# API: everything else This page lists every name `rietx` exports that the other two API pages do not, alphabetically. Most are the types a result, a report or a project is made of. You read their fields more often than you construct them. ### rx.\_\_version_\_ *= 1.10.0* A constant. ### *class* rx.AbsorptionCorrection Record of the specimen absorption applied (cylinder or flat plate). * `method: 'rouse_cylinder' | 'flat_plate_reflection' | 'flat_plate_transmission' = 'rouse_cylinder'` * `mu_r: float` * `mu_r_source: 'given' | 'estimated'` * `wavelength: float` * `equivalent_delta_biso: float` * `skipped: str | None = None` * `out_of_range: bool = False` * `unabsorbed_fraction: float | None = None` * `identifiable_fraction: float | None = None` * `intensity_fraction_of_optimal: float | None = None` ### *class* rx.AmbiguityPartner A distinct lattice whose calculated line *positions* match this one’s. * `cell: tuple[float, float, float, float, float, float]` * `transformation: list[list[int]]` * `index: int` * `system: str` * `volume: float` * `discriminating_reflections: list[tuple[int, int, int]] = []` * `discriminating_two_theta: list[float] = []` ### *class* rx.AngleRestraint A soft restraint on the i–j–k bond angle (vertex = the **middle** atom `atom_j`), contributing √weight·(angle − `target_deg`)/sigma degrees. * `atom_i: int` * `atom_j: int` * `atom_k: int` * `target_deg: float` * `sigma: float` * `weight: float = 1.0` * `op_index_i: int | None = None` * `translation_i: tuple[int, int, int] = (0 × 3)` * `op_index_k: int | None = None` * `translation_k: tuple[int, int, int] = (0 × 3)` ### *class* rx.Annotation An append-only overlay: labels, refs and scores, applied after nodes. * `node_id: str = ''` * `label: str | None = None` * `refs: dict[str, str] = {}` * `scores: dict[str, float] = {}` * `notes: dict[str, str] = {}` ### *class* rx.AntiBumpRestraint A one-sided distance restraint: zero beyond `min_distance`, linear inside. * `atom_i: int` * `atom_j: int` * `min_distance: float` * `sigma: float` * `weight: float = 1.0` * `op_index: int | None = None` * `translation: tuple[int, int, int] = (0 × 3)` ### *class* rx.Base Base for every rietx schema. ### *class* rx.BodyOrigin A rigid body’s origin: the point (0, 0, 0) of its template, fractional. * `x: Parameter` * `y: Parameter` * `z: Parameter` ### *class* rx.BodyTorsion A rotation of declared body atoms about the line through two others (WP-1808). * `name: str` * `axis: tuple[str, str]` * `moves: list[str]` * `angle: float = 0.0` * `vary: bool = False` ### *class* rx.BondRestraint A soft restraint on the distance between two atoms of one phase. * `atom_i: int` * `atom_j: int` * `target: float` * `sigma: float` * `weight: float = 1.0` * `op_index: int | None = None` * `translation: tuple[int, int, int] = (0 × 3)` ### *class* rx.BravaisOpinion What gemmi and spglib each say about a candidate’s lattice symmetry. * `system: str` * `system_loosest: str` * `system_gemmi: str` * `system_spglib: str` * `ambiguous: bool = False` * `methods_disagree: bool = False` * `reduced_cell: tuple[float, float, float, float, float, float] = (0.0 × 6)` ### *class* rx.CandidateEvidence One candidate’s evidence, collected for a consumer that can reason. * `index: int` * `cell: tuple[float, float, float, float, float, float]` * `cell_esd: tuple[float, float, float, float, float, float]` * `system: str` * `centring: str` * `volume: float` * `confidence: 'high' | 'medium' | 'low'` * `caveats: list[CaveatEvidence] = []` * `found_by: list[str] = []` * `n_indexed: int = 0` * `n_lines: int = 0` * `fom: dict[str, float] = {}` * `validated: bool = False` * `lebail_status: str | None = None` * `lebail_rwp: float | None = None` * `predicted_but_absent: int | None = None` * `unmatched_observed: int | None = None` * `ambiguity_partners: int = 0` ### *class* rx.CaveatEvidence One caveat, with the half of it the gate never wrote out: its kind. * `name: 'engines_disagree' | 'geometric_ambiguity' | 'fom_panel_disagrees' | 'fom_panel_reduced' | 'not_validated' | 'validation_failed' | 'predicted_but_absent' | 'indexed_fraction_low' | 'indexed_lines_low' | 'search_incomplete' | 'shift_allowance_assumed' | 'bravais_ambiguous' | 'volume_unphysical' | 'supercell_refuted'` * `kind: 'refuting' | 'capping'` ### *class* rx.CellCandidate One candidate lattice, with everything needed to rank or reject it. * `cell: tuple[float, float, float, float, float, float]` * `cell_esd: tuple[float, float, float, float, float, float]` * `system: str` * `centring: str = 'P'` * `lattice_group: str = ''` * `volume: float = 0.0` * `volume_esd: float = 0.0` * `af: tuple[float, float, float, float, float, float] = (0.0 × 6)` * `engine_cell: tuple[float, float, float, float, float, float] | None = None` * `change_of_basis: tuple[tuple[int, int, int], tuple[int, int, int], tuple[int, int, int]] | None = None` * `n_indexed: int = 0` * `n_lines: int = 0` * `n_search_unindexed: int | None = None` * `unindexed_two_theta: list[float] | None = None` * `chi2_red: float = 0.0` * `shift_template: str | None = None` * `shift_coefficient: float = 0.0` * `shift_esd: float = 0.0` * `fom: list[FigureOfMerit] = []` * `found_by: list[str] = []` * `ambiguity: list[AmbiguityPartner] = []` * `supercell_checks: list[SupercellCheck] | None = None` * `bravais: BravaisOpinion | None = None` * `lebail: LeBailValidation | None = None` * `confidence: 'high' | 'medium' | 'low' = 'low'` * `confidence_caveats: list['engines_disagree' | 'geometric_ambiguity' | 'fom_panel_disagrees' | 'fom_panel_reduced' | 'not_validated' | 'validation_failed' | 'predicted_but_absent' | 'indexed_fraction_low' | 'indexed_lines_low' | 'search_incomplete' | 'shift_allowance_assumed' | 'bravais_ambiguous' | 'volume_unphysical' | 'supercell_refuted'] = []` * `diagnostics: list[Diagnostic] = []` ### *class* rx.CellVolume One phase’s unit-cell volume in ų, with its esd (WP-1933). * `phase_index: int` * `volume: float` * `stderr: float | None = None` * `stderr_diagonal: float | None = None` ### *class* rx.CoordinateTable Each pattern’s coordinates: named columns, one row per pattern. * `columns: dict[str, list[float | None]]` * `units: dict[str, str] = {}` ### *class* rx.CorrelationPair One entry of the worst-|ρ| list (WP-1056). * `path_a: str` * `path_b: str` * `rho: float` ### *class* rx.DataQualityReport Is this peak list fit to index, and what does it already say? * `n_usable: int` * `n_total: int` * `two_theta_min: float` * `two_theta_max: float` * `source: 'fitted' | 'positions'` * `sigma_two_theta_median: float` * `sigma_two_theta_worst: float` * `relative_sigma_q_median: float` * `sigma_over_spacing: float` * `lines_per_dof: dict[str, float] = {}` * `systems_supported: list[str] = []` * `fom_undefined: dict[str, str] = {}` * `volume_envelope: dict[str, float] = {}` * `shift: ShiftScreen | None = None` * `supports_indexing: bool = True` * `abstained_reason: str | None = None` * `thresholds_version: str = '1.11'` * `diagnostics: list[Diagnostic] = []` ### *class* rx.DataRef The pattern a project is fitted against, held as a reference you can check. * `filename: str` * `sha256: str` * `fingerprint: str` * `reader: str` * `options: dict[str, str] = {}` * `n_points: int` * `two_theta_range: tuple[float, float]` * `has_sigma: bool` ### *class* rx.DataSupport How many observations the pattern actually holds (WP-1071). * `n_unique_reflections: int` * `n_effective_observations: float | None = None` * `n_structural_parameters: int` * `observations_per_parameter: float | None = None` * `effective_observations_per_parameter: float | None = None` ### *class* rx.EmissionLine One wavelength component of the incident spectrum. * `wavelength: Parameter` * `weight: Parameter = Parameter(1.0, min=0.0)` ### *class* rx.ExchangeRow How well the fitted parameters can imitate one held parameter. * `held: str` * `r2: float` * `partners: dict[str, float] = {}` ### *class* rx.ExtinctionCandidate One **extinction class**: the space groups that share an absence set. * `symbol: str` * `representative: str` * `space_groups: list[str] = []` * `excluded_groups: list[str] = []` * `laue_classes: dict[str, list[str]] = {}` * `conditions: list[str] = []` * `conditions_complete: bool = True` * `n_lines: int = 0` * `n_absent: int = 0` * `n_testable: int | None = None` * `n_present: int = 0` * `forbidden_hkl: list[tuple[int, int, int]] = []` * `forbidden_two_theta: list[float] = []` * `rwp: float = inf` * `gof: float = inf` * `chi2: float = inf` * `delta_bic: float = 0.0` * `absences_rejected: bool = False` * `screened: bool = False` * `refuted: bool = False` * `refuted_reason: str | None = None` * `diagnostics: list[Diagnostic] = []` ### *class* rx.ExtinctionPrior Declared facts about the specimen that remove space groups from a class. * `sohncke: bool | None = None` * `centrosymmetric: bool | None = None` * `polar: bool | None = None` ### *class* rx.ExtinctionScreen What `rietx.determine_extinction_symbol` returns. * `candidates: list[ExtinctionCandidate] = []` * `lattice_group: str = ''` * `cell: tuple[float, float, float, float, float, float] = (0.0 × 6)` * `system: str = ''` * `centring: str = 'P'` * `wavelength: float = 0.0` * `two_theta_range: tuple[float, float] = (0.0 × 2)` * `n_classes: int = 0` * `n_screened: int = 0` * `reference_rwp: float = inf` * `reference_chi2: float = inf` * `reference_lines: int = 0` * `n_points: int = 0` * `profile_rwp: float = inf` * `prior: ExtinctionPrior | None = None` * `status: str = 'converged'` * `thresholds_version: str = '1.11'` * `diagnostics: list[Diagnostic] = []` ### *class* rx.FigureOfMerit One figure of merit, and **what it cannot see**. * `name: str` * `value: float` * `n_lines: int` * `n_possible: int` * `k_sigma: float` * `mean_discrepancy: float = -1.0` * `blind_spot: str = ''` ### *class* rx.FractionProfile Every fraction of one phase the pattern admits along its width. * `phase: str` * `phase_index: int` * `axes: list[str]` * `weight_fraction: float` * `weight_fraction_stderr: float | None = None` * `chi2_fit: float` * `chi2_best: float` * `delta_chi2_cut: float` * `fit_admissible: bool` * `points: list[FractionProfilePoint] = []` * `range_low: float` * `range_high: float` * `excess: float | None = None` * `diagnostics: list[Diagnostic] = []` ### *class* rx.FractionProfilePoint One pinned width and what the refit made of the fraction there. * `axis: str` * `value: float` * `fwhm: float` * `admissible: bool` * `weight_fraction: float | None = None` * `chi2: float | None = None` * `delta_chi2: float | None = None` * `rwp: float | None = None` * `status: str | None = None` * `error: str | None = None` * `node_id: str | None = None` ### *class* rx.GeometryAngle One interatomic angle at `atom_2`, in degrees (WP-1072). * `phase_index: int` * `atom_1: str` * `atom_2: str` * `atom_3: str` * `atom_index_1: int` * `atom_index_2: int` * `atom_index_3: int` * `angle: float` * `stderr: float | None = None` * `stderr_diagonal: float | None = None` * `symmetry_1: str | None = '.'` * `symmetry_2: str = '.'` * `symmetry_3: str | None = '.'` ### *class* rx.GeometryDistance One interatomic distance, bonding or nonbonding (WP-1072). * `phase_index: int` * `atom_1: str` * `atom_2: str` * `atom_index_1: int` * `atom_index_2: int` * `distance: float` * `stderr: float | None = None` * `stderr_diagonal: float | None = None` * `symmetry_1: str = '.'` * `symmetry_2: str | None = '.'` * `bonded: bool = True` ### *class* rx.GeometryTable Bonding geometry of the converged model, with propagated esds (WP-1072). * `distances: list[GeometryDistance] = []` * `angles: list[GeometryAngle] = []` * `bond_slack: float = 0.0` * `contact_max: float = 0.0` * `notes: list[str] = []` ### *class* rx.GuardFinding One guard hit, as data: which parameters, which number, which code. * `code: str` * `paths: tuple[str, ...]` * `value: float | None` * `message: str` * `detail: str = ''` * `limit: tuple[str, float] | None = None` ### *class* rx.Harmonic An nth-order contribution at λ/n from a monochromator that passes order. * `order: int` * `weight: Parameter = Parameter(0.01, min=0.0)` ### rx.help_key_for(path: str) → str | None The family glob that claims a parameter dot-path, or `None`. ### rx.help_registry() → dict[str, object] The whole corpus as JSON-able data, for `GET /api/help`. ### *class* rx.HelpEntry What one name is, in the fields a reference entry always carries. * `title: str` * `description: str` * `unit: str | None = None` * `default: str | None = None` * `typical: str | None = None` * `anchor: str | None = None` * `label: str | None = None` ### *class* rx.HistogramResult One pattern’s slice of a multi-histogram joint refinement. * `label: str = ''` * `weight: float = 1.0` * `statistics: Statistics` * `two_theta: list[float] = []` * `y_obs: list[float] = []` * `y_calc: list[float] = []` * `y_background: list[float] = []` * `sigma: list[float] = []` * `ticks: dict[str, list[float]] = {}` * `tick_hkl: dict[str, list[list[int]]] = {}` * `qpa: QuantitativePhaseAnalysis | None = None` * `restraints: RestraintReport | None = None` * `phase_agreement: list[PhaseAgreement] = []` * `diagnostics: list[Diagnostic] = []` ### *class* rx.HistoryNode One immutable checkpoint in the refinement DAG. * `id: str` * `parents: list[str] = []` * `action: NodeAction` * `state: RefinementState` * `metrics: NodeMetrics = NodeMetrics(…)` * `diagnostics: list[Diagnostic] = []` * `label: str = ''` * `created_utc: str = ''` * `scores: dict[str, float] = {}` * `notes: dict[str, str] = {}` * `schema_version: str | None = None` ### *class* rx.HistoryRecord One JSONL line. * `record: 'header' | 'node' | 'annotation'` * `header: TreeHeader | None = None` * `node: HistoryNode | None = None` * `annotation: Annotation | None = None` ### *class* rx.HumpComponent One explicit broad Gaussian added on top of whatever background is in use. * `position: Parameter = Parameter(0.0)` * `height: Parameter = Parameter(0.0, min=0.0)` * `fwhm: Parameter = Parameter(5.0, min=0.1)` * `kind: 'hump' = 'hump'` * `label: str | None = None` ### *class* rx.Identifiability Degeneracy evidence measured on the **final Jacobian** (WP-1055/-1056). * `background_absorption: dict[str, float] = {}` * `extra_peak_absorption: dict[str, float] = {}` * `top_correlations: list[CorrelationPair] = []` * `soft_modes: list[SoftMode] = []` * `exchangeability: list[ExchangeRow] = []` ### *class* rx.IncidentSpectrum The moderator spectrum a time-of-flight bank still carries, or none. * `itype: int = 0` * `coefficients: list[Parameter] = []` * `tof_min_us: float | None = None` * `tof_max_us: float | None = None` ### *class* rx.IndexingControls Everything an indexing *run* is asked with that is not the data itself. * `search: SearchSpecSpec = SearchSpecSpec(…)` * `engines: list[str] | None = None` * `validate_candidates: bool = True` * `check_top: int | None = None` ### *class* rx.IndexingEvidence The reasoning consumer’s view of an `IndexingResult` (WP-1043). * `candidates: list[CandidateEvidence] = []` * `systems_searched: list[str] = []` * `search_complete: dict[str, bool] = {}` * `systems_supported: list[str] = []` * `n_usable_lines: int = 0` * `fom_ranked: list[str] = []` * `fom_undefined: dict[str, str] = {}` * `validated: bool = False` ### *class* rx.LeBailValidation A candidate cell tested against the **whole pattern** by a Le Bail fit. * `rwp: float` * `gof: float` * `space_group: str` * `n_reflections: int` * `predicted_but_absent: int = 0` * `unmatched_observed: int = 0` * `predicted_but_absent_two_theta: list[float] = []` * `unmatched_observed_two_theta: list[float] = []` * `status: str = 'converged'` * `n_stages: int = 0` * `diagnostics: list[Diagnostic] = []` ### *class* rx.MagneticOnset Where along the series axis the moment stops being supported (WP-1329). * `path: str = ''` * `atom: str = ''` * `x: float | None = None` * `x_esd: float | None = None` * `bracket: list[float] = []` * `bracket_labels: list[str] = []` * `sense: 'falls' | 'rises' | 'none' = 'none'` * `monotone: bool = True` * `boundaries: list[list[float]] = []` * `n_supported: int = 0` * `n_held: int = 0` * `n_unmeasured: int = 0` * `unmeasured_labels: list[str] = []` * `n_unconverged: int = 0` * `bracket_verdicts_final: bool | None = None` * `note: str = ''` ### *class* rx.MagneticSymmetry A magnetic (Shubnikov) space group as the two magCIF loops that state it. * `operations: list[str]` * `centerings: list[str] = ['x,y,z,+1']` * `bns_number: str | None = None` * `og_number: str | None = None` * `uni_number: int | None = None` * `symbol: str | None = None` * `setting: str | None = None` * `propagation_vector_parent: tuple[str, str, str] | None = None` ### *class* rx.MagneticTrajectory |m| against the series axis, with the held patterns marked as held. * `path: str` * `x: list[float] = []` * `x_label: str = 'index'` * `value: list[float] = []` * `stderr: list[float | None] = []` * `labels: list[str] = []` * `positions: list[int] = []` * `supported: list[bool] = []` * `measured: list[bool] = []` * `status: list[str] = []` * `atom: str = ''` * `ion: str = ''` * `onset: MagneticOnset | None = None` ### *class* rx.MicroabsorptionCorrection Mixture-level record of the Brindley correction (Brindley, 1945). * `method: 'brindley_sphere' = 'brindley_sphere'` * `wavelength: float` * `mu_mean_cm: float` ### *class* rx.MicrostructureTerm One profile coefficient read as the physical quantity behind it. * `path: str` * `kind: 'size' | 'strain'` * `coefficient: float` * `value: float | None = None` * `esd: float | None = None` * `unavailable: str | None = None` ### *class* rx.Moment A magnetic moment on a site, in crystal-axis components (μ_B). * `crystalaxis_x: Parameter = Parameter(0.0)` * `crystalaxis_y: Parameter = Parameter(0.0)` * `crystalaxis_z: Parameter = Parameter(0.0)` * `ion: str` * `g: float | None = None` ### *class* rx.MomentAngleTest One round of the stationary-angle test on a stage’s covariance (WP-1929). * `paths: list[str]` * `reached: bool` * `statistic: float | None = None` * `cut: float` * `zeroed: bool` * `stationary_at: dict[str, float] = {}` * `half_widths: dict[str, float] = {}` ### *class* rx.NodeAction The edge operation that produced a node from its parent or parents. * `kind: 'root' | 'stage' | 'set_vary' | 'set_value' | 'set_tie' | 'set_variable' | 'set_hold' | 'edit_model' | 'merge'` * `name: str = ''` * `turn_on: list[str] = []` * `turn_off: list[str] = []` * `values: dict[str, float] = {}` * `max_iter: int = 100` * `lebail_cycles: int = 3` * `seed: float = 0.0` * `strain_seed: float = 0.0` * `restraint_weight_scale: float = 1.0` * `ftol: float | None = None` * `window_slack_deg: float | None = None` * `window_area_tol: float | None = None` * `phase_support_sigma: float | None = 3.0` * `correlation_guard: float = 0.98` * `ties: dict[str, TieSpec] = {}` * `untied: list[str] = []` * `variables: dict[str, Parameter] = {}` * `removed_variables: list[str] = []` * `held: list[str] = []` * `unheld: list[str] = []` ### *class* rx.NodeMetrics Cached scalars so queries (`best`, `compare`) need no recompute. * `statistics: Statistics | None = None` * `status: 'converged' | 'max_iter' | 'diverged' | None = None` * `n_iterations: int = 0` * `cost_initial: float | None = None` * `cost_final: float | None = None` * `stderr: dict[str, float] = {}` * `held_scale_phases: list[int] = []` ### *exception* rx.NoPhasesError An exception. A refining verb was handed a model with no phases (WP-1207). ### *class* rx.ObservedPeak One measured line: a fitted position with its esd, width, shape, area. * `two_theta: float` * `two_theta_esd: float` * `two_theta_esd_fit: float | None = None` * `intensity: float` * `intensity_esd: float` * `q: float` * `q_esd: float` * `fwhm: float` * `eta: float` * `group: int` * `n_in_group: int` * `chi2_red: float` * `flags: list['ghost_kbeta' | 'ghost_tungsten' | 'excluded' | 'fit_failed' | 'sigma_assumed' | 'unresolved_shoulder' | 'position_at_bound' | 'asymmetry_unmodelled' | 'not_separable' | 'background_extrapolated' | 'axial_tail' | 'kalpha2_residual' | 'no_intensity' | 'unnamed_neighbour' | 'position_unmeasured' | 'duplicate_line' | 'weak_line' | 'unresolved_split' | 'width_capped'] = []` * `origin: 'fitted' | 'manual' | 'edited' = 'fitted'` ### *class* rx.ParameterCandidate One held-but-refinable parameter, scored at the current state. * `path: str` * `gain: float` * `gradient: float` * `absorption: float = 0.0` * `seeded: bool = False` * `seed_value: float | None = None` * `action_kind: str | None = None` ### *class* rx.ParameterInterval The profile interval for one refined parameter. * `path: str` * `value: float` * `stderr: float | None` * `at_bound: bool | None` * `level: float` * `one_sided: bool` * `quantile: float` * `delta_chi2_cut: float` * `lower: float | None` * `upper: float | None` * `lower_stop: 'threshold' | 'bound' | 'refits' | 'error' | 'period'` * `upper_stop: 'threshold' | 'bound' | 'refits' | 'error' | 'period'` * `chi2_fit: float` * `chi2_lowest: float` * `fit_is_minimum: bool` * `points: list[ParameterIntervalPoint] = []` * `n_refits: int` ### *class* rx.ParameterIntervalPoint One pinned value and the lowest data χ² its refits reached there. * `value: float` * `runs: int` * `chi2: float | None = None` * `delta_chi2: float | None = None` * `status: str | None = None` * `error: str | None = None` * `node_id: str | None = None` ### *class* rx.ParametricCoefficient One refined coefficient of a `ParametricEquation`, in user units. * `equation: str` * `target: str` * `term: str` * `path: str` * `value: float` * `esd: float | None` * `vary: bool` * `unit: str | None` * `reference: dict[str, float] | None` ### *class* rx.ParametricEquation One target refined as a declared linear function of the coordinates. * `name: str` * `target: str` * `basis: 'constant' | 'polynomial' | 'design'` * `terms: list[list[str]] | None = None` * `design: list[list[float]] | None = None` * `patterns: list[int] | None = None` * `reference: dict[str, float] | None = None` * `scale: dict[str, float] | None = None` ### *class* rx.ParametricFormReading One reading of a form test (`ParametricFormTest`), or of every tested declaration at once (`RefinementResult.parametric_form_joint `). * `dof: int` * `statistic: float | None` * `cut: float | None` * `rejected: bool | None` * `p_value: float | None` ### *class* rx.ParametricFormTest Whether one `ParametricEquation`’s form survives its own data. * `equation: str` * `target: str` * `n_patterns: int` * `n_subset: int` * `rejected: bool | None` * `tied: ParametricFormReading | None` * `others_freed: ParametricFormReading | None` * `provisional_on: list[str]` ### *class* rx.ParametricValue One declaration’s target evaluated at a coordinate, with its esd. * `equation: str` * `target: str` * `coordinates: dict[str, float]` * `row: list[float] | None` * `value: float` * `esd: float | None` * `unit: str | None` * `outside: list[str] | None` * `form_rejected: bool | None` * `provisional_on: list[str]` * `joint_rejected: bool | None` ### *class* rx.PeakComponent One declared sharp pseudo-Voigt peak the phases cannot account for. * `center: Parameter = Parameter(0.0)` * `area: Parameter = Parameter(0.0, min=0.0)` * `fwhm: Parameter = Parameter(0.1, min=0.005, max=0.5)` * `eta: Parameter = Parameter(0.5, min=0.0, max=1.0)` * `all_lines: bool = True` * `kind: 'peak' = 'peak'` * `label: str | None = None` ### *class* rx.PeakList Every resolvable line in one pattern, with per-line σ. * `peaks: list[ObservedPeak]` * `wavelength: float` * `two_theta_min: float` * `two_theta_max: float` * `source: 'fitted' | 'positions' = 'fitted'` * `thresholds_version: str = '1.11'` * `diagnostics: list[Diagnostic] = []` ### *class* rx.PhaseAgreement One phase’s structure-sensitive agreement indices (WP-1069). * `name: str` * `r_bragg: float | None = None` * `r_f: float | None = None` * `n_reflections: int = 0` ### *class* rx.PhaseMicrostructure A phase’s size and strain as physical numbers, with esds (WP-1131). * `phase_index: int` * `phase_name: str = ''` * `wavelength: float | None = None` * `scherrer_k: float` * `terms: list[MicrostructureTerm] = []` * `size_agreement: float | None = None` * `strain_agreement: float | None = None` * `separable: bool | None = None` * `size_strain_collinearity: float | None = None` ### *class* rx.PhaseQuantity One phase’s quantitative-analysis row (Hill & Howard, 1987). * `name: str` * `weight_fraction: float | None` * `weight_fraction_stderr: float | None = None` * `scale: float` * `z: int | None = None` * `molar_mass: float | None = None` * `cell_mass: float` * `cell_volume: float` * `zmv: float` * `weight_fraction_corrected: float | None = None` * `brindley_tau: float | None = None` * `mu_cm: float | None = None` * `mu_r: float | None = None` * `particle_radius_um: float | None = None` ### *class* rx.PhaseTexture One phase’s spherical-harmonics texture at the answer (WP-1960). * `name: str` * `texture_index: float` * `min_p_reflections: float` * `min_p_sphere: float` ### rx.PLAN_PRESETS A dict. Keys: `mccusker_default`, `mccusker_structural`, `lab_bragg_brentano`, `lab_calibrate`, `lab_sample_refine`, `profile_only`, `pawley_default`, `magnetic_width`. ### *class* rx.PlanInfo What a preset is for, in the words a chooser needs. * `title: str` * `description: str` * `modes: tuple[Mode, ...]` * `when_to_use: str` ### *class* rx.PlanSpec A staged plan as data that round-trips through JSON, mirroring `RefinementPlan`. * `stages: list[StageSpec] = []` * `correlation_guard: float = 0.98` * `intermediate_ftol: float | None = 1e-06` * `lebail_passes: int = 1` * `phase_support_sigma: float | None = 3.0` * `closing_window_tol: float | None = 0.001` ### *class* rx.ProfileTOF GSAS **type-3** time-of-flight profile coefficients. * `alpha0: Parameter = Parameter(0.0)` * `alpha1: Parameter = Parameter(0.0)` * `beta0: Parameter = Parameter(0.0)` * `beta1: Parameter = Parameter(0.0)` * `sig0: Parameter = Parameter(0.0, min=0.0)` * `sig1: Parameter = Parameter(0.0, min=0.0)` * `sig2: Parameter = Parameter(0.0, min=0.0)` * `gam0: Parameter = Parameter(0.0)` * `gam1: Parameter = Parameter(0.0)` * `gam2: Parameter = Parameter(0.0)` ### *class* rx.ProjectDoc The settings half of a project, stored as `project.json` (see the module docstring). * `format_version: str = '1.5'` * `package_version: str = ''` * `created_utc: str = ''` * `updated_utc: str = ''` * `patterns: list[DataRef] = []` * `plan: PlanSpec | None = None` * `mode: 'rietveld' | 'lebail' | 'pawley' = 'rietveld'` * `two_theta_limits: tuple[float, float] | None = None` * `excluded_regions: list[tuple[float, float]] = []` * `indexing: IndexingControls = IndexingControls(…)` * `history_file: str = 'history.jsonl'` * `ui: dict[str, Any] = {}` ### *class* rx.ProjectFormat One foreign refinement format this build reads, and how it is recognised. * `name: str` * `title: str` * `extensions: tuple[str, ...]` * `sniff: str` * `carries: tuple[str, ...]` * `reports_at: 'read' | 'build' | 'both'` * `matches: Callable[[Path], bool]` * `read: Callable[..., Any]` * `to_structure: Callable[..., Structure]` * `write: Callable[..., None] | None = None` * `refuses: str | None = None` ### *class* rx.ProjectModel What a foreign refinement file stated, and which format stated it. * `format: ProjectFormat` * `path: Path` * `stated: Any` * `diagnostics: tuple[Diagnostic, ...] = ()` ### *class* rx.Provenance Everything needed to reproduce a result. * `package_version: str` * `schema_version: str = '0.59'` * `backend: str = 'numpy'` * `dtype: str = 'float64'` * `solver: str = 'trf'` * `report_thresholds_version: str = '0.1'` * `created_utc: str | None = None` * `notes: dict[str, str] = {}` ### *class* rx.QuantitativePhaseAnalysis Per-phase weight fractions from the refined Rietveld scales. * `phases: list[PhaseQuantity]` * `method: 'zmv' = 'zmv'` * `crystalline_only: bool = True` * `unmeasured_phases: list[str] = []` * `unmeasured_held: list[str] = []` * `microabsorption: MicroabsorptionCorrection | None = None` * `microabsorption_skipped: str | None = None` ### *class* rx.Recipe One PowderLine recipe, resolved into what this package refines with. * `structure: Structure` * `instrument: Instrument` * `pattern: PatternData` * `plan: RefinementPlan` * `limits: tuple[float, float] | None` * `diagnostics: list[Diagnostic] = []` * `schema_name: str = 'GSASII_Rietveld'` * `schema_version: str = '0.26.0'` * `phase_names: tuple[str, ...] = ()` ### *exception* rx.RecipeError An exception. A recipe this reader refuses, naming the field that caused it. ### *class* rx.RefinedParametricEquation One parametric declaration as the fit resolved it, with what a reader needs to evaluate it anywhere (WP-1325). * `equation: ParametricEquation` * `unit: str | None` * `span: dict[str, tuple[float, float]]` * `covariance: list[list[float]] | None` ### *exception* rx.RefinementCancelled An exception. Raised out of a fit whose `CancelToken` was set. ### *class* rx.RefinementState Everything needed to reconstruct a refinement exactly. * `structure: Structure` * `instrument: Instrument` * `mode: 'rietveld' | 'lebail' | 'pawley' = 'rietveld'` * `free_paths: list[str] = []` * `free_declared: bool = False` * `two_theta_limits: tuple[float, float] | None = None` * `reflections: list[ReflectionState] = []` * `ties: dict[str, TieSpec] = {}` * `variables: dict[str, Parameter] = {}` * `holds: list[str] = []` ### *class* rx.RefinementTree(header: [TreeHeader](#rx.TreeHeader), \*, path: str | Path | None = None) A record of every state a refinement passed through, and how. ### *class* rx.ReflectionPairScreen Evidence behind a shift measured from harmonic reflection pairs. * `n_pairs: int` * `n_candidate_triples: int` * `n_clustered: int` * `null_k_mean: float` * `null_k_std: float` * `z: float` * `p_value: float` * `null_replicates: int` * `seed: int` * `scatter_deg: float` * `refuted_templates: list[str] = []` * `declined_reason: str | None = None` ### *class* rx.ReflectionRow One (emission line, reflection) row of a reflection table. * `phase: str` * `line: int` * `wavelength: float` * `h: int` * `k: int` * `l: int` * `d: float` * `two_theta: float` * `multiplicity: int` * `f_squared: float | None` * `intensity: float` * `satellite_order: int = 0` * `component: str = 'total'` * `phase_index: int = 0` ### *class* rx.ReflectionState Per-hkl intensities, the state that is *not* in the parameter vector. * `phase_index: int` * `hkl: list[list[int]] = []` * `satellite_order: list[int] | None = None` * `intensity: list[float] = []` * `kind: 'lebail_extracted' | 'pawley_refined' = 'lebail_extracted'` * `stderr: list[float] | None = None` * `varied: bool = False` ### *class* rx.RegionAttribution What a locally linear model says is wrong in one region. * `two_theta_lo: float` * `two_theta_hi: float` * `n_reflections: int` * `chi2_share: float` * `mean_two_theta: float` * `mean_fwhm: float` * `coefficients: list[BasisCoefficient] = []` * `r2: float` * `gram_condition: float` * `chi2_reduced: float = 0.0` * `has_significant_misfit: bool = True` * `gates_passed: bool` * `gate_failures: list[GateFailure] = []` ### *class* rx.RestraintReport Per-restraint deviations and the pooled restraint χ² (WP-0406). * `rows: list[RestraintRow]` * `restraint_chi2: float` * `n_restraints: int` * `weight_scale: float = 1.0` ### *class* rx.RestraintRow One soft restraint’s computed-vs-target deviation (WP-0406). * `phase_index: int | None = None` * `kind: 'bond' | 'angle' | 'value' | 'tether' | 'anti_bump'` * `atoms: list[int] | None = None` * `path: str | None = None` * `computed: float` * `target: float` * `sigma: float` * `weight: float = 1.0` * `deviation: float` * `deviation_over_sigma: float` ### *class* rx.RigidBody A set of a phase’s atoms that moves as one rigid template (WP-1805, #561). * `name: str` * `atoms: list[str]` * `template: list[tuple[float, float, float]]` * `origin: BodyOrigin` * `orientation: tuple[float, float, float, float] = (1.0, 0.0, 0.0, 0.0)` * `rotation_vary: bool = False` * `torsions: list[BodyTorsion] = []` * `riding: list[str] = []` ### *class* rx.RoughnessPitschke Surface-roughness intensity correction, Pitschke *et al.* (1993) form. * `kind: 'pitschke' = 'pitschke'` * `c: Parameter = Parameter(0.0, min=0.0, max=4.0)` * `tau: Parameter = Parameter(0.05, min=0.0, max=0.3)` ### *class* rx.RoughnessSuortti Surface-roughness intensity correction, Suortti (1972) form. * `kind: 'suortti' = 'suortti'` * `a: Parameter = Parameter(0.5, min=0.0, max=1.0)` * `b: Parameter = Parameter(0.0, min=0.0, max=5.0)` ### *class* rx.SearchSpecSpec Mirrors `indexing.engines.SearchSpec`; every engine reads the same one. * `systems: list[str] | None = None` * `centrings: dict[str, list[str]] | None = None` * `min_d_axis: float = 2.0` * `max_d_axis: float = 25.0` * `min_volume: float = 15.0` * `max_volume: float | None = None` * `n_unindexed: int | 'inliers' | None = None` * `n_search_lines: int = 20` * `k_sigma: float = 3.0` * `shift_allowance_deg: float = 0.0` * `shift_template: str | None = None` * `budget_seconds: float = 30.0` * `total_budget_seconds: float | None = None` * `preset: str | None = None` * `max_candidates: int = 12` * `seed: int = 0` * `prior_cells: list[tuple[float, float, float, float, float, float]] | None = None` * `prior_spacegroups: list[str] | None = None` ### *class* rx.SeriesFailure One pattern the chain could not fit at all. * `index: int` * `label: str` * `exception: str` ### *class* rx.SeriesStep One step `SEQUENTIAL_DISCONTINUITY` flagged, as fields (WP-1469). * `path: str` * `labels: tuple[str, str]` * `indices: tuple[int, int]` * `step: float` ### *class* rx.SharingMap Which parameter paths are shared across histograms vs. * `per_histogram: list[str] = []` * `shared: list[str] = []` ### *class* rx.ShiftScreen Which physical cause a systematic 2θ shift has, or that it has none that can be named over the range measured. * `n_lines: int` * `templates: list[ShiftTemplateFit] = []` * `best: str | None = None` * `separable: bool = False` * `separability_ratio: float = 0.0` * `max_collinearity: float = 0.0` * `sigma_sys_deg: float = 0.0` * `prediction_spread_deg: float = 0.0` * `allowance_deg: float = 0.0` * `source: 'measured' | 'reflection_pairs' | 'unavailable' = 'unavailable'` * `pairs: ReflectionPairScreen | None = None` ### *class* rx.ShiftTemplateFit One systematic-shift template fitted **alone** to the deviations. * `name: str` * `coefficient: float` * `stderr: float` * `r2: float` * `residual_ss: float` ### *class* rx.SoftMode One near-null direction of the scale-normalised normal matrix. * `eigenvalue: float` * `loadings: dict[str, float] = {}` ### *class* rx.SphericalHarmonicTexture Spherical-harmonics preferred-orientation correction (Von Dreele 1997). * `order: int` * `coefficients: dict[str, Parameter] = {}` ### *class* rx.StageSpec One stage of a staged plan as data that round-trips through JSON, mirroring `Stage`. * `name: str` * `turn_on: list[str] = []` * `max_iter: int = 100` * `ftol: float | None = None` * `lebail_cycles: int = 3` * `seed: float = 0.0` * `strain_seed: float = 0.0` * `restraint_weight_scale: float = 1.0` * `window_slack_deg: float | None = None` ### *class* rx.SuggestedAction An advisory, typed suggestion. * `kind: 'refine_zero_shift' | 'refine_sample_displacement' | 'refine_sample_transparency' | 'refine_capillary_offset_along_beam' | 'refine_capillary_offset_across_beam' | 'refine_cell' | 'refine_profile_widths' | 'refine_sample_size_broadening' | 'refine_sample_strain_broadening' | 'refine_axial_asymmetry' | 'refine_biso' | 'refine_preferred_orientation' | 'refine_scale' | 'add_impurity_phase' | 'increase_background_flexibility' | 'decrease_background_flexibility' | 'reindex_or_recheck_cell' | 'collect_better_data'` * `confidence: float` * `rationale: str` * `parameter_paths: list[str] = []` * `expected_delta_chi2: float | None = None` * `alternatives: list['refine_zero_shift' | 'refine_sample_displacement' | 'refine_sample_transparency' | 'refine_capillary_offset_along_beam' | 'refine_capillary_offset_across_beam' | 'refine_cell' | 'refine_profile_widths' | 'refine_sample_size_broadening' | 'refine_sample_strain_broadening' | 'refine_axial_asymmetry' | 'refine_biso' | 'refine_preferred_orientation' | 'refine_scale' | 'add_impurity_phase' | 'increase_background_flexibility' | 'decrease_background_flexibility' | 'reindex_or_recheck_cell' | 'collect_better_data'] = []` * `two_theta_range: tuple[float, float] | None = None` * `vetoed_by: str | None = None` * `execution: 'stage' | 'index' | 'advice' | None = None` ### *class* rx.SupercellCheck This candidate asked as a superlattice of another reported candidate. * `parent_cell: tuple[float, float, float, float, float, float]` * `parent_system: str` * `parent_centring: str` * `index: int` * `n_extra: int` * `n_seen: int` * `p0: float` * `p_value: float` * `n_seen_unexplained: int | None = None` * `verdict: 'supported' | 'refuted' | 'undecided'` * `absent_two_theta: list[float] = []` ### *class* rx.TetherRestraint A one-sided distance restraint: zero inside `max_distance`, linear outside. * `atom_i: int` * `atom_j: int` * `max_distance: float` * `sigma: float` * `weight: float = 1.0` * `op_index: int | None = None` * `translation: tuple[int, int, int] = (0 × 3)` ### *class* rx.TieSpec The JSON form of `params.vector.AffineTie`, value = Σ c·src + k. * `terms: list[tuple[str, float]] = []` * `const: float = 0.0` * `user: bool = False` ### *class* rx.TOFSource Neutron **time-of-flight** bank: a white beam, a fixed detector angle. * `kind: 'neutron_tof' = 'neutron_tof'` * `difc: Parameter` * `difa: Parameter = Parameter(0.0)` * `tzero: Parameter = Parameter(0.0)` * `difb: Parameter = Parameter(0.0)` * `two_theta_bank_deg: float` * `l1_m: float | None = None` * `l2_m: float | None = None` * `profile_tof: ProfileTOF = ProfileTOF(…)` * `incident_spectrum: IncidentSpectrum = IncidentSpectrum(…)` ### *class* rx.Trajectory One parameter’s path across the series, with its per-point esds. * `path: str` * `x: list[float] = []` * `x_label: str = 'index'` * `value: list[float] = []` * `stderr: list[float | None] = []` * `labels: list[str] = []` * `positions: list[int] = []` ### *class* rx.TreeHeader Identifies the tree and the pattern every node is fitted against. * `tree_id: str` * `created_utc: str = ''` * `data_fingerprint: str = ''` * `data_source: str = ''` * `n_points: int = 0` * `plan: PlanSpec | None = None` * `package_version: str = ''` * `schema_version: str = '0.59'` ### *class* rx.ValueRestraint A soft restraint pulling a single parameter toward `target`. * `path: str` * `target: float` * `sigma: float` * `weight: float = 1.0`