def fitFunction(x, *tmp_params):
model = load_model(equation)
data = empty_data1D(x)
param_dict = dict(zip(param_names, tmp_params))
model_wrapper = Model(model, **param_dict)
if value_ranges is not None:
for name, values in value_ranges.items():
model_wrapper.__dict__[name].range(values[0], values[1])
func_wrapper = Experiment(data=data, model=model_wrapper)
return func_wrapper.theory()
kernel = load_model(name, dtype="single")
cutoff = 1e-3
if name == "ellipsoid":
model = Model(
kernel,
scale=0.08,
background=35,
radius_polar=15,
radius_equatorial=800,
sld=.291,
sld_solvent=7.105,
theta=theta,
phi=phi,
theta_pd=0,
theta_pd_n=0,
theta_pd_nsigma=3,
phi_pd=0,
phi_pd_n=20,
phi_pd_nsigma=3,
radius_polar_pd=0.222296,
radius_polar_pd_n=1,
radius_polar_pd_nsigma=0,
radius_equatorial_pd=.000128,
radius_equatorial_pd_n=1,
radius_equatorial_pd_nsigma=0,
)
# SET THE FITTING PARAMETERS
model.radius_polar.range(15, 1000)
model.radius_equatorial.range(15, 1000)
datasets = load_data('latex_smeared.xml', index='all')
#[print(data) for data in datasets]
# A single sphere model to share between the datasets. We will use
# FreeVariables below to set the parameters that are independent between
# the datasets.
kernel = load_model('sphere')
pars = dict(
scale=0.01,
background=0.0,
sld=5.0,
sld_solvent=0.0,
radius=1500.,
#radius_pd=0.1, radius_pd_n=35,
)
model = Model(kernel, **pars)
# radius and polydispersity (if any) are shared
model.radius.range(0, inf)
#model.radius_pd.range(0, 1)
# Contrast and dilution are the same for both measurements, but are not
# separable with a single measurement (i.e., I(q) ~ F(q) contrast^2 Vf),
# so fit one of scale, sld or solvent sld. With absolute scaling from
# data reduction, can use the same parameter for both datasets.
model.scale.range(0, inf)
#model.sld.range(-inf, inf)
#model.sld_solvent.range(-inf, inf)
# Background is different for sans and usans so set it as a free variable
# in the model.
from sasmodels.bumps_model import Model, Experiment
from sasmodels.data import load_data, set_beam_stop, set_top
""" IMPORT THE DATA USED """
radial_data = load_data('DEC07267.DAT')
set_beam_stop(radial_data, 0.00669, outer=0.025)
set_top(radial_data, -.0185)
kernel = load_model("ellipsoid")
model = Model(kernel,
scale=0.08,
radius_polar=15, radius_equatorial=800,
sld=.291, sld_solvent=7.105,
background=0,
theta=90, phi=0,
theta_pd=15, theta_pd_n=40, theta_pd_nsigma=3,
radius_polar_pd=0.222296, radius_polar_pd_n=1, radius_polar_pd_nsigma=0,
radius_equatorial_pd=.000128, radius_equatorial_pd_n=1, radius_equatorial_pd_nsigma=0,
phi_pd=0, phi_pd_n=20, phi_pd_nsigma=3,
)
# SET THE FITTING PARAMETERS
model.radius_polar.range(15, 1000)
model.radius_equatorial.range(15, 1000)
model.theta_pd.range(0, 360)
model.background.range(0,1000)
model.scale.range(0, 10)
#cutoff = 0 # no cutoff on polydisperisity loops
#cutoff = 1e-5 # default cutoff
def scat_model(data, label):
if label == "ellipsoid":
pars = dict(
scale=1.0,
background=0.001,
)
kernel = load_model(label)
model = Model(kernel, **pars)
# SET THE FITTING PARAMETERS
model.radius_polar.range(0.0, 1000.0)
model.radius_equatorial.range(0.0, 1000.0)
model.sld.range(-0.56, 8.00)
model.sld_solvent.range(-0.56, 6.38)
model.radius_polar_pd.range(0, 0.11)
experiment = Experiment(data=data, model=model)
problem = FitProblem(experiment)
result = fit(problem, method='dream')
chisq = problem.chisq()
if label == "shell":
label = "core_shell_sphere"
pars = dict(
scale=1.0,
background=0.001,
)
kernel = load_model(label)
model = Model(kernel, **pars)
# SET THE FITTING PARAMETERS
model.radius.range(0.0, 1000.0)
model.thickness.range(0.0, 100.0)
model.sld_core.range(-0.56, 8.00)
model.sld_shell.range(-0.56, 8.00)
model.sld_solvent.range(-0.56, 6.38)
model.radius_pd.range(0.1, 0.11)
experiment = Experiment(data=data, model=model)
problem = FitProblem(experiment)
result = fit(problem, method='dream')
chisq = problem.chisq()
if label == "cylinder":
pars = dict(
scale=1.0,
background=0.001,
)
kernel = load_model(label)
model = Model(kernel, **pars)
# SET THE FITTING PARAMETERS
model.radius.range(0, 1000.0)
model.length.range(0, 1000.0)
model.sld.range(-0.56, 8.00)
model.sld_solvent.range(-0.56, 6.38)
model.radius_pd.range(0, 0.11)
experiment = Experiment(data=data, model=model)
problem = FitProblem(experiment)
result = fit(problem, method='dream')
chisq = problem.chisq()
if label == "sphere":
pars = dict(
scale=1.0,
background=0.001,
)
kernel = load_model(label)
model = Model(kernel, **pars)
# SET THE FITTING PARAMETERS
model.radius.range(0.0, 3200.0)
model.sld.range(-0.56, 8.00)
model.sld_solvent.range(-0.56, 6.38)
model.radius_pd.range(0.1, 0.11)
experiment = Experiment(data=data, model=model)
problem = FitProblem(experiment)
result = fit(problem, method='dream')
chisq = problem.chisq()
return np.round(chisq, 3)
usans.oriented = True
#print sans.dxl, usans.dxl
#import pprint; pprint.pprint(sans.__dict__)
kernel = load_model("ellipsoid")
model = Model(
kernel,
scale=0.08,
background=0,
sld=.291,
sld_solvent=7.105,
r_polar=1800,
r_polar_pd=0.222296,
r_polar_pd_n=0,
r_equatorial=2600,
r_equatorial_pd=0.28,
r_equatorial_pd_n=0,
theta=60,
theta_pd=0,
theta_pd_n=0,
phi=60,
phi_pd=0,
phi_pd_n=0,
)
# SET THE FITTING PARAMETERS
model.r_polar.range(1000, 10000)
model.r_equatorial.range(1000, 10000)
model.theta.range(0, 360)
model.phi.range(0, 360)
section = "radial" if len(sys.argv) < 3 else sys.argv[2]
if section not in ("radial","tangential","both"):
raise ValueError("section %r should be 'radial', 'tangential' or 'both'"
% section)
data = radial_data if section != "tangential" else tan_data
phi = 0 if section != "tangential" else 90
kernel = load_model(name, dtype="single")
cutoff = 1e-3
if name == "ellipsoid":
model = Model(kernel,
scale=0.08,
r_polar=15, r_equatorial=800,
sld=.291, sld_solvent=7.105,
background=0,
theta=90, phi=phi,
theta_pd=15, theta_pd_n=40, theta_pd_nsigma=3,
r_polar_pd=0.222296, r_polar_pd_n=1, r_polar_pd_nsigma=0,
r_equatorial_pd=.000128, r_equatorial_pd_n=1, r_equatorial_pd_nsigma=0,
phi_pd=0, phi_pd_n=20, phi_pd_nsigma=3,
)
# SET THE FITTING PARAMETERS
model.r_polar.range(15, 1000)
model.r_equatorial.range(15, 1000)
model.theta_pd.range(0, 360)
model.background.range(0,1000)
model.scale.range(0, 10)
def fit_function(key, sans_data, usans_data, actual_vol, actual_stdev_vol,
backgrounds, avg_scale, avg_rg, ps_s, ps_porod_exp, slds, cps,
matrix):
#np.savetxt('Sample_'+str(key)+'.txt', np.array(['Fitting']), fmt='%s')
kernel = load_model("guinier_porod+ellipsoid")
# loading the data
sans = sans_data[key]
sans.dx = sans.dx - sans.dx # removing smearing from sans segment
usans = usans_data[key]
vol = actual_vol[key] / 100 # cp volume fraction from uv-vis
vol_stdev = actual_stdev_vol[key] / 100
# initial parameter values
scale = Parameter(1, name=str(key) + 'scale')
background = Parameter(backgrounds[key][0], name=str(key) + 'background')
A_scale = Parameter(avg_scale * (1 - vol), name=str(key) + ' PS scale')
A_rg = Parameter(avg_rg, name=str(key) + ' PS rg')
A_s = Parameter(ps_s, name=str(key) + ' PS s')
A_porod_exp = Parameter(ps_porod_exp, name=str(key) + ' PS porod_exp')
B_scale_normal = bumps.bounds.Normal(mean=vol, std=vol_stdev)
B_scale = Parameter(vol,
name=str(key) + ' sphere scale',
bounds=B_scale_normal)
B_sld = Parameter(slds[cps[key]], name=str(key) + ' PS sld')
B_sld_solvent = Parameter(slds[matrix[key]], name=str(key) + ' PS solvent')
B_radius_polar = Parameter(1000,
limits=[0, inf],
name=str(key) + ' ellipsoid polar radius')
B_radius_polar_pd = Parameter(0.5,
name=str(key) + ' ellipsoid polar radius pd')
B_radius_polar_pd_n = Parameter(200,
name=str(key) +
' ellipsoid polar radius pd n')
B_radius_polar_pd_nsigma = Parameter(8,
name=str(key) +
' ellipsoid polar radius pd nsigma')
B_radius_equatorial = Parameter(1000,
limits=[0, inf],
name=str(key) +
' ellipsoid equatorial radius')
B_radius_equatorial_pd = Parameter(0.5,
name=str(key) +
' ellipsoid equatorial radius pd')
B_radius_equatorial_pd_n = Parameter(200,
name=str(key) +
' ellipsoid equatorial radius pd n')
B_radius_equatorial_pd_nsigma = Parameter(
8, name=str(key) + ' ellipsoid equatorial radius pd nsigma')
# setting up the combined model for fitting
sans_model = Model(
model=kernel,
scale=scale,
background=background,
A_scale=A_scale,
A_rg=A_rg,
A_s=A_s,
A_porod_exp=A_porod_exp,
B_scale=B_scale,
B_sld=B_sld,
B_sld_solvent=B_sld_solvent,
B_radius_polar=B_radius_polar,
B_radius_polar_pd_type='lognormal',
B_radius_polar_pd=B_radius_polar_pd,
B_radius_polar_pd_n=B_radius_polar_pd_n,
B_radius_polar_pd_nsigma=B_radius_polar_pd_nsigma,
B_radius_equatorial=B_radius_equatorial,
B_radius_equatorial_pd_type='lognormal',
B_radius_equatorial_pd=B_radius_equatorial_pd,
B_radius_equatorial_pd_n=B_radius_equatorial_pd_n,
B_radius_equatorial_pd_nsigma=B_radius_equatorial_pd_nsigma,
)
# setting parameter ranges as needed
sans_model.B_radius_polar.range(0, 200000)
sans_model.B_radius_equatorial.range(0, 200000)
sans_experiment = Experiment(data=sans, model=sans_model)
usans_experiment = Experiment(data=usans, model=sans_model)
usans_smearing = sasmodels.resolution.Slit1D(usans.x, 0.117)
usans_experiment.resolution = usans_smearing
experiment = [sans_experiment, usans_experiment]
problem = FitProblem(experiment)
result = fit(problem,
method='dream',
samples=1e6,
steps=1000,
verbose=True)
result.state.save(
'../data/sans/Sample_Fitting/fitting_results/ps_ellipsoid_match/CMW' +
str(key) + '_ps_ellipsoid_state')
theta=theta,
phi=phi,
theta_pd=0,
theta_pd_n=0,
theta_pd_nsigma=3,
phi_pd=0,
phi_pd_n=20,
phi_pd_nsigma=3,
radius_polar_pd=0.222296,
radius_polar_pd_n=1,
radius_polar_pd_nsigma=0,
radius_equatorial_pd=.000128,
radius_equatorial_pd_n=1,
radius_equatorial_pd_nsigma=0,
)
model = Model(kernel, **pars)
# SET THE FITTING PARAMETERS
model.radius_polar.range(15, 1000)
model.radius_equatorial.range(15, 1000)
#model.theta.range(0, 90)
#model.theta_pd.range(0,10)
model.phi_pd.range(0, 20)
model.phi.range(0, 180)
model.background.range(0, 1000)
model.scale.range(0, 10)
elif name == "lamellar":
pars = dict(
scale=0.08,
background=0.003,