis_function()
    • openghg_inversions.basis.algorithms
      • AllSplitAcceptancePolicies
      • AxisAlignedWeightedSplitStrategy
      • AxisParallelSplitStep
      • ContrastScoreSplitAcceptance
      • GreedyAxisParallelSplitStrategy
      • InertialSplitStep
      • LatLonGridGeometry
      • MaxChildPCAEccentricity
      • MinChildTargetWeightShare
      • MinChildWeightShare
      • PartitionStep
      • SplitAcceptancePolicy
      • SplitContrastScore
      • SplitGeometry
      • SplitStrategy
      • TargetSplitAcceptancePolicy
      • allocate_nbasis_by_class()
      • contrast_tau_from_multiplier_cv()
      • intersect_region_class_layers()
      • quadtree_algorithm()
      • region_constrained_basis()
      • split_contrast_score()
      • weighted_algorithm()
    • openghg_inversions.basis.basis_functions
      • BasisFunctions
      • FluxWeightedBasis
      • basis_functions_from_fp_all_flat_basis()
      • flux_from_fp_all()
    • openghg_inversions.basis.layout
      • BasisLayout
      • BasisLayoutResult
      • BasisPartition
      • BasisStateMetadata
    • openghg_inversions.basis.operators
      • Design goals
      • How to use
      • BasisMeta
      • BasisOperator
      • BucketBasisOperator
      • MultiSourceBucketBasisOperator
      • 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
    • 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
      • build_parser()
      • extract_mcmc_type()
      • fixed_basis_expected_param()
      • fixedbasis_params_to_rhime()
      • hbmcmc_extract_param()
      • main()
      • validate_rhime_params()
  • openghg_inversions.inversion_data
    • FixedBasisPreparedData
      • FixedBasisPreparedData.averaging_period
      • FixedBasisPreparedData.basis_artifact_path
      • FixedBasisPreparedData.basis_artifact_source
      • FixedBasisPreparedData.basis_objects
      • FixedBasisPreparedData.fp_all
      • FixedBasisPreparedData.fp_data
      • FixedBasisPreparedData.inv_inputs
      • FixedBasisPreparedData.sites
    • RhimePreparedInputs
      • RhimePreparedInputs.averaging_period
      • RhimePreparedInputs.basis_artifact_path
      • RhimePreparedInputs.basis_artifact_source
      • RhimePreparedInputs.basis_functions
      • RhimePreparedInputs.inv_inputs
      • RhimePreparedInputs.site_lats
      • RhimePreparedInputs.site_lons
      • RhimePreparedInputs.sites
    • data_processing_surface_notracer()
    • load_merged_data()
    • prepare_fixedbasis_inversion_data()
    • prepare_rhime_inputs()
    • 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.preparation
      • FixedBasisPreparedData
      • RhimePreparedInputs
      • prepare_fixedbasis_inversion_data()
      • prepare_rhime_inputs()
    • 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
    • RhimeModelSpec
      • RhimeModelSpec.add_offset
      • RhimeModelSpec.bc_prior
      • RhimeModelSpec.domain
      • RhimeModelSpec.no_model_error
      • RhimeModelSpec.offset_args
      • RhimeModelSpec.offset_prior
      • RhimeModelSpec.pollution_events_from_obs
      • RhimeModelSpec.power
      • RhimeModelSpec.sectors
      • RhimeModelSpec.sigma_per_site
      • RhimeModelSpec.sigma_prior
      • RhimeModelSpec.species
      • RhimeModelSpec.use_bc
    • SectorSpec
      • SectorSpec.flux_source
      • SectorSpec.name
      • SectorSpec.variable_suffix
      • SectorSpec.x_prior
    • add_coords()
    • add_inferpymc_likelihood_component()
    • add_linear_component()
    • add_model_data()
    • add_offset_component()
    • add_sigma_component()
    • attach_coord_registry()
    • build_rhime_model()
    • build_rhime_model_from_spec()
    • build_rhime_multisector_model()
    • build_rhime_multisector_model_from_spec()
    • get_coord_registry()
    • parse_prior()
    • restore_inferencedata_coords()
    • safe_pymc_name()
    • openghg_inversions.models.components
      • LinearComponentResult
      • 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
      • 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
      • RhimeModelSpec
      • SectorSpec
      • build_rhime_model()
      • build_rhime_model_from_spec()
      • build_rhime_multisector_model()
      • build_rhime_multisector_model_from_spec()
      • safe_pymc_name()
  • openghg_inversions.postprocessing
    • openghg_inversions.postprocessing.countries
      • Countries
      • CountryRegions
      • get_area_grid()
    • openghg_inversions.postprocessing.diagnostics
      • Diagnostic
      • bayes_r2_by_site()
      • bayes_r2_by_site_resample()
      • register_diagnostic()
      • summary()
    • openghg_inversions.postprocessing.inversion_output
      • InversionOutput
      • convert_idata_to_dataset()
      • filter_data_vars_by_prefix()
    • openghg_inversions.postprocessing.legacy_outputs
      • make_legacy_hbmcmc_output()
    • openghg_inversions.postprocessing.make_outputs
      • OutputSector
      • basic_output()
      • convert_suffixes_to_dim()
      • flat_basis_for_output()
      • flatten_post_prior()
      • make_concentration_outputs()
      • make_country_outputs()
      • make_flux_outputs()
      • make_multisector_country_trace_outputs()
      • make_multisector_flux_trace_outputs()
      • make_sector_flux_outputs()
      • model_error_output()
      • observation_and_error_outputs()
      • observation_inputs_for_outputs()
      • sort_data_vars()
      • total_error_output()
    • openghg_inversions.postprocessing.make_paris_outputs
      • ParisTemplateFiles
      • add_variable_attrs()
      • convert_time_to_unix_epoch()
      • get_data_var_attrs()
      • get_data_var_dtypes()
      • infer_flux_frequency()
      • make_global_attrs()
      • make_paris_outputs()
      • paris_concentration_outputs()
      • paris_concentration_outputs_latest()
      • paris_flux_output()
      • paris_flux_output_latest()
      • paris_template_files()
      • shift_measurement_time_to_midpoint()
    • openghg_inversions.postprocessing.stats
      • StatsFunction
      • 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.rhime
    • RhimeModelSpec
      • RhimeModelSpec.add_offset
      • RhimeModelSpec.bc_prior
      • RhimeModelSpec.domain
      • RhimeModelSpec.no_model_error
      • RhimeModelSpec.offset_args
      • RhimeModelSpec.offset_prior
      • RhimeModelSpec.pollution_events_from_obs
      • RhimeModelSpec.power
      • RhimeModelSpec.sectors
      • RhimeModelSpec.sigma_per_site
      • RhimeModelSpec.sigma_prior
      • RhimeModelSpec.species
      • RhimeModelSpec.use_bc
    • RhimeOutputSpec
      • RhimeOutputSpec.country_file
      • RhimeOutputSpec.output_filename_convention
      • RhimeOutputSpec.output_format
      • RhimeOutputSpec.output_name
      • RhimeOutputSpec.output_path
      • RhimeOutputSpec.paris_postprocessing_kwargs
      • RhimeOutputSpec.save_inversion_output
      • RhimeOutputSpec.save_trace
    • RhimeResult
      • RhimeResult.basis_functions
      • RhimeResult.idata
      • RhimeResult.inv_inputs
      • RhimeResult.inv_out
      • RhimeResult.model
      • RhimeResult.model_spec
      • RhimeResult.output_metadata
      • RhimeResult.output_spec
      • RhimeResult.outputs
      • RhimeResult.run_spec
      • RhimeResult.sampler
    • RhimeRunSpec
      • RhimeRunSpec.averaging_period
      • RhimeRunSpec.end_date
      • RhimeRunSpec.model
      • RhimeRunSpec.output
      • RhimeRunSpec.sites
      • RhimeRunSpec.split_by_sectors
      • RhimeRunSpec.start_date
    • RhimeSampler
      • RhimeSampler.burn
      • RhimeSampler.chains
      • RhimeSampler.draws
      • RhimeSampler.nuts_sampler
      • RhimeSampler.posterior_predictive_kwargs
      • RhimeSampler.progressbar
      • RhimeSampler.sample()
      • RhimeSampler.sample_kwargs
      • RhimeSampler.sample_posterior_predictive
      • RhimeSampler.sample_prior_predictive
      • RhimeSampler.tune
    • SectorSpec
      • SectorSpec.flux_source
      • SectorSpec.name
      • SectorSpec.variable_suffix
      • SectorSpec.x_prior
    • params_from_config()
    • resolve_flux_sources()
    • run_rhime()
    • run_rhime_multisector()
    • openghg_inversions.rhime.outputs
      • RhimeOutputBundle
      • make_multisector_output_bundle()
      • make_standard_output_bundle()
    • openghg_inversions.rhime.params
      • RhimeRunnerSetup
      • as_list()
      • coerce_simple_param_types()
      • is_missing_required_value()
      • make_rhime_runner_setup()
      • normalise_optional_mapping()
      • normalise_output_format_alias()
      • normalise_param_aliases()
      • normalise_rhime_params()
      • normalise_sector_priors()
      • normalise_sector_sources()
      • params_from_config()
      • required_run_params()
      • resolve_flux_sources()
      • validate_multisector_x_prior()
      • validate_required_params()
      • validate_rhime_param_types()
      • validate_supported_params()
    • openghg_inversions.rhime.runner
      • RhimeModelSpec
      • RhimeOutputSpec
      • RhimeResult
      • RhimeRunSpec
      • RhimeSampler
      • SectorSpec
      • params_from_config()
      • resolve_flux_sources()
      • run_rhime()
      • run_rhime_multisector()
    • openghg_inversions.rhime.sampling
      • RhimeSampler
    • openghg_inversions.rhime.specs
      • RhimeOutputSpec
      • RhimeRunSpec
      • make_output_spec()
      • validate_output_filename_convention()
      • validate_output_format()
      • validate_output_path_settings()
  • 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.flux_sanitization
    • FluxNonFiniteMetadata
      • FluxNonFiniteMetadata.checked
      • FluxNonFiniteMetadata.context
      • FluxNonFiniteMetadata.count
      • FluxNonFiniteMetadata.declares_zero_fill()
      • FluxNonFiniteMetadata.fill_value
      • FluxNonFiniteMetadata.fraction
      • FluxNonFiniteMetadata.from_attrs()
      • FluxNonFiniteMetadata.from_json()
      • FluxNonFiniteMetadata.policy
      • FluxNonFiniteMetadata.schema_version
      • FluxNonFiniteMetadata.source
      • FluxNonFiniteMetadata.to_json()
      • FluxNonFiniteMetadata.to_json_dict()
      • FluxNonFiniteMetadata.total
    • NonFiniteFluxWarning
    • copy_flux_nonfinite_attrs()
    • sanitize_flux_nonfinite()
  • 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.utils
    • areagrid()
    • combine_datasets()
    • datatree_ncdf_encoding()
    • get_country()
    • get_country_file_path()
    • ncdf_encoding()
    • open_ds()
    • read_netcdfs()
    • write_netcdf_preserving_bounds_attrs()