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spant (version 3.5.0)

MR Spectroscopy Analysis Tools

Description

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) , Wilson (2025) and spectral alignment: Wilson (2018) .

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install.packages('spant')

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3.5.0

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GPL-3

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Repository

https://github.com/martin3141/spant/

Homepage

https://spantdoc.wilsonlab.co.uk/

Maintainer

Martin Wilson

Last Published

August 18th, 2025

Functions in spant (3.5.0)

Return the total number of acquired transients for an MRS dataset.

Return the number of data points in an MRS dataset.

Return the total number of spectra in an MRS dataset.

Apply Mod operator to an MRS dataset.

Complex rounding function taken from complexplus package to reduce the number of spant dependencies.

Apply Conj operator to an MRS dataset.

Apply Im operator to an MRS dataset.

Return the total number of coil elements in an MRS dataset.

Return the total number of dynamic scans in an MRS dataset.

Apply Arg operator to an MRS dataset.

Apply Re operator to an MRS dataset.

add_noise_spec_snr

Add noise to an mrs_data object to match a given SNR.

Return the total number of z locations in an MRS dataset.

Return the total number of x locations in an MRS dataset.

Return a list of options for an ABfit analysis with regularision.

Return the total number of y locations in an MRS dataset.

Add noise to an mrs_data object.

Return a list of options for an ABfit analysis.

abfit_opts_v1_9_0

Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.

Apply a function over specified array axes.

Fit and subtract a polynomial to each spectrum in a dataset.

Apply a function across given dimensions of a MRS data object.

Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.

Baseline correction using the ALS method.

Apply and subtract a Gaussian smoother in the spectral domain.

Remove a constant baseline offset based on a reference spectral region.

calc_peak_info_vec

Calculate the FWHM of a peak from a vector of intensity values.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

Fit and subtract a smoothing spline to each spectrum in a dataset.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

comb_coils_mrsi_gls

Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

Combine a pair of basis set objects.

Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).

Combine coil data based on the first data point of a reference signal.

Bin equally spaced spectral regions.

Append MRS data across the coil dimension, assumes they matched across the other dimensions.

Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.

Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

Simulate pulse sequence acquisition.

Append multiple regressor data frames into a single data frame.

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

Perform zeroth-order phase correction based on expected baseline regions.

Simulate an RF pulse on a single spin.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

Back extrapolate time-domain data points using an autoregressive model.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

Check LCModel can be run

coherence_filter

Zero all coherence orders other than the one supplied as an argument.

Calculate the spectral SNR.

Crop mrs_data object data points in the time-domain.

Perform a polynomial fit, subtract and return the standard deviation of the residuals.

Crop mrs_data object based on a frequency range.

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

Calculate the sum of squares differences between two mrs_data objects.

Align spectra to a reference frequency using a convolution based method.

Convolve two MRS data objects.

Deconvolve two MRS data objects.

Return the default number of data points in the spectral dimension.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

Apodise MRSI data in the x-y direction with a k-space filter.

Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.

Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Check the TARQUIN binary can be run

comb_fit_tables

Combine all fitting data points into a single data frame.

Crop an MRSI dataset in the x-y direction

Create a logical circular mask spanning the full extent of an n x n matrix.

Combine a reference and metabolite mrs_data object.

Crop basis_set object based on a frequency range.

Return the default sampling frequency in Hz.

Eddy current correction.

elliptical_mask

Create an elliptical mask stored as a matrix of logical values.

Return (and optionally modify using the input arguments) a list of the default acquisition parameters.

comb_fit_list_fit_tables

Combine all fitting data points from a list of fits into a single data frame.

comb_fit_list_result_tables

Combine the fit result tables from a list of fit results.

downsample_mrs_td

Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.

Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.

Transform frequency-domain data to the time-domain.

Estimate the standard deviation of the noise from a segment of an mrs_data object.

decimate_mrs_td

Decimate an MRS signal by filtering in the time domain before downsampling.

decimate_mrs_fd

Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.

Apply the diff operator to an MRS dataset in the FID/spectral dimension.

Frequency-domain convolution based filter.

Apply a Gaussian smoother in the spectral domain.

downsample_mrs_fd

Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter.

Return the default transmitter frequency in Hz.

Search for MRS data files in a BIDS filesystem structure.

Return the default nucleus.

Find valid MRS data files recursively from a directory path.

fit_t2_te_array

Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes.

comb_fit_list_dyns

Combine a list of fit results into a single fit result object across the dynamic dimension.

GUI interface for the standard SVS 1H brain analysis pipeline, this is a work in progress, and not ready for serious use.

fit_svs_group_results

Combine fitting results for group analysis.

Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

comb_coils_svs_gls

Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

get_1h_brain_basis_paras_v2

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

get_1h_brain_basis_paras_v1

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

crop_td_pts_end

Crop mrs_data object data points at the end of the FID.

Perform a fft and ffshift on a vector.

Return the phase of the first data point in the time-domain.

Generate the I product operator for a single spin.

Generate regressors by convolving a specified response function with a stimulus.

Generate the Fxy product operator with a specified phase.

Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

Return acquisition parameters from a MRS data object.

get_basis_subset

Return a subset of the input basis.

Generate trapezoidal regressors.

Return the default reference value for ppm scale.

crop_td_pts_pot

Crop mrs_data object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.

Standard SVS 1H brain analysis pipeline.

Perform a fit based analysis of MRS data.

Print the command to run the LCModel command-line program.

Generate a MRSI VOI from an mrs_data object.

Extract the metabolite component from an mrs_data object.

Get a data array from a fit result.

Generate a MRSI voxel from an mrs_data object.

Get a mol_parameters object for a named molecule.

gen_numeric_reg

Generate a regressor from a numeric vector.

Extract a subset of MRS data.

Return a character array of names that may be used with the get_mol_paras function.

gen_impulse_reg

Generate impulse regressors.

Extract a subset of dynamic scans.

Generate BOLD regressors.

fp_phase_correct

Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.

Scale the first time-domain data point in an mrs_data object.

gen_baseline_reg

Generate baseline regressor.

Generate polynomial regressors.

Return the first half of a dynamic series.

Calculate the partial volume estimates for each voxel in a 2D MRSI dataset.

Apply the Fourier transform over the dynamic dimension.

get_guassian_pulse

Generate a gaussian pulse shape.

Return even numbered dynamic scans starting from 1 (2,4,6...).

Return the first time-domain data point.

Return odd numbered dynamic scans starting from 1 (1,3,5...).

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

A very simple DICOM reader.

Extract the fit amplitudes from an object of class fit_result.

Perform a GLM analysis of dynamic MRS data in the spectral domain.

Expand a regressor matrix for a group analysis.

Write fit results table to a csv file.

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

Generate an affine for nifti generation.

Return a single voxel from a larger mrs dataset.

Return the spin number for a given nucleus.

Return the sampling frequency in Hz of an MRS dataset.

Edited SVS 1H brain analysis pipeline.

Image plot method for objects of class mrs_data.

Generate a SVS acquisition volume from an mrs_data object.

Invert odd numbered dynamic scans starting from 1 (1,3,5...).

Calculate diagnostic information for object of class fit_result.

Check if an object is defined, which is the same as being not NULL.

Return the last scans of a dynamic series.

Transform 2D MRSI data from k-space to image space in the x-y direction.

get_1h_brain_basis_paras_v3

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

Mask an MRSI dataset in the x-y direction

get_voi_seg_psf

Return the white matter, gray matter and CSF composition of a volume.

Check if the chemical shift dimension of an MRS data object is in the frequency domain.

Grid shift MRSI data in the x/y dimension.

Return the white matter, gray matter and CSF composition of a volume.

Transform 2D MRSI data to k-space in the x-y direction.

mask_xy_corners

Mask the four corners of an MRSI dataset in the x-y plane.

make_basis_from_raw

Make a basis-set object from a directory containing LCModel formatted RAW files.

HSVD of an mrs_data object.

Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

Generate a double gamma model of the HRF as used in SPM.

get_1h_braino_basis_names

Return a character vector of molecules included in the GE BRAINO phantom.

Extract the reference component from an mrs_data object.

HSVD based signal filter.

Calculate the centre of gravity for an image containing 0 and 1's.

get_uncoupled_mol

Generate a mol_parameters object for a simple spin system with one resonance.

Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.

Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.

Calculate the mean dynamic data.

Return the first scans of a dynamic series.

Apply the max operator to an interpolated MRS dataset.

fit_t1_ti_array

Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes.

Apply the max operator to an MRS dataset.

Apply the Modulus operator to the time-domain MRS signal.

Create a BIDS file structure from a vector of data paths or list of mri/mrs data objects.

Return the frequency scale of an MRS dataset in Hz.

HSVD of a complex vector.

fit_t1_tr_array

Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes.

Create a two dimensional Gaussian window function stored as a matrix.

Generate the F product operator.

get_1h_brain_basis_names

Return a character vector of common 1H molecules found in healthy human brain.

Install the spant command-line interface scripts to a system path.

Perform an ifftshift on a matrix, with each column replaced by its shifted result.

Return the mean of a list of mrs_data objects.

Plot a 2D slice from an MRSI fit result object.

Plot regressors as an image.

Perform a fftshift on a matrix, with each column replaced by its shifted result.

Plot the spectral standard deviation.

Get the quantum coherence matrix for a spin system.

get_1h_brain_basis_paras

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

Integrate a spectral region.

plot_slice_map_inter

Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.

get_1h_spectre_basis_names

Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.

Robust Alignment to a Target Spectrum (RATS).

Get the point spread function (PSF) for a 2D phase encoded MRSI scan.

Return the second half of a dynamic series.

Return a single slice from a larger MRSI dataset.

Get the indices of data points lying between two values (end > x > start).

glm_spec_fmrs_fl

Perform first-level spectral GLM analysis of an fMRS dataset.

Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.

glm_spec_fmrs_group

Perform group-level spectral GLM analysis of an fMRS dataset.

Perform an iffshift and ifft on a vector.

interleave_dyns

Interleave the first and second half of a dynamic series.

gridplot.mrs_data

Arrange spectral plots in a grid.

Invert even numbered dynamic scans starting from 1 (2,4,6...).

Arrange spectral plots in a grid.

Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.

Print the command to run the TARQUIN command-line program.

Perform l2 regularisation artefact suppression.

Apply line-broadening (apodisation) to MRS data or basis object.

Convert mrs_data object to a vector.

mrs_data2spec_mat

Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

Print fit coordinates from a single index.

Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).

Calculate the mean spectrum from an mrs_data object.

Mask fit result spectra depending on a vector of bool values.

Mask an MRS dataset in the dynamic dimension.

read_ima_dyn_dir

Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.

Replicate a scan in the dynamic dimension.

Calculate the mean spectrum from an mrs_data object.

phase_ref_1h_brain

Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.

read_pulse_ascii

Read an ASCII formatted pulse file.

read_pulse_bruker

Read a Bruker formatted pulse file

Read an LCModel formatted coord file containing fit information.

plot.fit_result

Plot the fitting results of an object of class fit_result.

preproc_svs_dataset

Preprocess and perform quality assessment of one or more SVS data sets.

Preprocess and perform quality assessment of a single SVS data set.

Replicate a scan over a given dimension.

scale_amp_molar2molal_pvc

Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.

Search for the highest peak in a spectral region and return the frequency, height and FWHM.

Return the ppm scale of an MRS dataset or fit result.

Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

rectangular_mask

Create a rectangular mask stored as a matrix of logical values.

Read MRS data using the TARQUIN software package.

Split MRS data containing multiple spectra into a list of single spectra datasets.

print.fit_result

Print a summary of an object of class fit_result.

Read MRS data from the filesystem.

Print a summary of mrs_data parameters.

recon_twix_2d_mrsi

Reconstruct 2D MRSI data from a twix file loaded with read_mrs.

mask_xy_ellipse

Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.

Save function results to file and load on subsequent calls to avoid repeat computation.

Display an interactive orthographic projection plot of a nifti object.

Correct linear frequency drift.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Calculate the median dynamic data.

Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).

Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.

read_tqn_result

Reader for csv results generated by TARQUIN.

Calculate the standard deviation spectrum from an mrs_data object.

Remove a subset of dynamic scans.

Export a one-page pdf of a single fit result

Reader for csv fit results generated by TARQUIN.

Plotting method for objects of class mrs_data.

Display an orthographic projection plot of a nifti object.

Calculate the standard deviation spectrum from an mrs_data object.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Mask a 2D MRSI dataset in the x-y dimension.

Set the number of transients for an mrs_data object.

Calculate the pairwise means across a dynamic data set.

Return a time scale vector to match the FID of an MRS data object.

Segment T1 weighted MRI data using FSL FAST and write to file. Runs deface and bet as preprocessing steps by default.

Scale an mrs_data object by a scalar or vector or amplitudes.

set_def_acq_paras

Set the default acquisition parameters.

Convenience function to plot a baseline estimate with the original data.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

Simulate MRS data with a similar appearance to normal brain (by default).

Simulate a mol_parameter object.

seq_slaser_ideal

sLASER sequence with ideal pulses.

Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation.

Scale mrs_data to a spectral region.

sim_basis_mm_lip_lcm

Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.

Simulate a basis file using TARQUIN.

set_precomp_mode

Set the precompute mode.

set_mask_xy_mat

Set the masked voxels in a 2D MRSI dataset to given spectrum.

Sort the basis-set elements alphabetically.

Smooth data across the dynamic dimension with a Gaussian kernel.

Simulate a basis set object.

Set the command to run the LCModel command-line program.

Apply line-broadening to an mrs_data object to achieve a specified linewidth.

Decompose an mrs_data object into white and gray matter spectra.

Apply frequency shifts to basis set signals.

Reconstruct complex time-domain data from the real part of frequency-domain data.

Read a basis file in LCModel .basis format.

Reconstruct complex time-domain data from the real part of frequency-domain data.

Apply a weighting to the FID to enhance spectral resolution.

Apply phasing parameters to MRS data.

plot_slice_fit_inter

Plot a 2D slice from an MRSI fit result object.

plot_voi_overlay

Plot a volume as an image overlay.

plot_voi_overlay_seg

Plot a volume as an overlay on a segmented brain volume.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

stackplot.fit_result

Plot the fitting results of an object of class fit_result with individual basis set components shown.

Perform a mathematical operation on a spectral region.

Subtract the mean dynamic spectrum from a dynamic series.

Subtract the first dynamic spectrum from a dynamic series.

Plot a slice from a 7 dimensional array.

Perform a t-test on spectral data points.

Read a .pta formatted pulse file compatible with Siemens PulseTool.

scale_amp_legacy

Apply water reference scaling to a fitting results object to yield metabolite quantities in units of "mmol per Kg wet weight".

Repeat an array over a given dimension.

seq_steam_ideal_cof

STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.

read_siemens_txt_hdr

Read the text format header found in Siemens IMA and TWIX data files.

scale_amp_molal

Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

Objects exported from other packages

read_dkd_moco_log

Read the log from Dinesh's MoCo sLASER sequence.

svs_1h_brain_batch_analysis

Batch interface to the standard SVS 1H brain analysis pipeline.

Resample a VOI to match a target image space using nearest-neighbour interpolation.

scale_amp_molal_pvc

Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

Calculate the sum across receiver coil elements.

Transform time-domain data to the frequency-domain.

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

read_ima_coil_dir

Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.

seq_press_ideal

PRESS sequence with ideal pulses.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

seq_mega_press_ideal

MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.

Output a table of fit amplitudes and error estimates for a single-voxel fit.

Return the sum of a list of mrs_data objects.

Reslice a nifti object to match the orientation of mrs data.

scale_amp_molar

Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue). This function is depreciated, please use scale_amp_legacy instead.

Resample a basis-set to match a mrs_data acquisition.

scale_basis_amp

Scale a basis object by a scalar.

CPMG style sequence with ideal pulses.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

set_precomp_verbose

Set the verbosity of the precompute function.

scale_amp_water_ratio

Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude.

Resample an image to match a target image space.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

sim_th_excit_profile

Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.

Set the ppm reference value (eg ppm value at 0Hz).

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Simulate an mrs_data object containing complex zero valued samples.

seq_steam_ideal_young

STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).

seq_steam_ideal

STEAM sequence with ideal pulses.

scale_basis_from_singlet

Scale a basis-set to be consistent with spant assumptions for water scaling.

Set the repetition time of an MRS dataset.

Return a list of options for VARPRO based fitting.

Zero-fill MRSI data in the k-space x-y direction.

Time-domain spectral registration.

Apply a frequency shift to MRS data.

sim_basis_1h_brain_press

Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

sim_basis_1h_brain

Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

spm_pve2categorical

Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.

Create a spin system object for pulse sequence simulation.

Time-domain convolution based filter.

Convert a vector into a mrs_data object.

spant: spectroscopy analysis tools.

spant_abfit_benchmark

Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.

Write a basis object to an LCModel .basis formatted file.

Return the repetition time of an MRS dataset.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

varpro_3_para_opts

Return a list of options for VARPRO based fitting with 3 free parameters.

Set the number of time-domain data points, truncating or zero-filling as appropriate.

spant_sim_fmrs_dataset

Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.

Zero-fill MRS data in the time domain.

Simulate an mrs_data object containing simulated Gaussian noise.

Simulate a MRS data object containing a set of simulated resonances.

Set the command to run the TARQUIN command-line program.

Signal space projection method for lipid suppression.

Return the echo time of an MRS dataset.

Sum two mrs_data objects.

Calculate the sum of data dynamics.

zero_td_pts_end

Set mrs_data object data points at the end of the FID to zero.

spant_simulation_benchmark

Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.

Produce a plot with multiple traces.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.

write_pulse_ascii

Write an ASCII formatted pulse file.

write_basis_tqn

Generate a basis file using TARQUIN.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

zero_higher_orders

Zero all coherences including and above a given order.

Write MRS data object to file.