doc: fitting and constraints with scripts

lavakyan · Feb 8, 2020 · 18d4d8f · 18d4d8f
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diff --git a/doc/source/scripting/experiment.dat b/doc/source/scripting/experiment.dat
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diff --git a/doc/source/scripting/fit_by_Mie.py b/doc/source/scripting/fit_by_Mie.py
@@ -0,0 +1,27 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+from mstm_studio.alloy_AuAg import AlloyAuAg
+from mstm_studio.contributions import LinearBackground, MieLognormSpheresCached
+from mstm_studio.fit_spheres_optic import Fitter
+
+fitter = Fitter(exp_filename='experiment.dat')        # load experiment from tabbed file
+fitter.set_extra_contributions(
+    [LinearBackground(fitter.wls),                    # wavelengths from experiment
+     MieLognormSpheresCached(fitter.wls, 'LN Mie')],  # cached version for faster fittting
+    [0.02, 0.0001, 0.1, 2.0, 0.4])                    # initial values for a, b, C, mu, sigma
+fitter.extra_contributions[1].set_material(AlloyAuAg(1.), 1.5)  # gold particles in glass
+fitter.set_spheres(None)  # no spheres - no slow MSTM runs
+
+# run fit (takes ~20 seconds on 2GHz CPU)
+fitter.run()
+
+fitter.report_result()
+
+# plot results
+import matplotlib.pyplot as plt
+plt.plot(fitter.wls, fitter.exp,  'ro', label='exp.')
+plt.plot(fitter.wls, fitter.calc, 'b-', label='fit')
+plt.xlabel('Wavelength, nm')
+plt.ylabel('Exctinction, a.u.')
+plt.legend()
+plt.savefig('fit_by_Mie.png', bbox_inches='tight')
diff --git a/doc/source/scripting/fit_by_core-shell.py b/doc/source/scripting/fit_by_core-shell.py
@@ -0,0 +1,51 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+from mstm_studio.alloy_AuAg import AlloyAuAg
+from mstm_studio.contributions import LinearBackground, MieLognormSpheresCached
+from mstm_studio.mstm_spectrum import ExplicitSpheres, Profiler
+from mstm_studio.fit_spheres_optic import Fitter, FixConstraint, ConcentricConstraint
+
+fitter = Fitter(exp_filename='experiment.dat')        # load experiment from tabbed file
+fitter.set_extra_contributions(
+    [LinearBackground(fitter.wls)],     # wavelengths from experiment
+    [0.02, 0.0001])                     # initial values for a, b
+
+spheres = ExplicitSpheres(2, [0,0,0,10,0,0,0,12], mat_filename=[AlloyAuAg(1.),AlloyAuAg(0.)])
+fitter.set_spheres(spheres) # core-shell Au@Ag particle
+fitter.set_matrix(1.5)      # in glass
+
+fitter.add_constraint(ConcentricConstraint(0, 1))  # 0 -> 1
+fitter.add_constraint(FixConstraint('x00'))
+fitter.add_constraint(FixConstraint('y00'))
+fitter.add_constraint(FixConstraint('z00'))
+
+# run fit (takes ~200 seconds on 2GHz CPU)
+with Profiler():
+    fitter.run()
+
+fitter.report_result()
+
+# plot results
+import matplotlib.pyplot as plt
+plt.plot(fitter.wls, fitter.exp,  'ro', label='exp.')
+plt.plot(fitter.wls, fitter.calc, 'b-', label='fit')
+plt.xlabel('Wavelength, nm')
+plt.ylabel('Exctinction, a.u.')
+plt.legend()
+plt.savefig('fit_by_core-shell.png', bbox_inches='tight')
+
+
+# ~ ChiSq:      0.002354
+# ~ Optimal parameters
+        # ~ a00:        1.284882        (Varied:True)
+        # ~ a01:        1.958142        (Varied:True)
+        # ~ ext00:      0.186312        (Varied:True)
+        # ~ ext01:      -0.000247       (Varied:True)
+        # ~ scale:      -0.063814       (Varied:True)
+        # ~ x00:        0.000000        (Varied:False)
+        # ~ x01:        0.000000        (Varied:False)
+        # ~ y00:        0.000000        (Varied:False)
+        # ~ y01:        0.000000        (Varied:False)
+        # ~ z00:        0.000000        (Varied:False)
+        # ~ z01:        0.000000        (Varied:False)
+