Getting started

This page takes about ten minutes. It loads and plots a 1D and a 2D spectrum, and processes a raw FID into a spectrum.

Installing NMRTools

Install NMRTools.jl and the CairoMakie plotting package through the Julia package manager:

using Pkg
Pkg.add(["NMRTools", "CairoMakie"])

Use GLMakie instead of CairoMakie for interactive plots in a window.

loadnmr loads a spectrum from the path of a Bruker experiment folder or an nmrPipe file. Example data, from NMRExampleData.jl, are found with example(name), which gives the path to load, downloading the dataset the first time.

using NMRTools, CairoMakie
spec = loadnmr(example("1d_19f_fragments"))
size(spec), label(spec)

((524288,), "19F{1H} broadband 1D")

nmrplot plots it, with axes labelled from the spectrum's metadata:

fig = nmrplot(spec)

Select a chemical shift range with .. to zoom in. The y-axis rescales to fit:

fig = nmrplot(spec[-124.5 .. -123])

Plot a 2D spectrum

Two-dimensional spectra are plotted in the same way. Contour levels start at five times the noise level:

spec2d = loadnmr(example("2d_hn_ubq"))
fig = nmrplot(spec2d)

Ranges can be selected in both dimensions, and levels and spacing change the contours:

fig = nmrplot(spec2d[7 .. 9, 115 .. 125]; levels=8, spacing=1.5, title="")

Figures can be saved as vector graphics or bitmaps with save("spectrum.pdf", fig).

Look inside a spectrum

A spectrum is an array with axes and metadata attached:

spec2d[Near(8.5), Near(120)]       # the intensity nearest 8.5 ppm, 120 ppm

2808.2490234375

spec2d[:ns], spec2d[F2Dim, :nucleus]   # number of scans; nucleus of the second dimension

(2, N15)

Process a FID

loadfid loads raw time-domain data, and autoprocess turns it into a phased spectrum: apodization, zero-filling, Fourier transformation and automatic phasing.

fid = loadfid(example("1d_1h_ubq"))
spec1h = autoprocess(fid)
fig = nmrplot(spec1h[-1 .. 10]; title="")

autoprocess returns the real spectrum. For a ¹H spectrum in H₂O, it also removes the residual water signal with a solvent filter.

Next steps