diff --git a/Examples/python/fitting/ex08_SimultaneousFitOfTwoDatasets/SimultaneousFitOfTwoDatasets.py b/Examples/python/fitting/ex08_SimultaneousFitOfTwoDatasets/SimultaneousFitOfTwoDatasets.py
index ed2c227f83886e1c25980964644143b5ad66aeca..8821793f3fcec6b5f3340afda7ecb2e39d9bc4eb 100644
--- a/Examples/python/fitting/ex08_SimultaneousFitOfTwoDatasets/SimultaneousFitOfTwoDatasets.py
+++ b/Examples/python/fitting/ex08_SimultaneousFitOfTwoDatasets/SimultaneousFitOfTwoDatasets.py
@@ -80,31 +80,23 @@ class DrawObserver(ba.IFitObserver):
self.fig.canvas.draw()
plt.ion()
- def plot_colormap(self, data, title, min=1.0, max=1e6):
- im = plt.imshow(
- data.getArray(),
- norm=matplotlib.colors.LogNorm(min, max),
- extent=[data.getXmin()/deg, data.getXmax()/deg,
- data.getYmin()/deg, data.getYmax()/deg],
- aspect='auto')
- plt.colorbar(im)
- plt.title(title)
-
def plot_datasets(self, fit_suite, canvas):
for i_dataset in range(0, fit_suite.numberOfFitObjects()):
- real_data = fit_suite.getRealData(i_dataset)
- simul_data = fit_suite.getSimulationData(i_dataset)
- chi2_map = fit_suite.getChiSquaredMap(i_dataset)
+ real_data = fit_suite.experimentalData(i_dataset)
+ simul_data = fit_suite.simulationResult(i_dataset)
+ chi2_map = fit_suite.relativeDifference(i_dataset)
+
+ zmax = real_data.histogram2d().getMaximum()
plt.subplot(canvas[i_dataset*3])
- self.plot_colormap(real_data, "\"Real\" data - #"+str(i_dataset+1),
- min=1.0, max=real_data.getMaximum())
+ ba.plot_colormap(real_data, title="\"Real\" data - #"+str(i_dataset+1),
+ zmin=1.0, zmax=zmax, zlabel="")
plt.subplot(canvas[1+i_dataset*3])
- self.plot_colormap(simul_data, "Simulated data - #"+str(i_dataset+1),
- min=1.0, max=real_data.getMaximum())
+ ba.plot_colormap(simul_data, title="Simulated data - #"+str(i_dataset+1),
+ zmin=1.0, zmax=zmax, zlabel="")
plt.subplot(canvas[2+i_dataset*3])
- self.plot_colormap(chi2_map, "Chi2 map - #"+str(i_dataset+1),
- min=0.001, max=10.0)
+ ba.plot_colormap(chi2_map, title="Chi2 map - #"+str(i_dataset+1),
+ zmin=0.001, zmax=10.0, zlabel="")
def plot_fit_parameters(self, fit_suite, canvas):
# fit parameters
@@ -125,7 +117,7 @@ class DrawObserver(ba.IFitObserver):
# most of the space
canvas = matplotlib.gridspec.GridSpec(
3, 3, width_ratios=[1, 1, 1], height_ratios=[4, 4, 1])
- canvas.update(left=0.05, right=0.95, hspace=0.4, wspace=0.2)
+ canvas.update(left=0.05, right=0.95, hspace=0.5, wspace=0.2)
self.plot_datasets(fit_suite, canvas)
self.plot_fit_parameters(fit_suite, canvas)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
index 2d4d2c65f482096b7c69516df2a5fcf4e59090d2..b478a6d1307605e39f82f994b05d12110f4c515f 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/Interference1DLattice.py
@@ -1,34 +1,37 @@
"""
-Long boxes on a 1D lattice
+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
import bornagain as ba
from bornagain import deg, angstrom, nm
-def get_sample():
+def get_sample(lattice_rotation_angle=45*deg):
"""
- Returns a sample with a grating on a substrate.
- The structure is modelled by infinitely long boxes forming a 1D lattice.
+ Returns a sample with a grating on a substrate,
+ modelled by very long boxes forming a 1D lattice with Cauchy correlations.
"""
# defining materials
m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
+ box_length, box_width, box_height = 10*nm, 10000*nm, 10*nm
+ lattice_length = 30*nm
+
# collection of particles
- lattice_length = 30.0*nm
- lattice_rotation_angle = 0.0*deg
interference = ba.InterferenceFunction1DLattice(
lattice_length, lattice_rotation_angle)
- pdf = ba.FTDecayFunction1DCauchy(20./2./numpy.pi*nm)
+ pdf = ba.FTDecayFunction1DCauchy(1000.0)
interference.setDecayFunction(pdf)
- box_ff = ba.FormFactorBox(1000*nm, 10*nm, 15.0*nm)
+ box_ff = ba.FormFactorBox(box_length, box_width, box_height)
box = ba.Particle(m_particle, box_ff)
- transform = ba.RotationZ(25.0*deg)
+
particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform)
+ particle_layout.addParticle(
+ box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), ba.RotationZ(lattice_rotation_angle))
particle_layout.setInterferenceFunction(interference)
# assembling the sample
@@ -49,7 +52,8 @@ def get_simulation():
simulation = ba.GISASSimulation()
simulation.setDetectorParameters(200, -1.0*deg, 1.0*deg,
200, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(24.0*angstrom, 0.2*deg, 0.0*deg)
+ simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
@@ -59,10 +63,11 @@ def run_simulation():
"""
simulation = get_simulation()
simulation.setSample(get_sample())
+ simulation.setTerminalProgressMonitor()
simulation.runSimulation()
return simulation.result()
if __name__ == '__main__':
result = run_simulation()
- ba.plot_simulation_result(result)
+ ba.plot_simulation_result(result, 1e-03)
diff --git a/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py b/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
index bdb63ec0fa301151fc5cbed1fc875249d7fd1354..c5e7b472662ddb33dec040db2d7e38fa4aeb6c2c 100644
--- a/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
+++ b/Examples/python/simulation/ex03_InterferenceFunctions/RectangularGrating.py
@@ -4,30 +4,31 @@ Monte-carlo integration is used to get rid of
large-particle form factor oscillations.
"""
import bornagain as ba
-from bornagain import deg, angstrom, nm
+from bornagain import deg, angstrom, nm, micrometer
-def get_sample(lattice_rotation_angle=45*deg):
+def get_sample(lattice_rotation_angle=0.0*deg):
"""
- Returns a sample with a grating on a substrate,
- modelled by very long boxes forming a 1D lattice with Cauchy correlations.
+ Returns a sample with a grating on a substrate.
+ lattice_rotation_angle = 0 - beam parallel to grating lines
+ lattice_rotation_angle = 90*deg - beam perpendicular to grating lines
"""
# defining materials
m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
- m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
+ m_si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7)
- box_length, box_width, box_height = 10*nm, 10000*nm, 10*nm
- lattice_length = 30*nm
+ box_length, box_width, box_height = 50*micrometer, 70*nm, 50*nm
+ lattice_length = 150*nm
# collection of particles
interference = ba.InterferenceFunction1DLattice(
- lattice_length, lattice_rotation_angle)
- pdf = ba.FTDecayFunction1DCauchy(1000.0)
+ lattice_length, 90.0*deg - lattice_rotation_angle)
+
+ pdf = ba.ba.FTDecayFunction1DGauss(450.0)
interference.setDecayFunction(pdf)
- box_ff = ba.FormFactorBox(box_length, box_width, box_height)
- box = ba.Particle(m_particle, box_ff)
+ box_ff = ba.FormFactorLongBoxLorentz(box_length, box_width, box_height)
+ box = ba.Particle(m_si, box_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(
@@ -37,11 +38,16 @@ def get_sample(lattice_rotation_angle=45*deg):
# assembling the sample
air_layer = ba.Layer(m_ambience)
air_layer.addLayout(particle_layout)
- substrate_layer = ba.Layer(m_substrate)
+ substrate_layer = ba.Layer(m_si)
+
+ roughness = ba.LayerRoughness()
+ roughness.setSigma(5.0 * nm)
+ roughness.setHurstParameter(0.5)
+ roughness.setLatteralCorrLength(10.0 * nm)
multi_layer = ba.MultiLayer()
multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
+ multi_layer.addLayerWithTopRoughness(substrate_layer, roughness)
return multi_layer
@@ -50,9 +56,10 @@ def get_simulation():
Create and return GISAXS simulation with beam and detector defined
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, -1.0*deg, 1.0*deg,
- 200, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ simulation.setDetectorParameters(200, -0.5*deg, 0.5*deg,
+ 200, 0.0*deg, 0.6*deg)
+ simulation.setBeamParameters(1.34*angstrom, 0.4*deg, 0.0*deg)
+ simulation.setBeamIntensity(1e+08)
simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
diff --git a/GUI/coregui/Views/widgetbox/images/Lattice2DFinite.png b/GUI/coregui/Views/widgetbox/images/Lattice2DFinite.png
new file mode 100644
index 0000000000000000000000000000000000000000..87b601e84ef60aabda663b6413bcb2c4df39d02b
Binary files /dev/null and b/GUI/coregui/Views/widgetbox/images/Lattice2DFinite.png differ
diff --git a/GUI/coregui/Views/widgetbox/widgetbox.qrc b/GUI/coregui/Views/widgetbox/widgetbox.qrc
index 848b11fc1f23c61d21ba202020a1b637089f66ca..861427053d77c33a56363eb93c39b6c933db03a3 100644
--- a/GUI/coregui/Views/widgetbox/widgetbox.qrc
+++ b/GUI/coregui/Views/widgetbox/widgetbox.qrc
@@ -36,5 +36,6 @@
<file>images/SizeDistribution.png</file>
<file>images/Lattice1D.png</file>
<file>images/sample_layers2.png</file>
+ <file>images/Lattice2DFinite.png</file>
</qresource>
</RCC>
diff --git a/GUI/coregui/Views/widgetbox/widgetbox.xml b/GUI/coregui/Views/widgetbox/widgetbox.xml
index 066096c1b45aabf4c9271d50a62971b3fa4f6693..f26b6eefa82af3b55430d4d94dd7a51978ebeb7c 100644
--- a/GUI/coregui/Views/widgetbox/widgetbox.xml
+++ b/GUI/coregui/Views/widgetbox/widgetbox.xml
@@ -67,7 +67,7 @@
</widget>
</categoryentry>
- <categoryentry name="Finite 2D lattice" icon="images/Lattice2D.png">
+ <categoryentry name="Finite 2D lattice" icon="images/Lattice2DFinite.png">
<widget class="InterferenceFinite2DLattice">
<property name="objectName">
<string notr="true">somestring</string>
diff --git a/Tests/Functional/Python/PyPersistence/CMakeLists.txt b/Tests/Functional/Python/PyPersistence/CMakeLists.txt
index 41ddb1ff5942b87d021be16168f689c3b17a2b6a..48f340e77a09cc06a937731f52a9f76734ba0ae0 100644
--- a/Tests/Functional/Python/PyPersistence/CMakeLists.txt
+++ b/Tests/Functional/Python/PyPersistence/CMakeLists.txt
@@ -36,7 +36,7 @@ test_example("simulation/ex03_InterferenceFunctions/ApproximationDA" 2e-10)
test_example("simulation/ex03_InterferenceFunctions/ApproximationLMA" 2e-10)
test_example("simulation/ex03_InterferenceFunctions/ApproximationSSCA" 2e-10)
test_example("simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice" 2e-10)
-test_example("simulation/ex03_InterferenceFunctions/Interference1DLattice" 2e-10)
+test_example("simulation/ex03_InterferenceFunctions/Interference1DLattice" 1.5)
test_example("simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal" 2e-10)
test_example("simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice" 2e-10)
test_example("simulation/ex03_InterferenceFunctions/Interference2DParaCrystal" 2e-10)
diff --git a/Tests/ReferenceData/Python/Interference1DLattice.ref.int.gz b/Tests/ReferenceData/Python/Interference1DLattice.ref.int.gz
index e8001e5bf71180634769eaa2dd9c85c8742252d1..834d93bd01543fa71c32f7a1e2f70d19e73741e6 100644
Binary files a/Tests/ReferenceData/Python/Interference1DLattice.ref.int.gz and b/Tests/ReferenceData/Python/Interference1DLattice.ref.int.gz differ
diff --git a/Tests/ReferenceData/Python/RectangularGrating.ref.int.gz b/Tests/ReferenceData/Python/RectangularGrating.ref.int.gz
index 3ba9799af330a01a4d84949b0204c5d66be280fb..0d7e955b23bf83f827995fe6c6d65f4d71d854a4 100644
Binary files a/Tests/ReferenceData/Python/RectangularGrating.ref.int.gz and b/Tests/ReferenceData/Python/RectangularGrating.ref.int.gz differ
diff --git a/dev-tools/code-tools/update-website.py b/dev-tools/code-tools/update-website.py
new file mode 100644
index 0000000000000000000000000000000000000000..6e0982b1ccf286d8833f80c660880f35ceeea43a
--- /dev/null
+++ b/dev-tools/code-tools/update-website.py
@@ -0,0 +1,120 @@
+"""
+To update examples on website:
+
+1) Run in your build directory
+ctest -R PyExamples
+This will run all existing examples and generate intensity images for web site.
+
+2) Modify variables in this script
+WEBSITE_DIR, BORNAGAIN_SOURCE, EXAMPLE_IMAGES
+
+3) Run this script
+python update-examples.py
+
+TODO: move the script under ctest control
+"""
+import os
+import shutil
+
+WEBSITE_DIR = "/home/pospelov/development/BornAgain-website"
+BORNAGAIN_SOURCE = "/home/pospelov/development/BornAgainHub/BornAgain"
+EXAMPLE_IMAGES = "/home/pospelov/development/BornAgainHub/build/test_output/Functional/Python/PyExamples"
+
+
+def copy_file_to_file(source, destination):
+ """
+ Copies file to another.
+ """
+ shutil.copyfile(source, destination)
+
+
+def find_files(dir_name):
+ """
+ Yield recursive list of files in given dir_name
+ """
+ for subdir, dirs, files in os.walk(dir_name):
+ for filename in files:
+ yield subdir, filename
+
+
+def get_files(dir_name, extension):
+ """
+ Return list of all files in subdirectories of dir_name with given extension
+ """
+ result = []
+ for subdir, filename in find_files(dir_name):
+ name, ext = os.path.splitext(filename)
+ if ext in extension:
+ result.append(os.sep.join([subdir, filename]))
+ return result
+
+
+def find_files_with_same_name(filename_list, name_to_find):
+ same_names = []
+ for filename in filename_list:
+ if os.path.basename(filename) == name_to_find:
+ same_names.append(filename)
+
+ return same_names
+
+
+def copy_files(source_list, destination_list):
+ """
+ Every file in destination_list will be replaced by the file with the same
+ basename found in source_list
+ """
+ missed_files = []
+ updated_files = []
+ for f in destination_list:
+ found_source = find_files_with_same_name(source_list, os.path.basename(f))
+ if len(found_source) == 1:
+ updated_files.append(f)
+ copy_file_to_file(found_source[0], f)
+ else:
+ print(len(found_source), "Problem with ", f)
+ missed_files.append(f)
+
+ print("Summary:")
+
+ print("Following files have been updated on website:")
+ for f in updated_files:
+ print(f)
+
+ if len(missed_files):
+ print("Following files exist on website but not in source dir:")
+ for f in missed_files:
+ print(f)
+
+
+def update_example_images():
+ """
+ Copies example intensity images from build directory to website directory
+ """
+ website = os.path.join(WEBSITE_DIR, "content/documentation/sample-models")
+ source = EXAMPLE_IMAGES
+ website_files = get_files(website, ".png")
+ source_files = get_files(source, ".png")
+
+ copy_files(source_files, website_files)
+
+
+def update_example_scripts():
+ """
+ Copies example scripts from BornAgain directory to website directory
+ """
+ website = os.path.join(WEBSITE_DIR, "static/files/python")
+ source = os.path.join(BORNAGAIN_SOURCE, "Examples/python")
+ website_files = get_files(website, ".py")
+ source_files = get_files(source, ".py")
+
+ copy_files(source_files, website_files)
+
+
+def update_website():
+ update_example_images()
+ update_example_scripts()
+
+
+if __name__ == '__main__':
+ update_website()
+