config

tit.analyzer.config

Configuration dataclass for the analyzer runner.

Pure Python -- no SimNIBS, numpy, nibabel, or other heavy dependencies. Mirrors the tit.opt.config / tit.sim.config pattern: a thin, typed wrapper around the dict keys :mod:tit.analyzer.__main__ already reads (both its "single" and "group" dispatch branches), so :mod:tit.config_io can generate a JSON Schema for it and the desktop UI can validate a form against that schema before submitting the job.

This module does not change tit.analyzer.__main__ in any way -- it is a read of what that entry point already accepts (see its docstring and the _run_single / _run_group dict lookups), not a new contract the runner must adopt. See AnalyzerConfig's "Notes" for the one runner behavior this dataclass does not express.

See Also

tit.analyzer.main : Reads the exact dict keys this dataclass mirrors. tit.analyzer.group.run_group_analysis : Consumed by the "group" branch. tit.analyzer.analyzer.Analyzer : Consumed by the "single" branch.

AnalysisMode

Bases: StrEnum

Which entry-point branch handles this config.

Attributes

SINGLE : str One subject, via :class:tit.analyzer.Analyzer. GROUP : str Multiple subjects, via :func:tit.analyzer.run_group_analysis.

AnalyzerSpace

Bases: StrEnum

Where the field is read from.

Attributes

MESH : str SimNIBS surface/volume mesh. VOXEL : str MNI-space NIfTI volume.

AnalysisType

Bases: StrEnum

Region-of-interest shape.

Attributes

SPHERICAL : str A sphere at center with radius radius. CORTICAL : str An atlas region on atlas. SUBCORTICAL : str Label(s) region of the volume atlas atlas, in coordinate_space (a subject atlas, or a shipped MNI atlas warped to the subject). MASK : str The positive voxels of the NIfTI mask_path.

AnalyzerCoordinateSpace

Bases: StrEnum

Space of center for a spherical ROI.

Attributes

SUBJECT : str Native subject-space coordinates (mm). MNI : str MNI coordinates, transformed to subject space before analysis.

AnalyzerConfig dataclass

AnalyzerConfig(mode: AnalysisMode = SINGLE, subject_id: str | None = None, subject_ids: list[str] = field(default_factory=list), simulation: str = '', space: AnalyzerSpace = MESH, tissue_type: str = 'GM', analysis_type: AnalysisType = SPHERICAL, field: str | None = None, center: list[float] | None = None, radius: float | None = None, coordinate_space: AnalyzerCoordinateSpace = SUBJECT, atlas: str | None = None, region: str | list[str] | None = None, output_dir: str | None = None, visualize: bool = True, mask_path: str | None = None)

Configuration for one analyzer run (single subject or group).

Attributes

mode : AnalysisMode "single" (one subject, subject_id) or "group" (multiple subjects, subject_ids). subject_id : str or None Subject identifier. Required when mode is "single". subject_ids : list of str Subject identifiers. Required (non-empty) when mode is "group". simulation : str Simulation (montage) folder name. space : AnalyzerSpace "mesh" or "voxel". tissue_type : str "GM", "WM", or "both" (voxel space only). analysis_type : AnalysisType ROI shape; see :class:AnalysisType. field : str or None Field to analyze (a name from constants.FIELD_REGISTRY). None resolves the TI_max/mTI_max envelope automatically. center : list of float or None [x, y, z] sphere center in mm. Required for analysis_type="spherical". radius : float or None Sphere radius in mm. Required for analysis_type="spherical". coordinate_space : AnalyzerCoordinateSpace Space of center (spherical), of the volume atlas (subcortical) or of mask_path (mask). atlas : str or None Atlas name. Required for analysis_type="cortical" and "subcortical". region : str or list of str or None Region name(s) within atlas (cortical, subcortical). mask_path : str or None NIfTI mask; positive voxels select the ROI in coordinate_space. output_dir : str or None Override output directory. None derives it from PathManager. visualize : bool Generate visualization artifacts.

Raises

ValueError If mode is "single" without subject_id, "group" without subject_ids, if analysis_type is "spherical" without both center and radius, or "cortical"/"subcortical" without atlas.

Notes

region is a single canonical field here; the runner reads data.get("regions") or data.get("region") (two keys, "regions" preferred). Serializing this dataclass writes only "region", which the runner already falls back to, so single-region submissions work unchanged; only the plural alias is not reproduced.

See Also

tit.analyzer.main : The entry point whose accepted keys this dataclass mirrors.