From 630a9ef19200fc9b107d7120f0cf39a1da5b00f4 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Mon, 23 Nov 2020 11:12:34 +0100
Subject: [PATCH] Restore example FindPeaks; additional output from
update-website
---
Examples/Python/sim03_Structures/FindPeaks.py | 90 +++++++++++++++++++
devtools/code-tools/update-website.py | 11 ++-
2 files changed, 99 insertions(+), 2 deletions(-)
create mode 100644 Examples/Python/sim03_Structures/FindPeaks.py
diff --git a/Examples/Python/sim03_Structures/FindPeaks.py b/Examples/Python/sim03_Structures/FindPeaks.py
new file mode 100644
index 00000000000..67e819af38a
--- /dev/null
+++ b/Examples/Python/sim03_Structures/FindPeaks.py
@@ -0,0 +1,90 @@
+"""
+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())
+ 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()
+
diff --git a/devtools/code-tools/update-website.py b/devtools/code-tools/update-website.py
index cac48d9f04b..0a5d0efafbe 100755
--- a/devtools/code-tools/update-website.py
+++ b/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:
@@ -55,7 +55,8 @@ 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 +68,7 @@ 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 +105,11 @@ 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):
"""
--
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