From 48dc6a0727d40cac7a751c5095690d1273eebcd8 Mon Sep 17 00:00:00 2001
From: Gennady Pospelov <g.pospelov@fz-juelich.de>
Date: Mon, 18 Dec 2017 17:33:43 +0100
Subject: [PATCH] Fitting example explaining how to set minimizer options.
---
.../ex02_FitBasics/MinimizerOptions.py | 113 ++++++++++++++++++
1 file changed, 113 insertions(+)
create mode 100644 Examples/python/fitting/ex02_FitBasics/MinimizerOptions.py
diff --git a/Examples/python/fitting/ex02_FitBasics/MinimizerOptions.py b/Examples/python/fitting/ex02_FitBasics/MinimizerOptions.py
new file mode 100644
index 00000000000..2d8e657b4e8
--- /dev/null
+++ b/Examples/python/fitting/ex02_FitBasics/MinimizerOptions.py
@@ -0,0 +1,113 @@
+"""
+Fitting example: running same fit using various minimizer and their settings.
+"""
+import bornagain as ba
+from bornagain import deg, angstrom, nm
+
+
+def get_sample(cylinder_height=5.0*nm, cylinder_radius=5.0*nm,
+ prism_length=5.0*nm, prism_height=5.0*nm):
+ """
+ Returns a sample with uncorrelated cylinders and prisms on a substrate.
+ """
+ # defining materials
+ 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)
+
+ # collection of particles
+ cylinder_ff = ba.FormFactorCylinder(cylinder_radius, cylinder_height)
+ cylinder = ba.Particle(m_particle, cylinder_ff)
+ prism_ff = ba.FormFactorPrism3(prism_length, prism_height)
+ prism = ba.Particle(m_particle, prism_ff)
+ particle_layout = ba.ParticleLayout()
+ particle_layout.addParticle(cylinder, 0.5)
+ particle_layout.addParticle(prism, 0.5)
+ interference = ba.InterferenceFunctionNone()
+ particle_layout.setInterferenceFunction(interference)
+
+ # air layer with particles and substrate form multi layer
+ 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 run_fitting():
+ """
+ run fitting
+ """
+
+ # prints info about available minimizers
+ print(ba.MinimizerFactory().catalogueToString())
+
+ # prints detailed info about available minimizers and their options
+ print(ba.MinimizerFactory().catalogueDetailsToString())
+
+ sample = get_sample()
+ simulation = get_simulation()
+ simulation.setSample(sample)
+
+ real_data = ba.IntensityDataIOFactory.readIntensityData(
+ 'refdata_fitcylinderprisms.int.gz')
+
+ fit_suite = ba.FitSuite()
+ fit_suite.addSimulationAndRealData(simulation, real_data)
+ fit_suite.initPrint(10)
+
+ # setting fitting parameters with starting values
+ fit_suite.addFitParameter("*Cylinder/Height", 4.*nm).setLowerLimited(0.01)
+ fit_suite.addFitParameter("*Cylinder/Radius", 6.*nm).setLowerLimited(0.01)
+ fit_suite.addFitParameter("*Prism3/Height", 4.*nm).setLowerLimited(0.01)
+ fit_suite.addFitParameter("*Prism3/BaseEdge", 12.*nm).setLowerLimited(0.01)
+
+ # Uncomment one of the line below to adjust minimizer settings
+
+ # setting Minuit2 minimizer with Migrad algorithm, limiting number of iterations
+ # Minimization will try to respect MaxFunctionCalls value and will stop around this value
+ # fit_suite.setMinimizer("Minuit2", "Migrad", "MaxFunctionCalls=100")
+
+ # Setting two options at once.
+ # Strategy=2 promises more accurate fit.
+ # fit_suite.setMinimizer("Minuit2", "Simplex", "MaxFunctionCalls=100;Strategy=2")
+
+ # setting Minuit2 minimizer with Fumili algorithm
+ # fit_suite.setMinimizer("Minuit2", "Fumili")
+
+ # Setting Levenberg-Marquardt algorithm
+ # fit_suite.setMinimizer("GSLLMA")
+
+ # Setting Genetic algorithm
+ # It requires all parameters to be limited, so we recreate parameters with min and max defined
+ # fit_suite.fitParameters().clear()
+ # fit_suite.addFitParameter("*Cylinder/Height", 4.*nm).setLimited(3.0, 8.0)
+ # fit_suite.addFitParameter("*Cylinder/Radius", 6.*nm).setLimited(3.0, 8.0)
+ # fit_suite.addFitParameter("*Prism3/Height", 4.*nm).setLimited(3.0, 8.0)
+ # fit_suite.addFitParameter("*Prism3/BaseEdge", 4.*nm).setLimited(3.0, 8.0)
+ # fit_suite.setMinimizer("Genetic", "Default", "MaxIterations=2;PopSize=200;RandomSeed=1")
+
+ # running fit with default minimizer
+ fit_suite.runFit()
+
+ print("Fitting completed.")
+ print("chi2:", fit_suite.getChi2())
+ for par in fit_suite.fitParameters():
+ print(par.name(), par.value(), par.error())
+
+if __name__ == '__main__':
+ run_fitting()
--
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