diff --git a/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice.py b/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice.py
deleted file mode 100644
index 9e8e86c8809d0171ad9aa563ed980d734ba66e7f..0000000000000000000000000000000000000000
--- a/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice.py
+++ /dev/null
@@ -1,112 +0,0 @@
-"""
-Two parameter fit of spheres in a hex lattice.
-See FitSpheresInHexLattice_builder.py example which performs same fitting task
-using advanced sample construction techniques.
-"""
-
-import numpy as np
-from matplotlib import pyplot as plt
-import bornagain as ba
-from bornagain import deg, angstrom, nm
-
-
-def get_sample(radius=5.0*nm, lattice_constant=10.0*nm):
- """
- Returns a sample with cylinders and pyramids on a substrate,
- forming a hexagonal lattice.
- """
- m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0)
- m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
-
- sphere_ff = ba.FormFactorFullSphere(radius)
- sphere = ba.Particle(m_particle, sphere_ff)
- particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(sphere)
-
- interference = ba.InterferenceFunction2DLattice.createHexagonal(lattice_constant)
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm)
- interference.setDecayFunction(pdf)
-
- particle_layout.setInterferenceFunction(interference)
-
- air_layer = ba.Layer(m_air)
- air_layer.addLayout(particle_layout)
- substrate_layer = ba.Layer(m_substrate, 0)
- multi_layer = ba.MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
- return multi_layer
-
-
-def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
- 100, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- simulation.setBeamIntensity(1e+08)
- return simulation
-
-
-def create_real_data():
- """
- Generating "real" data by adding noise to the simulated data.
- """
- sample = get_sample(5.0*nm, 10.0*nm)
- simulation = get_simulation()
- simulation.setSample(sample)
- simulation.runSimulation()
-
- # retrieving simulated data in the form of numpy array
- real_data = simulation.result().array()
-
- # spoiling simulated data with noise to produce "real" data
- # random seed made as in FitSPheresInHexLattice_builder.py example
- np.random.seed(0)
- noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
- noisy[noisy < 0.1] = 0.1
- return noisy
-
-
-def run_fitting():
- """
- main function to run fitting
- """
- simulation = get_simulation()
- sample = get_sample()
- simulation.setSample(sample)
-
- real_data = create_real_data()
-
- fit_suite = ba.FitSuite()
- #fit_suite.setMinimizer("GSLLMA")
- fit_suite.addSimulationAndRealData(simulation, real_data)
- fit_suite.initPrint(10)
-
- draw_observer = ba.DefaultFitObserver(draw_every_nth=10)
- fit_suite.attachObserver(draw_observer)
-
- fit_suite.addFitParameter(
- "*/FullSphere/Radius", 8.*nm, ba.AttLimits.limited(4., 12.))
- fit_suite.addFitParameter(
- "*HexagonalLattice/LatticeLength", 8.*nm, ba.AttLimits.limited(4., 12.))
-
- print(fit_suite.treeToString())
- print(fit_suite.parametersToString())
-
- # running fit
- fit_suite.runFit()
-
- print("Fitting completed.")
- print("chi2:", fit_suite.getChi2())
- for fitPar in fit_suite.fitParameters():
- print(fitPar.name(), fitPar.value(), fitPar.error())
-
-
-if __name__ == '__main__':
- run_fitting()
- plt.show()
diff --git a/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py b/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
deleted file mode 100644
index 9f2e6724095a16fa0bb158ff21194edd9882f693..0000000000000000000000000000000000000000
--- a/Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
+++ /dev/null
@@ -1,130 +0,0 @@
-"""
-Two parameter fit of spheres in a hex lattice.
-Sample builder approach is used.
-"""
-
-import numpy as np
-import ctypes
-import bornagain as ba
-from matplotlib import pyplot as plt
-from bornagain import deg, angstrom, nm
-
-
-class MySampleBuilder(ba.IMultiLayerBuilder):
- """
- Sample builder is used to build complex samples from set of parameters.
- Given builder produces the sample representing spheres at hex lattice
- using two parameters as an input:
- radius - radius of spheres
- lattice_constant - hexagonal lattice constant
- """
- def __init__(self):
- ba.IMultiLayerBuilder.__init__(self)
- self.sample = None
- # parameters describing the sample
- self.radius = ctypes.c_double(5.0*nm)
- self.lattice_constant = ctypes.c_double(10.0*nm)
- # register parameters
- self.registerParameter("radius", ctypes.addressof(self.radius))
- self.registerParameter("lattice_constant",
- ctypes.addressof(self.lattice_constant))
-
- # constructs the sample for current values of parameters
- def buildSample(self):
- m_air = ba.HomogeneousMaterial("Air", 0.0, 0.0)
- m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
-
- sphere_ff = ba.FormFactorFullSphere(self.radius.value)
- sphere = ba.Particle(m_particle, sphere_ff)
- particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(sphere)
-
- interference = ba.InterferenceFunction2DLattice.createHexagonal(
- self.lattice_constant.value)
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm)
- interference.setDecayFunction(pdf)
-
- particle_layout.setInterferenceFunction(interference)
-
- air_layer = ba.Layer(m_air)
- air_layer.addLayout(particle_layout)
- substrate_layer = ba.Layer(m_substrate, 0)
- multi_layer = ba.MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
- return multi_layer
-
-
-def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
- 100, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- simulation.setBeamIntensity(1e+08)
-
- return simulation
-
-
-def create_real_data():
- """
- Generating "real" data by adding noise to the simulated data.
- """
- sample_builder = MySampleBuilder()
- sample_builder.setParameterValue("radius", 5.0*nm)
- sample_builder.setParameterValue("lattice_constant", 10.0*nm)
- simulation = get_simulation()
- simulation.setSampleBuilder(sample_builder)
- simulation.runSimulation()
-
- # retrieving simulated data in the form of numpy array
- real_data = simulation.result().array()
-
- # spoiling simulated data with the noise to produce "real" data
- # random seed made as in FitSPheresInHexLattice.py example
- np.random.seed(0)
- noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
- noisy[noisy < 0.1] = 0.1
- return noisy
-
-
-def run_fitting():
- """
- main function to run fitting
- """
- simulation = get_simulation()
- simulation.setSampleBuilder(MySampleBuilder())
-
- real_data = create_real_data()
-
- fit_suite = ba.FitSuite()
- fit_suite.addSimulationAndRealData(simulation, real_data)
- fit_suite.initPrint(10)
-
- draw_observer = ba.DefaultFitObserver(draw_every_nth=10)
- fit_suite.attachObserver(draw_observer)
-
- # setting fitting parameters with starting values
- fit_suite.addFitParameter("*radius", 8.*nm, ba.AttLimits.limited(4., 12.))
- fit_suite.addFitParameter("*lattice_constant",
- 8.*nm, ba.AttLimits.limited(4., 12.))
-
- print(fit_suite.treeToString())
- print(fit_suite.parametersToString())
-
- # running fit
- fit_suite.runFit()
-
- print("Fitting completed.")
- print("chi2:", fit_suite.getChi2())
- for fitPar in fit_suite.fitParameters():
- print(fitPar.name(), fitPar.value(), fitPar.error())
-
-
-if __name__ == '__main__':
- run_fitting()
- plt.show()