Read raw FIDs and process to spectra

Reads Bruker 1D NMR FIDs, corrects the digital filter (group delay), applies apodisation (windowing), optional zero-filling, FFT, phasing and ppm calibration.

Returns either absorption-, dispersion-, or magnitude-mode spectra.

If to_global = TRUE, objects are assigned to the global environment.

Usage

read1d_raw(
  path,
  exp_type = list(exp = "PROF_PLASMA_CPMG128_3mm", pulprog = "noesygppr1d"),
  apodisation = list(fun = "exponential", lb = 0.2),
  zerofill = 1L,
  mode = c("absorption", "dispersion", "magnitude"),
  verbose = 1,
  recursive = TRUE,
  n_max = 1000,
  filter = TRUE,
  to_global = FALSE
)

Arguments

path

Character. Path to the root directory containing Bruker experiment folders.

exp_type

Named list. Acquisition-parameter filter to select experiments (e.g., list(PULPROG = "noesygppr1d")).

apodisation

Named list. Apodisation function and parameters. fun must be one of "exponential", "cosine", "sine", "sem".

zerofill

Integer. Zero-filling exponent (1 doubles points, 2 quadruples, …).

mode

Character. Spectrum type to return: "absorption", "dispersion", or "magnitude".

verbose

Integer. Verbosity level: 0 = silent, 1 = summary (default), 2 = detailed, 3 = debug.

recursive

Logical. Recursively search subdirectories for FIDs.

n_max

Integer. Maximum number of experiments to process.

filter

Logical. Remove experiments with incomplete file structures.

to_global

Logical. If TRUE, objects are also assigned to the global environment; otherwise, only an invisible list is returned.

Value

A named list with three elements:

X

A numeric matrix of spectra (rows = samples, columns = ppm values).

ppm

A numeric vector of chemical-shift axis (ppm).

meta

A data frame of acquisition metadata, row-aligned with X.

If to_global = TRUE, these objects are also assigned to the global environment. In that case, any existing objects with the same names will be overwritten.

Details

FIDs are read from Bruker acquisition folders and processed by the following pipeline:

1. Digital-filter (group-delay) correction: the initial n complex points are invalid due to the causal DSP decimation filter and are discarded; n equals GRPDLY when present, or is looked up from Bruker tables indexed by DECIM and DSPFVS on older systems.

2. Apodisation (windowing).

3. Zero-filling (optional).

4. FFT to the frequency domain.

5. Phase correction.

6. PPM calibration (e.g., to TSP).

A common ppm scale is then interpolated across spectra.

Digital filter note: On newer systems GRPDLY is written in acqus/acqu2s and should be used directly. For older data sets (GRPDLY < 0 or missing), the group delay is derived from DECIM and DSPFVS via an internal look-up table.

Apodisation functions:

• "uniform"

• "cosine",

• "sine",

• "exponential" (parameter: lb)

• "sem" (sine * exponential, parameter: lb)

• "gauss" (parameter: lb, 'gb', and 'para')

• "expGaus_resyG" (parameter: lb, 'gb', and 'aq_t')

See also

read1d_proc for importing TopSpin-processed spectra

Examples

path <- system.file("extdata", package = "metabom8")
read1d_raw(
  path,
  exp_type    = list(PULPROG = "noesygppr1d"),
  apodisation = list(fun = "exponential", lb = 0.2),
  zerofill    = 1,
  n_max       = 3
)
#> Processing 2 experiments.