processing.phasing

processing.phasing

Functions¶

Name	Description
autophase	Automatically calculate and apply phase correction to a spectrum.
phase	Apply zero- and first-order (linear) phase correction to a spectrum.

autophase¶

processing.phasing.autophase(
    da,
    dim=None,
    method='acme',
    mode='single',
    peak_width=0.5,
    target_coord=None,
    p0_only=False,
    lb=0.0,
    temp_time_dim=DIMS.time,
    **kwargs,
)

Automatically calculate and apply phase correction to a spectrum.

Parameters¶

Name	Type	Description	Default
da	xr.DataArray	The input frequency-domain spectrum. Can be N-dimensional.	required
dim	str or None	The spectral dimension to operate on. If `None` (default) it is resolved automatically to the spectral dim present (`frequency` [Hz] or `chemical_shift` [ppm]); time-domain input is transformed to a spectrum first.	`None`
method	(acme, peak_minima, positivity)	The scoring algorithm to use. “acme” relies on entropy and is best for multi-peak high SNR spectra. “positivity” and “peak_minima” are optimized for sparse/noisy spectra. By default “acme”.	`"acme"`
mode	(single, all)	Determines how N-dimensional data is handled. - “single”: Calculates the phase parameters using only the 1D slice with the global maximum signal, then applies those parameters across the entire dataset. - “all”: Calculates and applies unique phase parameters for every 1D spectrum individually. By default “single”.	`"single"`
peak_width	float	Width of the ROI (in units of `dim`, e.g., Hz or ppm) for the local methods. Concentrates the solver on the region surrounding the target peak. By default 0.5.	`0.5`
target_coord	float \| None	The explicit coordinate (e.g. 171.0 ppm) to target for local methods. If None, the coordinate of the maximum absolute magnitude is used.	`None`
p0_only	bool	If True, locks p1=0 and only optimizes the zero-order phase. Highly recommended for sparse spectra evaluated over a narrow `peak_width`.	`False`
lb	float	Optional exponential line broadening (in Hz). Can help smooth extreme noise for ACME, but usually unnecessary for local methods. By default 0.0.	`0.0`
temp_time_dim	str	The name used for the temporary time dimension if lb > 0.	`DIMS.time`
**kwargs		Additional keyword arguments passed to `scipy.optimize.differential_evolution`.	`{}`

Returns¶

Name	Type	Description
	xr.DataArray	The phased spectrum.

phase¶

processing.phasing.phase(da, dim=DIMS.frequency, p0=0.0, p1=0.0, pivot=None)

Apply zero- and first-order (linear) phase correction to a spectrum.

Parameters¶

Name	Type	Description	Default
da	xr.DataArray	The input frequency-domain spectrum. Must be complex-valued. Can be N-dimensional; phase will be broadcast across non-dim dimensions.	required
dim	str	The coordinate dimension along which to apply phase correction, by default `DIMS.frequency`.	`DIMS.frequency`
p0	float	Zero-order phase angle in degrees. This is a constant phase shift applied uniformly to all coordinates. By default 0.0.	`0.0`
p1	float	First-order phase angle in degrees. This represents the total phase twist applied across the entire spectral range (`max_coord - min_coord`). By default 0.0.	`0.0`
pivot	float	The coordinate value (e.g., ppm or Hz) around which `p1` is anchored. At this exact coordinate, the first-order phase contribution is 0.0. If None, standard maximum-magnitude pivoting is used safely across N-D.	`None`

Returns¶

Name	Type	Description
	xr.DataArray	The phase-corrected spectrum. Phase parameters (p0, p1, pivot, and pivot_coord) are appended to the dataset attributes to preserve lineage.