def test_read_write_methods():
for item in methods:
kwargs = {
"channels": ["93Nb"],
"spectral_dimensions": [{
"count": 1024,
"spectral_width": 100
} for _ in range(item.ndim)],
}
if item.__name__ == "SSB2D":
kwargs["rotor_frequency"] = 1e3
fn1 = item(**kwargs)
# Parse against self
assert_parsing(item, fn1)
# Parse against Method class
assert_parsing(Method, fn1)
# Parse against Method1D/Method2D classes
mth_d = Method1D if item.ndim == 1 else Method2D
assert_parsing(mth_d, fn1)
# save test
sim = Simulator(spin_systems=[sys], methods=[fn1])
# save/load with units
sim.run()
sim.save("test.mrsim")
sim2 = Simulator.load("test.mrsim")
check_sim_save(sim, sim2, "with units")
# save/load with out units
sim.run()
sim.save("test.mrsim", with_units=False)
sim2 = Simulator.load("test.mrsim", parse_units=False)
check_sim_save(sim, sim2, "without units")
# save/load methods
sim.run()
sim.export_methods("test.mrmtd")
sim2 = sim.copy()
sim2.load_methods("test.mrmtd")
check_methods_save_load(sim, sim2)
# save/load spin systems
sim.run()
sim.export_spin_systems("test.mrsys")
sim2 = sim.copy()
sim2.load_spin_systems("test.mrsys")
assert sim.spin_systems == sim2.spin_systems
os.remove("test.mrsim")
os.remove("test.mrsys")
os.remove("test.mrmtd")
def test_sim_coesite():
# coesite
O17_1 = Site(
isotope="17O",
isotropic_chemical_shift=29,
quadrupolar=dict(Cq=6.05e6, eta=0.000),
)
O17_2 = Site(
isotope="17O",
isotropic_chemical_shift=41,
quadrupolar=dict(Cq=5.43e6, eta=0.166),
)
O17_3 = Site(
isotope="17O",
isotropic_chemical_shift=57,
quadrupolar=dict(Cq=5.45e6, eta=0.168),
)
O17_4 = Site(
isotope="17O",
isotropic_chemical_shift=53,
quadrupolar=dict(Cq=5.52e6, eta=0.169),
)
O17_5 = Site(
isotope="17O",
isotropic_chemical_shift=58,
quadrupolar=dict(Cq=5.16e6, eta=0.292),
)
sites = [O17_1, O17_2, O17_3, O17_4, O17_5]
abundance = [0.83, 1.05, 2.16, 2.05, 1.90] # abundance of each spin system
spin_systems = [
SpinSystem(sites=[s], abundance=a) for s, a in zip(sites, abundance)
]
method = BlochDecayCTSpectrum(
channels=["17O"],
rotor_frequency=14000,
spectral_dimensions=[{
"count": 2048,
"spectral_width": 50000
}],
)
sim_coesite = Simulator()
sim_coesite.spin_systems += spin_systems
sim_coesite.methods += [method]
sim_coesite.save("sample.mrsim")
sim_load = Simulator.load("sample.mrsim")
assert sim_coesite == sim_load
os.remove("sample.mrsim")
def test_simulator_2():
sim = Simulator()
sim.spin_systems = [
SpinSystem(
sites=[Site(isotope="1H"),
Site(isotope="23Na")],
couplings=[Coupling(site_index=[0, 1], isotropic_j=15)],
)
]
sim.methods = [
BlochDecaySpectrum(
channels=["1H"],
spectral_dimensions=[{
"count": 10
}],
experiment=cp.as_csdm(np.arange(10)),
)
]
sim.name = "test"
sim.label = "test0"
sim.description = "testing-testing 1.2.3"
sim.run()
# save
sim.save("test_sim_save.temp")
sim_load = Simulator.load("test_sim_save.temp")
sim_load_data = sim_load.methods[0].simulation
sim_data = sim.methods[0].simulation
sim_load_data._timestamp = ""
assert sim_load_data.dict() == sim_data.dict()
sim_load.methods[0].simulation = None
sim.methods[0].simulation = None
assert sim_load.spin_systems == sim.spin_systems
assert sim_load.methods == sim.methods
assert sim_load.name == sim.name
assert sim_load.description == sim.description
os.remove("test_sim_save.temp")
def test_read_write_methods():
def assert_parsing(method, fn1):
fn2 = method.parse_dict_with_units(fn1.json())
assert fn1 == fn2, f"Error with {method} parse with units."
fn3 = method(**fn1.json(units=False))
assert fn1 == fn3, f"Error with {method} parse with units."
event_error = "Event objects are immutable for"
serialize = fn1.json()
ent = serialize["spectral_dimensions"][0]["events"]
ent[0]["transition_query"][0]["ch1"]["P"] = [-100]
if method not in [Method, Method1D, Method2D]:
with pytest.raises(ImmutableEventError,
match=f".*{event_error}.*"):
method.parse_dict_with_units(serialize)
with pytest.raises(ImmutableEventError,
match=f".*{event_error}.*"):
method(**serialize)
with pytest.raises(ImmutableEventError,
match=f".*{event_error}.*"):
ent.append({"transition_query": [{"ch1": {"P": [-100]}}]})
method.parse_dict_with_units(serialize)
def check_sim_save(sim1, sim2, message):
for mth in sim2.methods:
mth.simulation._timestamp = ""
_ = [
item.to("ppm", "nmr_frequency_ratio")
for item in mth.simulation.x
]
data1 = sim.methods[0].simulation.copy()
sim.methods[0].simulation = None
data2 = sim2.methods[0].simulation.copy()
sim2.methods[0].simulation = None
assert data1 == data2, f"data saved and loaded is not equal: type {message}."
assert sim == sim2, f".mrsim saved and loaded is not equal: type {message}."
for item in methods:
kwargs = {
"channels": ["93Nb"],
"spectral_dimensions": [{
"count": 1024,
"spectral_width": 100
} for _ in range(item.ndim)],
}
if item.__name__ == "SSB2D":
kwargs["rotor_frequency"] = 1e3
fn1 = item(**kwargs)
# Parse against self
assert_parsing(item, fn1)
# Parse against Method class
assert_parsing(Method, fn1)
# Parse against Method1D/Method2D classes
mth_d = Method1D if item.ndim == 1 else Method2D
assert_parsing(mth_d, fn1)
# save test
sim = Simulator(spin_systems=[sys], methods=[fn1])
# save/load with units
sim.run()
sim.save("test.mrsim")
sim2 = Simulator.load("test.mrsim")
check_sim_save(sim, sim2, "with units")
# save/load with out units
sim.run()
sim.save("test.mrsim", with_units=False)
sim2 = Simulator.load("test.mrsim", parse_units=False)
check_sim_save(sim, sim2, "without units")
os.remove("test.mrsim")
def test_simulator_1():
sim = Simulator()
sim.spin_systems = [SpinSystem(sites=[Site(isotope="1H"), Site(isotope="23Na")])]
sim.methods = [BlochDecaySpectrum(channels=["1H"])]
sim.name = "test"
sim.label = "test0"
sim.description = "testing-testing 1.2.3"
red_dict = sim.json(units=False)
_ = [item.pop("description") for item in red_dict["methods"]]
assert red_dict == {
"name": "test",
"label": "test0",
"description": "testing-testing 1.2.3",
"spin_systems": [
{
"sites": [
{"isotope": "1H", "isotropic_chemical_shift": 0.0},
{"isotope": "23Na", "isotropic_chemical_shift": 0.0},
],
}
],
"methods": [
{
"channels": ["1H"],
"name": "BlochDecaySpectrum",
"magnetic_flux_density": 9.4,
"rotor_angle": 0.9553166181245,
"rotor_frequency": 0.0,
"spectral_dimensions": [
{
"count": 1024,
"events": [{"transition_queries": [{"ch1": {"P": [-1]}}]}],
"spectral_width": 25000.0,
}
],
}
],
"config": {
"decompose_spectrum": "none",
"integration_density": 70,
"integration_volume": "octant",
"number_of_sidebands": 64,
},
}
# save
sim.save("test_sim_save.temp")
sim_load = Simulator.load("test_sim_save.temp")
assert sim_load.spin_systems == sim.spin_systems
assert sim_load.methods == sim.methods
assert sim_load.name == sim.name
assert sim_load.description == sim.description
assert sim_load == sim
# without units
sim.save("test_sim_save_no_unit.temp", with_units=False)
sim_load = Simulator.load("test_sim_save_no_unit.temp", parse_units=False)
assert sim_load == sim
os.remove("test_sim_save.temp")
os.remove("test_sim_save_no_unit.temp")
