plot_2d.m

Contour plotting utility with non-linear adaptive contour spacing. The function is useful for NMR data where small cross-peaks must be adequately contoured next to large diagonal peaks.

Syntax

    [axis_f1,axis_f2,spectrum]=plot_2d(spin_system,spectrum,...
                                               parameters,ncont,delta,...
                                               k,ncol,m,signs)

Parameters

    spectrum - a real matrix containing the 2D NMR spectrum

    parameters.sweep       -  one or two sweep widths, Hz

    parameters.spins       -  cell array with one ot two character
                              strings specifying the working spins

    parameters.offset      -  one or two transmitter offsets, Hz

    parameters.axis_units  -  axis units ('ppm','Hz','Gauss')

    ncont     - the number of contours, a reasonable value is 20

    delta     - minimum and maximum elevation (as a fraction of the
                total intensity) of the contours above the baseline.
                A good starting value is [0.02 0.2 0.02 0.2]. The
                first pair of numbers refers to the positive conto-
                urs and the second pair to the negative ones.

    k    - a coefficient that controls the curvature of the contour
           spacing function: k=1 corresponds to linear spacing and
           k>1 bends the spacing curve to increase the sampling den-
           sity near the baseline. A reasonable value is 2.

    ncol - number of colours in the colour map; around 256 is fine

    m    - the curvature of the colour map: m=1 corresponds to a li-
           near colour ramp into the red for positive contours, and
           into the blue for negative contours. A reasonable value
           for high-contrast plotting is 6.

    signs   - can be set to 'positive', 'negative' or 'both' - this
              will cause the corresponding contours to be plotted.

Outputs

    a figure is drawn and the following parameters are returned

    axis_f1, axis_f2 - F1 and F2 axis ticks for external
                        plotting utilities

    spectrum         - 2D spectrum array for external
                        plotting utilities

Examples

Below is the output of examples/esr_solids/hyscore_nitroxide_powder.m example file.

Notes

The following functions are used to compute contour levels:

 cont_levs_pos=delta(2)*smax*linspace(0,1,ncont).^k+smax*delta(1);
 cont_levs_neg=delta(2)*smin*linspace(0,1,ncont).^k+smin*delta(1);

where smin and smax are computed from the spectrum matrix.

See also

plot_1d.m, plot_3d.m, volplot.m, molplot.m, mri_2d_plot.m, slice_2d.m, int_2d.m, hfc_display.m, cst_display.m, apodisation.m, axis_1d.m, bwr_cmap.m, contspacing.m, crop_2d.m, cylgrid.m, fid2ascii.m, ft_axis.m, heterodyne.m, plot_uf.m, s2json.m, scale_figure.m, stack_2d.m, sweep2ticks.m, write_movie.m, xyz2pd.m, zoom_3d.m, Import,_export,_and_visualisation, Kernel_utilities

Version 2.3, authors: Ilya Kuprov