Merge pull request #1111 from jwuttke/nov23

devtools/update-website ctd: error messages upon mismatch with website

Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py

@@ -48,7 +48,8 @@ def get_simulation(integration_flag):
     simulation.setDetectorParameters(200, -2.0*deg, 2.0*deg, 200, 0.0*deg, 2.0*deg)
     simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
     simulation.getOptions().setMonteCarloIntegration(integration_flag, 50)
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
     return simulation
 
 

Examples/Python/sim03_Structures/FindPeaks.py

+"""
+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 bornagain as ba
+from bornagain import deg, angstrom, nm, micrometer
+from matplotlib import pyplot as plt
+
+
+def get_sample(lattice_rotation_angle=0.0*deg):
+    """
+    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_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
+    m_si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7)
+
+    box_length, box_width, box_height = 50*micrometer, 70*nm, 50*nm
+    lattice_length = 150*nm
+
+    # collection of particles
+    interference = ba.InterferenceFunction1DLattice(
+        lattice_length, 90.0*deg - lattice_rotation_angle)
+
+    pdf = ba.ba.FTDecayFunction1DGauss(450.0)
+    interference.setDecayFunction(pdf)
+
+    box_ff = ba.FormFactorLongBoxLorentz(box_length, box_width, box_height)
+    box = ba.Particle(m_si, box_ff)
+
+    particle_layout = ba.ParticleLayout()
+    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
+    vacuum_layer = ba.Layer(m_vacuum)
+    vacuum_layer.addLayout(particle_layout)
+    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(vacuum_layer)
+    multi_layer.addLayerWithTopRoughness(substrate_layer, roughness)
+    return multi_layer
+
+
+def get_simulation():
+    """
+    Create and return GISAXS simulation with beam and detector defined
+    """
+    simulation = ba.GISASSimulation()
+    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
+
+
+def run_simulation():
+    """
+    Runs simulation and returns intensity map.
+    """
+    simulation = get_simulation()
+    simulation.setSample(get_sample())
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
+    simulation.runSimulation()
+    return simulation.result()
+
+
+if __name__ == '__main__':
+    result = run_simulation().histogram2d()
+    ba.plot_histogram(result, cmap='jet', aspect='auto')
+
+    peaks = ba.FindPeaks(result, 2, "nomarkov", 0.001)
+    xpeaks = [peak[0] for peak in peaks]
+    ypeaks = [peak[1] for peak in peaks]
+    print(peaks)
+    plt.plot(xpeaks, ypeaks, linestyle='None', marker='x', color='white',
+             markersize=10)
+    plt.show()

Examples/Python/sim03_Structures/Interference1DLattice.py

@@ -62,7 +62,8 @@ def run_simulation():
     """
     simulation = get_simulation()
     simulation.setSample(get_sample())
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
     simulation.runSimulation()
     return simulation.result()
 

Examples/Python/sim03_Structures/Interference2DParaCrystal.py

@@ -59,7 +59,8 @@ def run_simulation():
     """
     simulation = get_simulation()
     simulation.setSample(get_sample())
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
     simulation.runSimulation()
     return simulation.result()
 

Examples/Python/sim03_Structures/RectangularGrating.py

@@ -69,7 +69,8 @@ def run_simulation():
     """
     simulation = get_simulation()
     simulation.setSample(get_sample())
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
     simulation.runSimulation()
     return simulation.result()
 

Examples/Python/sim04_Multilayers/GratingMC.py

@@ -70,12 +70,14 @@ def run_simulation():
     """
     simulation = get_simulation()
     simulation.setSample(get_sample())
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
     simulation.runSimulation()
     return simulation.result()
 
 
 if __name__ == '__main__':
+    interactive = True
     result = run_simulation().histogram2d()
     ba.plot_histogram(result, cmap='jet', aspect='auto')
 

Examples/Python/sim11_Device/ResonatorOffSpecSetup.py

@@ -55,7 +55,8 @@ def get_offspec_simulation():
 
     # create OffSpecular simulation
     simulation = ba.OffSpecSimulation()
-    simulation.setTerminalProgressMonitor()
+    if not "__no_terminal__" in globals():
+        simulation.setTerminalProgressMonitor()
 
     # define detector parameters
     n_alpha, alpha_min, alpha_max = 300, 0.0*deg, 4.0*deg

Tests/Functional/Python/PyExamples/CMakeLists.txt

@@ -14,7 +14,7 @@ file(GLOB fit_examples
 set(examples ${sim_examples} ${fit_examples})
 
 set(test_script ${output_dir}/check_functionality.py)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/check_functionality.py ${test_script} @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/check_functionality.in.py ${test_script} @ONLY)
 
 foreach(example_path ${examples})
     get_filename_component(example_name ${example_path} NAME_WE)

Tests/Functional/Python/PyExamples/check_functionality.py → Tests/Functional/Python/PyExamples/check_functionality.in.py

@@ -40,8 +40,9 @@ def exec_full(filepath):
     global_namespace = {
         "__file__": filepath,
         "__name__": "__main__",
+        "__no_terminal__": True
     }
-    sys.argv = []  # FIXME after cleanup in plot_utils
+    sys.argv = []  # TODO: FIXME after cleanup in plot_utils
     with open(filepath, 'rb') as file:
         exec(compile(file.read(), filepath, 'exec'), global_namespace)
 
@@ -53,11 +54,12 @@ def run_example(filename):
     if not os.path.exists(filename):
         raise Exception("Example script '" + filename + "' not found")
 
-    print("Input script: " + filename)
+    print("Input script: " + filename, flush=True)
 
     fig = get_figure(filename)
 
     exec_full(filename)
+    print("Input script completed.", flush=True)
 
     plot_file_name = os.path.join(
         output_dir,
@@ -76,8 +78,6 @@ def run_example(filename):
 if __name__ == '__main__':
 
     if len(sys.argv) != 2:
-        exit(
-            "Auxiliary script check_functionality called with wrong number of arguments"
-        )
+        exit("check_functionality called with wrong number of arguments")
 
     run_example(sys.argv[1])

devtools/code-tools/update-website.py

@@ -24,7 +24,7 @@ def log2(msg):
 
 def find_files(dir_name):
     """
-    Return recursive list of files in given dir_name
+    Return recursive list of files in given dir_name.
     """
     for subdir, dirs, files in os.walk(dir_name):
         for filename in files:
@@ -37,9 +37,11 @@ def get_files(dir_name, 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]))
+        if os.path.basename(subdir)=="utils":
+            continue
+        name, ext = os.path.splitext(filename)
+        if ext in extension:
+            result.append(os.sep.join([subdir, filename]))
     return result
 
 
@@ -55,7 +57,8 @@ def find_files_with_same_name(filename_list, name_to_find):
 def update_one_file(source_list, dest):
     """
     Update destination file 'dest', using a suitable source file from 'source_dir'.
-    Returns 2=error, 1=modified, 0=unchanged
+    Returns 2=error, 1=modified, 0=unchanged.
+    On succes (0 or 1), the source file is removed from source_list.
     """
     likely_sources = find_files_with_same_name(source_list, os.path.basename(dest))
     if len(likely_sources) == 0:
@@ -67,6 +70,7 @@ def update_one_file(source_list, dest):
             log2(f'  - {f}')
         return 2
     src = likely_sources[0]
+    source_list.remove(src)
     if filecmp.cmp(src, dest):
         log(f'. {dest}\n    is same as {src}')
         return 0
@@ -103,6 +107,11 @@ def update_all_files_of_one_type(source_dir, dest_dir, extension):
 
     log2(f'=> {nUnchanged} files unchanged, {nModified} files updated, {nError} errors')
 
+    if len(source_list)>0:
+        log2(f'!! WARNING: {len(source_list)} source files are unused')
+        for src in source_list:
+            log(f'  unused: {src}')
+
 
 def update_website(website_source_dir, ba_source_dir, ba_build_dir):
     """