def test_summary():
all_defined_no_constant_spec_dims = [
{
"events": [
{
"label": "Mix0",
"query": {
"ch1": {
"angle": np.pi / 4,
"phase": np.pi / 2
}
},
},
{
"label": "Dur0",
"duration": 1,
"magnetic_flux_density": 1,
"rotor_frequency": 0, # in kHz
"rotor_angle": 0.1,
"transition_queries": [{
"ch1": {
"P": [0],
"D": [0]
}
}],
},
{
"label": "Spec0",
"fraction": 1,
"magnetic_flux_density": 2,
"rotor_frequency": 20000,
"rotor_angle": 0.2,
"transition_queries": [{
"ch1": {
"P": [1],
"D": [-2]
}
}],
},
]
},
{
"events": [
{
"label": "Mix1",
"query": {
"ch1": {
"angle": np.pi / 2,
"phase": np.pi
}
},
},
{
"label": "Dur1",
"duration": 2,
"magnetic_flux_density": 3,
"rotor_frequency": 0,
"rotor_angle": 0.3,
"transition_queries": [{
"ch1": {
"P": [3],
"D": [-4]
}
}],
},
{
"label": "Spec1",
"fraction": 1,
"magnetic_flux_density": 4,
"rotor_frequency": 0,
"rotor_angle": 0.4,
"transition_queries": [{
"ch1": {
"P": [4],
"D": [-6]
}
}],
},
]
},
]
const_mfd_rotor_ang_spec_dims = [
{
"events": [
{
"label": "Mix0",
"query": {
"ch1": {
"angle": np.pi / 2,
"phase": np.pi
}
},
},
{
"label": "Dur0",
"duration": 1,
"rotor_frequency": 0,
"rotor_angle": 0.5,
"transition_queries": [{
"ch1": {
"P": [0],
"D": [0]
}
}],
},
{
"label": "Spec0",
"fraction": 1,
"rotor_frequency": 20000,
"rotor_angle": 0.5,
"transition_queries": [{
"ch1": {
"P": [1],
"D": [0]
}
}],
},
]
},
{
"events": [
{
"label": "Mix1",
"query": {
"ch1": {
"angle": np.pi / 2,
"phase": np.pi
}
},
},
{
"label": "Dur1",
"duration": 2,
"rotor_frequency": 0,
"rotor_angle": 0.5,
"transition_queries": [{
"ch1": {
"P": [3],
"D": [0]
}
}],
},
{
"label": "Spec1",
"fraction": 1,
"rotor_frequency": 0,
"rotor_angle": 0.5,
"transition_queries": [{
"ch1": {
"P": [4],
"D": [0]
}
}],
},
]
},
]
method1 = Method(
name="test-method-1",
channels=["1H", "13C"],
spectral_dimensions=all_defined_no_constant_spec_dims,
)
# Constant 'magnetic_flux_density' and 'rotor_frequency'
method2 = Method(
name="test-method-2",
channels=["1H", "13C"],
spectral_dimensions=const_mfd_rotor_ang_spec_dims,
)
assert method1.name == "test-method-1"
assert len(method1.spectral_dimensions) == 2
basic_summary_tests(method1)
assert method2.name == "test-method-2"
assert len(method2.spectral_dimensions) == 2
args_summary_tests(method2)
assert isinstance(method2.plot(), Figure)
SpectralEvent(transition_queries=[
{
"ch1": {
"P": [-1],
"D": [2]
}
}, # inner satellite
])
],
)
],
)
# A graphical representation of the method object.
plt.figure(figsize=(4, 2.5))
method.plot()
plt.show()
# %%
# Create the Simulator object and add the method and the spin system object.
sim = Simulator(spin_systems=[spin_system], methods=[method])
sim.run()
# The plot of the simulation before signal processing.
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
ax.plot(sim.methods[0].simulation.real, color="black", linewidth=1)
ax.invert_xaxis()
plt.tight_layout()
plt.show()
reference_offset=-1.05e4, # in Hz
label="Isotropic dimension",
events=[
SpectralEvent(
rotor_angle=54.735 * np.pi / 180, # in rads
transition_queries=[{"ch1": {"P": [-1], "D": [0]}}],
)
],
),
],
affine_matrix=[[1, -1], [0, 1]],
)
# A graphical representation of the method object.
plt.figure(figsize=(5, 2.5))
maf.plot()
plt.show()
# %%
# Create the Simulator object, add the method and spin system objects, and run the
# simulation.
sim = Simulator(spin_systems=spin_systems, methods=[maf])
sim.run()
# %%
# Add post-simulation signal processing.
csdm_dataset = sim.methods[0].simulation
processor = sp.SignalProcessor(
operations=[
sp.IFFT(dim_index=(0, 1)),
sp.apodization.Gaussian(FWHM="50 Hz", dim_index=0),
# :math:`p=0`. A similar argument holds for ``[-1]`` query. By implementing query # objects, we decouple the method from the spin system, i.e., once a method is defined, # it can be used to simulate spectra from any given spin system. We will demonstrate # this momentarily by simulating a Hahn echo spectrum from single and two-site spin # systems. # # Besides the SpectralEvent, you may also notice a MixingEvent sandwiched in-between # the two SpectralEvent. A MixingEvent does not directly contribute to the frequencies. # As the name suggests, a mixing event is used for the mixing of transitions in a # multi-event method such as HahnEcho. In the above code, we define a mixing query # on channel-1 by setting the attributes ``angle`` and ``phase`` to :math:`\pi` and # 0, respectively. There two parameters are analogous to the pulse angle and phase. # %% plt.figure(figsize=(4, 2)) hahn_echo.plot() plt.show() # %% # As mentioned before, a method object is decoupled from the spin system object. Notice, # when we get the transition pathways from this method for a single-site spin system, we # get a single transition pathway. pprint(hahn_echo.get_transition_pathways(spin_system_1)) # %% # In the case of a homonuclear two-site spin 1/2 spin system, the same method returns # four transition pathways. pprint(hahn_echo.get_transition_pathways(spin_system_2)) # %% # Create the Simulator object, add the method and spin system objects, and run the
events=[
SpectralEvent(transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}])
],
),
],
affine_matrix=[[1, 0], [1 / 4, 3 / 4]],
)
# A graphical representation of the method object.
plt.figure(figsize=(5, 2.75))
coaster.plot()
plt.show()
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator(spin_systems=[spin_system], methods=[coaster])
# configure the simulator object. For non-coincidental tensors, set the value of the
# `integration_volume` attribute to `hemisphere`.
sim.config.integration_volume = "hemisphere"
sim.run()
# %%
# The plot of the simulation.
dataset = sim.methods[0].simulation
rotor_angle=54.74 * np.pi / 180, # in radians
transition_queries=[{
"ch1": {
"P": [-1],
"D": [0]
}
}],
)
],
),
],
)
# A graphical representation of the method object.
plt.figure(figsize=(5, 2.5))
sas.plot()
plt.show()
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator(spin_systems=spin_systems, methods=[sas])
sim.run()
# %%
# The plot of the simulation.
dataset = sim.methods[0].simulation
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
cb = ax.imshow(dataset.real / dataset.real.max(),
reference_offset=0, # in Hz
label="MAS dimension",
events=[
SpectralEvent(
rotor_angle=54.735 * np.pi / 180, # in rads
transition_queries=[{"ch1": {"P": [-1], "D": [0]}}],
)
],
),
],
)
sim.methods = [das] # add the method
# A graphical representation of the method object.
plt.figure(figsize=(5, 2.5))
das.plot()
plt.show()
# %%
# Run the simulation
sim.run()
# %%
# The plot of the simulation.
dataset = sim.methods[0].simulation
plt.figure(figsize=(4.25, 3.0))
ax = plt.subplot(projection="csdm")
cb = ax.imshow(dataset.real / dataset.real.max(), aspect="auto", cmap="gist_ncar_r")
plt.colorbar(cb)
ax.invert_xaxis()
spectral_width=2e5, # in Hz
reference_offset=2e4, # in Hz
label="Paramagnetic shift",
events=[
SpectralEvent(
transition_queries=[{"ch1": {"P": [-1]}}],
freq_contrib=["Shielding1_0", "Shielding1_2"],
)
],
),
],
)
# A graphical representation of the method object.
plt.figure(figsize=(4, 1.5))
shifting_d.plot()
plt.show()
# %%
# Create the Simulator object, add the method and spin system objects, and
# run the simulation.
sim = Simulator(spin_systems=spin_systems, methods=[shifting_d])
# Configure the simulator object. For non-coincidental tensors, set the value of the
# `integration_volume` attribute to `hemisphere`.
sim.config.integration_volume = "hemisphere"
sim.config.decompose_spectrum = "spin_system" # simulate spectra per spin system
sim.run()
# %%
# Add post-simulation signal processing.
dataset = sim.methods[0].simulation