Metadata

NMRData objects contain comprehensive metadata on processing and acquisition parameters. These are populated automatically when loading a spectrum. Entries are divided into spectrum metadata – associated with the experiment in general – and axis metadata, that are associated with a particular dimension of the data.

Examples of spectrum metadata include: number of scans, receiver gain, pulse program, experiment title, number of dimensions, noise level (calculated when the spectrum is loaded), acquisition parameters (pulse lengths etc, from the acqus file), contents of auxilliary files (e.g. vclists and vdlists).

Examples of axis metadata include: the number of points, the original time domain size (before zero filling, linear prediction or extraction of a subregion), carrier frequency, spectrum width, window function used for processing.

Accessing spectrum metadata

Metadata are stored in a dictionary labelled by symbols such as :ns or :pulseprogram. This dictionary can be accessed using the metadata function.

using NMRTools
# load an example 2D 1H,15N HMQC spectrum
spec = exampledata("2D_HN")

metadata(spec)

Dict{Symbol, Any} with 14 entries:
  :filename         => "/Users/runner/.julia/artifacts/278430abd2b28a265273e707…
  :label            => "13C,15N ubiquitin"
  :ns               => 2
  :format           => :pdata
  :noise            => 502.842
  :experimentfolder => "/Users/runner/.julia/artifacts/278430abd2b28a265273e707…
  :pulseprogram     => "sfhmqcf3gpph.cw"
  :ndim             => 2
  :title            => "13C,15N ubiquitin\n500 uM in 10% D2O, 20 mM Pi pH 6.5, …
  :acqusfilename    => "/Users/runner/.julia/artifacts/278430abd2b28a265273e707…
  :topspin          => v"6.0.0"
  :acqus            => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,…
  :acqu2s           => Dict{Symbol, Any}(:origin=>nothing, :sw=>21.9971, :sw_h=…
  :rg               => 203

For convenience, entries can be accessed by passing a second argument to the metadata function:

metadata(spec, :title)

"13C,15N ubiquitin\n500 uM in 10% D2O, 20 mM Pi pH 6.5, 277 K, SOFAST-HMQC"

or directly from the spectrum using a dictionary-style lookup:

spec[:ns]

Accessing axis metadata

Axis metadata can be accessed by providing an additional argument to the metadata function, specifying the axis numerically:

metadata(spec, 1)

Metadata{FrequencyDimension} of Dict{Symbol, Any} with 19 entries:
  :aq              => 0.0946176
  :label           => "1H"
  :region          => 600:1815
  :sf              => 600.203
  :swppm           => 18.0315
  :bf              => 600.2
  :offsethz        => 2819.0
  :window          => Cos²Window(0.0946176)
  :offsetppm       => 4.69677
  :pseudodim       => false
  :npoints         => 1216
  :referenceoffset => 0.0
  :swhz            => 10822.5
  :td              => 1024
  :units           => nothing
  :coherence       => nothing
  :tdzf            => 4096
  :mcindex         => nothing
  :procs           => Dict{Symbol, Any}(:alpha=>0, :ymin_p=>-44320020, :pscal=>…

Axes can also be accessed by their type, e.g. F1Dim or F2Dim:

metadata(spec, F2Dim)

Metadata{FrequencyDimension} of Dict{Symbol, Any} with 19 entries:
  :aq              => 0.0478336
  :label           => "15N"
  :region          => missing
  :sf              => 60.8249
  :swppm           => 21.9997
  :bf              => 60.8177
  :offsethz        => 7176.49
  :window          => CosWindow(0.0478336)
  :offsetppm       => 118.0
  :pseudodim       => false
  :npoints         => 512
  :referenceoffset => 0.0
  :swhz            => 1337.97
  :td              => 64
  :units           => nothing
  :coherence       => nothing
  :tdzf            => 512
  :mcindex         => nothing
  :procs           => Dict{Symbol, Any}(:alpha=>0, :ymin_p=>-44320020, :pscal=>…

Again, for convenience entries can be accessed by passing an additional argument to the metadata function:

metadata(spec, F1Dim, :label)

"1H"

or directly from the spectrum object using a dictionary-style lookup alongside an axis reference:

spec[2, :offsetppm]

117.99995292412437

Accessing acquisition parameters

Spectrometer acquisition parameters are automatically parsed from the acqus file when data are loaded. This is stored as a dictionary in the :acqus entry of the spectrum metadata, but can more conveniently be accessed through the function acqus(spec, parametername). Parameter names can be provided either as strings (case insensitive, e.g. "TE" for the temperature) or as lowercase symbols (e.g. :te).

acqus(spec, :te)

276.9988

Arrayed parameters such as pulse lengths are returned as dictionaries:

acqus(spec, :p)

Dict{Int64, Float64} with 64 entries:
  5  => 16.5
  56 => 500.0
  16 => 1000.0
  20 => 2000.0
  35 => 160.0
  55 => 1300.0
  60 => 400.0
  30 => 160.0
  19 => 600.0
  0  => 9.2
  32 => 20000.0
  6  => 25.0
  49 => 100000.0
  45 => 78.0
  44 => 200.0
  9  => 25.0
  31 => 810.0
  61 => 120.0
  29 => 4000.0
  ⋮  => ⋮

For convenience, particular entries can be accessed directly by supplying an additional index parameter:

acqus(spec, :cnst, 4)

92.0

Note

Arrayed parameters such as pulse lengths, delays, etc. are returned as dictionaries rather than lists to avoid indexing confusion between Bruker arrays, which are zero-based, and Julia arrays, which are unit-based.

Auxiliary files

If present, files such as vclist and vdlist are imported and can be accessed through the acqus function:

relaxation_experiment = exampledata("pseudo3D_HN_R2")
acqus(relaxation_experiment, :vclist)

11-element Vector{Int64}:
  0
  1
  2
  3
  4
  6
  8
 10
 12
 14
 16

Window functions

The window functions used for data processing are identified when experiments are loaded. These are represented by subtypes of WindowFunction, which contain appropriate parameters specifying the particular function applied together with the acquisition time $t_\mathrm{max}$ (calculated at the point of application, i.e. after linear prediction but before zero filling).

Window functions are stored as axis metadata and can be accessed through the :window parameter:

spec[2, :window] # get the window function for the second dimension

CosWindow(0.04783359999999993)

Available window functions are:

NullWindow(tmax): no window function applied
UnknownWindow(tmax): unrecognised window function
ExponentialWindow(lb, tmax): line broadening specified in Hz
SineWindow(offset, endpoint, power, tmax): a supertype encompassing some special cases
- CosWindow(tmax): apodization by a pure half-cosine window
- Cos²Window(tmax): apodization by a pure half-cosine-squared window
- GeneralSineWindow(offset, endpoint, power, tmax): other general cases
GaussWindow(expHz, gaussHz, center, tmax): a supertype encompassing some special cases
- LorentzToGaussWindow(expHz, gaussHz, tmax)
- GeneralGaussWindow(expHz, gaussHz, center, tmax): other general cases