.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gettingstarted/examples/gallery/auto_examples_processing/nmr/plot_processing_nmr_relax.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_gettingstarted_examples_gallery_auto_examples_processing_nmr_plot_processing_nmr_relax.py: Processing Relaxation measurement ================================= Processing NMR spectra taken for relaxation measurements .. GENERATED FROM PYTHON SOURCE LINES 15-17 Import API ---------- .. GENERATED FROM PYTHON SOURCE LINES 17-22 .. code-block:: default import spectrochempy as scp # short version of the unit registry U = scp.ur .. GENERATED FROM PYTHON SOURCE LINES 23-26 Importing a pseudo 2D NMR spectra --------------------------------- Define the folder where are the spectra .. GENERATED FROM PYTHON SOURCE LINES 26-31 .. code-block:: default datadir = scp.preferences.datadir nmrdir = datadir / "nmrdata" / "bruker" / "tests" / "nmr" dataset = scp.read_topspin(nmrdir / "relax" / "100" / "ser", use_list="vdlist") .. GENERATED FROM PYTHON SOURCE LINES 32-35 Analysing the data --------------------- Print dataset summary .. GENERATED FROM PYTHON SOURCE LINES 35-37 .. code-block:: default dataset .. raw:: html

name	relax expno:100 procno:1 (SER)
author	runner@fv-az1110-430
created	2024-05-12 03:10:12+02:00
DATA
title	intensity
values	R[[ 0.5522 2.137 ... -1.437 -0.02603] [ 1.099 3.404 ... -0.6497 -0.0129] ... [ 1.603 5.99 ... 4.959 0.09235] [ 1.61 6.14 ... -0.7725 -0.01501]] pp I[[ -1.513 -2.733 ... 4.471 0.08437] [ -2.496 -4.623 ... -6.003 -0.1152] ... [ -4.25 -7.726 ... 4.695 0.08693] [ -4.302 -7.69 ... 0.222 0.004867]] pp
shape	(y:9, x:1982(complex))
DIMENSION `x`
size	1982
title	F2 acquisition time
coordinates	[ 0 6.4 ... 1.267e+04 1.268e+04] µs
DIMENSION `y`
size	9
title	time
coordinates	[ 1 2 ... 20 50] s

.. GENERATED FROM PYTHON SOURCE LINES 38-39 Plot the dataset .. GENERATED FROM PYTHON SOURCE LINES 39-45 .. code-block:: default 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)) .. image-sg:: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_001.png :alt: plot processing nmr relax :srcset: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 46-47 Integrate a region .. GENERATED FROM PYTHON SOURCE LINES 47-51 .. code-block:: default dsint = ds[:, -90.0:-115.0].simpson() _ = dsint.plot(marker="^", ls=":") dsint.real .. image-sg:: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_002.png :alt: plot processing nmr relax :srcset: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/runner/micromamba/envs/scpy_docs/lib/python3.10/site-packages/spectrochempy/analysis/integration/integrate.py:178: DeprecationWarning: 'scipy.integrate.simps' is deprecated in favour of 'scipy.integrate.simpson' and will be removed in SciPy 1.14.0 return scipy.integrate.simps(dataset.data, **kwargs) .. raw:: html

name	relax expno:100 procno:1 (SER)
author	runner@fv-az1110-430
created	2024-05-12 03:10:12+02:00
description	Integration of NDDataset 'relax expno:100 procno:1 (SER)' along dim: 'x'.
history	2024-05-12 03:10:12+02:00> Dataset resulting from application of `simpson` method
DATA
title	area
values	[ 1556 2472 ... 4253 4284] pp.ppm
size	9
DIMENSION `y`
size	9
title	time
coordinates	[ 1 2 ... 20 50] s

.. GENERATED FROM PYTHON SOURCE LINES 52-55 Fit a model ----------- create an Optimize object using a simple leastsq method .. GENERATED FROM PYTHON SOURCE LINES 55-58 .. code-block:: default fitter = scp.Optimize(log_level="INFO", method="leastsq") .. GENERATED FROM PYTHON SOURCE LINES 59-60 Define the model to fit .. GENERATED FROM PYTHON SOURCE LINES 60-68 .. code-block:: default 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 .. GENERATED FROM PYTHON SOURCE LINES 69-70 Add the model to the fitter usermodels as it it not a built-in model .. GENERATED FROM PYTHON SOURCE LINES 70-72 .. code-block:: default fitter.usermodels = {"T1_model": T1_model} .. GENERATED FROM PYTHON SOURCE LINES 73-76 Define the parameter variables using a script (parameter: value, low_bound, high_bound) no underscore in parameters names. .. GENERATED FROM PYTHON SOURCE LINES 76-83 .. code-block:: default fitter.script = """ MODEL: T1 shape: T1_model $ I0: 1000.0, 1, none $ T1: 2.0, 0.1, none """ .. GENERATED FROM PYTHON SOURCE LINES 84-85 Performs the fit .. GENERATED FROM PYTHON SOURCE LINES 85-87 .. code-block:: default _ = fitter.fit(dsint) .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 88-91 .. code-block:: default som = fitter.predict() som .. raw:: html

name	relax expno:100 procno:1 (SER)_Optimize.inverse_transform
author	runner@fv-az1110-430
created	2024-05-12 03:10:12+02:00
history	2024-05-12 03:10:12+02:00> Created using method Optimize.inverse_transform
DATA
title	area
values	[ 1500 2467 ... 4223 4223] pp.ppm
size	9
DIMENSION `y`
size	9
title	time
coordinates	[ 1 2 ... 20 50] s

.. GENERATED FROM PYTHON SOURCE LINES 92-94 .. code-block:: default _ = fitter.plotmerit(dsint, som, method="scatter", title="T1 relaxation fitting") .. image-sg:: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_003.png :alt: T1 relaxation fitting :srcset: /gettingstarted/examples/gallery/auto_examples_processing/nmr/images/sphx_glr_plot_processing_nmr_relax_003.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 95-97 This ends the example ! The following line can be removed or commented when the example is run as a notebook (*.ipynb). .. GENERATED FROM PYTHON SOURCE LINES 97-99 .. code-block:: default # scp.show() .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 0.540 seconds) .. _sphx_glr_download_gettingstarted_examples_gallery_auto_examples_processing_nmr_plot_processing_nmr_relax.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_processing_nmr_relax.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_processing_nmr_relax.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_