Importing and plotting CSDM data

[pdellis01]

In all of your examples for host you utilize a web site address ... my data set resides in a directory on my computer ... when I write a path to the file I receive an error message saying there is no such file or directory. Any suggestions on my error?

[mgiammar]

Would you be able to copy and paste the few lines you are using to try and load a .csdm object into this thread? The issue might lie there.

Also, with regards to the host and filename variables in the online examples, they are just strings which get added together into a single string to load that file from a URL. For example

host = "https://nmr.cemhti.cnrs-orleans.fr/Dmfit/Help/csdm/"
filename = "31P Phosphate 6kHz.csdf"
experiment = cp.load(host + filename)

is equivalent to calling

experiment = cp.load("https://nmr.cemhti.cnrs-orleans.fr/Dmfit/Help/csdm/31P Phosphate 6kHz.csdf")

For local files, you won't need a https url, just the path to whatever file. For example,

experiment = cp.load("/Users/nmruser/Desktop/some_exp_spectrum.csdf")

[pdellis01]

Thank you as far as I see the cp.load worked ... then ... when I ran the program (very simple one):

import csdmpy as cp
import matplotlib.pyplot as plt
from lmfit import Minimizer

from mrsimulator import Simulator, SpinSystem, Site
from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator.utils import spectral_fitting as sf
from mrsimulator.utils import get_spectral_dimensions
from mrsimulator.spin_system.tensors import SymmetricTensor

read in the JEOL dataset file

experiment = cp.load ("/Users/pdellis/Desktop/SnO_Better.csdf")
experiment = experiment.real

plt.figure(4.25,3.0)
ax = plt.subplot(projection="csdm")
ax.plt(experiment, colors="black", linewidth=0.5, label ="Experiment")
ax.set_xlim(150,-150)
plt.grid()
plt.show()

I then received the following error message:
/usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/new_SnO.py
pdellis@dotynmr mrsim_fit % /usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/new_SnO.py
Traceback (most recent call last):
File "/Users/pdellis/Desktop/mrsim_fit/new_SnO.py", line 20, in
plt.figure(4.25,3.0)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/_api/deprecation.py", line 454, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/pyplot.py", line 840, in figure
manager = new_figure_manager(
^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/pyplot.py", line 384, in new_figure_manager
return _get_backend_mod().new_figure_manager(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 3573, in new_figure_manager
fig = fig_cls(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/_api/deprecation.py", line 454, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/figure.py", line 2536, in init
self.bbox_inches = Bbox.from_bounds(0, 0, *figsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: Value after * must be an iterable, not float
pdellis@dotynmr mrsim_fit %

[mgiammar]

Looks like just matplotlib issues now. Some of the arguments and functions called don't match what matplotlib is expecting. The following code should work for plotting:

plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(experiment, colors="black", linewidth=0.5, label ="Experiment")
ax.set_xlim(150,-150)
plt.grid()
plt.show()

Size figure passed as figsize=(width, height) to the plt.figure() call, cannot just be two numbers.

[pdellis01]

we are getting closer ... it did not like the word color:
usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/new_SnO.py
pdellis@dotynmr mrsim_fit % /usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/new_SnO.py
Traceback (most recent call last):
File "/Users/pdellis/Desktop/mrsim_fit/new_SnO.py", line 20, in
ax.plot(experiment, colors="black", linewidth=0.5, label ="Experiment")
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/csdmpy/helper_functions.py", line 56, in plot
return self.call_1D(csdm, "plot", *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/csdmpy/helper_functions.py", line 195, in call_1D
r_plt = super().plot(x, y, *args, **kwargs_)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_axes.py", line 1688, in plot
lines = [*self._get_lines(*args, data=data, **kwargs)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 311, in call
yield from self._plot_args(
^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 544, in _plot_args
return [l[0] for l in result]
^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 544, in
return [l[0] for l in result]
^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 537, in
result = (make_artist(x[:, j % ncx], y[:, j % ncy], kw,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 351, in _makeline
seg = mlines.Line2D(x, y, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/_api/deprecation.py", line 454, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/lines.py", line 393, in init
self._internal_update(kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/artist.py", line 1223, in _internal_update
return self._update_props(
^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/matplotlib/artist.py", line 1197, in _update_props
raise AttributeError(
AttributeError: Line2D.set() got an unexpected keyword argument 'colors'
pdellis@dotynmr mrsim_fit %

[mgiammar]

Try changing the colors argument to just color.

[pdellis01]

your suggestion worked! I got a nice blank box ... no spectrum. The csdf file has an asci header, the data as binary. Are you expecting asci?

[mgiammar]

Remove the line setting the x limits. Matplotlib should automatically set the limits for whatever dataset you're plotting.

[pdellis01]

Cool I am at play ground with my grand kids but I will give your suggestions a quick shot. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Matthew Giammar ***@***.***> Sent: Wednesday, May 31, 2023 9:13:38 AM To: deepanshs/mrsimulator ***@***.***> Cc: Paul Ellis ***@***.***>; Author ***@***.***> Subject: Re: [deepanshs/mrsimulator] "host" (Discussion #263) Remove the line setting the x limits. Matplotlib should automatically set the limits for whatever dataset you're plotting. — Reply to this email directly, view it on GitHub<#263 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A76PY3DLIDXRMZR67ESKYYDXI5GZFANCNFSM6AAAAAAYUQQFRE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[pdellis01]

Still having Fun ...

I still cannot get my simulated spectrum to display ... it is not an issue with plot limits. The code now runs to completion ... but I am sure it is NOT executing the simulation or the fit. However, I am getting an error message:

/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/astropy/units/quantity.py:673: RuntimeWarning: divide by zero encountered in divide
result = super().array_ufunc(function, method, *arrays, **kwargs)
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/astropy/units/quantity.py:673: RuntimeWarning: invalid value encountered in divide

I am attaching the program and one of the plots ...

The Plot:

The code:

from doctest import master
from gettext import ngettext
import locale
import csdmpy as cp
import matplotlib.pyplot as plt
from lmfit import Minimizer
from mrsimulator.spin_system.site import SymmetricTensor

from mrsimulator import Site, SpectralDimension, SpinSystem, Simulator, spin_system
from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator import signal_processor as sp
from mrsimulator.utils import spectral_fitting as sf
from mrsimulator.method import SpectralDimension
from mrsimulator.utils import get_spectral_dimensions

initialize nmrglue converter object

ax = plt.subplot(projection="csdm")

read in the JEOL dataset file

experiment = cp.load ("/Users/pdellis/Desktop/mrsim_fit/SnO_Transformed.csdf")
fig, ax = plt.subplots(1, 2, figsize=(9, 3.5), subplot_kw={"projection": "csdm"})

ax[0].plot(experiment.real)
ax[0].set_title("Full Spectrum")
ax[0].grid()
ax[1].plot(experiment.real,color= "red", label="real")
ax[1].set_title("Zoomed Spectrum")
ax[1].set_xlim(1.4e6, 1.8e6)
ax[1].grid()
plt.tight_layout()
plt.legend()
plt.show()

standard deviation of noise from the dataset

sigma = 0.6410905

Tin_119 = Site(
isotope = "119Sn",
isotropic_chemical_shift = 1.6e6,
shielding_symmetric = SymmetricTensor(zeta = 1.8e5,eta = 0.0)

)

Dict = {'origin_offset': 'Hz', 'reference_offset': 'Hz', 'spectral_width': 'Hz', 'reference_offset': 'Hz', 'origin_offset': 'Hz'},
spectral_dims = get_spectral_dimensions(experiment)
bloch = BlochDecaySpectrum(
channels = ["119Sn"],
magnetic_flux_density = 11.75, # in T
rotor_angle = 0.9553234193716164, # in rad
rotor_frequency = 6600, # in Hz
spectral_dimensions = [
SpectralDimension(
count = 8192,
spectral_width = 2000000, # in Hz
)
],
experiment = experiment, # add the measurement to the method
)

Use only the real part of the spectrum

experiment = experiment.real
sys = [SpinSystem(sites=[Tin_119]), ]

sim = Simulator(spin_systems = sys, methods=[bloch])

sim.config.decompose_spectrum = "spin_system"

sim.run()

relative_intensity_factor = experiment.max() / sim.methods[0].simulation.max()

Post Simulation Processing

processor = sp.SignalProcessor(
operations=[
sp.IFFT(),
sp.apodization.Gaussian(FWHM="50 Hz"),
sp.FFT(),
sp.Scale(factor=200)
]
)
dataset = experiment
processed_dataset = processor.apply_operations(dataset = sim.methods[0].simulation).real

Plot the spectrum

plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(experiment, linewidth=1, label="Experiment")
ax = plt.subplot(projection="csdm")
ax.plot(processed_dataset, linewidth=1, label="Simulation")
ax.set_xlim(1.4e6, 1.8e6)
plt.grid()
plt.legend()
plt.tight_layout()
plt.show()

params = sf.make_LMFIT_params(sim, processor, include={"rotor_frequency"})

fit_parameters = sf.make_LMFIT_params(sim, processor)
print(fit_parameters.pretty_print(columns=["value", "min", "max", "vary", "expr"]))

standard deviation of noise from the dataset

from lmfit import Minimizer
minner = Minimizer(sf.LMFIT_min_function, fit_parameters, fcn_args=(sim, processor, sigma))
result = minner.minimize()
result

best_fit = sf.bestfit(sim, processor)[0].real
residuals = sf.residuals(sim, processor)[0].real

Plot the spectrum

plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(experiment, linewidth=1, label="Experiment")
ax.plot(best_fit, linewidth=1, label="Best Fit")
ax.plot(residuals, linewidth=1, label="Residuals")
ax.set_xlim(1.4e6, 1.8e6)
plt.grid()
plt.legend()
plt.tight_layout()
plt.show()

[pdellis01]

WE are making progress --- Almost ... No error messages here is the output and I have attached the program and here are some plots:

pdellis@dotynmr ~ % /usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/SnO_Fitting_RMN.py
2023-06-25 14:42:50.758 Python[29615:723980] WARNING: Secure coding is not enabled for restorable state! Enable secure coding by implementing NSApplicationDelegate.applicationSupportsSecureRestorableState: and returning YES.
Name Value Min Max Vary Expr
SP_0_operation_1_Gaussian_FWHM 5 -inf inf True None
SP_0_operation_3_Scale_factor 5000 -inf inf True None
sys_0_abundance 100 0 100 False 100
sys_0_site_0_isotropic_chemical_shift -650 -inf inf True None
sys_0_site_0_shielding_symmetric_eta 0 0 1 True None
sys_0_site_0_shielding_symmetric_zeta 600 -inf inf True None
None
pdellis@dotynmr ~ %

For some reason I am having trouble pasting the spectra ... but you will see the issue when you run the program ...

SnO_Fitting_RMN.zip

[mgiammar]

Hi Paul,

I don't have the file SnO_Phased-1041.csdf, so I am unable to run the program. Are you able to attach it?

[pdellis01]

Here is the file ...

SnO_Phased-1041.csdf

[mgiammar]

Can you compress the file to zip, then drag and drop into the comment box? Otherwise it will not upload to GitHub.

[pdellis01]

Here you go ...
SnO_Phased-1041.zip

[mgiammar]

Find attached a Jupyter Notebook (in a zip file) which runs a fit on the spectrum you provided. You can run this in Google Colab; the script will install the requisite libraries. Note that the fit is not great mostly because I have not had time to play around with the starting parameters.

You are not seeing the simulated spectrum in the script above since the values for isotropic_chemical_shift and shielding_symmetric.zeta are still (presumably) in Hz. Mrsimulator does not accept these values in Hz; they must a ppm value. The simulated spectrum is therefore on the order of 10^6 ppm, far outside the spectral window of the experimental dataset, which is plotted first.

The sidebands in the spectrum also seem to have no width, that is, they are single points. Could you provide the raw JOEL time-domain dataset? Maybe there is an export discrepancy on their end or some pre-processing issue.

SnO_Fit.ipynb.zip

[pdellis01]

Oh Boy … thank you very much. I will send you the file in the morning … it is on another computer. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Matthew Giammar ***@***.***> Sent: Thursday, June 8, 2023 7:22:07 PM To: deepanshs/mrsimulator ***@***.***> Cc: Paul Ellis ***@***.***>; Author ***@***.***> Subject: Re: [deepanshs/mrsimulator] Importing and plotting CSDM data (Discussion #263) Find attached a Jupyter Notebook (in a zip file) which runs a fit on the spectrum you provided. You can run this in Google Colab<https://colab.research.google.com/>; the script will install the requisite libraries. Note that the fit is not great mostly because I have not had time to play around with the starting parameters. You are not seeing the simulated spectrum in the script above since the values for isotropic_chemical_shift and shielding_symmetric.zeta are still (presumably) in Hz. Mrsimulator does not accept these values in Hz; they must a ppm value. The simulated spectrum is therefore on the order of 10^6 ppm, far outside the spectral window of the experimental dataset, which is plotted first. The sidebands in the spectrum also seem to have no width, that is, they are single points. Could you provide the raw JOEL time-domain dataset? Maybe there is an export discrepancy on their end or some pre-processing issue. SnO_Fit.ipynb.zip<https://github.com/deepanshs/mrsimulator/files/11697001/SnO_Fit.ipynb.zip> — Reply to this email directly, view it on GitHub<#263 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A76PY3E5YSAZC4MF2EDFHLDXKJNB7ANCNFSM6AAAAAAYUQQFRE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[pdellis01]

Hi Mathew … I have attached the time domain file. I have my day tied up for a while I will send the raw data after lunch Paul From: Matthew Giammar ***@***.***> Date: Thursday, June 8, 2023 at 7:22 PM To: deepanshs/mrsimulator ***@***.***> Cc: Paul Ellis ***@***.***>, Author ***@***.***> Subject: Re: [deepanshs/mrsimulator] Importing and plotting CSDM data (Discussion #263) Find attached a Jupyter Notebook (in a zip file) which runs a fit on the spectrum you provided. You can run this in Google Colab<https://colab.research.google.com/>; the script will install the requisite libraries. Note that the fit is not great mostly because I have not had time to play around with the starting parameters. You are not seeing the simulated spectrum in the script above since the values for isotropic_chemical_shift and shielding_symmetric.zeta are still (presumably) in Hz. Mrsimulator does not accept these values in Hz; they must a ppm value. The simulated spectrum is therefore on the order of 10^6 ppm, far outside the spectral window of the experimental dataset, which is plotted first. The sidebands in the spectrum also seem to have no width, that is, they are single points. Could you provide the raw JOEL time-domain dataset? Maybe there is an export discrepancy on their end or some pre-processing issue. SnO_Fit.ipynb.zip<https://github.com/deepanshs/mrsimulator/files/11697001/SnO_Fit.ipynb.zip> — Reply to this email directly, view it on GitHub<#263 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A76PY3E5YSAZC4MF2EDFHLDXKJNB7ANCNFSM6AAAAAAYUQQFRE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[pdellis01]

Hi Mathew ...

Some progress ... Mike and I are on the same page (art least the same chapter) ... given that I am concerned about two of the error message I now have ... (see below)

pdellis@dotynmr ~ % /usr/local/bin/python3 /Users/pdellis/Desktop/mrsim_fit/SnO_Fitting.py
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_methods.py:226: RuntimeWarning: invalid value encountered in divide
arrmean = um.true_divide(arrmean, div, out=arrmean,
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_methods.py:261: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
Name Value Min Max Vary Expr
SP_0_operation_1_Gaussian_FWHM 10 -inf inf True None
SP_0_operation_3_Scale_factor 4000 -inf inf True None
sys_0_abundance 100 0 100 False 100
sys_0_site_0_isotropic_chemical_shift -650 -inf inf True None
sys_0_site_0_shielding_symmetric_eta 0 0 1 True None
sys_0_site_0_shielding_symmetric_zeta 700 -inf inf True None
None
Traceback (most recent call last):
File "/Users/pdellis/Desktop/mrsim_fit/SnO_Fitting.py", line 139, in
result = minner.minimize()
^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/lmfit/minimizer.py", line 2379, in minimize
return function(**kwargs)
^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/lmfit/minimizer.py", line 1703, in leastsq
lsout = scipy_leastsq(self.__residual, variables, **lskws)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/optimize/_minpack_py.py", line 413, in leastsq
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/optimize/_minpack_py.py", line 26, in _check_func
res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/lmfit/minimizer.py", line 604, in __residual
return _nan_policy(np.asfarray(out).ravel(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/lmfit/minimizer.py", line 2463, in _nan_policy
raise ValueError(msg)
ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do for more information.
pdellis@dotynmr ~ %

Clearly, I cannot see where the where the specific error is occurring ... but any advice would be welocome. I have copied the offending code below ...

Paul

import csdmpy as cp
import mrsimulator
from mrsimulator import SpectralDimension, signal_processor as sp
from mrsimulator import Site, SpinSystem, Simulator
from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator.utils import get_spectral_dimensions
from mrsimulator.spin_system.tensors import SymmetricTensor
from mrsimulator.method import Isotope

import matplotlib.pyplot as plt

import os
os.getcwd()

import math
import cmath

import numpy as np

from lmfit import Minimizer

read in the JEOL dataset file

testdata = cp.load ("/Users/pdellis/Desktop/mrsim_fit/SnO_Phased-1041.csdf")
testdata.description
x = testdata.dimensions
x

#As saved
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(testdata.real,color= "black", label="real")
ax.plot(testdata.imag,color= "red", label="Imaginary")
ax.grid()
plt.tight_layout()
plt.legend()
plt.show()

Reverse the data without reversing the axis

testdata_swap = testdata.real - cmath.sqrt(-1) * testdata.imag

processor = sp.SignalProcessor(
operations=[sp.apodization.Exponential(FWHM="10 Hz"), sp.FFT()]
)
processed_dataset = processor.apply_operations(dataset=testdata_swap)
processed_dataset.dimensions[0].to("ppm", "nmr_frequency_ratio")

x = processed_dataset.dimensions
x

#As Calculated / Collected
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(processed_dataset.real, color="black", linewidth=1)

ax.invert_xaxis()

ax.set_xlim(0, -1.7E3)
plt.tight_layout()
plt.show()

Use only the real part of the spectrum

exp_spectrum = processed_dataset.real

Use region below -20 ppm to calculate the noise standard deviation

loc = np.where(exp_spectrum.dimensions[0].coordinates < -2000)
sigma = exp_spectrum[loc].std()

test = np.abs(processed_dataset)

#As Calculated / Collected
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(test, color="black", linewidth=1)
#ax.invert_xaxis()
ax.set_xlim(0, -1700)
plt.tight_layout()
plt.show()

site = Site(
isotope = "119Sn",
isotropic_chemical_shift = -650.0,
shielding_symmetric = {"zeta" : 700,"eta" : 0.0},
)

Get the dimensions from the experimental dataset

spectral_dims = get_spectral_dimensions(test)
v_ref = test.dimensions[0].origin_offset - exp_spectrum.dimensions[0].coordinates_offset
B0 = v_ref.to("MHz").value / np.abs(Isotope(symbol="119Sn").gyromagnetic_ratio)

MAS = BlochDecaySpectrum(
channels=["119Sn"],
magnetic_flux_density = 11.75, # in T
rotor_frequency = 8067, # in Hz
spectral_dimensions = spectral_dims,

experiment = test,  # add the measurement to the method.Method

)

sys = SpinSystem(sites = [site])

sim = Simulator(spin_systems = [sys], methods = [MAS])
sim.config.number_of_sidebands = 60
sim.run()

Post Simulation Processing

--------------------------

relative_intensity_factor = exp_spectrum.max() / sim.methods[0].simulation.max()
processor = sp.SignalProcessor(
operations=[
sp.IFFT(),
sp.apodization.Gaussian(FWHM="10 Hz"),
sp.FFT(),
sp.Scale(factor=4000),
]
)
processed_dataset = processor.apply_operations(dataset=sim.methods[0].simulation).real

Plot of the guess spectrum

--------------------------

plt.figure(figsize=(6.0, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(test, label="Experiment")
ax.plot(processed_dataset, label="Guess Spectrum")
ax.set_xlim(0, -1700)
plt.legend()
plt.grid()
plt.tight_layout()
plt.show()

from mrsimulator.utils import spectral_fitting as sf
fit_parameters = sf.make_LMFIT_params(sim, processor)
print(fit_parameters.pretty_print(columns=["value", "min", "max", "vary", "expr"]))
fit_parameters["sys_0_site_0_shielding_symmetric_eta"].value = 0
fit_parameters["sys_0_site_0_shielding_symmetric_zeta"].vary = 0
fit_parameters["sys_0_site_0_isotropic_chemical_shift"].vary = 0

from lmfit import Minimizer
minner = Minimizer(sf.LMFIT_min_function, fit_parameters, fcn_args=(sim, processor, sigma))
result = minner.minimize()
result

best_fit = sf.bestfit(sim, processor)[0].real
residuals = sf.residuals(sim, processor)[0].real

Plot the spectrum

plt.figure(figsize=(6, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(exp_spectrum, label="Experiment")
ax.plot(best_fit, alpha=0.75, label="Best Fit")
ax.plot(residuals, alpha=0.75, label="Residuals")
ax.set_xlim(-15, 15)
plt.legend()
plt.grid()
plt.tight_layout()
plt.show()
fit_parameters["sys_0_site_0_shielding_symmetric_eta"].value = 0
fit_parameters["sys_0_site_0_shielding_symmetric_eta"].vary = True
minner = Minimizer(sf.LMFIT_min_function, fit_parameters, fcn_args=(sim, processor, sigma))
result = minner.minimize()
best_fit = sf.bestfit(sim, processor)[0].real
residuals = sf.residuals(sim, processor)[0].real

Plot the spectrum

plt.figure(figsize=(6, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(exp_spectrum, label="Experiment")
ax.plot(best_fit, alpha=0.75, label="Best Fit")
ax.plot(residuals, alpha=0.75, label="Residuals")
ax.set_xlim(-15, 15)
plt.legend()
plt.grid()
plt.tight_layout()
plt.show()

[pdellis01]

Double darn … I will send right away. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Matthew Giammar ***@***.***> Sent: Monday, June 26, 2023 8:13:31 AM To: deepanshs/mrsimulator ***@***.***> Cc: Paul Ellis ***@***.***>; Author ***@***.***> Subject: Re: [deepanshs/mrsimulator] Importing and plotting CSDM data (Discussion #263) Hi Paul, I don't have the file SnO_Phased-1041.csdf, so I am unable to run the program. Are you able to attach it? — Reply to this email directly, view it on GitHub<#263 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A76PY3HPD5TVB7YE3B7WSQTXNF4GXANCNFSM6AAAAAAYUQQFRE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[mgiammar]

@pdellis01 Attached is a zip file with a notebook and a processed 1D static spectrum of your SnO CPMG dataset. The notebook sets up a static Method object to simulate the experimental spectrum and subsequently fits the dataset; the residuals don't look too bad.

I think your issues are coming from trying to fit a spikelet pattern from a 1D echo train to a spinning sideband simulation. I don't know if this is possible, and mrsimulator is certainly not designed to handle such a case.

Hopefully this notebook helps!

SnO_fit_plus_dataset.zip

[pdellis01]

Mathew … I can’t thank you enough … Warmest regards … Paul From: Matthew Giammar ***@***.***> Date: Tuesday, June 27, 2023 at 11:38 AM To: deepanshs/mrsimulator ***@***.***> Cc: Paul Ellis ***@***.***>, Mention ***@***.***> Subject: Re: [deepanshs/mrsimulator] Importing and plotting CSDM data (Discussion #263) @pdellis01<https://github.com/pdellis01> Attached is a zip file with a notebook and a processed 1D static spectrum of your SnO CPMG dataset. The notebook sets up a static Method object to simulate the experimental spectrum and subsequently fits the dataset; the residuals don't look too bad. I think your issues are coming from trying to fit a spikelet pattern from a 1D echo train to a spinning sideband simulation. I don't know if this is possible, and mrsimulator is certainly not designed to handle such a case. Hopefully this notebook helps! SnO_fit_plus_dataset.zip<https://github.com/deepanshs/mrsimulator/files/11884553/SnO_fit_plus_dataset.zip> — Reply to this email directly, view it on GitHub<#263 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A76PY3G2TMQXE3KW7XFNJ4DXNL4UVANCNFSM6AAAAAAYUQQFRE>. You are receiving this because you were mentioned.Message ID: ***@***.***>