Comments (6)
I am assuming that the error is with the plotting function, where one of these two lines is failing:
ax['a'].plot(ppm_13C, f2proj)
ax['b'].plot(-f1proj, ppm_1H)
My best guess is that the udic
that is being generated is not consistent with the data shape. Are the shapes of ppm_13C
and f2_proj
(or f1proj and ppm_1H) the same? If not, then there is some inconsistency while reading in the parameters and generating the universal dictionary. one place this could occur is if you use non-zero STSR
and STSI
values for processing in Topspin. If so, you should indicate that when generating a universal dictionary.
udic_2d = ng.bruker.guess_udic(dic_2d, data_2d, strip_fake=True)
Also, as far as I can see, this should also work without the intermediate conversion to nmrpipe formats (unless you need that for something else). You can generate the unit conversion object from a universal dictionary and data using:
uc_13C = ng.fileiobase.uc_from_udic(udic_2d, dim=1)
uc_1H = ng.fileiobase.uc_from_udic(udic_2d, dim=0)
from nmrglue.
Everything seems fine with the F2 dimension since the shape is the same
f2proj.shape
(2048,)
ppm_13C.shape
(2048,)
The F1, the calculated projection has double the number of points
f1proj.shape
(256,)
ppm_1H.shape
(128,)
I've tried to use
udic_2d = ng.bruker.guess_udic(dic_2d, data_2d, strip_fake=True)
but the problem persists. But anyway both STSR and STSI are zero.
from nmrglue.
It is unlikely that the amax
function is giving the incorrect array size. So my guess is that the problem should be with the unit conversion. Can you confirm that the shape of data_pipe
is incompatible with the shape of ppm_1H
.
from nmrglue.
I believe it is. I was checking the dimension and
data_pipe.shape
(256, 2048)
But then when I run
uc_1H = ng.pipe.make_uc(dic_pipe, data_pipe, dim=0)
ppm_1H = uc_1H.ppm_scale()
The size is cut in half
ppm_1H.shape
(128,)
from nmrglue.
Does skipping the conversion back and forth from nmrpipe, and generating the unit conversion object from bruker data (as shown in this comment) give the same results? If yes, will it be possible to share the data for debugging this?
from nmrglue.
Not converting to NMRpipe solves the problem. For now its ok but maybe it would be worth it to solve this.
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Related Issues (20)
- nmrglue import fails with scipy=1.8 HOT 4
- 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
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- ng.analysis.peakpick.pick() generating deprecation warning due to np.float() HOT 3
- Suggestion: nmrglue/fileio/SPINit.py
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- How to Process and display multiple 1D Bruker data HOT 3
- Port tests away from nose HOT 2
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- Help plotting Bruker 2D spectra HOT 3
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