tomojax.io

Raw detector frames are read with tomojax.load_frames and corrected with tomojax.corrections. Expert helpers (acquisition readers, NXtomo containers, inspection, JSON) are in tomojax.io.api.

ProjectionDatasetCopy Anchor Link

class ProjectionDataset(
    projections: np.ndarray,
    angles: np.ndarray,
    volume: np.ndarray | jax.Array | None = None,
    detector: Detector | None = None,
    grid: Grid | None = None,
    geometry_type: str = 'parallel',
    geometry_metadata: dict[str, Any] = dict(),
    angle_offset_deg: np.ndarray | None = None,
    align_params: np.ndarray | None = None,
    align_gauge: dict[str, JsonValue] | None = None,
    misalign_spec: dict[str, JsonValue] | None = None,
    source_path: str | None = None,
    source_format: str | None = None,
    sample_name: str | None = None,
    _metadata: NXTomoMetadata | None = None,
)

Standard public in-memory projection dataset.

This is the current IO boundary. It contains measured projection data, normalized metadata needed by reconstruction/alignment code, and the optional reconstructed volume when a processed container stores one. angles holds each view's rotation angle, in degrees.

ParametersCopy Anchor Link

projections : numpy.ndarray Measured projections in (view, v, u) order. angles : numpy.ndarray One rotation angle per view, in degrees. volume : numpy.ndarray, jax.Array or None, optional Reconstructed volume in (x, y, z) order, when present. detector : Detector or None, optional Detector pixel counts, pitches and physical centre. grid : Grid or None, optional Reconstruction voxel grid. geometry_type : str, optional Geometry family, such as parallel, lamino or cone. geometry_metadata : dict, optional Additional geometry and acquisition metadata. angle_offset_deg : numpy.ndarray or None, optional Per-view angular corrections in degrees. align_params : numpy.ndarray or None, optional Saved per-view alignment parameters, with convention in align_gauge. align_gauge : dict or None, optional Gauge and frame metadata for saved alignment parameters. misalign_spec : dict or None, optional Simulation misalignment record; angles already include simulated offsets. source_path : str or None, optional Original input path. source_format : str or None, optional Original container format. sample_name : str or None, optional Sample name retained on output. _metadata : NXTomoMetadata or None, optional Internal retained acquisition metadata; normally populated by from_nxtomo.

ProjectionDataset.from_nxtomoCopy Anchor Link

@classmethod
from_nxtomo(
    payload: LoadedNXTomo,
    *,
    source_path: PathLike | None = None,
) -> ProjectionDataset

Build a public dataset from the lower-level NXtomo payload.

ParametersCopy Anchor Link

payload : LoadedNXTomo NXtomo projection payload and persistence metadata. source_path : str, pathlib.Path or None, optional Input path retained as provenance.

ReturnsCopy Anchor Link

ProjectionDataset Normalized in-memory dataset with arrays and typed grid/detector metadata.

RaisesCopy Anchor Link

ValueError If grid or detector metadata have invalid coordinate dimensions.

ProjectionDataset.to_nxtomo_metadataCopy Anchor Link

to_nxtomo_metadata() -> NXTomoMetadata

Return NXtomo metadata for saving this public dataset.

ReturnsCopy Anchor Link

NXTomoMetadata Persistence metadata reflecting the dataset's current fields.

ProjectionDataset.copy_metadataCopy Anchor Link

copy_metadata() -> NXTomoMetadata

Return writable persistence metadata for save/update workflows.

ReturnsCopy Anchor Link

NXTomoMetadata Writable metadata with copied arrays and retained acquisition information.

ProjectionDataset.geometry_inputsCopy Anchor Link

geometry_inputs() -> dict[str, Any]

Return normalized geometry metadata for reconstruction/alignment.

ReturnsCopy Anchor Link

dict Normalized geometry, detector, angle and alignment metadata.

RaisesCopy Anchor Link

ValueError If detector metadata are missing.

ProjectionDataset.prepare_center_seedCopy Anchor Link

prepare_center_seed() -> ProjectionDataset

Prepare axial centre inference from recorded pitches, without reading pixels.

The pending seed is not calibrated; loading must estimate its centre before returning frames. Inspection can check the remaining required metadata.

ReturnsCopy Anchor Link

ProjectionDataset Original record or a copy with an internal pending detector seed.

ValidationReportCopy Anchor Link

class ValidationReport()

Public dataset validation result.

AttributesCopy Anchor Link

issues : list of str Validation problems; an empty list means none were found.

build_geometry_from_dataset_metadataCopy Anchor Link

build_geometry_from_dataset_metadata(
    meta: Mapping[str, Any],
    *,
    grid_override: Grid | tuple[int, int, int] | list[int] | None = None,
    poses: bool = False,
    volume_shape: Sequence[int] | None = None,
) -> tuple[Grid, Detector, ScanGeometry]

Build geometry objects from normalized dataset metadata.

poses applies the per-view corrections and angle offsets saved with the data. Keeping this wrapper in tomojax.io makes the command/data dependency explicit and gives the ProjectionDataset solver contract one replacement point.

ParametersCopy Anchor Link

meta : mapping Normalized geometry metadata, as returned by geometry_inputs. grid_override : Grid, tuple of int, list of int or None, optional Replacement grid or (nx, ny, nz) dimensions. poses : bool, optional Apply saved per-view alignment and angle corrections; defaults to False. volume_shape : sequence of int or None, optional Fallback (nx, ny, nz) dimensions when no grid is recorded.

ReturnsCopy Anchor Link

grid : Grid Resolved reconstruction grid. detector : Detector Resolved detector geometry. geometry : ScanGeometry Per-view geometry, with saved corrections when requested.

RaisesCopy Anchor Link

ValueError If geometry metadata are incomplete or inconsistent.

load_datasetCopy Anchor Link

load_dataset(path: PathLike) -> ProjectionDataset

Load a standard TomoJAX projection dataset.

Supported direct inputs are NXtomo/HDF5 (.nx, .nxs, .h5, .hdf, .hdf5) and TomoJAX .npz payloads. TIFF stacks need explicit angle metadata, so use load_tiff_stack.

ParametersCopy Anchor Link

path : str or pathlib.Path NXtomo/HDF5 or TomoJAX NPZ dataset to read.

ReturnsCopy Anchor Link

ProjectionDataset Measured projections, normalized metadata and any saved volume.

RaisesCopy Anchor Link

ValueError If the format is unsupported or TIFF angles must be supplied separately. KeyError If required datasets are missing. OSError If the input cannot be opened.

load_tiff_stackCopy Anchor Link

load_tiff_stack(
    path: PathLike,
    *,
    angles: Sequence[float] | np.ndarray,
    detector: Detector | None = None,
    grid: Grid | None = None,
    geometry_type: str = 'parallel',
    geometry_metadata: Mapping[str, Any] | None = None,
) -> ProjectionDataset

Load grayscale TIFF pages with explicit view angles, in degrees.

ParametersCopy Anchor Link

path : str or pathlib.Path Multipage TIFF or folder of naturally sorted TIFF files. angles : array-like Finite one-dimensional view angles in degrees, one per grayscale page. detector : Detector or None, optional Detector geometry to attach to the dataset. grid : Grid or None, optional Reconstruction grid to attach to the dataset. geometry_type : str, optional Geometry family; defaults to parallel. geometry_metadata : mapping or None, optional Additional geometry metadata.

ReturnsCopy Anchor Link

ProjectionDataset Float32 TIFF samples and supplied metadata; no intensity correction is applied.

RaisesCopy Anchor Link

ValueError If pages are not consistent grayscale frames or angles do not match them. FileNotFoundError If the input contains no TIFF frames.

save_datasetCopy Anchor Link

save_dataset(path: PathLike, dataset: ProjectionDataset) -> None

Save a public projection dataset as NXtomo/HDF5 or NPZ.

ParametersCopy Anchor Link

path : str or pathlib.Path NXtomo/HDF5 or NPZ output path; existing files are overwritten. dataset : ProjectionDataset Projections, geometry and optional volume to persist.

ReturnsCopy Anchor Link

None Write the dataset to disk without changing its metadata.

RaisesCopy Anchor Link

ValueError If the output suffix is not supported. OSError If the output cannot be written.

validate_datasetCopy Anchor Link

validate_dataset(path: PathLike) -> ValidationReport

Validate a user dataset path using the public IO boundary.

ParametersCopy Anchor Link

path : str or pathlib.Path Dataset path to inspect for structural validity and missing raw calibration.

ReturnsCopy Anchor Link

ValidationReport Issues found in the file or format; an empty issues list means none were found.