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Commit c64f3f42 authored by Wuttke, Joachim's avatar Wuttke, Joachim
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In examples: back to shorter notation "deg", "nm"

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Examples/python/fitting/ex01_SampleParametersIntro/SampleParametersIntro.py
+ 12
− 12
View file @ c64f3f42
...@@ -6,7 +6,7 @@ from __future__ import print_function ...@@ -6,7 +6,7 @@ from __future__ import print_function
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(): def get_sample():
...@@ -20,9 +20,9 @@ def get_sample(): ...@@ -20,9 +20,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer) cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
prism_ff = ba.FormFactorPrism3(5*nanometer, 5*nanometer) prism_ff = ba.FormFactorPrism3(5*nm, 5*nm)
prism = ba.Particle(m_particle, prism_ff) prism = ba.Particle(m_particle, prism_ff)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 0.5) particle_layout.addParticle(cylinder, 0.5)
...@@ -45,9 +45,9 @@ def get_simulation(): ...@@ -45,9 +45,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -77,7 +77,7 @@ def run_simulations(): ...@@ -77,7 +77,7 @@ def run_simulations():
# one sample parameter (cylinder height) is changed using exact parameter name # one sample parameter (cylinder height) is changed using exact parameter name
sample.setParameterValue( sample.setParameterValue(
"/MultiLayer/Layer0/ParticleLayout/Particle0/Cylinder/Height", "/MultiLayer/Layer0/ParticleLayout/Particle0/Cylinder/Height",
10.0*nanometer) 10.0*nm)
simulation.setSample(sample) simulation.setSample(sample)
simulation.runSimulation() simulation.runSimulation()
...@@ -85,16 +85,16 @@ def run_simulations(): ...@@ -85,16 +85,16 @@ def run_simulations():
# simulation #3 # simulation #3
# all parameters matching criteria will be changed (cylinder height in this case) # all parameters matching criteria will be changed (cylinder height in this case)
sample.setParameterValue("*/Cylinder/Height", 100.0*nanometer) sample.setParameterValue("*/Cylinder/Height", 100.0*nm)
simulation.setSample(sample) simulation.setSample(sample)
simulation.runSimulation() simulation.runSimulation()
results.append(simulation.getIntensityData()) results.append(simulation.getIntensityData())
# simulation #4 # simulation #4
# all parameters which are matching criteria will be changed # all parameters which are matching criteria will be changed
sample.setParameterValue("*/Cylinder/Height", 10.0*nanometer) sample.setParameterValue("*/Cylinder/Height", 10.0*nm)
# set ba.FormFactorPrism3/half_side and ba.FormFactorPrism3/height to 10 nm # set ba.FormFactorPrism3/half_side and ba.FormFactorPrism3/height to 10 nm
sample.setParameterValue("*/Prism3/*", 10.0*nanometer) sample.setParameterValue("*/Prism3/*", 10.0*nm)
simulation.setSample(sample) simulation.setSample(sample)
simulation.runSimulation() simulation.runSimulation()
results.append(simulation.getIntensityData()) results.append(simulation.getIntensityData())
...@@ -112,8 +112,8 @@ def draw_results(results): ...@@ -112,8 +112,8 @@ def draw_results(results):
plt.imshow( plt.imshow(
hist.getArray(), hist.getArray(),
norm=matplotlib.colors.LogNorm(1, hist.getMaximum()), norm=matplotlib.colors.LogNorm(1, hist.getMaximum()),
extent=[hist.getXmin()/degree, hist.getXmax()/degree, extent=[hist.getXmin()/deg, hist.getXmax()/deg,
hist.getYmin()/degree, hist.getYmax()/degree]) hist.getYmin()/deg, hist.getYmax()/deg])
plt.show() plt.show()
......
Examples/python/fitting/ex02_FitCylindersAndPrisms/FitCylindersPrisms.py
+ 10
− 10
View file @ c64f3f42
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
Fitting example: 4 parameters fit with simple output Fitting example: 4 parameters fit with simple output
""" """
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(): def get_sample():
...@@ -15,9 +15,9 @@ def get_sample(): ...@@ -15,9 +15,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
cylinder_ff = ba.FormFactorCylinder(1.0*nanometer, 1.0*nanometer) cylinder_ff = ba.FormFactorCylinder(1.0*nm, 1.0*nm)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
prism_ff = ba.FormFactorPrism3(1.0*nanometer, 1.0*nanometer) prism_ff = ba.FormFactorPrism3(1.0*nm, 1.0*nm)
prism = ba.Particle(m_particle, prism_ff) prism = ba.Particle(m_particle, prism_ff)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 0.5) particle_layout.addParticle(cylinder, 0.5)
...@@ -40,9 +40,9 @@ def get_simulation(): ...@@ -40,9 +40,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined Returns a GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -62,13 +62,13 @@ def run_fitting(): ...@@ -62,13 +62,13 @@ def run_fitting():
fit_suite.initPrint(10) fit_suite.initPrint(10)
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter("*Cylinder/Height", 4.*nanometer, fit_suite.addFitParameter("*Cylinder/Height", 4.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Cylinder/Radius", 6.*nanometer, fit_suite.addFitParameter("*Cylinder/Radius", 6.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Prism3/Height", 4.*nanometer, fit_suite.addFitParameter("*Prism3/Height", 4.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Prism3/Length", 12.*nanometer, fit_suite.addFitParameter("*Prism3/Length", 12.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
# running fit # running fit
......
Examples/python/fitting/ex02_FitCylindersAndPrisms/FitCylindersPrisms_detailed.py
+ 13
− 13
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...@@ -11,11 +11,11 @@ from matplotlib import pyplot as plt ...@@ -11,11 +11,11 @@ from matplotlib import pyplot as plt
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(cylinder_height=1.0*nanometer, cylinder_radius=1.0*nanometer, def get_sample(cylinder_height=1.0*nm, cylinder_radius=1.0*nm,
prism_length=2.0*nanometer, prism_height=1.0*nanometer): prism_length=2.0*nm, prism_height=1.0*nm):
""" """
Returns a sample with uncorrelated cylinders and prisms on a substrate. Returns a sample with uncorrelated cylinders and prisms on a substrate.
""" """
...@@ -52,7 +52,7 @@ def create_real_data(): ...@@ -52,7 +52,7 @@ def create_real_data():
located in same directory. located in same directory.
""" """
# creating sample with set of parameters we will later try to find during the fit # creating sample with set of parameters we will later try to find during the fit
sample = get_sample(5.0*nanometer, 5.0*nanometer, 5.0*nanometer, 5.0*nanometer) sample = get_sample(5.0*nm, 5.0*nm, 5.0*nm, 5.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -80,9 +80,9 @@ def get_simulation(): ...@@ -80,9 +80,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined Returns a GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -106,8 +106,8 @@ class DrawObserver(ba.IFitObserver): ...@@ -106,8 +106,8 @@ class DrawObserver(ba.IFitObserver):
im = plt.imshow( im = plt.imshow(
data.getArray(), data.getArray(),
norm=matplotlib.colors.LogNorm(min, max), norm=matplotlib.colors.LogNorm(min, max),
extent=[data.getXmin()/degree, data.getXmax()/degree, extent=[data.getXmin()/deg, data.getXmax()/deg,
data.getYmin()/degree, data.getYmax()/degree]) data.getYmin()/deg, data.getYmax()/deg])
plt.colorbar(im) plt.colorbar(im)
plt.title(title) plt.title(title)
...@@ -165,13 +165,13 @@ def run_fitting(): ...@@ -165,13 +165,13 @@ def run_fitting():
fit_suite.attachObserver(draw_observer) fit_suite.attachObserver(draw_observer)
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter("*Cylinder/Height", 4.*nanometer, fit_suite.addFitParameter("*Cylinder/Height", 4.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Cylinder/Radius", 6.*nanometer, fit_suite.addFitParameter("*Cylinder/Radius", 6.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Prism3/Height", 4.*nanometer, fit_suite.addFitParameter("*Prism3/Height", 4.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
fit_suite.addFitParameter("*Prism3/BaseEdge", 12.*nanometer, fit_suite.addFitParameter("*Prism3/BaseEdge", 12.*nm,
ba.AttLimits.lowerLimited(0.01)) ba.AttLimits.lowerLimited(0.01))
# running fit # running fit
......
Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice.py
+ 9
− 9
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...@@ -6,10 +6,10 @@ from matplotlib import pyplot as plt ...@@ -6,10 +6,10 @@ from matplotlib import pyplot as plt
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(radius=5*nanometer, lattice_constant=10*nanometer): def get_sample(radius=5*nm, lattice_constant=10*nm):
""" """
Returns a sample with cylinders and pyramids on a substrate, Returns a sample with cylinders and pyramids on a substrate,
forming a hexagonal lattice. forming a hexagonal lattice.
...@@ -24,7 +24,7 @@ def get_sample(radius=5*nanometer, lattice_constant=10*nanometer): ...@@ -24,7 +24,7 @@ def get_sample(radius=5*nanometer, lattice_constant=10*nanometer):
particle_layout.addParticle(sphere) particle_layout.addParticle(sphere)
interference = ba.InterferenceFunction2DLattice.createHexagonal(lattice_constant) interference = ba.InterferenceFunction2DLattice.createHexagonal(lattice_constant)
pdf = ba.FTDecayFunction2DCauchy(10*nanometer, 10*nanometer) pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm)
interference.setDecayFunction(pdf) interference.setDecayFunction(pdf)
particle_layout.addInterferenceFunction(interference) particle_layout.addInterferenceFunction(interference)
...@@ -43,9 +43,9 @@ def get_simulation(): ...@@ -43,9 +43,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -53,7 +53,7 @@ def create_real_data(): ...@@ -53,7 +53,7 @@ def create_real_data():
""" """
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample = get_sample(5.0*nanometer, 10.0*nanometer) sample = get_sample(5.0*nm, 10.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -94,9 +94,9 @@ def run_fitting(): ...@@ -94,9 +94,9 @@ def run_fitting():
# this fit parameter will change both length_1 and length_2 simultaneously # this fit parameter will change both length_1 and length_2 simultaneously
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*2DLattice/LatticeLength*", 8.*nanometer, ba.AttLimits.limited(4., 12.)) "*2DLattice/LatticeLength*", 8.*nm, ba.AttLimits.limited(4., 12.))
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/FullSphere/Radius", 8.*nanometer, ba.AttLimits.limited(4., 12.)) "*/FullSphere/Radius", 8.*nm, ba.AttLimits.limited(4., 12.))
# running fit # running fit
fit_suite.runFit() fit_suite.runFit()
......
Examples/python/fitting/ex03_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
+ 11
− 11
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...@@ -7,7 +7,7 @@ import math ...@@ -7,7 +7,7 @@ import math
import random import random
import ctypes import ctypes
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
class MySampleBuilder(ISampleBuilder): class MySampleBuilder(ISampleBuilder):
...@@ -22,8 +22,8 @@ class MySampleBuilder(ISampleBuilder): ...@@ -22,8 +22,8 @@ class MySampleBuilder(ISampleBuilder):
ISampleBuilder.__init__(self) ISampleBuilder.__init__(self)
self.sample = None self.sample = None
# parameters describing the sample # parameters describing the sample
self.radius = ctypes.c_double(5.0*nanometer) self.radius = ctypes.c_double(5.0*nm)
self.lattice_constant = ctypes.c_double(10.0*nanometer) self.lattice_constant = ctypes.c_double(10.0*nm)
# register parameters # register parameters
self.registerParameter("radius", ctypes.addressof(self.radius)) self.registerParameter("radius", ctypes.addressof(self.radius))
self.registerParameter("lattice_constant", self.registerParameter("lattice_constant",
...@@ -42,7 +42,7 @@ class MySampleBuilder(ISampleBuilder): ...@@ -42,7 +42,7 @@ class MySampleBuilder(ISampleBuilder):
interference = ba.InterferenceFunction2DLattice.createHexagonal( interference = ba.InterferenceFunction2DLattice.createHexagonal(
self.lattice_constant.value) self.lattice_constant.value)
pdf = ba.FTDecayFunction2DCauchy(10*nanometer, 10*nanometer) pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm)
interference.setDecayFunction(pdf) interference.setDecayFunction(pdf)
particle_layout.addInterferenceFunction(interference) particle_layout.addInterferenceFunction(interference)
...@@ -62,9 +62,9 @@ def get_simulation(): ...@@ -62,9 +62,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -74,8 +74,8 @@ def create_real_data(): ...@@ -74,8 +74,8 @@ def create_real_data():
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample_builder = MySampleBuilder() sample_builder = MySampleBuilder()
sample_builder.setParameterValue("radius", 5.0*nanometer) sample_builder.setParameterValue("radius", 5.0*nm)
sample_builder.setParameterValue("lattice_constant", 10.0*nanometer) sample_builder.setParameterValue("lattice_constant", 10.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSampleBuilder(sample_builder) simulation.setSampleBuilder(sample_builder)
...@@ -114,9 +114,9 @@ def run_fitting(): ...@@ -114,9 +114,9 @@ def run_fitting():
fit_suite.attachObserver(draw_observer) fit_suite.attachObserver(draw_observer)
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter("*radius", 8.*nanometer, ba.AttLimits.limited(4., 12.)) fit_suite.addFitParameter("*radius", 8.*nm, ba.AttLimits.limited(4., 12.))
fit_suite.addFitParameter("*lattice_constant", fit_suite.addFitParameter("*lattice_constant",
8.*nanometer, ba.AttLimits.limited(4., 12.)) 8.*nm, ba.AttLimits.limited(4., 12.))
# running fit # running fit
fit_suite.runFit() fit_suite.runFit()
......
Examples/python/fitting/ex04_FitScaleAndShift/FitScaleAndShift.py
+ 8
− 8
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...@@ -12,10 +12,10 @@ import matplotlib ...@@ -12,10 +12,10 @@ import matplotlib
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(radius=5*nanometer, height=10*nanometer): def get_sample(radius=5*nm, height=10*nm):
""" """
Build the sample representing cylinders on top of substrate without interference. Build the sample representing cylinders on top of substrate without interference.
""" """
...@@ -44,9 +44,9 @@ def get_simulation(): ...@@ -44,9 +44,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
simulation.setBeamIntensity(1e12) simulation.setBeamIntensity(1e12)
return simulation return simulation
...@@ -59,7 +59,7 @@ def create_real_data(): ...@@ -59,7 +59,7 @@ def create_real_data():
During the fit we will try to find cylinder height and radius and During the fit we will try to find cylinder height and radius and
scale, background factors. scale, background factors.
""" """
sample = get_sample(5.0*nanometer, 10.0*nanometer) sample = get_sample(5.0*nm, 10.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -110,9 +110,9 @@ def run_fitting(): ...@@ -110,9 +110,9 @@ def run_fitting():
fit_suite.getFitObjects().printParameters() fit_suite.getFitObjects().printParameters()
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter("*/Cylinder/Radius", 6.*nanometer, fit_suite.addFitParameter("*/Cylinder/Radius", 6.*nm,
ba.AttLimits.limited(4., 8.)) ba.AttLimits.limited(4., 8.))
fit_suite.addFitParameter("*/Cylinder/Height", 9.*nanometer, fit_suite.addFitParameter("*/Cylinder/Height", 9.*nm,
ba.AttLimits.limited(8., 12.)) ba.AttLimits.limited(8., 12.))
fit_suite.addFitParameter("*/Normalizer/scale", 1.5, fit_suite.addFitParameter("*/Normalizer/scale", 1.5,
ba.AttLimits.limited(1.0, 3.0)) ba.AttLimits.limited(1.0, 3.0))
......
Examples/python/fitting/ex05_FitWithMasks/FitWithMasks.py
+ 20
− 20
View file @ c64f3f42
...@@ -7,10 +7,10 @@ from matplotlib import pyplot as plt ...@@ -7,10 +7,10 @@ from matplotlib import pyplot as plt
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(radius=5*nanometer, height=10*nanometer): def get_sample(radius=5*nm, height=10*nm):
""" """
Build the sample representing cylinders on top of Build the sample representing cylinders on top of
substrate without interference. substrate without interference.
...@@ -40,9 +40,9 @@ def get_simulation(): ...@@ -40,9 +40,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -50,7 +50,7 @@ def create_real_data(): ...@@ -50,7 +50,7 @@ def create_real_data():
""" """
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample = get_sample(5.0*nanometer, 10.0*nanometer) sample = get_sample(5.0*nm, 10.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -89,33 +89,33 @@ def add_mask_to_simulation(simulation): ...@@ -89,33 +89,33 @@ def add_mask_to_simulation(simulation):
# set mask to simulate pacman's head # set mask to simulate pacman's head
simulation.addMask( simulation.addMask(
ba.Ellipse(0.0*degree, 1.0*degree, 0.5*degree, 0.5*degree), False) ba.Ellipse(0.0*deg, 1.0*deg, 0.5*deg, 0.5*deg), False)
# set mask for pacman's eye # set mask for pacman's eye
simulation.addMask( simulation.addMask(
ba.Ellipse(0.11*degree, 1.25*degree, 0.05*degree, 0.05*degree), True) ba.Ellipse(0.11*deg, 1.25*deg, 0.05*deg, 0.05*deg), True)
# set mask for pacman's mouth # set mask for pacman's mouth
points = [[0.0*degree, 1.0*degree], [0.5*degree, 1.2*degree], points = [[0.0*deg, 1.0*deg], [0.5*deg, 1.2*deg],
[0.5*degree, 0.8*degree], [0.0*degree, 1.0*degree]] [0.5*deg, 0.8*deg], [0.0*deg, 1.0*deg]]
simulation.addMask(ba.Polygon(points), True) simulation.addMask(ba.Polygon(points), True)
# giving pacman something to eat # giving pacman something to eat
simulation.addMask( simulation.addMask(
ba.Rectangle(0.45*degree, 0.95*degree, 0.55*degree, 1.05*degree), False) ba.Rectangle(0.45*deg, 0.95*deg, 0.55*deg, 1.05*deg), False)
simulation.addMask( simulation.addMask(
ba.Rectangle(0.61*degree, 0.95*degree, 0.71*degree, 1.05*degree), False) ba.Rectangle(0.61*deg, 0.95*deg, 0.71*deg, 1.05*deg), False)
simulation.addMask( simulation.addMask(
ba.Rectangle(0.75*degree, 0.95*degree, 0.85*degree, 1.05*degree), False) ba.Rectangle(0.75*deg, 0.95*deg, 0.85*deg, 1.05*deg), False)
# other mask's shapes are possible too # other mask's shapes are possible too
# simulation.removeMasks() # simulation.removeMasks()
# # rotated ellipse: # # rotated ellipse:
# simulation.addMask(ba.Ellipse(0.11*degree, 1.25*degree, # simulation.addMask(ba.Ellipse(0.11*deg, 1.25*deg,
# 1.0*degree, 0.5*degree, 45.0*degree), True) # 1.0*deg, 0.5*deg, 45.0*deg), True)
# simulation.addMask(Line(-1.0*degree, 0.0*degree, 1.0*degree, 2.0*degree), True) # simulation.addMask(Line(-1.0*deg, 0.0*deg, 1.0*deg, 2.0*deg), True)
# simulation.addMask(ba.HorizontalLine(1.0*degree), False) # simulation.addMask(ba.HorizontalLine(1.0*deg), False)
# simulation.addMask(ba.VerticalLine(0.0*degree), False) # simulation.addMask(ba.VerticalLine(0.0*deg), False)
def run_fitting(): def run_fitting():
...@@ -139,9 +139,9 @@ def run_fitting(): ...@@ -139,9 +139,9 @@ def run_fitting():
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/Cylinder/Radius", 6.*nanometer, ba.AttLimits.limited(4., 8.)) "*/Cylinder/Radius", 6.*nm, ba.AttLimits.limited(4., 8.))
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/Cylinder/Height", 9.*nanometer, ba.AttLimits.limited(8., 12.)) "*/Cylinder/Height", 9.*nm, ba.AttLimits.limited(8., 12.))
# running fit # running fit
fit_suite.runFit() fit_suite.runFit()
......
Examples/python/fitting/ex06_FitStrategies/FitStrategyAdjustMinimizer.py
+ 8
− 8
View file @ c64f3f42
...@@ -15,10 +15,10 @@ import matplotlib ...@@ -15,10 +15,10 @@ import matplotlib
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(radius=5*nanometer, height=5*nanometer): def get_sample(radius=5*nm, height=5*nm):
""" """
Returns a sample with uncorrelated cylinders and pyramids on a substrate. Returns a sample with uncorrelated cylinders and pyramids on a substrate.
""" """
...@@ -47,9 +47,9 @@ def get_simulation(): ...@@ -47,9 +47,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, 0.0*degree, 2.0*degree, simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -57,7 +57,7 @@ def create_real_data(): ...@@ -57,7 +57,7 @@ def create_real_data():
""" """
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample = get_sample(5.0*nanometer, 5.0*nanometer) sample = get_sample(5.0*nm, 5.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -98,9 +98,9 @@ def run_fitting(): ...@@ -98,9 +98,9 @@ def run_fitting():
# Here we select starting values being quite far from true values # Here we select starting values being quite far from true values
# to puzzle our minimizer's as much as possible # to puzzle our minimizer's as much as possible
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*Height", 1.*nanometer, ba.AttLimits.limited(0.01, 30.), 0.04*nanometer) "*Height", 1.*nm, ba.AttLimits.limited(0.01, 30.), 0.04*nm)
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*Radius", 20.*nanometer, ba.AttLimits.limited(0.01, 30.), 0.06*nanometer) "*Radius", 20.*nm, ba.AttLimits.limited(0.01, 30.), 0.06*nm)
# Now we create first fig strategy which will run first minimization round # Now we create first fig strategy which will run first minimization round
# using the Genetic minimizer. # using the Genetic minimizer.
......
Examples/python/fitting/ex07_FitAlongSlices/FitAlongSlices.py
+ 16
− 16
View file @ c64f3f42
...@@ -8,14 +8,14 @@ from matplotlib import pyplot as plt ...@@ -8,14 +8,14 @@ from matplotlib import pyplot as plt
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
import numpy import numpy
phi_slice_value = 0.0*degree # position of vertical slice phi_slice_value = 0.0*deg # position of vertical slice
alpha_slice_value = 0.2*degree # position of horizontal slice alpha_slice_value = 0.2*deg # position of horizontal slice
def get_sample(radius=5*nanometer, height=10*nanometer): def get_sample(radius=5*nm, height=10*nm):
""" """
Returns a sample with uncorrelated cylinders on a substrate. Returns a sample with uncorrelated cylinders on a substrate.
""" """
...@@ -44,9 +44,9 @@ def get_simulation(): ...@@ -44,9 +44,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg,
100, 0.0*degree, 2.0*degree) 100, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -54,7 +54,7 @@ def create_real_data(): ...@@ -54,7 +54,7 @@ def create_real_data():
""" """
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample = get_sample(5.0*nanometer, 10.0*nanometer) sample = get_sample(5.0*nm, 10.0*nm)
simulation = get_simulation() simulation = get_simulation()
simulation.setSample(sample) simulation.setSample(sample)
...@@ -92,8 +92,8 @@ class DrawObserver(ba.IFitObserver): ...@@ -92,8 +92,8 @@ class DrawObserver(ba.IFitObserver):
im = plt.imshow( im = plt.imshow(
data.getArray(), data.getArray(),
norm=matplotlib.colors.LogNorm(1.0, data.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, data.getMaximum()),
extent=[data.getXmin()/degree, data.getXmax()/degree, extent=[data.getXmin()/deg, data.getXmax()/deg,
data.getYmin()/degree, data.getYmax()/degree]) data.getYmin()/deg, data.getYmax()/deg])
plt.colorbar(im) plt.colorbar(im)
plt.title("\"Real\" data") plt.title("\"Real\" data")
plt.xlabel(r'$\phi_f$', fontsize=12) plt.xlabel(r'$\phi_f$', fontsize=12)
...@@ -111,9 +111,9 @@ class DrawObserver(ba.IFitObserver): ...@@ -111,9 +111,9 @@ class DrawObserver(ba.IFitObserver):
plt.subplot(2, 2, nplot) plt.subplot(2, 2, nplot)
plt.subplots_adjust(wspace=0.2, hspace=0.3) plt.subplots_adjust(wspace=0.2, hspace=0.3)
for label, slice in slices: for label, slice in slices:
plt.semilogy(slice.getBinCenters()/degree, plt.semilogy(slice.getBinCenters()/deg,
slice.getBinValues(), label=label) slice.getBinValues(), label=label)
plt.xlim(slice.getXmin()/degree, slice.getXmax()/degree) plt.xlim(slice.getXmin()/deg, slice.getXmax()/deg)
plt.ylim(1.0, slice.getMaximum()*10.0) plt.ylim(1.0, slice.getMaximum()*10.0)
plt.legend(loc='upper right') plt.legend(loc='upper right')
plt.title(title) plt.title(title)
...@@ -154,7 +154,7 @@ class DrawObserver(ba.IFitObserver): ...@@ -154,7 +154,7 @@ class DrawObserver(ba.IFitObserver):
("simul", simul_data.projectionX(alpha_slice_value)) ("simul", simul_data.projectionX(alpha_slice_value))
] ]
title = ( "Horizontal slice at alpha =" + title = ( "Horizontal slice at alpha =" +
'{:3.1f}'.format(alpha_slice_value/degree) ) '{:3.1f}'.format(alpha_slice_value/deg) )
self.plot_slices(slices, title, nplot=2) self.plot_slices(slices, title, nplot=2)
# vertical slices # vertical slices
...@@ -162,7 +162,7 @@ class DrawObserver(ba.IFitObserver): ...@@ -162,7 +162,7 @@ class DrawObserver(ba.IFitObserver):
("real", real_data.projectionY(phi_slice_value)), ("real", real_data.projectionY(phi_slice_value)),
("simul", simul_data.projectionY(phi_slice_value)) ("simul", simul_data.projectionY(phi_slice_value))
] ]
title = "Vertical slice at phi =" + '{:3.1f}'.format(phi_slice_value/degree) title = "Vertical slice at phi =" + '{:3.1f}'.format(phi_slice_value/deg)
self.plot_slices(slices, title, nplot=3) self.plot_slices(slices, title, nplot=3)
# display fit parameters # display fit parameters
...@@ -198,9 +198,9 @@ def run_fitting(): ...@@ -198,9 +198,9 @@ def run_fitting():
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/Cylinder/Radius", 6.*nanometer, ba.AttLimits.limited(4., 8.)) "*/Cylinder/Radius", 6.*nm, ba.AttLimits.limited(4., 8.))
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/Cylinder/Height", 9.*nanometer, ba.AttLimits.limited(8., 12.)) "*/Cylinder/Height", 9.*nm, ba.AttLimits.limited(8., 12.))
# running fit # running fit
fit_suite.runFit() fit_suite.runFit()
......
Examples/python/fitting/ex08_SimultaneousFitOfTwoDatasets/SimultaneousFitOfTwoDatasets.py
+ 12
− 12
View file @ c64f3f42
...@@ -9,10 +9,10 @@ import matplotlib.gridspec as gridspec ...@@ -9,10 +9,10 @@ import matplotlib.gridspec as gridspec
import math import math
import random import random
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
def get_sample(radius_a=4.0*nanometer, radius_b=4.0*nanometer, height=4.0*nanometer): def get_sample(radius_a=4.0*nm, radius_b=4.0*nm, height=4.0*nm):
""" """
Returns a sample with uncorrelated cylinders and pyramids. Returns a sample with uncorrelated cylinders and pyramids.
""" """
...@@ -41,9 +41,9 @@ def get_simulation(incident_alpha=0.2): ...@@ -41,9 +41,9 @@ def get_simulation(incident_alpha=0.2):
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(50, -1.5*degree, 1.5*degree, simulation.setDetectorParameters(50, -1.5*deg, 1.5*deg,
50, 0.0*degree, 2.0*degree) 50, 0.0*deg, 2.0*deg)
simulation.setBeamParameters(1.0*angstrom, incident_alpha, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, incident_alpha, 0.0*deg)
return simulation return simulation
...@@ -52,7 +52,7 @@ def create_real_data(incident_alpha): ...@@ -52,7 +52,7 @@ def create_real_data(incident_alpha):
Generating "real" data by adding noise to the simulated data. Generating "real" data by adding noise to the simulated data.
""" """
sample = get_sample( sample = get_sample(
radius_a=5.0*nanometer, radius_b=6.0*nanometer, height=8.0*nanometer) radius_a=5.0*nm, radius_b=6.0*nm, height=8.0*nm)
simulation = get_simulation(incident_alpha) simulation = get_simulation(incident_alpha)
simulation.setSample(sample) simulation.setSample(sample)
...@@ -87,8 +87,8 @@ class DrawObserver(ba.IFitObserver): ...@@ -87,8 +87,8 @@ class DrawObserver(ba.IFitObserver):
im = plt.imshow( im = plt.imshow(
data.getArray(), data.getArray(),
norm=matplotlib.colors.LogNorm(min, max), norm=matplotlib.colors.LogNorm(min, max),
extent=[data.getXmin()/degree, data.getXmax()/degree, extent=[data.getXmin()/deg, data.getXmax()/deg,
data.getYmin()/degree, data.getYmax()/degree], data.getYmin()/deg, data.getYmax()/deg],
aspect='auto') aspect='auto')
plt.colorbar(im) plt.colorbar(im)
plt.title(title) plt.title(title)
...@@ -147,7 +147,7 @@ def run_fitting(): ...@@ -147,7 +147,7 @@ def run_fitting():
main function to run fitting main function to run fitting
""" """
incident_alpha_angles = [0.1*degree, 0.4*degree] incident_alpha_angles = [0.1*deg, 0.4*deg]
fit_suite = ba.FitSuite() fit_suite = ba.FitSuite()
sample = get_sample() sample = get_sample()
...@@ -163,11 +163,11 @@ def run_fitting(): ...@@ -163,11 +163,11 @@ def run_fitting():
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/HemiEllipsoid/RadiusX", 4.*nanometer, ba.AttLimits.limited(2., 10.)) "*/HemiEllipsoid/RadiusX", 4.*nm, ba.AttLimits.limited(2., 10.))
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/HemiEllipsoid/RadiusY", 6.*nanometer, ba.AttLimits.fixed()) "*/HemiEllipsoid/RadiusY", 6.*nm, ba.AttLimits.fixed())
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*/HemiEllipsoid/Height", 4.*nanometer, ba.AttLimits.limited(2., 10.)) "*/HemiEllipsoid/Height", 4.*nm, ba.AttLimits.limited(2., 10.))
# running fit # running fit
fit_suite.runFit() fit_suite.runFit()
......
Examples/python/fitting/ex10_FitGALAXIData/FitGALAXIData.py
+ 7
− 7
View file @ c64f3f42
...@@ -8,7 +8,7 @@ import bornagain as ba ...@@ -8,7 +8,7 @@ import bornagain as ba
from SampleBuilder import MySampleBuilder from SampleBuilder import MySampleBuilder
wavelength = 1.34*ba.angstrom wavelength = 1.34*ba.angstrom
alpha_i = 0.463*ba.degree alpha_i = 0.463*ba.deg
# detector setup as given from instrument responsible # detector setup as given from instrument responsible
pilatus_npx, pilatus_npy = 981, 1043 pilatus_npx, pilatus_npy = 981, 1043
...@@ -44,7 +44,7 @@ def create_simulation(): ...@@ -44,7 +44,7 @@ def create_simulation():
# ba.ResolutionFunction2DGaussian(0.5*pilatus_pixel_size, # ba.ResolutionFunction2DGaussian(0.5*pilatus_pixel_size,
# 0.5*pilatus_pixel_size)) # 0.5*pilatus_pixel_size))
# beam divergence # beam divergence
# alpha_distr = ba.DistributionGaussian(alpha_i, 0.02*ba.degree) # alpha_distr = ba.DistributionGaussian(alpha_i, 0.02*ba.deg)
# simulation.addParameterDistribution("*/Beam/Alpha", alpha_distr, 5) # simulation.addParameterDistribution("*/Beam/Alpha", alpha_distr, 5)
return simulation return simulation
...@@ -73,13 +73,13 @@ def run_fitting(): ...@@ -73,13 +73,13 @@ def run_fitting():
# setting fitting parameters with starting values # setting fitting parameters with starting values
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*radius", 5.0*ba.nanometer, ba.AttLimits.limited(4.0, 6.0), "*radius", 5.0*ba.nm, ba.AttLimits.limited(4.0, 6.0),
0.1*ba.nanometer) 0.1*ba.nm)
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*sigma", 0.55, ba.AttLimits.limited(0.2, 0.8), 0.01*ba.nanometer) "*sigma", 0.55, ba.AttLimits.limited(0.2, 0.8), 0.01*ba.nm)
fit_suite.addFitParameter( fit_suite.addFitParameter(
"*distance", 27.*ba.nanometer, ba.AttLimits.limited(20, 70), "*distance", 27.*ba.nm, ba.AttLimits.limited(20, 70),
0.1*ba.nanometer) 0.1*ba.nm)
use_two_minimizers_strategy = False use_two_minimizers_strategy = False
if use_two_minimizers_strategy: if use_two_minimizers_strategy:
......
Examples/python/fitting/ex10_FitGALAXIData/SampleBuilder.py
+ 9
− 9
View file @ c64f3f42
...@@ -15,13 +15,13 @@ class MySampleBuilder(ba.ISampleBuilder): ...@@ -15,13 +15,13 @@ class MySampleBuilder(ba.ISampleBuilder):
self.sample = None self.sample = None
# parameters describing the sample # parameters describing the sample
self.radius = ctypes.c_double(5.75*ba.nanometer) self.radius = ctypes.c_double(5.75*ba.nm)
self.sigma = ctypes.c_double(0.4) self.sigma = ctypes.c_double(0.4)
self.distance = ctypes.c_double(53.6*ba.nanometer) self.distance = ctypes.c_double(53.6*ba.nm)
self.disorder = ctypes.c_double(10.5*ba.nanometer) self.disorder = ctypes.c_double(10.5*ba.nm)
self.kappa = ctypes.c_double(17.5) self.kappa = ctypes.c_double(17.5)
self.ptfe_thickness = ctypes.c_double(22.1*ba.nanometer) self.ptfe_thickness = ctypes.c_double(22.1*ba.nm)
self.hmdso_thickness = ctypes.c_double(18.5*ba.nanometer) self.hmdso_thickness = ctypes.c_double(18.5*ba.nm)
# register parameters # register parameters
self.registerParameter("radius", ctypes.addressof(self.radius)) self.registerParameter("radius", ctypes.addressof(self.radius))
...@@ -49,7 +49,7 @@ class MySampleBuilder(ba.ISampleBuilder): ...@@ -49,7 +49,7 @@ class MySampleBuilder(ba.ISampleBuilder):
# self.radius.value, self.radius.value*1.5) # self.radius.value, self.radius.value*1.5)
sphere = ba.Particle(m_Ag, sphere_ff) sphere = ba.Particle(m_Ag, sphere_ff)
position = ba.kvector_t(0*ba.nanometer, 0*ba.nanometer, position = ba.kvector_t(0*ba.nm, 0*ba.nm,
-1.0*self.hmdso_thickness.value) -1.0*self.hmdso_thickness.value)
sphere.setPosition(position) sphere.setPosition(position)
ln_distr = ba.DistributionLogNormal(self.radius.value, self.sigma.value) ln_distr = ba.DistributionLogNormal(self.radius.value, self.sigma.value)
...@@ -62,7 +62,7 @@ class MySampleBuilder(ba.ISampleBuilder): ...@@ -62,7 +62,7 @@ class MySampleBuilder(ba.ISampleBuilder):
# interference function # interference function
interference = ba.InterferenceFunctionRadialParaCrystal( interference = ba.InterferenceFunctionRadialParaCrystal(
self.distance.value, 1e6*ba.nanometer) self.distance.value, 1e6*ba.nm)
interference.setKappa(self.kappa.value) interference.setKappa(self.kappa.value)
interference.setDomainSize(20000.0) interference.setDomainSize(20000.0)
pdf = ba.FTDistribution1DGauss(self.disorder.value) pdf = ba.FTDistribution1DGauss(self.disorder.value)
...@@ -76,8 +76,8 @@ class MySampleBuilder(ba.ISampleBuilder): ...@@ -76,8 +76,8 @@ class MySampleBuilder(ba.ISampleBuilder):
particle_layout.setTotalParticleSurfaceDensity(1) particle_layout.setTotalParticleSurfaceDensity(1)
# roughness # roughness
r_ptfe = ba.LayerRoughness(2.3*ba.nanometer, 0.3, 5.0*ba.nanometer) r_ptfe = ba.LayerRoughness(2.3*ba.nm, 0.3, 5.0*ba.nm)
r_hmdso = ba.LayerRoughness(1.1*ba.nanometer, 0.3, 5.0*ba.nanometer) r_hmdso = ba.LayerRoughness(1.1*ba.nm, 0.3, 5.0*ba.nm)
# layers # layers
air_layer = ba.Layer(m_air) air_layer = ba.Layer(m_air)
......
Examples/python/simulation/ex01_BasicParticles/AllFormFactorsAvailable.py
+ 11
− 11
View file @ c64f3f42
...@@ -5,18 +5,18 @@ import numpy ...@@ -5,18 +5,18 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom from bornagain import deg, angstrom
phi_min, phi_max = -2.0, 2.0 phi_min, phi_max = -2.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
formfactors = [ formfactors = [
ba.FormFactorAnisoPyramid(20.0, 16.0, 13.0, 60.0*degree), ba.FormFactorAnisoPyramid(20.0, 16.0, 13.0, 60.0*deg),
ba.FormFactorBox(20.0, 16.0, 13.0), ba.FormFactorBox(20.0, 16.0, 13.0),
ba.FormFactorCone(10.0, 13.0, 60.0*degree), ba.FormFactorCone(10.0, 13.0, 60.0*deg),
ba.FormFactorCone6(10.0, 13.0, 60.0*degree), ba.FormFactorCone6(10.0, 13.0, 60.0*deg),
ba.FormFactorCuboctahedron(20.0, 13.0, 0.7, 60.0*degree), ba.FormFactorCuboctahedron(20.0, 13.0, 0.7, 60.0*deg),
ba.FormFactorCylinder(8.0, 16.0), ba.FormFactorCylinder(8.0, 16.0),
ba.FormFactorDodecahedron(5.0), ba.FormFactorDodecahedron(5.0),
ba.FormFactorEllipsoidalCylinder(8.0, 13.0, 16.0), ba.FormFactorEllipsoidalCylinder(8.0, 13.0, 16.0),
...@@ -26,10 +26,10 @@ formfactors = [ ...@@ -26,10 +26,10 @@ formfactors = [
ba.FormFactorIcosahedron(8.0), ba.FormFactorIcosahedron(8.0),
ba.FormFactorPrism3(10.0, 13.0), ba.FormFactorPrism3(10.0, 13.0),
ba.FormFactorPrism6(5.0, 11.0), ba.FormFactorPrism6(5.0, 11.0),
ba.FormFactorPyramid(18.0, 13.0, 60.0*degree), ba.FormFactorPyramid(18.0, 13.0, 60.0*deg),
ba.FormFactorRipple1(27.0, 20.0, 14.0), ba.FormFactorRipple1(27.0, 20.0, 14.0),
ba.FormFactorRipple2(36.0, 25.0, 14.0, 3.0), ba.FormFactorRipple2(36.0, 25.0, 14.0, 3.0),
ba.FormFactorTetrahedron(15.0, 6.0, 60.0*degree), ba.FormFactorTetrahedron(15.0, 6.0, 60.0*deg),
ba.FormFactorTruncatedSphere(5.0, 7.0), ba.FormFactorTruncatedSphere(5.0, 7.0),
ba.FormFactorTruncatedSpheroid(7.5, 9.0, 1.2), ba.FormFactorTruncatedSpheroid(7.5, 9.0, 1.2),
ba.FormFactorTruncatedCube(15.0, 6.0) ba.FormFactorTruncatedCube(15.0, 6.0)
...@@ -63,8 +63,8 @@ def get_simulation(): ...@@ -63,8 +63,8 @@ def get_simulation():
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters( simulation.setDetectorParameters(
100, phi_min*degree, phi_max*degree, 100, alpha_min*degree, alpha_max*degree) 100, phi_min*deg, phi_max*deg, 100, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -95,8 +95,8 @@ def run_simulation(): ...@@ -95,8 +95,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
plt.tick_params(axis='both', which='major', labelsize=8) plt.tick_params(axis='both', which='major', labelsize=8)
plt.tick_params(axis='both', which='minor', labelsize=6) plt.tick_params(axis='both', which='minor', labelsize=6)
......
Examples/python/simulation/ex01_BasicParticles/CylindersAndPrisms.py
+ 8
− 8
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = -1.0, 1.0 phi_min, phi_max = -1.0, 1.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -21,9 +21,9 @@ def get_sample(): ...@@ -21,9 +21,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer) cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
prism_ff = ba.FormFactorPrism3(10*nanometer, 5*nanometer) prism_ff = ba.FormFactorPrism3(10*nm, 5*nm)
prism = ba.Particle(m_particle, prism_ff) prism = ba.Particle(m_particle, prism_ff)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 0.5) particle_layout.addParticle(cylinder, 0.5)
...@@ -47,9 +47,9 @@ def get_simulation(): ...@@ -47,9 +47,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(100, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(100, phi_min*deg, phi_max*deg,
100, alpha_min*degree, alpha_max*degree) 100, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -66,8 +66,8 @@ def run_simulation(): ...@@ -66,8 +66,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex01_BasicParticles/CylindersInBA.py
+ 7
− 7
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = -2.0, 2.0 phi_min, phi_max = -2.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -21,7 +21,7 @@ def get_sample(): ...@@ -21,7 +21,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer) cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0) particle_layout.addParticle(cylinder, 1.0)
...@@ -39,9 +39,9 @@ def get_simulation(): ...@@ -39,9 +39,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined Returns a GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -59,8 +59,8 @@ def run_simulation(): ...@@ -59,8 +59,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex01_BasicParticles/CylindersInDWBA.py
+ 7
− 7
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = -2.0, 2.0 phi_min, phi_max = -2.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -21,7 +21,7 @@ def get_sample(): ...@@ -21,7 +21,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer) cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0) particle_layout.addParticle(cylinder, 1.0)
...@@ -41,9 +41,9 @@ def get_simulation(): ...@@ -41,9 +41,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined Returns a GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -61,8 +61,8 @@ def run_simulation(): ...@@ -61,8 +61,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py
+ 7
− 7
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = 0.0, 2.0 phi_min, phi_max = 0.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -20,7 +20,7 @@ def get_sample(): ...@@ -20,7 +20,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# cylindrical particle # cylindrical particle
radius = 5*nanometer radius = 5*nm
height = radius height = radius
cylinder_ff = ba.FormFactorCylinder(radius, height) cylinder_ff = ba.FormFactorCylinder(radius, height)
cylinder = ba.Particle(m_particle, cylinder_ff) cylinder = ba.Particle(m_particle, cylinder_ff)
...@@ -54,9 +54,9 @@ def get_simulation(): ...@@ -54,9 +54,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -75,8 +75,8 @@ def run_simulation(): ...@@ -75,8 +75,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex01_BasicParticles/RotatedPyramids.py
+ 8
− 8
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = -2.0, 2.0 phi_min, phi_max = -2.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -21,9 +21,9 @@ def get_sample(): ...@@ -21,9 +21,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8) m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles # collection of particles
pyramid_ff = ba.FormFactorPyramid(10*nanometer, 5*nanometer, 54.73*degree) pyramid_ff = ba.FormFactorPyramid(10*nm, 5*nm, 54.73*deg)
pyramid = ba.Particle(m_particle, pyramid_ff) pyramid = ba.Particle(m_particle, pyramid_ff)
transform = ba.RotationZ(45.*degree) transform = ba.RotationZ(45.*deg)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
particle_layout.addParticle( particle_layout.addParticle(
pyramid, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform) pyramid, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform)
...@@ -43,9 +43,9 @@ def get_simulation(): ...@@ -43,9 +43,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -63,8 +63,8 @@ def run_simulation(): ...@@ -63,8 +63,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py
+ 8
− 8
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = 0.0, 2.0 phi_min, phi_max = 0.0, 2.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -24,7 +24,7 @@ def get_sample(): ...@@ -24,7 +24,7 @@ def get_sample():
nfwhm = 3.0 nfwhm = 3.0
# collection of particles #1 # collection of particles #1
radius1 = 5.0*nanometer radius1 = 5.0*nm
height1 = radius1 height1 = radius1
sigma1 = radius1*0.2 sigma1 = radius1*0.2
...@@ -38,7 +38,7 @@ def get_sample(): ...@@ -38,7 +38,7 @@ def get_sample():
part_coll1 = ba.ParticleDistribution(cylinder1, par_distr1) part_coll1 = ba.ParticleDistribution(cylinder1, par_distr1)
# collection of particles #2 # collection of particles #2
radius2 = 10.0*nanometer radius2 = 10.0*nm
height2 = radius2 height2 = radius2
sigma2 = radius2*0.02 sigma2 = radius2*0.02
...@@ -69,9 +69,9 @@ def get_simulation(): ...@@ -69,9 +69,9 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined Create and return GISAXS simulation with beam and detector defined
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree) simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
return simulation return simulation
...@@ -89,8 +89,8 @@ def run_simulation(): ...@@ -89,8 +89,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
Examples/python/simulation/ex02_LayeredStructures/BuriedParticles.py
+ 8
− 8
View file @ c64f3f42
...@@ -5,7 +5,7 @@ import numpy ...@@ -5,7 +5,7 @@ import numpy
import matplotlib import matplotlib
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
import bornagain as ba import bornagain as ba
from bornagain import degree, angstrom, nanometer from bornagain import deg, angstrom, nm
phi_min, phi_max = -1.0, 1.0 phi_min, phi_max = -1.0, 1.0
alpha_min, alpha_max = 0.0, 2.0 alpha_min, alpha_max = 0.0, 2.0
...@@ -22,7 +22,7 @@ def get_sample(): ...@@ -22,7 +22,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 0.0, 0.0) m_particle = ba.HomogeneousMaterial("Particle", 0.0, 0.0)
# collection of particles # collection of particles
ff_sphere = ba.FormFactorFullSphere(10.2*nanometer) ff_sphere = ba.FormFactorFullSphere(10.2*nm)
sphere = ba.Particle(m_particle, ff_sphere) sphere = ba.Particle(m_particle, ff_sphere)
sphere.setPosition(0.0, 0.0, -25.2) sphere.setPosition(0.0, 0.0, -25.2)
particle_layout = ba.ParticleLayout() particle_layout = ba.ParticleLayout()
...@@ -30,7 +30,7 @@ def get_sample(): ...@@ -30,7 +30,7 @@ def get_sample():
# assembling the sample # assembling the sample
air_layer = ba.Layer(m_ambience) air_layer = ba.Layer(m_ambience)
intermediate_layer = ba.Layer(m_interm_layer, 30.*nanometer) intermediate_layer = ba.Layer(m_interm_layer, 30.*nm)
intermediate_layer.addLayout(particle_layout) intermediate_layer.addLayout(particle_layout)
substrate_layer = ba.Layer(m_substrate, 0) substrate_layer = ba.Layer(m_substrate, 0)
...@@ -46,9 +46,9 @@ def get_simulation(): ...@@ -46,9 +46,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined. Returns a GISAXS simulation with beam and detector defined.
""" """
simulation = ba.GISASSimulation() simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, phi_min*degree, phi_max*degree, simulation.setDetectorParameters(200, phi_min*deg, phi_max*deg,
200, alpha_min*degree, alpha_max*degree) 200, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1.5*angstrom, 0.15*degree, 0.0*degree) simulation.setBeamParameters(1.5*angstrom, 0.15*deg, 0.0*deg)
return simulation return simulation
...@@ -66,8 +66,8 @@ def run_simulation(): ...@@ -66,8 +66,8 @@ def run_simulation():
im = plt.imshow( im = plt.imshow(
result.getArray(), result.getArray(),
norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()), norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
extent=[result.getXmin()/degree, result.getXmax()/degree, extent=[result.getXmin()/deg, result.getXmax()/deg,
result.getYmin()/degree, result.getYmax()/degree], result.getYmin()/deg, result.getYmax()/deg],
aspect='auto') aspect='auto')
cb = plt.colorbar(im) cb = plt.colorbar(im)
cb.set_label(r'Intensity (arb. u.)', size=16) cb.set_label(r'Intensity (arb. u.)', size=16)
......
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