Function phase_offset_removal 

pub fn phase_offset_removal(
    phases: &[impl AsRef<[f64]>],
    mags: &[impl AsRef<[f64]>],
    tes: &[f64],
    mask: &[u8],
    sigma: [f64; 3],
    echoes: [usize; 2],
    unwrap_method: UnwrapMethod,
    grid: &Grid,
) -> (Vec<Vec<f64>>, Vec<f64>)

MCPC-3D-S phase offset estimation for single-coil multi-echo data

Implements the MCPC-3D-S algorithm from MriResearchTools.jl for single-coil data. This estimates and removes the phase offset (φ₀) from each echo.

Arguments

• phases - Phase data for all echoes, shape [n_echoes][nxnynz]
• mags - Magnitude data for all echoes, shape [n_echoes][nxnynz]
• tes - Echo times in ms
• mask - Binary mask
• sigma - Smoothing sigma in voxels [sx, sy, sz], default [10, 10, 5]
• echoes - Which echoes to use for HIP calculation, default [0, 1] (first two)
• nx, ny, nz - Dimensions

Returns

(corrected_phases, phase_offset) where:

• corrected_phases: phases with offset removed
• phase_offset: estimated phase offset Remove phase offset from multi-echo phase data using HIP (Hermitian Inner Product).

Estimates the spatially-varying phase offset from the phase difference between two echoes, smooths it with a Gaussian filter, and subtracts it from all echoes.

Arguments

• phases - Wrapped phase per echo (n_echoes arrays of nxnynz)
• mags - Magnitude per echo
• tes - Echo times (any consistent unit)
• mask - Binary mask
• sigma - Gaussian smoothing sigma in voxels [x, y, z]
• echoes - Which two echoes to use for HIP [e1, e2]
• unwrap_method - Method to unwrap the HIP phase (Romeo or Laplacian)
• grid - Volume grid (dimensions and voxel sizes)

Returns

(corrected_phases, phase_offset) — offset-corrected phases and the estimated offset