nmr_autophase: Rephase 1D NMR data

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

Rephase 1D NMR data

Description

Use phasing algorithms to rephase data in the spectral domain.

This function may improve autophasing processing from instrument vendors. It wraps the NMRphasing::NMRphasing() function, to automatically rephase spectra, allowing you to choose from a number of algorithms of which NLS, MPC_DANM and SPC_DANM are the most recent.

Rephasing should happen before any spectra interpolation.

Please use the all_components = TRUE when calling nmr_read_samples() in order to load the complex spectra and fix NMR phasing correctly.

Usage

nmr_autophase(
  dataset,
  method = c("NLS", "MPC_DANM", "MPC_EMP", "SPC_DANM", "SPC_EMP", "SPC_AAM", "SPC_DSM"),
  withBC = FALSE,
  ...
)

Arguments

dataset	An nmr_dataset object
method	The autophasing method. See NMRphasing::NMRphasing() for details.
withBC	NMRphasing::NMRphasing may perform a baseline correction using modified polynomial fitting. By default AlpsNMR offers other baseline estimation methods and better visualization of its effect, so AlpsNMR by default disables the baseline correction offered by NMRphasing.
...	Other parameters passed on to NMRphasing::NMRphasing().

Value

A (hopefully better phased) nmr_dataset object, with updated real and imaginary parts.

Examples

if (requireNamespace("NMRphasing", quietly=TRUE)) {
  # Helpers to create a dataset:
  lorentzian <- function(x, x0, gamma, A) {
    A * (1 / (pi * gamma)) * ((gamma^2) / ((x - x0)^2 + gamma^2))
  }
  x <- seq(from=1, to=2, length.out = 300)
  y <- lorentzian(x, 1.3, 0.01, 1) + lorentzian(x, 1.6, 0.01, 1)
  dataset <- new_nmr_dataset(
    metadata = list(external = data.frame(NMRExperiment = "10")),
    data_fields = list(data_1r = list(y)),
    axis = list(list(x))
  )
  # Autophase, interpolate and plot:
  dataset <- nmr_autophase(dataset, method = "NLS")
  dataset <- nmr_interpolate_1D(dataset, axis = c(min = 1, max = 2, by = 0.01))
  plot(dataset)
}

sipss/AlpsNMR documentation built on Aug. 13, 2024, 5:11 p.m.