Processing Relaxation measurement

Processing NMR spectra taken for relaxation measurements

Requires the official spectrochempy-nmr plugin. Install with: pip install spectrochempy[nmr].

Import API

import spectrochempy as scp

# short version of the unit registry
U = scp.ur

Importing a pseudo 2D NMR spectra

Define the folder where are the spectra

datadir = scp.preferences.datadir
nmrdir = datadir / "nmrdata" / "bruker" / "tests" / "nmr"

dataset = scp.nmr.read_topspin(nmrdir / "relax" / "100" / "ser", use_list="vdlist")

/home/runner/work/spectrochempy/spectrochempy/.venv/lib/python3.13/site-packages/spectrochempy/core/readers/importer.py:226: UserWarning: No module named 'spectrochempy_hypercomplex'
  warning_(str(e))

Analysing the data

Print dataset summary

dataset

Plot the dataset

ds = dataset.em(lb=15 * U.Hz)
ds = ds.fft()
ds = ds.pk(phc0=-10 * U.deg, phc1=0 * U.deg)
ds.plot(xlim=(-60, -140))

Traceback (most recent call last):
  File "/home/runner/work/spectrochempy/spectrochempy/build/~gallery_examples/processing/nmr/plot_processing_nmr_relax.py", line 42, in <module>
    ds = dataset.em(lb=15 * U.Hz)
         ^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'em'

Integrate a region

dsint = ds[:, -90.0:-115.0].simpson()
dsint.plot(marker="^", ls=":")
dsint.real

Fit a model

create an Optimize object using a simple leastsq method

fitter = scp.Optimize(log_level="INFO", method="leastsq")

Define the model to fit

def T1_model(t, I0, T1):  # no underscore in parameters names.
    # T1 relaxation model
    import numpy as np

    I = I0 * (1 - np.exp(-t / T1))
    return I

Add the model to the fitter usermodels as it it not a built-in model

fitter.usermodels = {"T1_model": T1_model}

Define the parameter variables using a script (parameter: value, low_bound, high_bound) no underscore in parameters names.

fitter.script = """
MODEL: T1
shape: T1_model
  $ I0:  1000.0, 1, none
  $ T1:  2.0,    0.1, none
"""

Performs the fit

fitter.fit(dsint)

som = fitter.predict()
som

fitter.plotmerit(dsint, som, method="scatter", title="T1 relaxation fitting")

This ends the example ! The following line can be removed or commented when the example is run as a notebook (ipynb).

# scp.show()