def assertion(csdm, res, test_ref=""):
assert get_spectral_dimensions(csdm)[0] == res, f"failed ref {test_ref}"
csdm_coordinates = csdm.x[0].coordinates.to("Hz").value
if csdm.x[0].increment < 0:
csdm_coordinates = csdm_coordinates[::-1]
spectral_dimension = SpectralDimension(**res)
mrsim_coordinates = spectral_dimension.coordinates_Hz()
assert np.allclose(csdm_coordinates,
mrsim_coordinates), f"failed ref {test_ref}"
def test_get_spectral_dimensions():
# 1
csdm = cp.as_csdm(np.arange(10))
csdm.dimensions[0] = cp.LinearDimension(count=10,
increment="1 Hz",
complex_fft=True)
res = {"count": 10, "spectral_width": 10, "reference_offset": 0}
assert get_spectral_dimensions(csdm)[0] == res
# 2
csdm.dimensions[0] = cp.LinearDimension(count=10,
increment="1 Hz",
coordinates_offset="-0.05 kHz",
complex_fft=True)
res = {"count": 10, "spectral_width": 10, "reference_offset": -50}
assert get_spectral_dimensions(csdm)[0] == res
# 3
csdm.dimensions[0] = cp.LinearDimension(count=10, increment="1 Hz")
res = {"count": 10, "spectral_width": 10, "reference_offset": 5}
assert get_spectral_dimensions(csdm)[0] == res
# 4
csdm.dimensions[0] = cp.LinearDimension(count=10,
increment="1 Hz",
label="1H")
res = {
"count": 10,
"spectral_width": 10,
"reference_offset": 5,
"label": "1H"
}
assert get_spectral_dimensions(csdm)[0] == res
# %%
# Create a fitting model
# ----------------------
# **Spin System**
B11 = Site(
isotope="11B",
isotropic_chemical_shift=20.0, # in ppm
quadrupolar=SymmetricTensor(Cq=2.3e6, eta=0.03), # Cq in Hz
)
spin_systems = [SpinSystem(sites=[B11])]
# %%
# **Method**
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(experiment)
MAS_CT = BlochDecayCTSpectrum(
channels=["11B"],
magnetic_flux_density=14.1, # in T
rotor_frequency=12500, # in Hz
spectral_dimensions=spectral_dims,
experiment=experiment, # add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the method.
for sys in spin_systems:
sys.transition_pathways = MAS_CT.get_transition_pathways(sys)
# %%
isotope="13C",
isotropic_chemical_shift=0, #
shielding_symmetric={
"zeta": -70,
"eta": 0.8
},
)
spin_systems = [SpinSystem(sites=[site])]
# %%
# **Method**
#
# For the sideband-only cross-section, use the BlochDecaySpectrum method.
# Get the dimension information from the experiment.
spectral_dims = get_spectral_dimensions(pass_cross_section)
PASS = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=9.395, # in T
rotor_frequency=1500, # in Hz
spectral_dimensions=spectral_dims,
experiment=pass_cross_section, # also add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the method.
for sys in spin_systems:
sys.transition_pathways = PASS.get_transition_pathways(sys)
# %%
eta = [0.8, 0.4, 0.9, 0.3, 0.0, 0.0]
spin_systems = single_site_system_generator(
isotope="13C",
isotropic_chemical_shift=shifts,
shielding_symmetric={"zeta": zeta, "eta": eta},
abundance=100 / 6,
)
# %%
# **Method**
#
# Create the SSB2D method.
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(mat_dataset)
PASS = SSB2D(
channels=["13C"],
magnetic_flux_density=9.395, # in T
rotor_frequency=1500, # in Hz
spectral_dimensions=spectral_dims,
experiment=mat_dataset, # add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the method.
for sys in spin_systems:
sys.transition_pathways = PASS.get_transition_pathways(sys)
# %%
shielding_symmetric=SymmetricTensor(zeta=30, eta=0.5), # zeta in Hz
)
spin_systems = [
SpinSystem(sites=[C1], name="C1"),
SpinSystem(sites=[C2], name="C2")
]
# %%
# **Method**: Create the three MAS method objects with respective MAS spinning speeds.
# Get the spectral dimension parameters from the respective experiment and setup the
# corresponding method.
# Method for dataset 1
spectral_dims1 = get_spectral_dimensions(experiment1)
MAS1 = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=7.05, # in T
rotor_frequency=5000, # in Hz
spectral_dimensions=spectral_dims1,
experiment=experiment1, # add experimental dataset 1
)
# Method for dataset 2
spectral_dims2 = get_spectral_dimensions(experiment2)
MAS2 = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=7.05, # in T
rotor_frequency=1940, # in Hz
spectral_dimensions=spectral_dims2,
)
Rb_2 = Site(
isotope="87Rb",
isotropic_chemical_shift=40, # in ppm
quadrupolar=SymmetricTensor(Cq=2.2e6, eta=0.95), # Cq in Hz
)
spin_systems = [SpinSystem(sites=[s]) for s in [Rb_1, Rb_2]]
# %%
# **Method**
#
# Create the SSB2D method.
# Get the spectral dimension parameters from the experiment.
spectral_dims = get_spectral_dimensions(qmat_data)
PASS = SSB2D(
channels=["87Rb"],
magnetic_flux_density=9.395, # in T
rotor_frequency=2604, # in Hz
spectral_dimensions=spectral_dims,
experiment=qmat_data, # add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the method.
for sys in spin_systems:
sys.transition_pathways = PASS.get_transition_pathways(sys)
# %%
def add_measurement_to_a_method():
"""Add a measurement to the selected method."""
existing_data = ctx.states["local-mrsim-data.data"]
existing_data["trigger"] = {
"simulation": False,
"internal_processor": False,
}
trigger_id = ctx.triggered[0]["prop_id"].split(".")[0]
contents = ctx.inputs[f"{trigger_id}.contents"]
content_string = contents.split(",")[1]
decoded = base64.b64decode(content_string)
success, exp_data, error_message = load_csdm(decoded)
if not success:
return sim_utils.on_fail_message(f"FileLoadError: {error_message}")
index = ctx.states["select-method.value"]
method = existing_data["methods"][index]
method["experiment"] = exp_data.to_dict()
spectral_dim = method["spectral_dimensions"]
mrsim_spectral_dims = get_spectral_dimensions(exp_data, units=True)
for i, dim in enumerate(mrsim_spectral_dims):
spectral_dim[i].update(dim)
method_overview = method_UI.refresh(existing_data["methods"])
post_sim_overview = no_update
if existing_data["signal_processors"][index] in [None, {"operations": []}]:
vector = exp_data.y[0].components[0].real
increment = exp_data.x[0].increment.value
amp = vector.sum()
existing_data["signal_processors"][index]["operations"] = [
{
"dim_index": [0],
"function": "IFFT"
},
{
"dim_index": [0],
"FWHM": f"{abs(3*increment)} Hz",
"function": "apodization",
"type": "Exponential",
},
{
"dim_index": [0],
"function": "FFT"
},
{
"factor": abs(amp) / 30,
"function": "Scale"
},
]
post_sim_overview = post_sim_UI.refresh(existing_data)
out = {
"alert": ["", False],
"mrsim": [existing_data, no_update],
"children": [no_update, method_overview, no_update],
"mrsim_config": [no_update] * 4,
"processor": [post_sim_overview],
}
return sim_utils.expand_output(out)
"zeta": -70,
"eta": 0.8
},
)
spin_systems = [SpinSystem(sites=[site])]
# %%
# **Method**
#
# For the sideband only cross-section, use the BlochDecaySpectrum method.
# Get the dimension information from the experiment. Note, the following function
# returns an array of two spectral dimensions corresponding to the 2D PASS dimensions.
# Use the spectral dimension that is along the anisotropic dimensions for the
# BlochDecaySpectrum method.
spectral_dims = get_spectral_dimensions(pass_data)
method = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=9.4, # in T
rotor_frequency=1500, # in Hz
spectral_dimensions=[spectral_dims[0]],
experiment=data1D, # also add the measurement to the method.
)
# Optimize the script by pre-setting the transition pathways for each spin system from
# the method.
for sys in spin_systems:
sys.transition_pathways = method.get_transition_pathways(sys)
# %%
# **Guess Spectrum**
