Welcome to mrsimulator Discussions!

[deepanshs]

👋 Welcome!

We’re using Discussions as a place to connect with other members of our community. We hope that you:

• Ask questions you’re wondering about.
• Share ideas.
• Engage with other community members.
• Welcome others and are open-minded. Remember that this is a community we
  build together 💪.

To get started, comment below with an introduction of yourself and tell us about what you do with this community.

[Max-Kimball]

Hi, I'm trying to fit a spectrum with multiple sites and J-couplings, I'm trying to figure it out with mrsimulator, but it's my first time playing with code. I'm trying to follow the fitting tutorial, but with multiple spin systems and couplings. I have no problems up until I try to minimize the fit, then I get

C;\.....\anaconda3\lib\site-packages\mrsimulator\utils\spectral_fitting.py", line 447, in LMFIT_min_function
exp_data = mth.experiment.y[0].components[0]

AttributeError: 'NoneType' object has no attribute 'y'

Do you have any idea what might be causing this?

I can do everything on the app but add J-coupling. Is this something I'm missing? Or is it not implemented yet?

Thank you so much for your hard work! It's very impressive and very helpful.

[deepanshs]

Hi Max. For fitting, you need to add the measured data to method object, for example (See full example on readthedocs)

MAS = BlochDecaySpectrum
    channels=["119Sn"],
    magnetic_flux_density=9.395,  # in T
    rotor_frequency=10000,  # in Hz
    spectral_dimensions=spectral_dims,
    experiment=experiment,  # add the measurement to the method.
)

The error you see is from the missing experiment data.

---

The J-couplings are implement in v0.7. See the isotopomers example. To add coupling between two sites, use the Coupling class

CH3_coupling_1 = Coupling(site_index=[0, 6], isotropic_j=125)

where isotropic_j is the isotopic J-coupling.

[Max-Kimball]

Ah, I missed the experiment=experiment line. Thank you for the fast reply!

[Max-Kimball]

Hello again deepanshs,

I'm producing fits which is very exciting, but they're not very good with the limited processing I'm able to do via python. I have to do some baseline correction and first order phasing.

I managed to trick NMRglue to import my processed spectrum from topspin by saving it as an FID, but of course it's not in the correct units, so I can't move forward. I'm trying to read more of the documentation to figure it out, but I'm a bit out of my depth.

Is there a proper way to bring in the processed spectrum, or to correct the units so I can move on to fitting? Or a way to do the baseline correction and first order phasing?

I'm incredibly thankful for your work, it's very impressive. I'm trying to learn more about python to properly implement it.

[deepanshs]

I appreciate you using mrsimulator. Feel free to ask any questions. We'll be happy to assist.

We have an example that shows fitting starting from importing data/signal processing (zero and first-order phase correction). I would recommend following this example first.

---

If you follow the steps in the above example, you should not need to change the dimension unit.
Yes, you can change the dimension unit of a csdm object by multiplying it by appropriate units. For example, if csdm_ds has a unitless dimension, you can convert it to a time dimension by multiplying it by a time unit,

import csdmpy as cp
csdm_ds.dimensions[0] *= cp.ScalarQuantity("s")

---

We have a few baseline functions that you can use for fitting.