b2spinach.m
Imports time-domain NMR data recorded by Bruker instruments: reads the binary fid or ser file together with the acquisition and processing parameter files from the numbered experiment directory. The dimension of the data set is deduced from the presence of the acqu2s, acqu3s, and acqu4s status parameter files; data sets with more than four dimensions are refused. The parameter files are parsed from JCAMP-DX into Matlab structures, the binary byte order is taken from BYTORDA, the storage type and the file block size from DTYPA, the padding to whole 1024-byte blocks is stripped, complex fids are assembled in the Bruker sign convention as the real part minus the imaginary part times the imaginary unit, and the amplitudes are scaled by 2^NC. The group delay of the digital filter is zero when DIGMOD reports analogue filtering, is taken from GRPDLY when the hardware supplies it, comes from the tabulated DECIM and DSPFVS combinations for the DSP firmware families 10 to 12, and from the closed form 3-1/(2*DECIM) for firmware family 13. The difflist, vdlist, vclist, and nuslist files are read when they are present.
Syntax
bdata=b2spinach(inpath)
Parameters
inpath - character string with the path to the numbered
Bruker experiment directory containing the ac-
qus file and the fid or ser file
Outputs
bdata.fid - matrix of complex free induction de-
cays, one per column, in the order
they are stored in the file; for data
sets with three and more dimensions
the loop order over the indirect di-
mensions is determined by the AQSEQ
parameter of the acqus structure
bdata.acqus - structure with every parameter found
in the acqus file: numeric parameters
as scalars or column vectors, string
parameters as character strings or
cell arrays thereof
bdata.acqu2s - same for the acqu2s file of data sets
with two or more dimensions
bdata.acqu3s - same for the acqu3s file of data sets
with three or more dimensions
bdata.acqu4s - same for the acqu4s file of four-di-
mensional data sets
bdata.procs - same for the procs file of the first
processed data directory when present
bdata.dirname - experiment directory name
bdata.ndims_data - number of dimensions in the data set
bdata.arraydim - number of fids the status parameter
files declare as acquired
bdata.fids_in_file - number of fid slots held by the bina-
ry file, and the column count of the
fid matrix; exceeds arraydim when the
acquisition was preallocated or inter-
rupted, and falls short of it for non-
uniformly sampled data sets, where the
fids follow the acquisition order of
the sampling schedule in nus_list
bdata.npoints - complex points per fid
bdata.pulprog - pulse programme name
bdata.nucleus - observe nucleus, e.g. '1H'
bdata.gamma - magnetogyric ratio of the observe
nucleus, rad/(s*T)
bdata.sfrq - spectrometer frequency, MHz
bdata.at - acquisition time, seconds
bdata.sw_ppm - spectral width, ppm
bdata.spec_start - lower edge of the spectrum, ppm
bdata.digshift - group delay of the digital filter in
complex points; the first round(dig-
shift) points of each fid precede the
start of the true signal
bdata.grad_amps - gradient amplitudes, T/m, present
when the difflist file exists
bdata.vd_list - variable delay list, seconds, present
when the vdlist file exists
bdata.vc_list - variable counter list, present when
the vclist file exists
bdata.nus_list - non-uniform sampling schedule, pre-
sent when the nuslist file exists
Notes
The lower edge of the spectrum is taken from the OFFSET parameter of the procs file when the processed data directory is present, and computed from SFO1, BF1, and SW otherwise; the two routes need not agree to the last digit.
The function reads status parameter files (acqus, acqu2s, ...), not the acquisition input files (acqu, acqu2, ...), so the numbers it reports are those of the acquisition that actually took place.
Adapted from the brukerimport() function of the GNAT package by:
Dr. Mathias Nilsson
School of Chemistry, University of Manchester,
Oxford Road, Manchester M13 9PL, UK
mathias.nilsson@manchester.ac.uk
See also
v2spinach.m, c2spinach.m, g2spinach.m, x2spinach.m, read_wave.m, Import,_export,_and_visualisation
Version 2.13, authors: Ilya Kuprov, Mathias Nilsson
