Struct ScanMetadata 

pub struct ScanMetadata {
    pub dims: (usize, usize, usize),
    pub voxel_size: (f64, f64, f64),
    pub echo_times: Vec<f64>,
    pub field_strength: f64,
    pub b0_direction: (f64, f64, f64),
    pub slice_geometry: Option<SliceGeometry>,
    pub affine: Option<[f64; 16]>,
}

Metadata about the scan

Fields

dims: (usize, usize, usize)

Volume dimensions (nx, ny, nz)

voxel_size: (f64, f64, f64)

Voxel size in mm (vsx, vsy, vsz)

echo_times: Vec<f64>

Echo times in seconds

field_strength: f64

Main field strength in Tesla

b0_direction: (f64, f64, f64)

B0 direction as unit vector in voxel coordinates

slice_geometry: Option<SliceGeometry>

Slice thickness and slice axis, when the acquisition recorded them.

voxel_size along the slice axis is the slice-to-slice pitch; this supplies the thickness, and the two together say whether the sampled volume has holes in it. A 2D multi-slice acquisition often leaves a gap, and a gapped volume cannot be reconstructed at all — the FFT dipole and spherical-mean kernels are defined on a uniform grid, so on one with holes they compute a different convolution and produce a map that is wrong while still looking like a susceptibility map.

None means the acquisition did not say. BIDS only recommends SliceThickness, so this is common, and a gap then cannot be detected by this crate or by anything else reading the NIfTI alone. The stages run anyway rather than refusing the vast majority of data that has no gap — so a host that can read the field should set it, and a host that cannot should tell its user that this check could not run. See Grid::require_contiguous_slices_if_known.

affine: Option<[f64; 16]>

The image’s voxel→world affine (row-major 4×4, as in a NIfTI sform/qform), when the host has one. Only the steps that need the anatomical orientation read it — currently MaskOp::MindGrab, which errors without it; everything else works in voxel space.

Implementations

impl ScanMetadata

pub fn grid(&self) -> Grid

Get a Grid from this metadata’s dimensions and voxel sizes.

pub fn echo(&self, e: usize) -> ScanMetadata

This scan’s metadata for echo e alone (echo_times = [echo_times[e]]), for the stages of a per-echo reconstruction (QsmPipelineConfig::qsm_per_echo): each echo’s field, local field and χ are computed at that echo’s time. Panics if e is out of range.

pub fn require_contiguous_slices(&self) -> Result<(), PipelineError>

Refuse an acquisition whose slices are not contiguous.

Every stage that convolves with a kernel defined on the voxel grid calls this first — background removal, dipole inversion, TGV, chi-separation. They call it unconditionally rather than per algorithm, because every one of those is three-dimensional: a complete background removal needs a 3D stage to have the mean value property at all, and the dipole kernel is inherently 3D, so there is no variant for which a gap is harmless.

Phase unwrapping deliberately does not call this. A gap degrades 3D unwrapping too, but the remedy there is to unwrap in plane (crate::unwrap::unwrap_slicewise) rather than to refuse, and refusing would block the one path that handles the case.

Returns PipelineError::InvalidInput carrying the measured thickness, pitch and gap.

Trait Implementations

impl Clone for ScanMetadata

fn clone(&self) -> ScanMetadata

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ScanMetadata

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.