BuriedParticles.py copied as ex02_BuriedParticles.py into test directory. In...

BuriedParticles.py copied as ex02_BuriedParticles.py into test directory. In the next step it will be converted into a wrapper.
Also simplified things in CMakeLists.txt and PyPersistenceTest.cpp.

Tests/Functional/PyCore/persistence/CMakeLists.txt

@@ -29,52 +29,53 @@ target_link_libraries(PyPersistenceTest BornAgainCore BornAgainTestMachinery)
 foreach(example ${PY_EXAMPLES})
 endforeach()
 
-# ppt = python persistence test:
-function(ppt example tolerance)
-    set(script ${PY_EXAMPLES_DIR}/${example})
-    get_filename_component(script_dir  ${script} DIRECTORY)
-    get_filename_component(script_name ${script} NAME_WE)
-    get_filename_component(script_ext  ${script} EXT)
-    if (NOT ${script_ext} STREQUAL ".py" )
-        message(SEND_ERROR
-            "Unexpected file name extension '${script_ext}' in Python script ${script}")
-        continue()
-    endif()
+# lppt = legacy python persistence test:
+function(lppt example tolerance)
+    set(script_path ${PY_EXAMPLES_DIR}/${example}.py)
+    get_filename_component(script_name ${script_path} NAME_WE)
     add_test(PyPersistenceTest/${script_name} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/PyPersistenceTest
-        ${script_dir} ${script_name} ${tolerance})
+        ${script_path} ${script_name} ${tolerance})
+endfunction()
+
+lppt("simulation/ex01_BasicParticles/AllFormFactorsAvailable" 2e-10)
+lppt("simulation/ex01_BasicParticles/CylindersAndPrisms" 2e-10)
+lppt("simulation/ex01_BasicParticles/CylindersInBA" 2e-10)
+lppt("simulation/ex01_BasicParticles/CylindersInDWBA" 2e-10)
+lppt("simulation/ex01_BasicParticles/CylindersWithSizeDistribution" 2e-10)
+lppt("simulation/ex01_BasicParticles/RotatedPyramids" 2e-10)
+lppt("simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution" 2e-10)
+lppt("simulation/ex02_LayeredStructures/BuriedParticles" 2e-10)
+lppt("simulation/ex02_LayeredStructures/CorrelatedRoughness" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/ApproximationDA" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/ApproximationLMA" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/ApproximationSSCA" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference1DLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference2DParaCrystal" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/Interference2DSquareLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/RectangularGrating" 0.5)
+lppt("simulation/ex03_InterferenceFunctions/SpheresAtHexLattice" 2e-10)
+lppt("simulation/ex03_InterferenceFunctions/TriangularRipple" 2e-10)
+lppt("simulation/ex04_ComplexShapes/CoreShellNanoparticles" 2e-10)
+lppt("simulation/ex04_ComplexShapes/CustomFormFactor" 2e-10)
+lppt("simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis" 2e-10)
+lppt("simulation/ex04_ComplexShapes/LargeParticlesFormFactor" 0.5)
+lppt("simulation/ex05_BeamAndDetector/BeamDivergence" 2e-10)
+lppt("simulation/ex05_BeamAndDetector/DetectorResolutionFunction" 2e-10)
+lppt("simulation/ex05_BeamAndDetector/OffSpecularSimulation" 2e-10)
+lppt("simulation/ex05_BeamAndDetector/RectangularDetector" 2e-10)
+lppt("simulation/ex05_BeamAndDetector/SpecularSimulation" 2e-10)
+lppt("simulation/ex06_Miscellaneous/AxesInDifferentUnits" 2e-10)
+lppt("fitting/ex01_SampleParametersIntro/SampleParametersIntro" 2e-10)
+
+# ppt = python persistence test:
+function(ppt script tolerance)
+    add_test(PyPersistenceTest/${script} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/PyPersistenceTest
+        ${CMAKE_CURRENT_SOURCE_DIR}/${script}.py ${script} ${tolerance})
 endfunction()
 
-ppt("simulation/ex01_BasicParticles/AllFormFactorsAvailable.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/CylindersAndPrisms.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/CylindersInBA.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/CylindersInDWBA.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/RotatedPyramids.py" 2e-10)
-ppt("simulation/ex01_BasicParticles/TwoTypesOfCylindersWithSizeDistribution.py" 2e-10)
-ppt("simulation/ex02_LayeredStructures/BuriedParticles.py" 2e-10)
-ppt("simulation/ex02_LayeredStructures/CorrelatedRoughness.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/ApproximationDA.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/ApproximationLMA.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/ApproximationSSCA.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/CosineRipplesAtRectLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference1DLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference1DRadialParaCrystal.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference2DCenteredSquareLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference2DLatticeSumOfRotated.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference2DParaCrystal.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference2DRotatedSquareLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/Interference2DSquareLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/RectangularGrating.py" 0.5)
-ppt("simulation/ex03_InterferenceFunctions/SpheresAtHexLattice.py" 2e-10)
-ppt("simulation/ex03_InterferenceFunctions/TriangularRipple.py" 2e-10)
-ppt("simulation/ex04_ComplexShapes/CoreShellNanoparticles.py" 2e-10)
-ppt("simulation/ex04_ComplexShapes/CustomFormFactor.py" 2e-10)
-ppt("simulation/ex04_ComplexShapes/HexagonalLatticesWithBasis.py" 2e-10)
-ppt("simulation/ex04_ComplexShapes/LargeParticlesFormFactor.py" 0.5)
-ppt("simulation/ex05_BeamAndDetector/BeamDivergence.py" 2e-10)
-ppt("simulation/ex05_BeamAndDetector/DetectorResolutionFunction.py" 2e-10)
-ppt("simulation/ex05_BeamAndDetector/OffSpecularSimulation.py" 2e-10)
-ppt("simulation/ex05_BeamAndDetector/RectangularDetector.py" 2e-10)
-ppt("simulation/ex05_BeamAndDetector/SpecularSimulation.py" 2e-10)
-ppt("simulation/ex06_Miscellaneous/AxesInDifferentUnits.py" 2e-10)
-ppt("fitting/ex01_SampleParametersIntro/SampleParametersIntro.py" 2e-10)
+ppt("ex02_BuriedParticles" 2e-10)

Tests/Functional/PyCore/persistence/PyPersistenceTest.cpp

@@ -28,9 +28,9 @@
 #include <iomanip>
 
 PyPersistenceTest::PyPersistenceTest(
-    const std::string& directory, const std::string& name, double threshold)
+    const std::string& path, const std::string& name, double threshold)
     : IReferencedTest(name, "persistence test on script "+name, threshold)
-    , m_directory(directory)
+    , m_path(path)
 {}
 
 //! Runs a Python script, and returns true if the output of the script agrees with reference data.
@@ -43,10 +43,9 @@ bool PyPersistenceTest::runTest()
         std::cout << "Removed old output " << fname.c_str() << "\n";
     }
 
-    // Run Python script
-    std::string pyscript_filename = FileSystemUtils::jointPath(m_directory, getName()+".py");
+    // Run Python script, which writes output to PYPERSIST_OUT_DIR.
     std::string dat_stem = FileSystemUtils::jointPath(PYPERSIST_OUT_DIR, getName());
-    if (!runPython(pyscript_filename + " " + dat_stem))
+    if (!runPython(m_path + " " + dat_stem))
         return false;
 
     // Retrieve new output and reference files
@@ -62,9 +61,7 @@ bool PyPersistenceTest::runTest()
 
     // Compare files one by one
     for (auto const& it: dat)
-        if (!compareFilePair(
-                FileSystemUtils::jointPath(PYPERSIST_OUT_DIR, it.second),
-                FileSystemUtils::jointPath(PYPERSIST_REF_DIR, ref[it.first])))
+        if (!compareFilePair(it.second, ref[it.first]))
             return false;
     return true;
 }
@@ -78,7 +75,8 @@ PyPersistenceTest::glob2map(const std::string& dir, const std::string& stem)
     for (const std::string& fname: FileSystemUtils::glob(dir, stem+"\\.\\w+\\..+")) {
         std::vector<std::string> fname_segments =
             StringUtils::split(FileSystemUtils::filename(fname), ".");
-        ret.insert(make_pair(fname_segments[1]+"."+fname_segments[2], fname));
+        ret.insert(make_pair(fname_segments[1]+"."+fname_segments[2],
+                             FileSystemUtils::jointPath(dir, fname)));
     }
     return ret;
 }
@@ -92,7 +90,7 @@ bool PyPersistenceTest::compareFileMaps(
     // All dat files present in ref?
     for (auto const& it: dat) {
         if (ref.find(it.first)==ref.end()) {
-            std::cerr << "For test output " << it.second
+            std::cerr << "For test output "  << it.second
                       << " there is no reference file in " << PYPERSIST_REF_DIR << "\n";
             success = false;
         }
@@ -100,7 +98,7 @@ bool PyPersistenceTest::compareFileMaps(
     // All ref files present in dat?
     for (auto const& it: ref) {
         if (dat.find(it.first)==dat.end()) {
-            std::cerr << "For reference file " << it.second
+            std::cerr << "For reference file "  << it.second
                       << " there is no test output in " << PYPERSIST_OUT_DIR << "\n";
             success = false;
         }

Tests/Functional/PyCore/persistence/PyPersistenceTest.h

@@ -36,13 +36,13 @@ namespace YAML {
 class PyPersistenceTest : public IReferencedTest
 {
 public:
-    PyPersistenceTest(const std::string& directory, const std::string& name, double threshold);
+    PyPersistenceTest(const std::string& path, const std::string& name, double threshold);
     ~PyPersistenceTest() final {}
 
     bool runTest() final;
 
 private:
-    std::string m_directory;
+    std::string m_path;
 
     static std::map<const std::string, const std::string>
         glob2map(const std::string& dir, const std::string& stem);

Tests/Functional/PyCore/persistence/ex02_BuriedParticles.py

+"""
+Spherical particles embedded in the middle of the layer on top of substrate.
+"""
+import numpy
+import bornagain as ba
+from bornagain import deg, angstrom, nm
+
+def get_sample():
+    """
+    Returns a sample with spherical particles in an layer between air and substrate.
+    """
+    # defining materials
+    m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
+    m_interm_layer = ba.HomogeneousMaterial("IntermLayer", 3.45e-6, 5.24e-9)
+    m_substrate = ba.HomogeneousMaterial("Substrate", 7.43e-6, 1.72e-7)
+    m_particle = ba.HomogeneousMaterial("Particle", 0.0, 0.0)
+
+    # collection of particles
+    ff_sphere = ba.FormFactorFullSphere(10.2*nm)
+    sphere = ba.Particle(m_particle, ff_sphere)
+    sphere.setPosition(0.0, 0.0, -25.2)
+    particle_layout = ba.ParticleLayout()
+    particle_layout.addParticle(sphere, 1.0)
+
+    # assembling the sample
+    air_layer = ba.Layer(m_ambience)
+    intermediate_layer = ba.Layer(m_interm_layer, 30.*nm)
+    intermediate_layer.addLayout(particle_layout)
+    substrate_layer = ba.Layer(m_substrate, 0)
+
+    multi_layer = ba.MultiLayer()
+    multi_layer.addLayer(air_layer)
+    multi_layer.addLayer(intermediate_layer)
+    multi_layer.addLayer(substrate_layer)
+    return multi_layer
+
+
+def get_simulation():
+    """
+    Returns a GISAXS simulation.
+    """
+    simulation = ba.GISASSimulation()
+    simulation.setSample(get_sample())
+    simulation.setDetectorParameters(200, -1*deg, +1*deg, 200, 0*deg, +2*deg)
+    simulation.setBeamParameters(1.5*angstrom, 0.15*deg, 0.0*deg)
+    return simulation
+
+
+if __name__ == '__main__':
+    simulation = get_simulation()
+    simulation.runSimulation()
+    result = simulation.getIntensityData()
+    ba.plot_intensity_data(result)