From ecca5d3ec2910957ca8b40d7167740ed1f03578b Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Fri, 5 Aug 2016 16:24:14 +0200
Subject: [PATCH] Converted ex01-ex04; the others temporarily broken
---
Core/CMakeLists.txt | 1 +
.../ex07_FitAlongSlices/FitAlongSlices.py | 2 +-
.../ex10_FitGALAXIData/FitGALAXIData.py | 2 +-
.../AllFormFactorsAvailable.py | 6 +-
.../ex01_BasicParticles/CylindersAndPrisms.py | 30 +----
.../ex01_BasicParticles/CylindersInBA.py | 31 +----
.../ex01_BasicParticles/CylindersInDWBA.py | 22 +---
.../CylindersWithSizeDistribution.py | 21 +---
.../ex01_BasicParticles/RotatedPyramids.py | 21 +---
...TwoTypesOfCylindersWithSizeDistribution.py | 21 +---
.../ex02_LayeredStructures/BuriedParticles.py | 22 +---
.../CorrelatedRoughness.py | 22 +---
.../ApproximationDA.py | 21 +---
.../ApproximationLMA.py | 22 +---
.../ApproximationSSCA.py | 21 +---
.../CosineRipplesAtRectLattice.py | 21 +---
.../Interference1DLattice.py | 21 +---
.../Interference1DRadialParaCrystal.py | 21 +---
.../Interference2DCenteredSquareLattice.py | 21 +---
.../Interference2DLatticeSumOfRotated.py | 21 +---
.../Interference2DParaCrystal.py | 21 +---
.../Interference2DRotatedSquareLattice.py | 21 +---
.../Interference2DSquareLattice.py | 21 +---
.../RectangularGrating.py | 21 +---
.../SpheresAtHexLattice.py | 21 +---
.../TriangularRipple.py | 21 +---
.../CoreShellNanoparticles.py | 21 +---
.../ex04_ComplexShapes/CustomFormFactor.py | 21 +---
.../HexagonalLatticesWithBasis.py | 21 +---
.../LargeParticlesFormFactor.py | 110 ++++++++++--------
.../ex05_BeamAndDetector/BeamDivergence.py | 6 +-
.../DetectorResolutionFunction.py | 6 +-
.../OffSpecularSimulation.py | 6 +-
.../RectangularDetector.py | 4 +-
.../SpecularSimulation.py | 4 +-
.../AccessingSimulationResults.py | 6 +-
.../AxesInDifferentUnits.py | 12 +-
Examples/python/utils/plot_intensity_data.py | 2 +-
.../python/utils/plot_intensity_data_diff.py | 2 +-
Examples/python/utils/show2d_root.py | 2 +-
Wrap/swig/CorePython.py | 22 +++-
auto/Wrap/libBornAgainCore.py | 36 +++++-
42 files changed, 222 insertions(+), 555 deletions(-)
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index a1d48e8828a..848472e5e2a 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -71,6 +71,7 @@ if(BORNAGAIN_PYTHON)
${WRAP_DIR}/swig/ignores.i
${WRAP_DIR}/swig/shared_pointers.i
${WRAP_DIR}/swig/warnings.i
+ ${WRAP_DIR}/swig/CorePython.py
)
foreach(FNAM ${swig_dependencies})
if(NOT EXISTS ${FNAM})
diff --git a/Examples/python/fitting/ex07_FitAlongSlices/FitAlongSlices.py b/Examples/python/fitting/ex07_FitAlongSlices/FitAlongSlices.py
index 6b485d549a0..475038acfaf 100644
--- a/Examples/python/fitting/ex07_FitAlongSlices/FitAlongSlices.py
+++ b/Examples/python/fitting/ex07_FitAlongSlices/FitAlongSlices.py
@@ -9,7 +9,7 @@ import math
import random
import bornagain as ba
from bornagain import deg, angstrom, nm
-import numpy, sys
+import numpy
phi_slice_value = 0.0*deg # position of vertical slice
alpha_slice_value = 0.2*deg # position of horizontal slice
diff --git a/Examples/python/fitting/ex10_FitGALAXIData/FitGALAXIData.py b/Examples/python/fitting/ex10_FitGALAXIData/FitGALAXIData.py
index 1bd6e7943fd..cde1ee93b72 100644
--- a/Examples/python/fitting/ex10_FitGALAXIData/FitGALAXIData.py
+++ b/Examples/python/fitting/ex10_FitGALAXIData/FitGALAXIData.py
@@ -3,7 +3,7 @@ Real life example: experiment at GALAXY
"""
import matplotlib
from matplotlib import pyplot as plt
-import numpy, sys
+import numpy
import bornagain as ba
from SampleBuilder import MySampleBuilder
diff --git a/Examples/python/simulation/ex01_BasicParticles/AllFormFactorsAvailable.py b/Examples/python/simulation/ex01_BasicParticles/AllFormFactorsAvailable.py
index 2686f86b886..6a7c182442e 100644
--- a/Examples/python/simulation/ex01_BasicParticles/AllFormFactorsAvailable.py
+++ b/Examples/python/simulation/ex01_BasicParticles/AllFormFactorsAvailable.py
@@ -1,7 +1,7 @@
"""
All formfactors available in BornAgain in the Born Approximation
"""
-import numpy, sys
+import numpy
import bornagain as ba
from bornagain import deg, angstrom
@@ -114,7 +114,7 @@ if __name__ == '__main__':
for nplot in range(len(formfactors)):
ff = formfactors[nplot]
name = ff.__class__.__name__.replace("FormFactor","")
- print("Generating intensity map.or " + name)
+ print("Generating intensity map for " + name)
intensities = simulate(ff)
plot(intensities, nplot+1, name)
plt.show()
@@ -124,4 +124,4 @@ if __name__ == '__main__':
intensities = simulate(ff)
fname = "%s.%s.int" % (sys.argv[1], name)
ba.IntensityDataIOFactory.writeIntensityData(intensities, fname)
- print("Stored intensity map.n " + fname)
+ print("Stored intensity map in " + fname)
diff --git a/Examples/python/simulation/ex01_BasicParticles/CylindersAndPrisms.py b/Examples/python/simulation/ex01_BasicParticles/CylindersAndPrisms.py
index cefa41da822..95c47f396c5 100644
--- a/Examples/python/simulation/ex01_BasicParticles/CylindersAndPrisms.py
+++ b/Examples/python/simulation/ex01_BasicParticles/CylindersAndPrisms.py
@@ -1,7 +1,7 @@
"""
Mixture of cylinders and prisms without interference
"""
-import numpy, sys
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -61,32 +61,6 @@ def simulate():
simulation.runSimulation()
return simulation.getIntensityData()
-def plot(result):
- """
- Plots intensity map.
- """
- import matplotlib
- from matplotlib import pyplot as plt
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
if __name__ == '__main__':
- if len(sys.argv)<=1:
- print('Usage:')
- print(' '+sys.argv[0]+' -p # to plot result')
- print(' '+sys.argv[0]+' <fname> # to save result in <fname>.int')
- sys.exit(1)
- result = simulate()
- if sys.argv[1] != '-p':
- ba.IntensityDataIOFactory.writeIntensityData(result, sys.argv[1]+".int")
- else:
- plot(result)
+ ba.simulateThenPlotOrSave(simulate, standardIntensityPlot)
diff --git a/Examples/python/simulation/ex01_BasicParticles/CylindersInBA.py b/Examples/python/simulation/ex01_BasicParticles/CylindersInBA.py
index 5c1335deab3..df65592d9e0 100644
--- a/Examples/python/simulation/ex01_BasicParticles/CylindersInBA.py
+++ b/Examples/python/simulation/ex01_BasicParticles/CylindersInBA.py
@@ -1,7 +1,7 @@
"""
Cylinder formfactor in Born approximation
"""
-import numpy, sys
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -54,32 +54,5 @@ def simulate():
return simulation.getIntensityData()
-def plot(result):
- """
- Plots intensity map.
- """
- import matplotlib
- from matplotlib import pyplot as plt
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
-
if __name__ == '__main__':
- if len(sys.argv)<=1:
- print('Usage:')
- print(' '+sys.argv[0]+' -p # to plot result')
- print(' '+sys.argv[0]+' <fname> # to save result in <fname>.int')
- sys.exit(1)
- result = simulate()
- if sys.argv[1] != '-p':
- ba.IntensityDataIOFactory.writeIntensityData(result, sys.argv[1]+".int")
- else:
- plot(result)
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex01_BasicParticles/CylindersInDWBA.py b/Examples/python/simulation/ex01_BasicParticles/CylindersInDWBA.py
index a069b24920a..06387541b0d 100644
--- a/Examples/python/simulation/ex01_BasicParticles/CylindersInDWBA.py
+++ b/Examples/python/simulation/ex01_BasicParticles/CylindersInDWBA.py
@@ -1,7 +1,7 @@
"""
Cylinder formfactor in DWBA
"""
-import numpy, sys
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -55,24 +55,6 @@ def simulate():
simulation.runSimulation()
return simulation.getIntensityData()
-def plot(result):
- """
- Plots intensity map.
- """
- import matplotlib
- from matplotlib import pyplot as plt
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
-
if __name__ == '__main__':
- ba.simulate_then_plot_or_save(simulate, plot)
+ ba.simulateThenPlotOrSave(simulate, standardIntensityPlot)
diff --git a/Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py b/Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py
index d6325506770..ac2849c08d3 100644
--- a/Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py
+++ b/Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py
@@ -1,9 +1,7 @@
"""
Cylinders with size distribution
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -69,21 +67,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex01_BasicParticles/RotatedPyramids.py b/Examples/python/simulation/ex01_BasicParticles/RotatedPyramids.py
index 6c2ca1e52cc..f3254acd119 100644
--- a/Examples/python/simulation/ex01_BasicParticles/RotatedPyramids.py
+++ b/Examples/python/simulation/ex01_BasicParticles/RotatedPyramids.py
@@ -1,9 +1,7 @@
"""
Rotated pyramids on top of substrate
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -57,21 +55,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py b/Examples/python/simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py
index 00cc0cbeba4..a0af5935bfd 100644
--- a/Examples/python/simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py
+++ b/Examples/python/simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py
@@ -1,9 +1,7 @@
"""
Mixture cylinder particles with different size distribution
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -83,21 +81,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex02_LayeredStructures/BuriedParticles.py b/Examples/python/simulation/ex02_LayeredStructures/BuriedParticles.py
index 10cd4b2c87b..a2a8fd5d892 100644
--- a/Examples/python/simulation/ex02_LayeredStructures/BuriedParticles.py
+++ b/Examples/python/simulation/ex02_LayeredStructures/BuriedParticles.py
@@ -1,9 +1,7 @@
"""
Spherical particles embedded in the middle of the layer on top of substrate.
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -60,21 +58,7 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
-
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex02_LayeredStructures/CorrelatedRoughness.py b/Examples/python/simulation/ex02_LayeredStructures/CorrelatedRoughness.py
index fd549e6be02..9b5d61cc93e 100644
--- a/Examples/python/simulation/ex02_LayeredStructures/CorrelatedRoughness.py
+++ b/Examples/python/simulation/ex02_LayeredStructures/CorrelatedRoughness.py
@@ -1,9 +1,7 @@
"""
MultiLayer with correlated roughness
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -67,22 +65,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(result.getMaximum()/1000.,
- result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
index 8c2779fec36..3980879060f 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
@@ -1,9 +1,7 @@
"""
Cylinders of two different sizes in Decoupling Approximation
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -72,21 +70,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
index 78482676904..5b248db6887 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
@@ -1,9 +1,7 @@
"""
Cylinders of two different sizes in Local Monodisperse Approximation
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -81,21 +79,7 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
-
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
index aa688431c4f..4c78b21b133 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
@@ -1,9 +1,7 @@
"""
Cylinders of two different sizes in Size-Spacing Coupling Approximation
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -74,21 +72,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice.py
index cd2ed9e273a..78da8ef6e9f 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice.py
@@ -1,9 +1,7 @@
"""
Cosine ripple on a 2D lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -65,21 +63,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
index 55f72df30ac..b3359474c1a 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
@@ -1,9 +1,7 @@
"""
Long boxes on a 1D lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -66,21 +64,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal.py
index 332e18c6782..a2f8db7a5c2 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal.py
@@ -1,9 +1,7 @@
"""
radial paracrystal
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -63,21 +61,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice.py
index 6dfcd3050f1..bbfc555456d 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice.py
@@ -1,9 +1,7 @@
"""
2D lattice with disorder, centered square lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -68,21 +66,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated.py
index 4b0507c2cf5..074eb75f171 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated.py
@@ -1,7 +1,5 @@
# 2D lattice with different disorder (IsGISAXS example #6), sum of rotated lattices
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -83,21 +81,8 @@ def simulate():
OutputData_total += single_output
OutputData_total.scale(1.0/total_weight)
- result = OutputData_total
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return OutputData_total
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DParaCrystal.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DParaCrystal.py
index ed17848a097..38cbd8e4fbc 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DParaCrystal.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DParaCrystal.py
@@ -1,9 +1,7 @@
"""
2D paracrystal
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
from bornagain import micrometer
@@ -64,21 +62,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice.py
index 6268332b237..7da27bb23a9 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice.py
@@ -1,9 +1,7 @@
"""
Cylinders on a rotated 2D lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -65,21 +63,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DSquareLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DSquareLattice.py
index 5910e22f015..92c9b115ee1 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DSquareLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference2DSquareLattice.py
@@ -1,9 +1,7 @@
"""
Cylinders on a 2D square lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -62,21 +60,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py b/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
index a0486576c2e..d3b6aef158d 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
@@ -3,9 +3,7 @@ Simulation of grating using very long boxes and 1D lattice.
Monte-carlo integration is used to get rid of
large-particle form factor oscillations.
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -72,21 +70,8 @@ def simulate():
simulation = get_simulation(monte_carlo_integration=True)
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/SpheresAtHexLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/SpheresAtHexLattice.py
index 93f99af6e34..1fede9b2f0b 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/SpheresAtHexLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/SpheresAtHexLattice.py
@@ -1,9 +1,7 @@
"""
Spheres on a hexagonal lattice
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -59,21 +57,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/TriangularRipple.py b/Examples/python/simulation/ex03_InterferenceFunctions/TriangularRipple.py
index 6dfdb249702..eb41a7cdb8b 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/TriangularRipple.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/TriangularRipple.py
@@ -1,9 +1,7 @@
"""
Sample from the article D. Babonneau et. al., Phys. Rev. B 85, 235415, 2012 (Fig.3)
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -66,21 +64,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex04_ComplexShapes/CoreShellNanoparticles.py b/Examples/python/simulation/ex04_ComplexShapes/CoreShellNanoparticles.py
index b2bcc020f3b..36d02a2bd88 100644
--- a/Examples/python/simulation/ex04_ComplexShapes/CoreShellNanoparticles.py
+++ b/Examples/python/simulation/ex04_ComplexShapes/CoreShellNanoparticles.py
@@ -1,9 +1,7 @@
"""
Core shell nanoparticles
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -61,21 +59,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex04_ComplexShapes/CustomFormFactor.py b/Examples/python/simulation/ex04_ComplexShapes/CustomFormFactor.py
index 002c945f124..1215ef13275 100644
--- a/Examples/python/simulation/ex04_ComplexShapes/CustomFormFactor.py
+++ b/Examples/python/simulation/ex04_ComplexShapes/CustomFormFactor.py
@@ -1,9 +1,7 @@
"""
Custom form factor in DWBA.
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
import cmath
@@ -98,21 +96,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis.py b/Examples/python/simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis.py
index e7fc0ef1cbf..c3e0c9c1a3a 100644
--- a/Examples/python/simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis.py
+++ b/Examples/python/simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis.py
@@ -1,9 +1,7 @@
"""
Spheres on two hexagonal close packed layers
"""
-import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
+import numpy
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -65,21 +63,8 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # showing the result
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.show()
+ return simulation.getIntensityData()
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex04_ComplexShapes/LargeParticlesFormFactor.py b/Examples/python/simulation/ex04_ComplexShapes/LargeParticlesFormFactor.py
index bbe28dbaeab..0178f580627 100644
--- a/Examples/python/simulation/ex04_ComplexShapes/LargeParticlesFormFactor.py
+++ b/Examples/python/simulation/ex04_ComplexShapes/LargeParticlesFormFactor.py
@@ -7,8 +7,6 @@ oscillates rapidly within one detector bin and analytical calculations
In this case Monte-Carlo integration over detector bin should be used.
"""
import numpy, sys
-import matplotlib
-from matplotlib import pyplot as plt
import bornagain as ba
from bornagain import deg, angstrom, nm
@@ -57,59 +55,79 @@ def get_simulation(integration_flag):
return simulation
-def simulate():
+def simulate(condi):
"""
- Runs simulation and plots 4 results:
-for small and large cylinders, with and without integration
+ Runs simulation and returns result.
"""
+ scale = condi['scale']
+ integration_flag = condi['integration']
+ sample = get_sample(default_cylinder_radius*scale,
+ default_cylinder_height*scale)
+ simulation = get_simulation(integration_flag)
+ simulation.setSample(sample)
+ simulation.runSimulation()
+ return simulation.getIntensityData()
+
+def plot(result, nframe, title):
+ plt.subplot(2, 2, nframe+1)
+ plt.subplots_adjust(wspace=0.3, hspace=0.3)
+ im = plt.imshow(
+ result.getArray(),
+ norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
+ extent=[result.getXmin()/deg, result.getXmax()/deg,
+ result.getYmin()/deg, result.getYmax()/deg],
+ aspect='auto')
+ cb = plt.colorbar(im)
+ cb.set_label(r'Intensity (arb. u.)', size=16)
+ plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
+ plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
+ plt.text(0.0, 2.1,
+ title,
+ horizontalalignment='center',
+ verticalalignment='center',
+ fontsize=13)
- fig = plt.figure(figsize=(12.80, 10.24))
+if __name__ == '__main__':
+ """
+ Runs one simulation for each condition, and plots results on a single canvas.
+ Conditions are small and large cylinders, with and without integration.
+ """
+ if len(sys.argv)<2:
+ print( "Usage:" )
+ print( " " + sys.argv[0] + " -p # to plot results" )
+ print( " " + sys.argv[0] + " <filename without extension> # to save results" )
+ sys.exit()
# conditions to define cylinders scale factor and Monte-Carlo integration flag
conditions = [
- {'title': "Small cylinders, analytical calculations", 'scale': 1,
+ {'name': "SmallAn",
+ 'title': "Small cylinders, analytical calculations", 'scale': 1,
'integration': False, 'max': 1e+08},
- {'title': "Small cylinders, Monte-Carlo integration", 'scale': 1,
+ {'name': "SmallMC",
+ 'title': "Small cylinders, Monte-Carlo integration", 'scale': 1,
'integration': True, 'max': 1e+08},
- {'title': "Large cylinders, analytical calculations", 'scale': 100,
+ {'name': "LargeAn",
+ 'title': "Large cylinders, analytical calculations", 'scale': 100,
'integration': False, 'max': 1e+12},
- {'title': "Large cylinders, Monte-Carlo integration", 'scale': 100,
+ {'name': "LargeMC",
+ 'title': "Large cylinders, Monte-Carlo integration", 'scale': 100,
'integration': True, 'max': 1e+12}
]
- # run simulation 4 times and plot results
- for i_plot in range(0, len(conditions)):
- scale = conditions[i_plot]['scale']
- integration_flag = conditions[i_plot]['integration']
-
- sample = get_sample(default_cylinder_radius*scale,
- default_cylinder_height*scale)
- simulation = get_simulation(integration_flag)
- simulation.setSample(sample)
- simulation.runSimulation()
- result = simulation.getIntensityData()
-
- # plotting results
- plt.subplot(2, 2, i_plot+1)
- plt.subplots_adjust(wspace=0.3, hspace=0.3)
- im = plt.imshow(
- result.getArray(),
- norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
- extent=[result.getXmin()/deg, result.getXmax()/deg,
- result.getYmin()/deg, result.getYmax()/deg],
- aspect='auto')
- cb = plt.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- plt.text(0.0, 2.1,
- conditions[i_plot]['title'],
- horizontalalignment='center',
- verticalalignment='center',
- fontsize=13)
-
- plt.show()
-
-
-if __name__ == '__main__':
- simulate()
+ if sys.argv[1] == "-p":
+ import matplotlib
+ from matplotlib import pyplot as plt
+ plt.figure(figsize=(12.80, 10.24))
+ for nplot in range(len(conditions)):
+ condi = conditions[nplot]
+ title = condi['title']
+ print("Generating intensity map for " + title)
+ intensities = simulate(condi)
+ plot(intensities, nplot, title)
+ plt.show()
+ else:
+ for condi in conditions:
+ intensities = simulate(condi)
+ fname = "%s.%s.int" % (sys.argv[1], condi['name'])
+ ba.IntensityDataIOFactory.writeIntensityData(intensities, fname)
+ print("Stored intensity map in " + fname)
diff --git a/Examples/python/simulation/ex05_BeamAndDetector/BeamDivergence.py b/Examples/python/simulation/ex05_BeamAndDetector/BeamDivergence.py
index 84ba9f54ce9..635ccd38e36 100644
--- a/Examples/python/simulation/ex05_BeamAndDetector/BeamDivergence.py
+++ b/Examples/python/simulation/ex05_BeamAndDetector/BeamDivergence.py
@@ -1,7 +1,7 @@
"""
Cylinder form factor in DWBA with beam divergence
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -64,7 +64,7 @@ def simulate():
simulation.printParameters()
simulation.runSimulation()
- result = simulation.getIntensityData()
+ return simulation.getIntensityData()
# showing the result
im = plt.imshow(
@@ -81,4 +81,4 @@ def simulate():
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex05_BeamAndDetector/DetectorResolutionFunction.py b/Examples/python/simulation/ex05_BeamAndDetector/DetectorResolutionFunction.py
index 44167c48fb4..a21f5857154 100644
--- a/Examples/python/simulation/ex05_BeamAndDetector/DetectorResolutionFunction.py
+++ b/Examples/python/simulation/ex05_BeamAndDetector/DetectorResolutionFunction.py
@@ -1,7 +1,7 @@
"""
Cylinder form factor in DWBA with detector resolution function applied
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -59,7 +59,7 @@ def simulate():
simulation.setSample(sample)
simulation.printParameters()
simulation.runSimulation()
- result = simulation.getIntensityData()
+ return simulation.getIntensityData()
# showing the result
im = plt.imshow(
@@ -76,4 +76,4 @@ def simulate():
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex05_BeamAndDetector/OffSpecularSimulation.py b/Examples/python/simulation/ex05_BeamAndDetector/OffSpecularSimulation.py
index a6d2c4073f4..5a3745a9bb8 100644
--- a/Examples/python/simulation/ex05_BeamAndDetector/OffSpecularSimulation.py
+++ b/Examples/python/simulation/ex05_BeamAndDetector/OffSpecularSimulation.py
@@ -1,7 +1,7 @@
"""
Long boxes at 1D lattice, ba.OffSpecular simulation
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -72,7 +72,7 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
+ return simulation.getIntensityData()
# showing the result
im = plt.imshow(
@@ -89,4 +89,4 @@ def simulate():
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex05_BeamAndDetector/RectangularDetector.py b/Examples/python/simulation/ex05_BeamAndDetector/RectangularDetector.py
index 218421abc06..1e8fb2786cd 100644
--- a/Examples/python/simulation/ex05_BeamAndDetector/RectangularDetector.py
+++ b/Examples/python/simulation/ex05_BeamAndDetector/RectangularDetector.py
@@ -2,7 +2,7 @@
Simulation with rectangular detector. Pilatus3-1M detector is used as an example.
Results will be compared against simulation with spherical detector.
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -146,4 +146,4 @@ def simulate():
plot_results(result_sph, result_rect)
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex05_BeamAndDetector/SpecularSimulation.py b/Examples/python/simulation/ex05_BeamAndDetector/SpecularSimulation.py
index 577104f53b4..76e2446b35a 100644
--- a/Examples/python/simulation/ex05_BeamAndDetector/SpecularSimulation.py
+++ b/Examples/python/simulation/ex05_BeamAndDetector/SpecularSimulation.py
@@ -1,7 +1,7 @@
"""
R and T coefficients in multilayer, ba.Specular simulation.
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -93,4 +93,4 @@ def simulate():
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex06_Miscellaneous/AccessingSimulationResults.py b/Examples/python/simulation/ex06_Miscellaneous/AccessingSimulationResults.py
index 6f3aabc8e0c..7cce1159543 100644
--- a/Examples/python/simulation/ex06_Miscellaneous/AccessingSimulationResults.py
+++ b/Examples/python/simulation/ex06_Miscellaneous/AccessingSimulationResults.py
@@ -3,7 +3,7 @@ Extended example for simulation results treatment (cropping, slicing, exporting)
The standard "Cylinders in DWBA" sample is used to setup the simulation.
"""
import math
-import numpy, sys
+import numpy
import matplotlib
import random
from matplotlib import pyplot as plt
@@ -186,10 +186,10 @@ def simulate():
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
- result = simulation.getIntensityData()
+ return simulation.getIntensityData()
plot_results(result)
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/simulation/ex06_Miscellaneous/AxesInDifferentUnits.py b/Examples/python/simulation/ex06_Miscellaneous/AxesInDifferentUnits.py
index b9d6ab9036d..dd7bca4e5f6 100644
--- a/Examples/python/simulation/ex06_Miscellaneous/AxesInDifferentUnits.py
+++ b/Examples/python/simulation/ex06_Miscellaneous/AxesInDifferentUnits.py
@@ -2,7 +2,7 @@
In this example we demonstrate how to plot simulation results with
axes in different units (nbins, mm, degs and QyQz).
"""
-import numpy, sys
+import numpy
import matplotlib
from matplotlib import pyplot as plt
import bornagain as ba
@@ -89,22 +89,22 @@ def simulate():
plt.subplot(2, 2, 1)
# default units for rectangular detector are millimeters
- result = simulation.getIntensityData()
+ return simulation.getIntensityData()
plot_as_colormap.esult, "In default units",
r'$X_{mm}$', r'$Y_{mm}$')
plt.subplot(2, 2, 2)
- result = simulation.getIntensityData(ba.IDetector2D.NBINS)
+ return simulation.getIntensityData(ba.IDetector2D.NBINS)
plot_as_colormap.esult, "In number of bins",
r'$X_{nbins}$', r'$Y_{nbins}$')
plt.subplot(2, 2, 3)
- result = simulation.getIntensityData(ba.IDetector2D.DEGREES)
+ return simulation.getIntensityData(ba.IDetector2D.DEGREES)
plot_as_colormap.esult, "In degs",
r'$\phi_f ^{\circ}$', r'$\alpha_f ^{\circ}$')
plt.subplot(2, 2, 4)
- result = simulation.getIntensityData(ba.IDetector2D.QYQZ)
+ return simulation.getIntensityData(ba.IDetector2D.QYQZ)
plot_as_colormap.esult, "Q-space",
r'$Q_{y} [1/nm]$', r'$Q_{z} [1/nm]$')
@@ -113,4 +113,4 @@ def simulate():
if __name__ == '__main__':
- simulate()
+ ba.simulateThenPlotOrSave(simulate, ba.standardIntensityPlot)
diff --git a/Examples/python/utils/plot_intensity_data.py b/Examples/python/utils/plot_intensity_data.py
index 9b84198af96..9acbf973d7c 100755
--- a/Examples/python/utils/plot_intensity_data.py
+++ b/Examples/python/utils/plot_intensity_data.py
@@ -2,7 +2,7 @@
# Plots intensity data stored in BornAgain "*.int" or "*.int.gz" format
# Usage: python plot_intensity_data.py intensity_file.int.gz
-import matplotlib, numpy, sys
+import matplotlib, numpy
from matplotlib import pyplot as plt
import bornagain as ba
from bornagain import deg, angstrom, nm
diff --git a/Examples/python/utils/plot_intensity_data_diff.py b/Examples/python/utils/plot_intensity_data_diff.py
index be8d01e9479..f6ad420ab79 100755
--- a/Examples/python/utils/plot_intensity_data_diff.py
+++ b/Examples/python/utils/plot_intensity_data_diff.py
@@ -2,7 +2,7 @@
# Plots intensity data difference stored in BornAgain "*.int" or "*.int.gz" format
# Usage: python plot_intensity_data.py intensity_reference.int.gz intensity_other.int.gz
-import matplotlib, numpy, sys
+import matplotlib, numpy
from matplotlib import pyplot as plt
import bornagain as ba
from bornagain import deg, angstrom, nm
diff --git a/Examples/python/utils/show2d_root.py b/Examples/python/utils/show2d_root.py
index 3a74514b4bb..cb3d1dbaf05 100755
--- a/Examples/python/utils/show2d_root.py
+++ b/Examples/python/utils/show2d_root.py
@@ -5,7 +5,7 @@
from __future__ import print_function
import argparse
import os
-import numpy, sys
+import numpy
import ROOT
from pylab import *
diff --git a/Wrap/swig/CorePython.py b/Wrap/swig/CorePython.py
index 799ce9edba9..147840503cc 100644
--- a/Wrap/swig/CorePython.py
+++ b/Wrap/swig/CorePython.py
@@ -10,13 +10,13 @@
#
# @homepage http://apps.jcns.fz-juelich.de/BornAgain
# @license GNU General Public License v3 or higher (see COPYING)
-# @copyright Forschungszentrum Jülich GmbH 2016
+# @copyright Forschungszentrum Juelich GmbH 2016
# @authors Scientific Computing Group at MLZ Garching
# @authors J. Fisher, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
#
# ************************************************************************** #
-def simulate_then_plot_or_save(simulate, plot):
+def simulateThenPlotOrSave(simulate, plot):
"""
Runs a simulation. Then plots the function or saves the result, depending on given argument.
"""
@@ -32,4 +32,22 @@ def simulate_then_plot_or_save(simulate, plot):
else:
plot(result)
+def standardIntensityPlot(result):
+ """
+ Plots intensity map.
+ """
+ import matplotlib
+ from matplotlib import pyplot as plt
+ im = plt.imshow(
+ result.getArray(),
+ norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
+ extent=[result.getXmin()/deg, result.getXmax()/deg,
+ result.getYmin()/deg, result.getYmax()/deg],
+ aspect='auto')
+ cb = plt.colorbar(im)
+ cb.set_label(r'Intensity (arb. u.)', size=16)
+ plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
+ plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
+ plt.show()
+
%}
diff --git a/auto/Wrap/libBornAgainCore.py b/auto/Wrap/libBornAgainCore.py
index e6599ea2d73..7d3a6aee6d6 100644
--- a/auto/Wrap/libBornAgainCore.py
+++ b/auto/Wrap/libBornAgainCore.py
@@ -24529,7 +24529,23 @@ SimulationFactory_swigregister(SimulationFactory)
-def simulate_then_plot_or_save(simulate, plot):
+# ************************************************************************** #
+#
+# BornAgain: simulate and fit scattering at grazing incidence
+#
+# @file Wrap/swig/CorePython.py
+# @brief Python extensions of the SWIG-genrated Python module bornagain.
+# This file is included by libBornAgainCore.i.
+#
+# @homepage http://apps.jcns.fz-juelich.de/BornAgain
+# @license GNU General Public License v3 or higher (see COPYING)
+# @copyright Forschungszentrum Juelich GmbH 2016
+# @authors Scientific Computing Group at MLZ Garching
+# @authors J. Fisher, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+#
+# ************************************************************************** #
+
+def simulateThenPlotOrSave(simulate, plot):
"""
Runs a simulation. Then plots the function or saves the result, depending on given argument.
"""
@@ -24545,6 +24561,24 @@ def simulate_then_plot_or_save(simulate, plot):
else:
plot(result)
+def standardIntensityPlot(result):
+ """
+ Plots intensity map.
+ """
+ import matplotlib
+ from matplotlib import pyplot as plt
+ im = plt.imshow(
+ result.getArray(),
+ norm=matplotlib.colors.LogNorm(1.0, result.getMaximum()),
+ extent=[result.getXmin()/deg, result.getXmax()/deg,
+ result.getYmin()/deg, result.getYmax()/deg],
+ aspect='auto')
+ cb = plt.colorbar(im)
+ cb.set_label(r'Intensity (arb. u.)', size=16)
+ plt.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
+ plt.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
+ plt.show()
+
# This file is compatible with both classic and new-style classes.
--
GitLab