Changelog

v0.8.0dev0

What’s new

Features

  • Support gamma angle averaging.

v0.7.0

What’s new

Features

  • Support for complex amplitude simulation.

  • New isotropic interpolation schemes. Added isotropic_interpolation as a sim.config parameter. Allowed values are linear and Gaussian.

  • New larmor_freq(B0) function added to the Isotope class which returns the Larmor frequency of the isotope, given a magnetic flux density. For example, H1.larmor_freq(B0=9.40)

  • New weak J and dipolar coupling enumerations added to freq_contrib.

  • New command-line interface (CLI) tools for mrsimulator.

  • Added 200+ NMR active isotopes to the library.

  • Support for python 3.10

Method

  • New Event classes—SpectralEvent and MixingEvent. The MixingEvent controls the transition amplitude mixing in a multi-event method.

  • New TotalMixing and NoMixing mixing query enumerations for quick scripting of common mixing events.

  • New weights attribute for the TransitionPathway object, which holds the probability of the transition pathway based on the mixing events defined within the method.

  • New plot() function in Method class, which generates a visual representation of the method’s events, transition pathways, rotor angle, etc.

  • Support for concurrent mixing events.

  • Support for negative spectral width in a spectral dimension.

  • Deprecated Method1D and Method2D classes. Use the generic mrsimulator.method.Method object for custom 1D and 2D methods.

SpinSystem

  • New function simplify() to simplifies a spin system object to a list of irreducible spin systems.

  • New function site_generator() added to the utility collection sub-module, which simplifies the process of creating Site objects in bulk.

  • Added gyromagnetic ratio and quadrupole moment metadata for all isotopes, including unstable isotopes.

SignalProcessor

  • New SkewGaussian, TopHat, and Mask apodization functions were added to the signal processor module.

Documentation

  • Restructured documentation layout

  • Improved troubleshooting section.

  • Added section User Guide detailing the use and attributes of most objects.

  • Added section Method demonstrating how to create custom Method objects.

  • Condensed simulation/fitting gallery by removing redundant examples.

  • New gallery demonstrating signal processing functions.

Changes

  • reduced_dict function is deprecated, use json(units=False) instead.

  • The mrsimulator.signal_processing module is renamed to mrsimulator.signal_processor

  • Drop support for Python version 3.6

  • Added Channel validation for named methods #177

  • Optimized memory usage and performance of the single_site_system_generator utility function.

Bug fixes

  • Fixed bug where spectral interpolation resulted in a segmentation fault.

  • Fixed memory leak issue in the C code.

  • Fixed bug in query combination involving multiple quadrupolar queries. #188.

  • Fixed bug related to unsigned/signed integers crashing on M1 macs.

Breaking changes

For most users Mrsimulator is currently in development, and the new release includes breaking changes from v0.6. Please review these changes and make changes according.

  • The mrsimulator.methods module is renamed as mrsimulator.method.lib.

  • The mrsimulator.signal_processing module is renamed to mrsimulator.signal_processor.

  • The data attribute of SignalProcessor.apply_operations(data=…) is renamed to dataset. Use SignalProcessor.apply_operations(dataset=…)

  • The transition_query attribute of the mrsimulator.method.SpectralEvent class is renamed to transition_queries.

  • The mrsimulator.method.query.RotationalQuery class is renamed to mrsimulator.method.query.RotationQuery

For advanced users - Complete redesign of the TransitionQuery object. Please refer to the documentation for details.

v0.6.0

What’s new

  • ⭐ Improved simulation performance. ⭐ See our Performance benchmark.

  • Simulation of one-dimensional spectra of coupled spin systems. The frequency contributions from the coupled sites include weak J-couplings and weak dipolar couplings.

  • New Coupling class.

  • Added a new Sites class that holds a list of Site objects. The Sites class method, to_pd(), exports the sites as a pandas data frame.

  • A new method, sites(), is added to the Simulator object, which returns a list of unique Sites objects within the Simulator object across multiple spin systems.

  • Added three new arguments to the single_site_system_generator() method, ‘site_labels’, ‘site_names’, and ‘site_descriptions’.

Changes

  • The get_isotopes() method from the SpinSystem object, will now return Isotope objects by default. Use the symbol=True argument of the method to get a list of string isotopes.

  • The to_freq_dict() function is deprecated.

  • The D symmetry of transition_query attribute from Method2D method is now None by default.

  • BlochDecayCTSpectrum is an alias for BlochDecayCentralTransitionSpectrum class.

Bug fixes

  • Fixed a bug related to get_spectral_dimensions() utility method in cases when CSDM dimension objects have negative increment.

  • Fixed a bug resulting in the non-conserved spectral area after a Gaussian apodization.

  • Fixed a bug in Gaussian apodization, which raised an error when the FWHM argument is a scalar.

  • Fixed bug causing multi-dataset fit to fail.

v0.5.1

Bug fixes

  • Fixed a bug that was causing incorrect spectral binning when the frequency contribution is pure isotropic.

Other changes

  • The to_dict_with_units() method is deprecated and is replaced with json()

  • The json() function returns a python dictionary object with minimal required keywords, where the event keys are globally serialized at the root method object. In the case where the event key value is different from the global value, the respective key is serialized within the event object.

  • The json() function will no longer serialize the transition_query objects for the named objects.

v0.5.0

What’s new

The update introduces various two-dimensional methods for simulating NMR spectrum.

  • Introduces a generic one-dimensional method, Method1D.

  • Introduces a generic two-dimensional method, Method2D.

  • Specialized two-dimensional methods for multi-quantum variable-angle spinning with build-in affine transformations.

  • Specialized two-dimensional methods for satellite-transition variable-angle spinning with build-in affine transformations.

  • Specialized two-dimensional isotropic/anisotropic sideband correlation method, SSB2D.

Other changes

  • The get_transition_pathways() method no longer return a numpy array, instead a python list.

  • Renamed mrsimulator.methods module to mrsimulator.method.lib.

v0.4.0

What’s new!

v0.3.0

What’s new!

  • ⭐ Improved simulation performance. ⭐ See our Performance benchmark.

  • Removed the Dimension class and added a new Method class instead.

  • New methods for simulating the NMR spectrum:

    • BlochDecaySpectrum and

    • BlochDecayCentralTransitionSpectrum.

    The Bloch decay spectrum method simulates all p=Δm=-1 transition pathways, while the Bloch decay central transition selective spectrum method simulates all transition pathways with p=Δm=-1 and d=0.

  • New Isotope, Transition, and ZeemanState classes.

  • Every class now includes a reduced_dict() method. The reduced_dict method returns a dictionary with minimal key-value pairs required to simulate the spectrum. Note, this may cause metadata loss, if any.

  • Added a label and description attributes to the Site class.

  • Added a new label attribute to the SpinSystem class.

  • New SignalProcessor class for post-simulation signal processing.

  • Improved usage of least-squares minimization using python LMFIT package.

  • Added a new get_spectral_dimensions utility function to extract the spectral dimensions information from the CSDM object.

Bug fixes

  • Fixed bug resulting from the rotation of the fourth rank tensor with non-zero euler angles.

  • Fixed bug causing a change in the spectral area as the sampling points change. Now the area is constant.

  • Fixed bug resulting in an incorrect spectrum when non-coincidental quad and shielding tensors are given.

  • Fixed bug causing incorrect generation of transition pathways when multiple events are present.

Other changes

  • Renamed the decompose attribute from the ConfigSimulator class to decompose_spectrum. The attribute is an enumeration with the following literals:

    • none: Computes a spectrum which is an integration of the spectra from all spin systems.

    • spin_system: Computes a series of spectra each corresponding to a single spin system.

  • Renamed Isotopomer class to SpinSystem.

  • Renamed isotopomers attribute from Simulator class to spin_systems.

  • Renamed dimensions attribute from Simulator class to methods.

  • Changed the default value of name and description attribute from the SpinSystem class from "" to None.

v0.2.x

What’s new!

Bug fixes

  • Fixed amplitude normalization. The spectral amplitude no longer change when the integration_density, integration_volume`, or the number_of_sidebands attributes change.

Other changes

  • Removed plotly-dash app to its own repository.

  • Renamed the class Spectrum to Dimension

v0.1.3

  • Fixed missing files from source tar.

v0.1.2

  • Initial release on pypi.

v0.1.1

  • Added solid state quadrupolar spectrum simulation.

  • Added mrsimulator plotly-dash app.

v0.1.0

  • Solid state chemical shift anisotropy spectrum simulation.