From 27c185bf4db09b9c0e7e5b692f89002cad3afd15 Mon Sep 17 00:00:00 2001
From: Walter Van Herck <w.van.herck@fz-juelich.de>
Date: Tue, 17 Feb 2015 14:33:41 +0100
Subject: [PATCH] Added functional test for python script generation of
LatticeBasis and readded old isgisaxs06b functional test
---
Core/StandardSamples/IsGISAXS06Builder.cpp | 28 +--
Core/StandardSamples/SimulationRegistry.cpp | 4 +
Core/StandardSamples/StandardSimulations.cpp | 19 +-
Core/StandardSamples/StandardSimulations.h | 1 +
Core/Tools/src/LabelSample.cpp | 12 +-
Core/Tools/src/PyGenVisitor.cpp | 213 +++++++++---------
Tests/FunctionalTests/TestCore/CMakeLists.txt | 2 +-
.../FunctionalTests/TestPyCore/CMakeLists.txt | 1 +
.../PyScript_isgisaxs06b.cpp | 14 ++
.../FunctionalTests/TestPyCore/isgisaxs06.py | 2 +-
10 files changed, 170 insertions(+), 126 deletions(-)
create mode 100644 Tests/FunctionalTests/TestPyCore/PyScript_isgisaxs06b/PyScript_isgisaxs06b.cpp
diff --git a/Core/StandardSamples/IsGISAXS06Builder.cpp b/Core/StandardSamples/IsGISAXS06Builder.cpp
index 235f3fa89f3..5191c5f481a 100644
--- a/Core/StandardSamples/IsGISAXS06Builder.cpp
+++ b/Core/StandardSamples/IsGISAXS06Builder.cpp
@@ -24,6 +24,8 @@
#include "IntensityDataIOFactory.h"
#include "Utils.h"
+#include <LatticeBasis.h>
+
// -----------------------------------------------------------------------------
// lattice #1:
@@ -82,23 +84,21 @@ ISample *IsGISAXS06Lattice2Builder::buildSample() const
100.0*Units::nanometer/2.0/M_PI);
interference_function.setProbabilityDistribution(pdf);
- ParticleLayout particle_layout1;
- // particle 1
FormFactorCylinder ff_cyl(5.0*Units::nanometer, 5.0*Units::nanometer);
- kvector_t position(0.0, 0.0, 0.0);
- Particle p(particle_material, ff_cyl);
- ParticleInfo particle_info(p, position, 1.0);
- particle_layout1.addParticleInfo(particle_info);
- particle_layout1.addInterferenceFunction(interference_function);
- ParticleLayout particle_layout2;
- // particle 2
+ Particle cylinder(particle_material, ff_cyl);
+ std::vector<kvector_t > positions;
+ kvector_t position_1(0.0, 0.0, 0.0);
kvector_t position_2(5.0*Units::nanometer, 5.0*Units::nanometer, 0.0);
- particle_info.setPosition(position_2);
- particle_layout2.addParticleInfo(particle_info);
- particle_layout2.addInterferenceFunction(interference_function);
+ positions.push_back(position_1);
+ positions.push_back(position_2);
+ LatticeBasis basis;
+ basis.addParticle(cylinder, positions);
- air_layer.addLayout(particle_layout1);
- air_layer.addLayout(particle_layout2);
+ ParticleLayout particle_layout;
+ particle_layout.addParticle(basis);
+ particle_layout.addInterferenceFunction(interference_function);
+ particle_layout.setTotalParticleSurfaceDensity(0.5);
+ air_layer.addLayout(particle_layout);
multi_layer->addLayer(air_layer);
multi_layer->addLayer(substrate_layer);
diff --git a/Core/StandardSamples/SimulationRegistry.cpp b/Core/StandardSamples/SimulationRegistry.cpp
index 4727226763f..34bbbb17068 100644
--- a/Core/StandardSamples/SimulationRegistry.cpp
+++ b/Core/StandardSamples/SimulationRegistry.cpp
@@ -131,6 +131,10 @@ SimulationRegistry::SimulationRegistry()
"gui_isgisaxs06a", StandardSimulations::gui_IsGISAXS06L1,
"GUI: 2D lattice with disorders");
+ registerItem(
+ "gui_isgisaxs06b", StandardSimulations::gui_IsGISAXS06L2,
+ "GUI: 2D lattice centered");
+
registerItem(
"gui_isgisaxs07", StandardSimulations::gui_IsGISAXS07,
"GUI: Mixture of fixed particles");
diff --git a/Core/StandardSamples/StandardSimulations.cpp b/Core/StandardSamples/StandardSimulations.cpp
index aa248be833a..23bdb931801 100644
--- a/Core/StandardSamples/StandardSimulations.cpp
+++ b/Core/StandardSamples/StandardSimulations.cpp
@@ -383,7 +383,7 @@ Simulation *StandardSimulations::PolarizedDWBAMagCylinders1()
Simulation *result = new Simulation();
- result->setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree,
+ result->setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree,
100, 0.0*Units::degree, 2.0*Units::degree);
result->setBeamParameters(1.0*Units::angstrom, 0.2*Units::degree,
0.0*Units::degree);
@@ -557,6 +557,23 @@ Simulation *StandardSimulations::gui_IsGISAXS06L1()
return result;
}
+Simulation *StandardSimulations::gui_IsGISAXS06L2()
+{
+ SampleBuilderFactory factory;
+ SampleBuilder_t builder = factory.createBuilder("isgisaxs06b");
+
+ Simulation *result = new Simulation();
+
+ result->setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree,
+ 100, 0.0*Units::degree, 2.0*Units::degree);
+ result->setBeamParameters(1.0*Units::angstrom, 0.2*Units::degree,
+ 0.0*Units::degree);
+
+ result->setSampleBuilder( builder );
+
+ return result;
+}
+
Simulation *StandardSimulations::gui_IsGISAXS07()
{
SampleBuilderFactory factory;
diff --git a/Core/StandardSamples/StandardSimulations.h b/Core/StandardSamples/StandardSimulations.h
index 9e6ad4b4b84..04eccd4a6c8 100644
--- a/Core/StandardSamples/StandardSimulations.h
+++ b/Core/StandardSamples/StandardSimulations.h
@@ -53,6 +53,7 @@ Simulation *gui_IsGISAXS041DDL();
Simulation *gui_IsGISAXS042DDL();
Simulation *gui_IsGISAXS11();
Simulation *gui_IsGISAXS06L1();
+Simulation *gui_IsGISAXS06L2();
Simulation *gui_IsGISAXS07();
Simulation *gui_MultipleLayouts();
}
diff --git a/Core/Tools/src/LabelSample.cpp b/Core/Tools/src/LabelSample.cpp
index 28b3d7b7e15..0ee39e1951b 100644
--- a/Core/Tools/src/LabelSample.cpp
+++ b/Core/Tools/src/LabelSample.cpp
@@ -13,6 +13,7 @@
//
// ************************************************************************** //
+#include <LatticeBasis.h>
#include <iostream>
#include "LabelSample.h"
#include "ParticleCoreShell.h"
@@ -53,10 +54,13 @@ std::string LabelSample::getLabel(const MultiLayer *sample)
std::string LabelSample::getLabel(const IParticle *sample)
{
- if (const ParticleCoreShell *pcs = dynamic_cast<const ParticleCoreShell*>(sample))
- return m_ParticleCoreShellLabel[pcs];
- if (const Particle *p = dynamic_cast<const Particle*>(sample))
- return m_ParticleLabel[p];
+ if (const ParticleCoreShell *core_shell_particle =
+ dynamic_cast<const ParticleCoreShell*>(sample))
+ return m_ParticleCoreShellLabel[core_shell_particle];
+ if (const Particle *particle = dynamic_cast<const Particle*>(sample))
+ return m_ParticleLabel[particle];
+ if (const LatticeBasis *lattice_basis = dynamic_cast<const LatticeBasis*>(sample))
+ return m_LatticeBasisLabel[lattice_basis];
throw Exceptions::NotImplementedException("LabelSample::getLabel: called"
" for unknown IParticle type");
}
diff --git a/Core/Tools/src/PyGenVisitor.cpp b/Core/Tools/src/PyGenVisitor.cpp
index 6cbbf879d8b..82880adc6d1 100644
--- a/Core/Tools/src/PyGenVisitor.cpp
+++ b/Core/Tools/src/PyGenVisitor.cpp
@@ -244,8 +244,9 @@ std::string PyGenVisitor::definePreamble() const
std::ostringstream result;
result << "import numpy\n";
result << "from libBornAgainCore import *\n";
- result << "#NOTE: Uncomment the next import statement for plotting\n";
- result << "#import pylab\n\n";
+ result << "#NOTE: Uncomment the next import statements for plotting\n";
+ result << "#import pylab\n";
+ result << "#import matplotlib\n\n";
result << "#NOTE: All the ANGLES are displayed in RADIANS\n\n";
result << "#NOTE: Running this Script by default will write output data"
<< "to \"output.int\" file\n";
@@ -308,7 +309,7 @@ std::string PyGenVisitor::defineMaterials() const
if (p_material->isScalarMaterial()) {
result << "\t" << m_label->getLabel(p_material)
<< " = HomogeneousMaterial(\"" << p_material->getName();
- result << "\"," << PyGenTools::printDouble(delta) << ","
+ result << "\", " << PyGenTools::printDouble(delta) << ", "
<< PyGenTools::printDouble(beta) << ")\n";
}
else {
@@ -327,7 +328,7 @@ std::string PyGenVisitor::defineMaterials() const
<< ")\n";
result << "\t" << m_label->getLabel(p_material)
<< " = HomogeneousMagneticMaterial(\"" << p_material->getName();
- result << "\"," << PyGenTools::printDouble(delta) << ", "
+ result << "\", " << PyGenTools::printDouble(delta) << ", "
<< PyGenTools::printDouble(beta) << ", "
<< "magnetic_field)\n";
}
@@ -352,7 +353,7 @@ std::string PyGenVisitor::defineLayers() const
<< m_label->getLabel(layer->getMaterial());
if (layer->getThickness() != 0)
{
- result << "," << layer->getThickness();
+ result << ", " << layer->getThickness();
}
result << ")\n";
it++;
@@ -377,9 +378,9 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorAnisoPyramid *>(p_ff))
{
result << " = FormFactorAnisoPyramid("
- << anisoPyramid->getLength()<< "*nanometer,"
- << anisoPyramid->getWidth() << "*nanometer,"
- << anisoPyramid->getHeight() << "*nanometer,"
+ << anisoPyramid->getLength()<< "*nanometer, "
+ << anisoPyramid->getWidth() << "*nanometer, "
+ << anisoPyramid->getHeight() << "*nanometer, "
<< anisoPyramid->getAlpha() << ")\n";
}
@@ -387,8 +388,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorBox *>(p_ff))
{
result << " = FormFactorBox("
- << box->getLength() << "*nanometer,"
- << box->getWidth() << "*nanometer,"
+ << box->getLength() << "*nanometer, "
+ << box->getWidth() << "*nanometer, "
<< box->getHeight() << "*nanometer)\n";
}
@@ -396,8 +397,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorCone *>(p_ff))
{
result << " = FormFactorCone("
- << cone->getRadius() << "*nanometer,"
- << cone->getHeight() << "*nanometer,"
+ << cone->getRadius() << "*nanometer, "
+ << cone->getHeight() << "*nanometer, "
<< cone->getAlpha() << ")\n";
}
@@ -405,8 +406,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorCone6 *>(p_ff))
{
result << " = FormFactorCone6("
- << cone6->getRadius() << "*nanometer,"
- << cone6->getHeight() << "*nanometer,"
+ << cone6->getRadius() << "*nanometer, "
+ << cone6->getHeight() << "*nanometer, "
<< cone6->getAlpha() << ")\n";
}
@@ -414,9 +415,9 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorCuboctahedron *>(p_ff))
{
result << " = FormFactorCuboctahedron("
- << cuboctahedron->getLength() << "*nanometer,"
- << cuboctahedron->getHeight() << "*nanometer,"
- << cuboctahedron->getHeightRatio() << "*nanometer"
+ << cuboctahedron->getLength() << "*nanometer, "
+ << cuboctahedron->getHeight() << "*nanometer, "
+ << cuboctahedron->getHeightRatio() << "*nanometer, "
<< cuboctahedron->getAlpha() << ")\n";
}
@@ -424,7 +425,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorCylinder *>(p_ff))
{
result << " = FormFactorCylinder("
- << cylinder->getHeight() << "*nanometer,"
+ << cylinder->getHeight() << "*nanometer, "
<< cylinder->getRadius() << "*nanometer)\n";
}
@@ -432,8 +433,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorEllipsoidalCylinder *>(p_ff))
{
result << " = FormFactorEllipsoidalCylinder("
- << ellipsoidalCylinder->getRadiusA() << "*nanometer,"
- << ellipsoidalCylinder->getRadiusB() << "*nanometer,"
+ << ellipsoidalCylinder->getRadiusA() << "*nanometer, "
+ << ellipsoidalCylinder->getRadiusB() << "*nanometer, "
<< ellipsoidalCylinder->getHeight() << "*nanometer)\n";
}
@@ -448,7 +449,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorFullSpheroid *>(p_ff))
{
result << " = FormFactorFullSpheroid("
- << fullSpheroid->getRadius() << "*nanometer,"
+ << fullSpheroid->getRadius() << "*nanometer, "
<< fullSpheroid->getHeight() << "*nanometer)\n";
}
@@ -463,7 +464,7 @@ std::string PyGenVisitor::defineFormFactors() const
else
{
result << " = FormFactorGauss("
- << gauss->getRadius() << "*nanometer,"
+ << gauss->getRadius() << "*nanometer, "
<< gauss->getHeight() << "*nanometer)\n";
}
}
@@ -472,8 +473,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorHemiEllipsoid *>(p_ff))
{
result << " = FormFactorHemiEllipsoid("
- << hemiEllipsoid->getRadiusA() << "*nanometer,"
- << hemiEllipsoid->getRadiusB() << "*nanometer,"
+ << hemiEllipsoid->getRadiusA() << "*nanometer, "
+ << hemiEllipsoid->getRadiusB() << "*nanometer, "
<< hemiEllipsoid->getHeight() << "*nanometer)\n";
}
@@ -481,7 +482,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorInfLongBox *>(p_ff))
{
result << " = FormFactorInfLongBox("
- << infLongBox->getWidth() << "*nanometer,"
+ << infLongBox->getWidth() << "*nanometer, "
<< infLongBox->getHeight() << "*nanometer)\n";
}
@@ -489,7 +490,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorInfLongRipple1 *>(p_ff))
{
result << " = FormFactorInfLongRipple1("
- << infLongRipple1->getWidth() << "*nanometer,"
+ << infLongRipple1->getWidth() << "*nanometer, "
<< infLongRipple1->getHeight() << "*nanometer)\n";
}
@@ -497,8 +498,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorInfLongRipple2 *>(p_ff))
{
result << " = FormFactorInfLongRipple2("
- << infLongRipple2->getWidth() << "*nanometer,"
- << infLongRipple1->getHeight() << "*nanometer,"
+ << infLongRipple2->getWidth() << "*nanometer, "
+ << infLongRipple1->getHeight() << "*nanometer, "
<< infLongRipple2->getAsymetry() << "*nanometer)\n";
}
@@ -513,7 +514,7 @@ std::string PyGenVisitor::defineFormFactors() const
else
{
result << " = FormFactorLorentz("
- << lorentz->getRadius() << "*nanometer,"
+ << lorentz->getRadius() << "*nanometer, "
<< lorentz->getHeight() << "*nanometer)\n";
}
}
@@ -522,7 +523,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorPrism3 *>(p_ff))
{
result << " = FormFactorPrism3("
- << prism3->getLength() << "*nanometer,"
+ << prism3->getLength() << "*nanometer, "
<< prism3->getHeight() << "*nanometer)\n";
}
@@ -530,7 +531,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorPrism6 *>(p_ff))
{
result << " = FormFactorPrism6("
- << prism6->getRadius() << "*nanometer,"
+ << prism6->getRadius() << "*nanometer, "
<< prism6->getHeight() << "*nanometer)\n";
}
@@ -538,8 +539,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorPyramid *>(p_ff))
{
result << " = FormFactorPyramid("
- << pyramid->getLength() << "*nanometer,"
- << pyramid->getHeight() << "*nanometer,"
+ << pyramid->getLength() << "*nanometer, "
+ << pyramid->getHeight() << "*nanometer, "
<< pyramid->getAlpha() << ")\n";
}
@@ -547,8 +548,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorRipple1 *>(p_ff))
{
result << " = FormFactorRipple1("
- << ripple1->getLength() << "*nanometer,"
- << ripple1->getWidth() << "*nanometer,"
+ << ripple1->getLength() << "*nanometer, "
+ << ripple1->getWidth() << "*nanometer, "
<< ripple1->getHeight() << "*nanometer)\n";
}
@@ -556,9 +557,9 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorRipple2 *>(p_ff))
{
result << " = FormFactorRipple2("
- << ripple2->getLength() << "*nanometer,"
- << ripple2->getWidth() << "*nanometer,"
- << ripple2->getHeight() << "nanometer,"
+ << ripple2->getLength() << "*nanometer, "
+ << ripple2->getWidth() << "*nanometer, "
+ << ripple2->getHeight() << "nanometer, "
<< ripple2->getAsymmetry() << "*nanometer)\n";
}
@@ -566,8 +567,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorTetrahedron *>(p_ff))
{
result << " = FormFactorTetrahedron("
- << tetrahedron->getLength() << "*nanometer,"
- << tetrahedron->getHeight() << "*nanometer,"
+ << tetrahedron->getLength() << "*nanometer, "
+ << tetrahedron->getHeight() << "*nanometer, "
<< tetrahedron->getAlpha() << ")\n";
}
@@ -575,7 +576,7 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorTruncatedSphere *>(p_ff))
{
result << " = FormFactorTruncatedSphere("
- << truncatedSphere->getRadius() << "*nanometer,"
+ << truncatedSphere->getRadius() << "*nanometer, "
<< truncatedSphere->getHeight() << "*nanometer)\n";
}
@@ -583,8 +584,8 @@ std::string PyGenVisitor::defineFormFactors() const
dynamic_cast<const FormFactorTruncatedSpheroid *>(p_ff))
{
result << " = FormFactorTruncatedSpheroid("
- << truncatedSpheroid->getRadius() << "*nanometer,"
- << truncatedSpheroid->getHeight() << "*nanometer,"
+ << truncatedSpheroid->getRadius() << "*nanometer, "
+ << truncatedSpheroid->getHeight() << "*nanometer, "
<< truncatedSpheroid->getHeightFlattening()
<< "*nanometer)\n";
}
@@ -645,11 +646,11 @@ std::string PyGenVisitor::defineParticles() const
}
result << "\t" << it->second
<< " = Particle(" << m_label->getLabel(particle->getMaterial())
- << "," << m_label->getLabel(particle->getFormFactor());
+ << ", " << m_label->getLabel(particle->getFormFactor());
if (particle->getTransform3D())
{
- result << "," << it->second << "_rotation";
+ result << ", " << it->second << "_rotation";
}
result << ")\n";
@@ -672,12 +673,12 @@ std::string PyGenVisitor::defineCoreShellParticles() const
kvector_t position = it->first->getRelativeCorePosition();
result << "\t" << it->second
<< "_relPosition = kvector_t("
- << position.x() << "*nanometer,"
- << position.y() << "*nanometer,"
+ << position.x() << "*nanometer, "
+ << position.y() << "*nanometer, "
<< position.z() << "*nanometer)";
result << "\n\t" << it->second
<< " = ParticleCoreShell("
- << m_label->getLabel(it->first->getShellParticle()) << ","
+ << m_label->getLabel(it->first->getShellParticle()) << ", "
<< m_label->getLabel(it->first->getCoreParticle()) << ", "
<< it->second << "_relPosition)\n";
it++;
@@ -700,16 +701,16 @@ std::string PyGenVisitor::defineLatticeBases() const
for (size_t i=0; i<it->first->getNbrParticles(); ++i) {
std::vector<kvector_t> position_vector = it->first->getParticlePositions(i);
for (size_t j=0; j<position_vector.size(); ++j) {
- result << "\tparticle_" << i
- << "_position_" << j << " = kvector_t("
- << position_vector[j].x() << "*nanometer,"
- << position_vector[j].y() << "*nanometer,"
+ result << "\tparticle_" << i+1
+ << "_position_" << j+1 << " = kvector_t("
+ << position_vector[j].x() << "*nanometer, "
+ << position_vector[j].y() << "*nanometer, "
<< position_vector[j].z() << "*nanometer)\n";
}
result << "\t" << it->second << ".addParticle("
<< m_label->getLabel(it->first->getParticle(i)) << ", [";
for (size_t j=0; j<position_vector.size(); ++j) {
- result << "particle_" << i << "_position_" << j;
+ result << "particle_" << i+1 << "_position_" << j+1;
if (j!=position_vector.size()-1) result << ", ";
}
result << "])\n";
@@ -771,7 +772,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution1DVoigt("
- << PyGenTools::printDouble(fTD1DVoigt->getOmega()) << ","
+ << PyGenTools::printDouble(fTD1DVoigt->getOmega()) << ", "
<< PyGenTools::printDouble(fTD1DVoigt->getEta()) << ")\n";
}
@@ -842,7 +843,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< " = InterferenceFunctionRadialParaCrystal("
- << oneDParaCrystal->getPeakDistance() << "*nanometer,"
+ << oneDParaCrystal->getPeakDistance() << "*nanometer, "
<< oneDParaCrystal->getDampingLength() << "*nanometer)\n";
if (oneDParaCrystal->getKappa() != 0.0)
@@ -869,7 +870,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution1DVoigt("
- << PyGenTools::printDouble(fTD1DVoigt->getOmega()) << ","
+ << PyGenTools::printDouble(fTD1DVoigt->getOmega()) << ", "
<< PyGenTools::printDouble(fTD1DVoigt->getEta()) << ")\n";
}
@@ -956,7 +957,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
result << "\t" << it->second
<< "_pdf = FTDistribution2DCauchy("
<< PyGenTools::printDouble(fTD2DCauchy->getCoherenceLengthX())
- << "*nanometer,"
+ << "*nanometer, "
<< PyGenTools::printDouble(fTD2DCauchy->getCoherenceLengthY())
<< "*nanometer" << ")\n";
if (fTD2DCauchy->getGamma() != 0.0)
@@ -973,7 +974,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution2DCone("
- << fTD2DCone->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DCone->getCoherenceLengthX() << "*nanometer, "
<< fTD2DCone->getCoherenceLengthY() << "*nanometer"
<< ")\n";
@@ -991,7 +992,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution2DGate("
- << fTD2DGate->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGate->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGate->getCoherenceLengthY() << "*nanometer"
<< ")\n";
@@ -1009,7 +1010,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution2DGauss("
- << fTD2DGauss->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGauss->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGauss->getCoherenceLengthY() << "*nanometer"
<< ")\n";
@@ -1027,8 +1028,8 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf = FTDistribution2DVoigt("
- << fTD2DVoigt->getCoherenceLengthX() << "*nanometer,"
- << fTD2DVoigt->getCoherenceLengthY() << "*nanometer,"
+ << fTD2DVoigt->getCoherenceLengthX() << "*nanometer, "
+ << fTD2DVoigt->getCoherenceLengthY() << "*nanometer, "
<< PyGenTools::printDouble(fTD2DVoigt->getEta()) << ")\n";
if (fTD2DVoigt->getGamma() != 0.0)
@@ -1065,9 +1066,9 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< " = InterferenceFunction2DParaCrystal.createSquare("
- << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer,"
- << twoDParaCrystal->getDampingLength() << "*nanometer,"
- << domainSize[0] << "*nanometer,"
+ << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer, "
+ << twoDParaCrystal->getDampingLength() << "*nanometer, "
+ << domainSize[0] << "*nanometer, "
<< domainSize[1] << "*nanometer)\n";
}
@@ -1078,9 +1079,9 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< " = InterferenceFunction2DParaCrystal.createHexagonal("
- << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer,"
- << twoDParaCrystal->getDampingLength() << "*nanometer,"
- << domainSize[0] << "*nanometer,"
+ << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer, "
+ << twoDParaCrystal->getDampingLength() << "*nanometer, "
+ << domainSize[0] << "*nanometer, "
<< domainSize[1] << "*nanometer)\n";
}
@@ -1088,12 +1089,12 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< " = InterferenceFunction2DParaCrystal"
- << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer,"
- << twoDParaCrystal->getLatticeLengths()[1] << "*nanometer,"
+ << twoDParaCrystal->getLatticeLengths()[0]<< "*nanometer, "
+ << twoDParaCrystal->getLatticeLengths()[1] << "*nanometer, "
<< PyGenTools::printDouble(
- twoDParaCrystal->getAlphaLattice()) << ","
+ twoDParaCrystal->getAlphaLattice()) << ", "
<< PyGenTools::printDouble(
- twoDParaCrystal->getLatticeOrientation()) << ","
+ twoDParaCrystal->getLatticeOrientation()) << ", "
<< twoDParaCrystal->getDampingLength() << "*nanometer)\n";
@@ -1102,7 +1103,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< ".setDomainSizes("
- << domainSize[0] << "*nanometer,"
+ << domainSize[0] << "*nanometer, "
<< domainSize[1] << "*nanometer)\n";
}
@@ -1122,7 +1123,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_1 = FTDistribution2DCauchy("
- << fTD2DCauchy->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DCauchy->getCoherenceLengthX() << "*nanometer, "
<< fTD2DCauchy->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DCauchy->getGamma() != 0.0)
@@ -1138,7 +1139,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_1 = FTDistribution2DCone("
- << fTD2DCone->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DCone->getCoherenceLengthX() << "*nanometer, "
<< fTD2DCone->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DCone->getGamma() != 0.0)
@@ -1154,7 +1155,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_1 = FTDistribution2DGate("
- << fTD2DGate->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGate->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGate->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DGate->getGamma() != 0.0)
@@ -1170,7 +1171,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_1 = FTDistribution2DGauss("
- << fTD2DGauss->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGauss->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGauss->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DGauss->getGamma() != 0.0)
@@ -1186,8 +1187,8 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_1 = FTDistribution2DVoigt("
- << fTD2DVoigt->getCoherenceLengthX() << "*nanometer,"
- << fTD2DVoigt->getCoherenceLengthY() << "*nanometer,"
+ << fTD2DVoigt->getCoherenceLengthX() << "*nanometer, "
+ << fTD2DVoigt->getCoherenceLengthY() << "*nanometer, "
<< PyGenTools::printDouble(fTD2DVoigt->getEta()) << ")\n";
if (fTD2DVoigt->getGamma() != 0.0)
@@ -1214,7 +1215,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_2 = FTDistribution2DCauchy("
- << fTD2DCauchy->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DCauchy->getCoherenceLengthX() << "*nanometer, "
<< fTD2DCauchy->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DCauchy->getGamma() != 0.0)
@@ -1230,7 +1231,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_2 = FTDistribution2DCone("
- << fTD2DCone->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DCone->getCoherenceLengthX() << "*nanometer, "
<< fTD2DCone->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DCone->getGamma() != 0.0)
@@ -1246,7 +1247,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_2 = FTDistribution2DGate("
- << fTD2DGate->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGate->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGate->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DGate->getGamma() != 0.0)
@@ -1262,7 +1263,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_2 = FTDistribution2DGauss("
- << fTD2DGauss->getCoherenceLengthX() << "*nanometer,"
+ << fTD2DGauss->getCoherenceLengthX() << "*nanometer, "
<< fTD2DGauss->getCoherenceLengthY() << "*nanometer)\n";
if (fTD2DGauss->getGamma() != 0.0)
@@ -1278,8 +1279,8 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
{
result << "\t" << it->second
<< "_pdf_2 = FTDistribution2DVoigt("
- << fTD2DVoigt->getCoherenceLengthX() << "*nanometer,"
- << fTD2DVoigt->getCoherenceLengthY() << "*nanometer,"
+ << fTD2DVoigt->getCoherenceLengthX() << "*nanometer, "
+ << fTD2DVoigt->getCoherenceLengthY() << "*nanometer, "
<< PyGenTools::printDouble(fTD2DVoigt->getEta()) << ")\n";
if (fTD2DVoigt->getGamma() != 0.0)
@@ -1301,7 +1302,7 @@ std::string PyGenVisitor::defineInterferenceFunctions() const
result << "\t" << it->second
<< ".setProbabilityDistributions("
- << it->second << "_pdf_2," << it->second << "_pdf_2)\n\n";
+ << it->second << "_pdf_2, " << it->second << "_pdf_2)\n\n";
}
else
@@ -1347,9 +1348,9 @@ std::string PyGenVisitor::defineParticleLayouts() const
<< m_label->getLabel(particleInfo->getParticle())
<< "_position = kvector_t("
<< pos.x()
- << "*nanometer,"
+ << "*nanometer, "
<< pos.y()
- << "*nanometer,"
+ << "*nanometer, "
<< pos.z()
<< "*nanometer)\n";
@@ -1357,9 +1358,9 @@ std::string PyGenVisitor::defineParticleLayouts() const
<< m_label->getLabel(particleInfo->getParticle())
<< "_positionInfo = ParticleInfo("
<< m_label->getLabel(particleInfo->getParticle())
- << ","
+ << ", "
<< m_label->getLabel(particleInfo->getParticle())
- << "_position,"
+ << "_position, "
<< PyGenTools::printDouble(particleInfo->getAbundance())
<< ")\n";
@@ -1373,8 +1374,8 @@ std::string PyGenVisitor::defineParticleLayouts() const
result << "\t" << it->second
<< ".addParticle("
<< m_label->getLabel(particleInfo->getParticle())
- << ","
- << PyGenTools::printDouble(particleInfo->getDepth()) << ","
+ << ", "
+ << PyGenTools::printDouble(particleInfo->getDepth()) << ", "
<< PyGenTools::printDouble(particleInfo->getAbundance()) <<")\n";
}
particleIndex++;
@@ -1403,7 +1404,9 @@ std::string PyGenVisitor::defineParticleLayouts() const
result << "\t" << it->second << ".setApproximation(ILayout.";
result << "ISGISAXSMOR)\n";
break;
- }
+ }
+ result << "\t" << it->second << ".setTotalParticleSurfaceDensity("
+ << it->first->getTotalParticleSurfaceDensity() << ")\n";
}
it++;
}
@@ -1422,8 +1425,8 @@ std::string PyGenVisitor::defineRoughnesses() const
{
result << "\t" << it->second
<< " = LayerRoughness("
- << it->first->getSigma() << "*nanometer,"
- << it->first->getHurstParameter() << ","
+ << it->first->getSigma() << "*nanometer, "
+ << it->first->getHurstParameter() << ", "
<< it->first->getLatteralCorrLength() << "*nanometer)\n";
it++;
}
@@ -1490,7 +1493,7 @@ std::string PyGenVisitor::defineMultiLayers() const
result << "\t" << it->second
<< ".addLayerWithTopRoughness("
<< m_label->getLabel(it->first->getLayer(layerIndex))
- << ","
+ << ", "
<< m_label->getLabel(layerInterface->getRoughness())
<< ")\n";
}
@@ -1517,11 +1520,11 @@ std::string PyGenVisitor::defineDetector(const Simulation *simulation) const
size_t index = 0;
while (index < numberOfDetectorDimensions)
{
- if (index != 0) {result << ",";}
+ if (index != 0) {result << ", ";}
result << simulation->getInstrument().getDetectorAxis(index).getSize()
- << ","
+ << ", "
<< simulation->getInstrument().getDetectorAxis(index).getMin()
- << ","
+ << ", "
<< simulation->getInstrument().getDetectorAxis(index).getMax();
index++;
}
@@ -1535,8 +1538,8 @@ std::string PyGenVisitor::defineBeam(const Simulation *simulation) const
result << std::setprecision(12);
result << "\t# Defining Beam Parameters\n";
result << "\tsimulation.setBeamParameters(" ;
- result << simulation->getInstrument().getBeam().getWavelength() << "*nanometer,"
- << simulation->getInstrument().getBeam().getAlpha() << ","
+ result << simulation->getInstrument().getBeam().getWavelength() << "*nanometer, "
+ << simulation->getInstrument().getBeam().getAlpha() << ", "
<< simulation->getInstrument().getBeam().getPhi() << ")\n";
return result.str();
}
@@ -1550,8 +1553,8 @@ std::string PyGenVisitor::definePlotting(const Simulation *simulation) const
result << "#def plotSimulation(simulation):\n";
result << "#\tresult = simulation.getIntensityData().getArray()"
<< "+ 1 # +1 for log scale\n";
- result << "#\tim = pylab.imshow(numpy.rot90(result, 1),"
- << "norm=pylab.colors.LogNorm(), extent=[";
+ result << "#\tim = pylab.imshow(numpy.rot90(result, 1), "
+ << "norm=matplotlib.colors.LogNorm(), extent=[";
size_t index = 0;
size_t numberOfDetectorDimensions =
simulation->getInstrument().getDetectorDimension();
@@ -1559,10 +1562,10 @@ std::string PyGenVisitor::definePlotting(const Simulation *simulation) const
{
if (index != 0)
{
- result << ",";
+ result << ", ";
}
result << simulation->getInstrument().getDetectorAxis(index).getMin()
- << ","
+ << ", "
<< simulation->getInstrument().getDetectorAxis(index).getMax();
index++;
}
diff --git a/Tests/FunctionalTests/TestCore/CMakeLists.txt b/Tests/FunctionalTests/TestCore/CMakeLists.txt
index 6a7deb64c6d..11f74a6958e 100644
--- a/Tests/FunctionalTests/TestCore/CMakeLists.txt
+++ b/Tests/FunctionalTests/TestCore/CMakeLists.txt
@@ -13,7 +13,7 @@ set(list_of_tests
"IsGISAXS041DDL"
"IsGISAXS042DDL"
"IsGISAXS06L1"
-# "IsGISAXS06L2"
+ "IsGISAXS06L2"
"IsGISAXS06L3"
"IsGISAXS06L4"
"IsGISAXS07"
diff --git a/Tests/FunctionalTests/TestPyCore/CMakeLists.txt b/Tests/FunctionalTests/TestPyCore/CMakeLists.txt
index 93818677813..41af8e39c69 100644
--- a/Tests/FunctionalTests/TestPyCore/CMakeLists.txt
+++ b/Tests/FunctionalTests/TestPyCore/CMakeLists.txt
@@ -35,6 +35,7 @@ set(list_of_cpp_python_tests
"PyScript_isgisaxs04_1DDL"
"PyScript_isgisaxs04_2DDL"
"PyScript_isgisaxs06a"
+ "PyScript_isgisaxs06b"
"PyScript_isgisaxs07"
"PyScript_isgisaxs11"
"PyScript_multiplelayoutbuilder"
diff --git a/Tests/FunctionalTests/TestPyCore/PyScript_isgisaxs06b/PyScript_isgisaxs06b.cpp b/Tests/FunctionalTests/TestPyCore/PyScript_isgisaxs06b/PyScript_isgisaxs06b.cpp
new file mode 100644
index 00000000000..c5ac5755ddd
--- /dev/null
+++ b/Tests/FunctionalTests/TestPyCore/PyScript_isgisaxs06b/PyScript_isgisaxs06b.cpp
@@ -0,0 +1,14 @@
+#include "PyGenTools.h"
+#include "SimulationRegistry.h"
+
+int main()
+{
+ SimulationRegistry simulationRegistry;
+ Simulation *simulation =
+ simulationRegistry.createSimulation("gui_isgisaxs06b");
+ bool test = PyGenTools::testPyScript(simulation);
+ std::cout << "Python Script Generation Test for isgisaxs06b"
+ << "(2D lattice centered):"
+ << (test? "[OK]" : "[FAILED]") << std::endl;
+ return (test ? 0 : 1);
+}
diff --git a/Tests/FunctionalTests/TestPyCore/isgisaxs06.py b/Tests/FunctionalTests/TestPyCore/isgisaxs06.py
index 5de5b25d055..6d4d32e28f3 100644
--- a/Tests/FunctionalTests/TestPyCore/isgisaxs06.py
+++ b/Tests/FunctionalTests/TestPyCore/isgisaxs06.py
@@ -62,7 +62,7 @@ def run_simulation_centered():
pdf = FTDistribution2DCauchy(300.0*nanometer/2.0/numpy.pi, 100.0*nanometer/2.0/numpy.pi)
interference.setProbabilityDistribution(pdf)
- # particle 1
+ # two cylinders at fixed position of each other
cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
cylinder = Particle(mParticle, cylinder_ff)
position1 = kvector_t(0.0, 0.0, 0.0)
--
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