RHIME Terminology And Quickstart

RHIME runners use the modern spec vocabulary below. New Python examples and new config files should use these names.

Terminology

species

Primary gas or tracer name used for object-store lookup and output naming.

source

OpenGHG metadata key used to retrieve flux data. In sector-resolved RHIME inputs, source is also the xarray coordinate on flux and sensitivity data.

flux_sources

RHIME config/API field containing the requested OpenGHG flux source values.

sector

Model component optimized separately in a multi-sector RHIME run. A sector is usually backed by one flux source.

sector_sources

Optional mapping from sector names to OpenGHG source values. Use this when sector labels such as FF or ocean differ from the source names used to retrieve flux data.

tracer

Additional species used to constrain the primary species, normally with linked forward models. The current RHIME preparation path does not support tracer inversions.

emissions_name

Legacy compatibility spelling accepted only when flux_sources is absent.

Python API

from openghg_inversions.rhime import run_rhime, run_rhime_multisector

result = run_rhime(
    species="ch4",
    sites=["TAC"],
    averaging_period=["1h"],
    domain="EUROPE",
    start_date="2019-01-01",
    end_date="2019-01-02",
    output_path="outputs",
    output_name="example",
    flux_sources=["total-ukghg-edgar7"],
)

multi_sector_result = run_rhime_multisector(
    species="ch4",
    sites=["TAC"],
    averaging_period=["1h"],
    domain="EUROPE",
    start_date="2019-01-01",
    end_date="2019-01-02",
    output_path="outputs",
    output_name="example_multisector",
    flux_sources=["ff-inventory", "gpp-inventory", "ter-inventory", "ocean-inventory"],
    sector_sources={
        "FF": "ff-inventory",
        "GPP": "gpp-inventory",
        "TER": "ter-inventory",
        "ocean": "ocean-inventory",
    },
    sector_priors={
        "FF": {"pdf": "lognormal", "mean": 1.0, "stdev": 1.0},
        "GPP": {"pdf": "normal", "mu": 1.0, "sigma": 0.5},
        "TER": {"pdf": "normal", "mu": 1.0, "sigma": 0.5},
        "ocean": {"pdf": "lognormal", "mean": 1.0, "stdev": 1.0},
    },
)

Config Files

New RHIME config files should use flux_sources:

[INPUT.MEASUREMENTS]
species = "ch4"
sites = ["TAC"]
averaging_period = ["1h"]
start_date = "2019-01-01"
end_date = "2019-01-02"

[INPUT.PRIORS]
domain = "EUROPE"
flux_sources = ["total-ukghg-edgar7"]

[RHIME.OUTPUT]
output_path = "outputs"
output_name = "example"

For multi-sector RHIME, use sector_sources when the optimized sector names are not the same strings as the OpenGHG source values.

[INPUT.PRIORS]
domain = "EUROPE"
flux_sources = ["ff-inventory", "gpp-inventory", "ter-inventory", "ocean-inventory"]
sector_sources = {
    "FF": "ff-inventory",
    "GPP": "gpp-inventory",
    "TER": "ter-inventory",
    "ocean": "ocean-inventory"
}

[RHIME.PDF]
sector_priors = {
    "FF": {"pdf": "lognormal", "mean": 1.0, "stdev": 1.0},
    "GPP": {"pdf": "normal", "mu": 1.0, "sigma": 0.5},
    "TER": {"pdf": "normal", "mu": 1.0, "sigma": 0.5},
    "ocean": {"pdf": "lognormal", "mean": 1.0, "stdev": 1.0}
}

Generated Basis Functions

RHIME can load saved flux basis functions with fp_basis_case or generate a basis with basis_algorithm and nbasis. The legacy generated-basis choices exposed through RHIME config are still "quadtree" and "weighted".

The lower-level Python basis API also supports "region_constrained" when a caller supplies an already loaded region_classes DataArray. That path keeps generated labels from crossing land/sea, country, inner/outer, or other class boundaries, but RHIME config and run_hbmcmc.py do not yet load region_classes from files. For RHIME runs that need these masks today, build and save the basis through the Python basis API, then load it as a saved basis case.

Region-constrained algorithms have split-stopping policies at the lower-level strategy boundary. MinChildWeightShare is a parent-relative balance guard: it compares the lightest proposed child with the current parent partition. MinChildTargetWeightShare is an equal-target low-weight guard: it compares the lightest proposed child with weights.sum() / target_regions for the class/source-local field being partitioned. Thresholds such as 0.1 mean different things for those policies, and generated region counts become upper targets when split stopping rejects remaining candidates. These child-share policies are not currently routed through RHIME config options.

Output Formats

Standard single-sector RHIME supports inv_out, basic, paris, and legacy output formats. legacy writes the old HBMCMC-compatible NetCDF product from the modern InversionOutput. The deprecated names hbmcmc and hbmcmc_postprocessing are accepted as aliases for legacy.

Modern RHIME preparation, InversionOutput artifacts, and postprocessing use retained BasisFunctions / BasisOperator objects as the primary basis representation. Derived flux, country, PARIS, and legacy-format products record basis_reconstruction_path="operator-backed" plus the retained basis artifact source/path when known. Legacy flat basis NetCDF files remain readable as an explicit compatibility fallback, and flat basis maps may still be emitted by compatibility output formats, but new workflows should save and load DataTree BasisFunctions artifacts instead of relying on flat-basis reconstruction.

run_hbmcmc.py is now a compatibility wrapper for old fixedbasis-style INI files. It translates legacy option names to the modern run_rhime API and uses the legacy filename convention. New scripts and new configs should use openghg-inversions run-rhime or run_rhime(...) directly. This compatibility route no longer preserves the exact historical fixedbasisMCMC / inferpymc passthrough behaviour. Use release 0.6 or earlier if you need the old fixedbasis implementation. Direct fixedbasisMCMC(...) calls are a temporary legacy Python path, not a wrapper around run_rhime(...).