Compatibility Layer Documentation#

The compat module converts pyglotaran v0.8 Result objects to a flat dataset format compatible with v0.7-style plotting functions.

v0.8 Result Structure#

Result
├── optimization_results: dict[str, OptimizationResult]
│   └── OptimizationResult
│       ├── elements: dict[str, xr.Dataset]      # Element results by name
│       ├── activations: dict[str, xr.Dataset]   # Activation (IRF) results
│       ├── input_data: xr.DataArray | xr.Dataset
│       ├── residuals: xr.DataArray | xr.Dataset
│       ├── fitted_data: property (input_data - residuals)
│       └── meta: OptimizationResultMetaData
├── scheme: Scheme
│   └── experiments: dict[str, ExperimentModel]
├── optimization_info: OptimizationInfo
├── initial_parameters: Parameters
└── optimized_parameters: Parameters

Element Identification#

Each element dataset has an element_uid attribute:

Element Type	`element_uid`
Kinetic	`glotaran.builtin.elements.kinetic.element.KineticElement`
Damped Oscillation	`glotaran.builtin.elements.damped_oscillation.element.DampedOscillationElement`
Coherent Artifact	`glotaran.builtin.elements.coherent_artifact.element.CoherentArtifactElement`

Variable Mappings#

Core Data#

v0.8 Source	v0.7 Target
`OptimizationResult.input_data`	`data`
`OptimizationResult.residuals`	`residual`
`OptimizationResult.fitted_data`	`fitted_data`

Global Result Element#

Global v0.8 fits store the model and global matrices in a generic result element. For plotting, these are exposed under the v0.7 full-model names:

v0.8 Source	v0.7 Target
`global_concentrations`	`species_concentration`
`model_concentrations`	`species_spectra`

Dimension rename: amplitude_label → species_model

Kinetic Element#

v0.8 Source	v0.7 Target
`concentrations`	`species_concentration_{element_name}`
`amplitudes`	`species_associated_spectra_{element_name}`
`kinetic_amplitudes.isel(activation=0)`	`decay_associated_spectra_{element_name}`

Dimension rename: compartment → species_{element_name}

Damped Oscillation Element#

v0.8 Source	v0.7 Target
`cos_concentrations`	`damped_oscillation_cos`
`sin_concentrations`	`damped_oscillation_sin`
`amplitudes`	`damped_oscillation_associated_spectra`
`phase_amplitudes`	`damped_oscillation_phase`

Coordinate renames: oscillation → damped_oscillation, oscillation_frequency → damped_oscillation_frequency, oscillation_rate → damped_oscillation_rate

Coherent Artifact Element#

v0.8 Source	v0.7 Target
`concentrations`	`coherent_artifact_response`
`amplitudes`	`coherent_artifact_associated_spectra`

Dimension rename: derivative → coherent_artifact_order

Activation (IRF) Data#

v0.8 Source	v0.7 Target
`attrs["center"]`	`irf_center`
`attrs["width"]`	`irf_width`
`attrs["scale"]`	`irf_scale`
`"trace"` variable	`irf`
`"center"` variable	`irf_center_location`

Dimension rename for irf_center_location: component_index → irf_nr

Dataset Attributes#

v0.8 Source (`meta`)	v0.7 Attribute
`root_mean_square_error`	`root_mean_square_error`
`weighted_root_mean_square_error`	`weighted_root_mean_square_error`
`global_dimension`	`global_dimension`
`model_dimension`	`model_dimension`
`scale`	`scale`

CompatResult Properties#

v0.7 Property	v0.8 Source
`data`	Flattened datasets (via `_compat_datasets`)
`model`	First experiment from `scheme.experiments`
`number_of_function_evaluations`	`optimization_info.number_of_function_evaluations`
`number_of_residuals`	`optimization_info.number_of_data_points`
`number_of_free_parameters`	`optimization_info.number_of_parameters`
`success`, `termination_reason`, `glotaran_version`, `number_of_clps`, `degrees_of_freedom`, `chi_square`, `reduced_chi_square`, `root_mean_square_error`, `additional_penalty`	Delegated to `optimization_info`