def load_spin_systems(self, filename: str):
"""Load a list of spin systems from the given JSON serialized file.
See an
`example <https://raw.githubusercontent.com/deepanshs/mrsimulator-examples/
master/spin_systems_v0.3.json>`_ of a JSON serialized file. For details, refer
to the :ref:`load_spin_systems` section of this documentation.
Args:
str filename: A local or remote address to a JSON serialized file.
Example
-------
>>> sim.load_spin_systems(filename) # doctest:+SKIP
"""
contents = import_json(filename)
self.spin_systems = [
SpinSystem.parse_dict_with_units(obj) for obj in contents
]
def test_6_coupled():
sim = Simulator()
spin_system = {"sites": [H, C], "couplings": [CH], "abundance": "100%"}
system_object = SpinSystem.parse_dict_with_units(spin_system)
sim.spin_systems += [system_object]
post_sim = sp.SignalProcessor(operations=op_list)
params = sf.make_LMFIT_params(sim, post_sim)
valuesdict_system = {
"sys_0_site_0_isotropic_chemical_shift": 10,
"sys_0_site_0_shielding_symmetric_zeta": 5,
"sys_0_site_0_shielding_symmetric_eta": 0.1,
"sys_0_site_0_shielding_symmetric_alpha": 3.12,
"sys_0_site_0_shielding_symmetric_gamma": 0.341,
"sys_0_site_1_isotropic_chemical_shift": -10,
"sys_0_site_1_shielding_symmetric_zeta": 15,
"sys_0_site_1_shielding_symmetric_eta": 0.2,
"sys_0_site_1_shielding_symmetric_beta": 4.12,
"sys_0_coupling_0_isotropic_j": 10,
"sys_0_coupling_0_j_symmetric_zeta": 60,
"sys_0_coupling_0_j_symmetric_eta": 0.4,
"sys_0_abundance": 100,
}
valuedict_proc = {
"SP_0_operation_1_Exponential_FWHM": 100,
"SP_0_operation_3_Scale_factor": 10,
}
assert params.valuesdict() == {
**valuesdict_system,
**valuedict_proc,
}, "Parameter creation failed"
params = sf.make_LMFIT_params(sim)
assert params.valuesdict(
) == valuesdict_system, "Parameter creation failed"
# alias
params = sf.make_LMFIT_parameters(sim)
assert params.valuesdict(
) == valuesdict_system, "Parameter creation failed"
def test_6_coupled():
sim = Simulator()
spin_system = {"sites": [H, C], "couplings": [CH], "abundance": "100%"}
system_object = SpinSystem.parse_dict_with_units(spin_system)
sim.spin_systems += [system_object]
post_sim = sp.SignalProcessor(operations=op_list)
params = sf.make_LMFIT_params(sim, post_sim)
valuesdict_system = {
"sys_0_site_0_isotropic_chemical_shift": 10,
"sys_0_site_0_shielding_symmetric_zeta": 5,
"sys_0_site_0_shielding_symmetric_eta": 0.1,
"sys_0_site_0_shielding_symmetric_alpha": 3.12,
"sys_0_site_0_shielding_symmetric_gamma": 0.341,
"sys_0_site_1_isotropic_chemical_shift": -10,
"sys_0_site_1_shielding_symmetric_zeta": 15,
"sys_0_site_1_shielding_symmetric_eta": 0.2,
"sys_0_site_1_shielding_symmetric_beta": 4.12,
"sys_0_coupling_0_isotropic_j": 10,
"sys_0_coupling_0_j_symmetric_zeta": 60,
"sys_0_coupling_0_j_symmetric_eta": 0.4,
"sys_0_abundance": 100,
}
compare_result(params, valuesdict_system, sim)
def parse_dict_with_units(cls, py_dict: dict):
"""Parse the physical quantity from a dictionary representation of the Simulator
object, where the physical quantity is expressed as a string with a number and
a unit.
Args:
dict py_dict: A required python dict object.
Returns:
A :ref:`simulator_api` object.
Example
-------
>>> sim_py_dict = {
... 'config': {
... 'decompose_spectrum': 'none',
... 'integration_density': 70,
... 'integration_volume': 'octant',
... 'number_of_sidebands': 64
... },
... 'spin_systems': [
... {
... 'abundance': '100 %',
... 'sites': [{
... 'isotope': '13C',
... 'isotropic_chemical_shift': '20.0 ppm',
... 'shielding_symmetric': {'eta': 0.5, 'zeta': '10.0 ppm'}
... }]
... },
... {
... 'abundance': '100 %',
... 'sites': [{
... 'isotope': '1H',
... 'isotropic_chemical_shift': '-4.0 ppm',
... 'shielding_symmetric': {'eta': 0.1, 'zeta': '2.1 ppm'}
... }]
... },
... {
... 'abundance': '100 %',
... 'sites': [{
... 'isotope': '27Al',
... 'isotropic_chemical_shift': '120.0 ppm',
... 'shielding_symmetric': {'eta': 0.1, 'zeta': '2.1 ppm'}
... }]
... }
... ]
... }
>>> sim = Simulator.parse_dict_with_units(sim_py_dict)
>>> len(sim.spin_systems)
3
"""
py_copy_dict = deepcopy(py_dict)
if "spin_systems" in py_copy_dict:
spin_sys = py_copy_dict["spin_systems"]
spin_sys = [SpinSystem.parse_dict_with_units(obj) for obj in spin_sys]
py_copy_dict["spin_systems"] = spin_sys
if "methods" in py_copy_dict:
methods = py_copy_dict["methods"]
methods = [Method.parse_dict_with_units(obj) for obj in methods]
py_copy_dict["methods"] = methods
return Simulator(**py_copy_dict)
{"count": 2048, "spectral_width": "25 kHz", "reference_offset": "0 Hz",}
],
}
method2 = {
"channels": ["1H"],
"magnetic_flux_density": "9.4 T",
"rotor_frequency": "1 kHz",
"rotor_angle": "54.735 deg",
"spectral_dimensions": [
{"count": 2048, "spectral_width": "25 kHz", "reference_offset": "0 Hz",}
],
}
sim = Simulator()
sim.spin_systems = [SpinSystem.parse_dict_with_units(item) for item in spin_systems]
sim.methods = [
BlochDecaySpectrum.parse_dict_with_units(method1),
BlochDecaySpectrum.parse_dict_with_units(method2),
]
sim.run()
freq1, amp1 = sim.methods[0].simulation.to_list()
freq2, amp2 = sim.methods[1].simulation.to_list()
fig, ax = plt.subplots(1, 2, figsize=(6, 3))
ax[0].plot(freq1, amp1, linewidth=1.0, color="k")
ax[0].set_xlabel(f"frequency ratio / {freq2.unit}")
ax[0].grid(color="gray", linestyle="--", linewidth=0.5, alpha=0.5)
ax[0].set_title("Static")
def test_direct_init_spin_system():
# test-1 # empty spin system
the_spin_system = SpinSystem(sites=[],
abundance=10,
transition_pathways=None)
assert the_spin_system.sites == []
assert the_spin_system.abundance == 10.0
assert the_spin_system.transition_pathways is None
assert the_spin_system.json() == {"abundance": "10.0 %"}
assert the_spin_system.json(units=False) == {
"abundance": 10.0,
}
# test-2 # site
test_site = Site(isotope="29Si", isotropic_chemical_shift=10)
assert test_site.isotope.symbol == "29Si"
assert test_site.isotropic_chemical_shift == 10.0
assert test_site.property_units["isotropic_chemical_shift"] == "ppm"
assert test_site.json() == {
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm",
}
assert test_site.json(units=False) == {
"isotope": "29Si",
"isotropic_chemical_shift": 10.0,
}
# test-3 # one site spin system
the_spin_system = SpinSystem(sites=[test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
}],
"abundance": "10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
}],
"abundance": 10,
}
# test-4 # two sites spin system
the_spin_system = SpinSystem(sites=[test_site, test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"abundance":
10,
}
# test-5 # coupling
test_coupling = Coupling(site_index=[0, 1],
isotropic_j=10,
dipolar={"D": 100})
assert test_coupling.site_index == [0, 1]
assert test_coupling.isotropic_j == 10.0
assert test_coupling.property_units["isotropic_j"] == "Hz"
assert test_coupling.dipolar.D == 100.0
assert test_coupling.dipolar.property_units["D"] == "Hz"
assert test_coupling.json() == {
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}
assert test_coupling.json(units=False) == {
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
},
}
# test-6 # two sites and one coupling spin system
the_spin_system = SpinSystem(sites=[test_site, test_site],
couplings=[test_coupling],
abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert isinstance(the_spin_system.couplings[0], Coupling)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
}
}],
"abundance":
10,
}
# test-5
the_spin_system = SpinSystem(
name="Just a test",
description="The same",
sites=[
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10,
"quadrupolar": {
"Cq": 5.1e6,
"eta": 0.5
},
},
],
couplings=[{
"site_index": [0, 1],
"isotropic_j": 34
}],
abundance=4.23,
)
assert the_spin_system.name == "Just a test"
assert the_spin_system.description == "The same"
assert the_spin_system.sites[0].isotope.symbol == "1H"
assert the_spin_system.sites[0].isotropic_chemical_shift == 0
assert the_spin_system.sites[1].isotope.symbol == "17O"
assert the_spin_system.sites[1].isotropic_chemical_shift == -10
assert the_spin_system.sites[1].quadrupolar.Cq == 5.1e6
assert the_spin_system.sites[1].quadrupolar.eta == 0.5
assert the_spin_system.couplings[0].site_index == [0, 1]
assert the_spin_system.couplings[0].isotropic_j == 34.0
assert the_spin_system.abundance == 4.23
serialize = the_spin_system.json()
assert serialize == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": "0.0 ppm"
},
{
"isotope": "17O",
"isotropic_chemical_shift": "-10.0 ppm",
"quadrupolar": {
"Cq": "5100000.0 Hz",
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "34.0 Hz"
}],
"abundance":
"4.23 %",
}
assert the_spin_system == SpinSystem.parse_dict_with_units(serialize)
json_no_unit = the_spin_system.json(units=False)
assert json_no_unit == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10.0,
"quadrupolar": {
"Cq": 5100000,
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 34.0
}],
"abundance":
4.23,
}
assert the_spin_system == SpinSystem(**json_no_unit)
import csdmpy as cp
import numpy as np
from mrsimulator import signal_processing as sp
from mrsimulator import Simulator
from mrsimulator import SpinSystem
from mrsimulator.methods import BlochDecaySpectrum
from .test_signal_processing import setup_read_write
__author__ = "Maxwell C. Venetos"
__email__ = "*****@*****.**"
sim = Simulator()
the_site = {"isotope": "1H", "isotropic_chemical_shift": "0 ppm"}
the_spin_system = {"name": "site A", "sites": [the_site], "abundance": "80%"}
spin_system_object = SpinSystem.parse_dict_with_units(the_spin_system)
sim.spin_systems += [
spin_system_object, spin_system_object, spin_system_object
]
sim.config.decompose_spectrum = "spin_system"
sim.methods += [
BlochDecaySpectrum(
channels=["1H"],
magnetic_flux_density=9.4,
spectral_dimensions=[{
"count": 65536,
"spectral_width": 25000
}],
)
]
