From 569c628a7da7523dd3c42b9ab37b301e00a963d4 Mon Sep 17 00:00:00 2001
From: pospelov <pospelov@fz-juelich.de>
Date: Mon, 8 Jul 2013 15:16:12 +0200
Subject: [PATCH] isgisaxs1 and isgisaxs4 examples
---
Core/Algorithms/inc/Simulation.h | 3 -
Core/Algorithms/src/Simulation.cpp | 11 --
Examples/README | 7 --
Examples/python/README | 10 ++
.../CylindersAndPrisms.py | 57 +++++++++
.../CylindersParaCrystal_1DDL.py | 55 ++++++++
.../CylindersParaCrystal_2DDL.py | 59 +++++++++
Examples/python/utils/__init__.py | 1 +
Examples/python/utils/show2d.py | 119 +++++++++---------
Examples/python/utils/show2d_root.py | 75 +++++++++++
10 files changed, 320 insertions(+), 77 deletions(-)
delete mode 100644 Examples/README
create mode 100644 Examples/python/README
create mode 100644 Examples/python/ex001_CylindersAndPrisms/CylindersAndPrisms.py
create mode 100644 Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_1DDL.py
create mode 100644 Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_2DDL.py
create mode 100644 Examples/python/utils/__init__.py
create mode 100755 Examples/python/utils/show2d_root.py
diff --git a/Core/Algorithms/inc/Simulation.h b/Core/Algorithms/inc/Simulation.h
index 4e88964ea89..c933e0b9bbd 100644
--- a/Core/Algorithms/inc/Simulation.h
+++ b/Core/Algorithms/inc/Simulation.h
@@ -114,9 +114,6 @@ class BA_CORE_API_ Simulation : public IParameterized, public ICloneable
//! Apply smearing of intensity due to tilting of z-axis (DEPRECATED)
void smearIntensityFromZAxisTilting();
- //! creates default IsGISAXS simulation which is used for comparison
- static Simulation *createDefaultIsGISAXS();
-
protected:
Simulation(const Simulation& other);
diff --git a/Core/Algorithms/src/Simulation.cpp b/Core/Algorithms/src/Simulation.cpp
index 5113bcfbeb2..404a6c1a0be 100644
--- a/Core/Algorithms/src/Simulation.cpp
+++ b/Core/Algorithms/src/Simulation.cpp
@@ -409,15 +409,4 @@ void Simulation::addToIntensityMap(double alpha, double phi, double value)
}
-Simulation *Simulation::createDefaultIsGISAXS()
-{
- // Build simulation
- Simulation *result = new Simulation();
- result->setDetectorParameters(
- 100,-1.0*Units::degree, 1.0*Units::degree, 100,
- 0.0*Units::degree, 2.0*Units::degree, true);
- result->setBeamParameters(
- 1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
- return result;
-}
diff --git a/Examples/README b/Examples/README
deleted file mode 100644
index 46df19ff930..00000000000
--- a/Examples/README
+++ /dev/null
@@ -1,7 +0,0 @@
-BornAgain usage examples.
-
-Content:
-
-
-
-
diff --git a/Examples/python/README b/Examples/python/README
new file mode 100644
index 00000000000..fffd712f200
--- /dev/null
+++ b/Examples/python/README
@@ -0,0 +1,10 @@
+BornAgain usage examples.
+
+Content:
+
+ex001_CylindersAndPrisms - Mixture of cylinders and prisms without interference (IsGISAXS example #1)
+ex004_CylindersParaCrystal - 1D and 2D paracrystal (IsGISAXS example #4)
+
+
+
+
diff --git a/Examples/python/ex001_CylindersAndPrisms/CylindersAndPrisms.py b/Examples/python/ex001_CylindersAndPrisms/CylindersAndPrisms.py
new file mode 100644
index 00000000000..c084fad503c
--- /dev/null
+++ b/Examples/python/ex001_CylindersAndPrisms/CylindersAndPrisms.py
@@ -0,0 +1,57 @@
+# IsGISAXS01 example: Mixture of cylinders and prisms without interference
+import sys, os, numpy
+
+sys.path.append(os.path.abspath(
+ os.path.join(os.path.split(__file__)[0], '..', '..', '..', 'lib')
+ ))
+
+sys.path.append(os.path.abspath(os.path.join(os.path.split(__file__)[0],'..')))
+
+from libBornAgainCore import *
+from utils.show2d import PlotNumpyArray
+
+
+# ----------------------------------
+# describe sample and run simulation
+# ----------------------------------
+def RunSimulation():
+ # defining materials
+ mAmbience = MaterialManager.getHomogeneousMaterial("Air", 1.0, 0.0 )
+ mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 1.0-6e-6, 2e-8 )
+ # collection of particles
+ n_particle = complex(1.0-6e-4, 2e-8)
+ cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder = Particle(n_particle, cylinder_ff)
+ prism_ff = FormFactorPrism3(5*nanometer, 5*nanometer)
+ prism = Particle(n_particle, prism_ff)
+ particle_decoration = ParticleDecoration()
+ particle_decoration.addParticle(cylinder, 0.0, 0.5)
+ particle_decoration.addParticle(prism, 0.0, 0.5)
+ interference = InterferenceFunctionNone()
+ particle_decoration.addInterferenceFunction(interference)
+ # air layer with particles and substrate form multi layer
+ air_layer = Layer(mAmbience)
+ air_layer_decorator = LayerDecorator(air_layer, particle_decoration)
+ substrate_layer = Layer(mSubstrate, 0)
+ multi_layer = MultiLayer()
+ multi_layer.addLayer(air_layer_decorator)
+ multi_layer.addLayer(substrate_layer)
+
+ # build and run experiment
+ simulation = Simulation()
+ simulation.setDetectorParameters(100,-1.0*degree, 1.0*degree, 100, 0.0*degree, 2.0*degree, True)
+ simulation.setBeamParameters(1.0*angstrom, -0.2*degree, 0.0*degree)
+ simulation.setSample(multi_layer)
+ simulation.runSimulation()
+ ## intensity data
+ return GetOutputData(simulation)
+
+
+#-------------------------------------------------------------
+# main()
+#-------------------------------------------------------------
+if __name__ == '__main__':
+ result = RunSimulation()
+ PlotNumpyArray(result)
+
+
diff --git a/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_1DDL.py b/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_1DDL.py
new file mode 100644
index 00000000000..7f45de5f82d
--- /dev/null
+++ b/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_1DDL.py
@@ -0,0 +1,55 @@
+# IsGISAXS04 example: 1D paracrystal
+import sys, os, numpy
+
+sys.path.append(os.path.abspath(
+ os.path.join(os.path.split(__file__)[0], '..', '..', '..', 'lib')
+ ))
+
+sys.path.append(os.path.abspath(os.path.join(os.path.split(__file__)[0],'..')))
+
+from libBornAgainCore import *
+from utils.show2d import PlotNumpyArray
+
+
+# ----------------------------------
+# describe sample and run simulation
+# ----------------------------------
+def RunSimulation():
+ # defining materials
+ mAmbience = MaterialManager.getHomogeneousMaterial("Air", 1.0, 0.0 )
+ mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 1.0-6e-6, 2e-8 )
+ # collection of particles
+ n_particle = complex(1.0-6e-4, 2e-8)
+ cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder = Particle(n_particle, cylinder_ff)
+ interference = InterferenceFunction1DParaCrystal(20.0*nanometer,7*nanometer, 1e3*nanometer)
+ particle_decoration = ParticleDecoration()
+ particle_decoration.addParticle(cylinder, 0.0, 1.0)
+ particle_decoration.addInterferenceFunction(interference)
+
+ air_layer = Layer(mAmbience)
+ air_layer_decorator = LayerDecorator(air_layer, particle_decoration)
+ substrate_layer = Layer(mSubstrate, 0)
+
+ multi_layer = MultiLayer()
+ multi_layer.addLayer(air_layer_decorator)
+ multi_layer.addLayer(substrate_layer)
+ # build and run experiment
+ simulation = Simulation()
+ simulation.setDetectorParameters(100,0.0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree, True)
+ simulation.setBeamParameters(1.0*angstrom, -0.2*degree, 0.0*degree)
+ simulation.setSample(multi_layer)
+ simulation.runSimulation()
+ ## intensity data
+ return GetOutputData(simulation)
+
+
+#-------------------------------------------------------------
+# main()
+#-------------------------------------------------------------
+if __name__ == '__main__':
+ result = RunSimulation()
+ PlotNumpyArray(result)
+
+
+
diff --git a/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_2DDL.py b/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_2DDL.py
new file mode 100644
index 00000000000..a6272baf3a0
--- /dev/null
+++ b/Examples/python/ex004_CylindersParaCrystal/CylindersParaCrystal_2DDL.py
@@ -0,0 +1,59 @@
+# IsGISAXS04 example: 2D paracrystal
+import sys, os, numpy
+
+sys.path.append(os.path.abspath(
+ os.path.join(os.path.split(__file__)[0], '..', '..', '..', 'lib')
+ ))
+
+sys.path.append(os.path.abspath(os.path.join(os.path.split(__file__)[0],'..')))
+
+from libBornAgainCore import *
+from utils.show2d import PlotNumpyArray
+
+
+# ----------------------------------
+# describe sample and run simulation
+# ----------------------------------
+def RunSimulation():
+ # defining materials
+ mAmbience = MaterialManager.getHomogeneousMaterial("Air", 1.0, 0.0 )
+ mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate", 1.0-6e-6, 2e-8 )
+ # collection of particles
+ n_particle = complex(1.0-6e-4, 2e-8)
+
+ cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder = Particle(n_particle, cylinder_ff)
+
+ interference = InterferenceFunction2DParaCrystal.createHexagonal(20.0*nanometer, 0.0,20.0*micrometer, 20.0*micrometer)
+ pdf = FTDistribution2DCauchy(1.0*nanometer, 1.0*nanometer)
+ interference.setProbabilityDistributions(pdf, pdf)
+
+ particle_decoration = ParticleDecoration()
+ particle_decoration.addParticle(cylinder, 0.0, 1.0)
+ particle_decoration.addInterferenceFunction(interference)
+
+ air_layer = Layer(mAmbience)
+ air_layer_decorator = LayerDecorator(air_layer, particle_decoration)
+ substrate_layer = Layer(mSubstrate, 0)
+
+ multi_layer = MultiLayer()
+ multi_layer.addLayer(air_layer_decorator)
+ multi_layer.addLayer(substrate_layer)
+
+ # build and run experiment
+ simulation = Simulation()
+ simulation.setDetectorParameters(100,0.0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree, True)
+ simulation.setBeamParameters(1.0*angstrom, -0.2*degree, 0.0*degree)
+ simulation.setSample(multi_layer)
+ simulation.runSimulation()
+ return GetOutputData(simulation)
+
+
+#-------------------------------------------------------------
+# main()
+#-------------------------------------------------------------
+if __name__ == '__main__':
+ result = RunSimulation()
+ PlotNumpyArray(result)
+
+
diff --git a/Examples/python/utils/__init__.py b/Examples/python/utils/__init__.py
new file mode 100644
index 00000000000..b0c679daaa6
--- /dev/null
+++ b/Examples/python/utils/__init__.py
@@ -0,0 +1 @@
+__author__ = ''
diff --git a/Examples/python/utils/show2d.py b/Examples/python/utils/show2d.py
index 18a0548bb80..54ee913b416 100755
--- a/Examples/python/utils/show2d.py
+++ b/Examples/python/utils/show2d.py
@@ -1,69 +1,76 @@
#!/usr/bin/env python
+# Draws two dimensional numpy array using matplotlib
+# Usage: python show2d.py file_name
from pylab import *
from matplotlib.colors import LogNorm
import argparse
import os
-# Define the arguments to the script
-parser = argparse.ArgumentParser(description='Plot 2D data table on log scale.')
-parser.add_argument('-m', '--minz', dest='zmin', metavar='MINZ',
- help='minimum z-value to display [default: 1]',
- default='1')
-parser.add_argument('-M', '--maxz', dest='zmax', metavar='MAXZ',
- help='maximum z-value to display [default: maximum value of data set]',
- default=None)
-parser.add_argument('filename', metavar='filename',
- help='filename of the data file')
-
-# Parse the script's arguments
-args = parser.parse_args()
-zmin = float(args.zmin)
-if (args.zmax):
- zmax = float(args.zmax)
-else:
- zmax = None
-filename = args.filename
# Define a nice colormap
-cdict = {'red': ((0.0, 0.0, 0.0),
- (0.5, 0.0, 0.0),
- (1.0, 1.0, 1.0)),
- 'green': ((0.0, 0.0, 0.0),
- (0.5, 0.0, 0.0),
- (1.0, 1.0, 1.0)),
- 'blue': ((0.0, 0.0, 0.0),
- (0.5, 1.0, 1.0),
- (1.0, 1.0, 1.0))}
+cdict = {'red': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
+ 'green': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
+ 'blue': ((0.0, 0.0, 0.0), (0.5, 1.0, 1.0), (1.0, 1.0, 1.0))}
blue_cmap = matplotlib.colors.LinearSegmentedColormap('blue_map', cdict, 256)
-# Load the file's data
-print( "loading..." )
-a=np.loadtxt(filename)
-file_no_prefix = os.path.splitext(os.path.basename(filename))[0]
-print 'Filename: ', file_no_prefix
-print 'Data shape: ', a.shape
-print 'Minimum value of data: ', a.flatten().min()
-print 'Maximum value of data: ', a.flatten().max()
-# Make a plot of the data
-print( "plotting..." )
-amax=a.flatten().max()
-amean=np.sum(a)/a.size
-aminplot=amean**2/amax
-a=np.maximum(a, zmin)
-dataarray=np.flipud(np.transpose(a))
-plt.xlabel(r'$\phi_f$', fontsize=20)
-plt.ylabel(r'$\alpha_f$', fontsize=20)
-# Use one of the predefined colormaps or the above defined 'blue_cmap':
-im=plt.imshow(dataarray, norm=LogNorm(), vmax=zmax, cmap=cm.jet) #, interpolation='none')
-plt.gca().axes.get_xaxis().set_ticks([])
-plt.gca().axes.get_yaxis().set_ticks([])
-plt.colorbar(im)
+def PlotNumpyArray(a, zmin = 1, zmax = None):
+ # Make a plot of the data
+ #print( "plotting..." )
+ amax=a.flatten().max()
+ amean=np.sum(a)/a.size
+ aminplot=amean**2/amax
+ a=np.maximum(a, zmin)
+ dataarray=np.flipud(np.transpose(a))
+ plt.xlabel(r'$\phi_f$', fontsize=20)
+ plt.ylabel(r'$\alpha_f$', fontsize=20)
+ # Use one of the predefined colormaps or the above defined 'blue_cmap':
+ im=plt.imshow(dataarray, norm=LogNorm(), vmax=zmax, cmap=cm.jet) #, interpolation='none')
+ plt.gca().axes.get_xaxis().set_ticks([])
+ plt.gca().axes.get_yaxis().set_ticks([])
+ plt.colorbar(im)
+
+ # Show the plot
+ #print( "showing..." )
+ # Uncomment the next lines to generate a pdf from the plot
+ #extension = 'pdf'
+ #plt.savefig(file_no_prefix + '.%s' %extension, format=extension)
+ plt.show()
+
+
+#-------------------------------------------------------------
+# main()
+#-------------------------------------------------------------
+if __name__ == '__main__':
+ # Define the arguments to the script
+ parser = argparse.ArgumentParser(description='Plot 2D data table on log scale.')
+ parser.add_argument('-m', '--minz', dest='zmin', metavar='MINZ',
+ help='minimum z-value to display [default: 1]',
+ default='1')
+ parser.add_argument('-M', '--maxz', dest='zmax', metavar='MAXZ',
+ help='maximum z-value to display [default: maximum value of data set]',
+ default=None)
+ parser.add_argument('filename', metavar='filename',
+ help='filename of the data file')
+
+ # Parse the script's arguments
+ args = parser.parse_args()
+ zmin = float(args.zmin)
+ if (args.zmax):
+ zmax = float(args.zmax)
+ else:
+ zmax = None
+ filename = args.filename
+
+ # Load the file's data
+ print( "loading..." )
+ a=np.loadtxt(filename)
+ file_no_prefix = os.path.splitext(os.path.basename(filename))[0]
+ print 'Filename: ', file_no_prefix
+ print 'Data shape: ', a.shape
+ print 'Minimum value of data: ', a.flatten().min()
+ print 'Maximum value of data: ', a.flatten().max()
+
+ PlotNumpyArray(a, zmin, zmax)
-# Show the plot
-print( "showing..." )
-# Uncomment the next lines to generate a pdf from the plot
-#extension = 'pdf'
-#plt.savefig(file_no_prefix + '.%s' %extension, format=extension)
-plt.show()
diff --git a/Examples/python/utils/show2d_root.py b/Examples/python/utils/show2d_root.py
new file mode 100755
index 00000000000..3691c0e7ce8
--- /dev/null
+++ b/Examples/python/utils/show2d_root.py
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+# Draws two dimensional numpy array using ROOT
+# Usage: python show2d.py file_name
+
+import argparse
+import os
+import numpy
+import ROOT
+from pylab import *
+
+
+def PlotNumpyArrayWithROOT(a, zmin = 1, zmax = None):
+ nx = a.shape[0]
+ ny = a.shape[1]
+ hist = ROOT.TH2D("hist","hist",nx,0,nx, ny, 0, ny)
+ for (x,y), value in numpy.ndenumerate(a):
+ hist.Fill(x,y,value)
+
+ c1 = ROOT.TCanvas("c1","numpy array", 1024,768)
+ c1.cd()
+ c1.SetLogz()
+ hist.Draw("CONT4Z")
+ c1.Update()
+ #ROOT.gApplication.Run()
+ Interrupt = False
+ while not Interrupt:
+ Interrupt = ROOT.gSystem.ProcessEvents()
+ ROOT.gSystem.Sleep(10)
+
+
+#-------------------------------------------------------------
+# main()
+#-------------------------------------------------------------
+if __name__ == '__main__':
+ # Define the arguments to the script
+ parser = argparse.ArgumentParser(description='Plot 2D data table on log scale.')
+ parser.add_argument('-m', '--minz', dest='zmin', metavar='MINZ',
+ help='minimum z-value to display [default: 1]',
+ default='1')
+ parser.add_argument('-M', '--maxz', dest='zmax', metavar='MAXZ',
+ help='maximum z-value to display [default: maximum value of data set]',
+ default=None)
+ parser.add_argument('filename', metavar='filename',
+ help='filename of the data file')
+
+ # Parse the script's arguments
+ args = parser.parse_args()
+ zmin = float(args.zmin)
+ if (args.zmax):
+ zmax = float(args.zmax)
+ else:
+ zmax = None
+ filename = args.filename
+
+ # Load the file's data
+ print( "loading..." )
+ a=np.loadtxt(filename)
+ file_no_prefix = os.path.splitext(os.path.basename(filename))[0]
+ print 'Filename: ', file_no_prefix
+ print 'Data shape: ', a.shape
+ print 'Minimum value of data: ', a.flatten().min()
+ print 'Maximum value of data: ', a.flatten().max()
+
+ PlotNumpyArrayWithROOT(a, zmin, zmax)
+
+ #rep = ''
+ #while not rep in [ 'q', 'Q' ]:
+ #rep = raw_input( 'enter "q" to quit: ' )
+ #if 1 < len(rep):
+ #rep = rep[0]
+
+ ROOT.gApplication.Run()
+
+ #while ROOT.gSystem.ProcessEvent():
+ #print "aaa"
\ No newline at end of file
--
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