GESeries.MRSSeries

GESeries.MRSSeries(DATA_FOLDER, SERIES_ID)

A single-voxel MRS series: FIDs, spectra, averaging, and fitting.

Attributes¶

Name	Description
`averages`
`avg_fid`	The FID averaged across all averages.
`avg_spec`	The spectrum averaged across all averages.
`fids`	The FIDs from RawMRISeries, with the id coordinate renamed to averages.
`npts`
`ppm`
`spec`

Name	Description
average_fids	Average FIDs by grouping consecutive acquisitions.
average_fids_by_duration	Average FIDs by grouping acquisitions within a time duration.
average_spectra	Average spectra by grouping consecutive acquisitions.
average_spectra_by_duration	Average spectra by grouping acquisitions within a time duration.
fit_average_fid	Fit the averaged FID (avg_fid) with AMARES, normalizing it first.
group_size_by_duration	Calculate number of consecutive FIDs to average for a target duration.
limit_spec_to_ppm_range	Return the spectra limited to the chemical_shift range [ppm_min, ppm_max].
phase_avg_spec	Phase (or autophase) the average spectrum, limited to a ppm range.

GESeries.MRSSeries.average_fids(group_size=8)

Average FIDs by grouping consecutive acquisitions.

Name	Type	Description	Default
group_size	int	Number of consecutive FIDs to average together. Defaults to 8.	`8`

Name	Type	Description
	xarray.DataArray	Averaged FIDs, shape `(n_groups, n_timepoints)`.

GESeries.MRSSeries.average_fids_by_duration(group_duration=10)

Average FIDs by grouping acquisitions within a time duration.

Name	Type	Description	Default
group_duration	int	Duration in seconds for each group. Defaults to 10.	`10`

Name	Type	Description
	xarray.DataArray	Averaged FIDs grouped by duration.

GESeries.MRSSeries.average_spectra(group_size=8)

Average spectra by grouping consecutive acquisitions.

Name	Type	Description	Default
group_size	int	Number of consecutive FIDs to average together. Defaults to 8.	`8`

Name	Type	Description
	xarray.DataArray	Averaged spectra, shape `(n_groups, n_points)`.

GESeries.MRSSeries.average_spectra_by_duration(group_duration=10)

Average spectra by grouping acquisitions within a time duration.

Name	Type	Description	Default
group_duration	int	Duration in seconds for each group. Defaults to 10.	`10`

Name	Type	Description
	xarray.DataArray	Averaged spectra grouped by duration.

GESeries.MRSSeries.fit_average_fid(
    init_params,
    fit_params=None,
    normalisation_factor=None,
    filter_by_ppm=None,
)

Fit the averaged FID (avg_fid) with AMARES, normalizing it first.

GESeries.MRSSeries.group_size_by_duration(group_duration)

Calculate number of consecutive FIDs to average for a target duration.

Name	Type	Description	Default
group_duration	float	Target duration in seconds for each group.	required

Name	Type	Description
	int	Number of consecutive FIDs to average together.

GESeries.MRSSeries.limit_spec_to_ppm_range(ppm_min=-2, ppm_max=6)

Return the spectra limited to the chemical_shift range [ppm_min, ppm_max].

GESeries.MRSSeries.phase_avg_spec(
    zero_order=0.0,
    first_order=0.0,
    autophase=False,
    ppm_min=-np.inf,
    ppm_max=np.inf,
)

Phase (or autophase) the average spectrum, limited to a ppm range.