Comments (3)
@ndbryant21 do you want to only plot the processed data, or process it from scratch and then plot it?
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@kaustubhmote For now I would like to plot the processed data. Though I have been generating a few hundred 2D spectra per year and would eventually like to process from scratch.
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This should work:
# read data
dic, data = ng.bruker.read_pdata("datafolder/1/pdata/1")
# read in axis ppm parameters
udic = ng.bruker.guess_udic(dic, data, strip_fake=True)
uc = {i: ng.fileiobase.uc_from_udic(udic, dim=i) for i in (0, 1)}
axis_limits = [*uc[1].ppm_limits(), *uc[0].ppm_limits()]
# contour levels
levels = [data.max() / 20 * 1.4**i for i in range(10)] # change as needed
# plot
fig, ax = plt.subplots()
ax.contour(
data.real,
levels=levels,
extent=axis_limits,
cmap=plt.cm.Greys_r, # change as per your preference
linewidths=0.5, # change as per your preference
)
ax.set_xlim(11.5, 6) # change as needed
ax.set_ylim(135, 105) # change as needed
plt.show()
I will not recommend processing multidimensional data with nmrglue if you need to apply linear prediction to the indirect dimensions as nmrglue's linear prediction functions are not very well tested. It would be better process it in nmrpipe or some other software and then use nmrglue to convert the data to numpy arrays for plotting.
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Related Issues (20)
- nmrglue import fails with scipy=1.8
- Installation fails with setuptools v61.2.0 HOT 2
- Import error - scipy version 1.8.0 HOT 1
- integrate_2d: how to get limits.in? HOT 2
- Problem with 1D plotting - maybe HOT 3
- Failed to load Bruker Data HOT 2
- Give up on Python 3.6 HOT 1
- Process_pipe_3d:There seems to be some issues with the processing script HOT 13
- nmrglue fails loading due to scipy.minpack deprecation (1.9.3) HOT 2
- Does the spectral raw data obtained by 'Echo-Antiecho', 'States', 'TPPI' and 'States-TPPI' require additional manual operations? HOT 2
- ng.analysis.peakpick.pick() generating deprecation warning due to np.float() HOT 3
- Suggestion: nmrglue/fileio/SPINit.py
- Issue when trying to convert Varian data to Pipe HOT 2
- How to Process and display multiple 1D Bruker data HOT 3
- Port tests away from nose HOT 2
- New release HOT 4
- Issue with ng.peakpick.pick for "thres" and "thres-fast" algorithms with Numpy ^v1.22 HOT 2
- Peak picking from a 2D contour plot HOT 1
- Reading JEOL NMR Data (*.jdf) HOT 2
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