Save spectra and FIDs

savenmr writes a frequency-domain spectrum as Bruker processed data, and savefid writes time-domain data as a raw Bruker fid/ser. Both produce experiments that TopSpin opens directly.

using NMRTools
fid = exampledata("1D_1H"; fid=true)
spec = autoprocess(fid)
out = mktempdir()

Spectra

Give the experiment folder and a processing number. If the folder does not exist, it is created, with the parameter files copied from the experiment the data were loaded from:

expt = joinpath(out, "1")
savenmr(expt, spec; procno=2)
readdir(joinpath(expt, "pdata", "2"))

4-element Vector{String}:
 "1r"
 "proc"
 "procs"
 "title"

savenmr writes the real part (1r, 2rr, 3rrr) and, for multicomplex 1D and 2D data, the imaginary parts, as 32-bit integers scaled by NC_proc. The processing parameter files, both current (proc, proc2, …) and status (procs, proc2s, …), record the axes, the window function and the phase correction applied. Reading the result back gives the same spectrum:

back = loadnmr(joinpath(expt, "pdata", "2"))
maximum(abs, back - spec) / maximum(abs, back)

1.2294405786393842e-9

FIDs

savefid writes time-domain data as a new experiment, for example after linear prediction or solvent filtering:

savefid(joinpath(out, "2"), solventfilter(fid))
readdir(joinpath(out, "2"))[1:5]

5-element Vector{String}:
 "EA"
 "README.md"
 "acqu"
 "acqus"
 "audita.txt"

savefid undoes the steps taken by loadfid: it restores the first points and the digital-filter group delay, re-encodes each indirect dimension with its original quadrature scheme and puts the dimensions back in acquisition order. loadfid on the written experiment returns the same data. Data are written as Float64 (DTYPA=2, as recorded by Avance NEO spectrometers) by default; pass dtype=Int32 for older TopSpin versions.

Parameter files

Both functions copy the acquisition parameter files (acqus, acqu2s, pulse programme, lists, …) from the experiment the data were loaded from (its :experimentfolder metadata), updating only the parameters that describe the written data, such as TD. If there is no source experiment, minimal parameter files are generated from the dimension metadata.

Existing data are not overwritten unless overwrite=true is passed.

Opening the result in TopSpin

Open the experiment folder in TopSpin and select the processing number. The spectrum appears as processed by NMRTools; reprocessing it in TopSpin overwrites it.

Peak lists

Peak lists are saved with savepeaks; see Save and load peak lists.

Pipeline forms

Both functions have forms for the end of a pipeline:

loadfid("expt/1") |> autoprocess |> savenmr("expt/1"; procno=2)