diff --git a/Base/Axis/IAxis.cpp b/Base/Axis/IAxis.cpp
index 5b56e268500e76560ec4944f93193ae9de427001..051c9ba8a9b9cc29ff4f1554e8c02e314ffb372e 100644
--- a/Base/Axis/IAxis.cpp
+++ b/Base/Axis/IAxis.cpp
@@ -37,3 +37,7 @@ bool IAxis::contains(double value) const {
double IAxis::span() const {
return upperBound() - lowerBound();
}
+
+double IAxis::center() const {
+ return (upperBound() + lowerBound())/2;
+}
diff --git a/Base/Axis/IAxis.h b/Base/Axis/IAxis.h
index 21154ced4bad5d5a51e53f486a639e6e02817b53..f4ba5bf2186e587853d7130b6ff48dac95409ff3 100644
--- a/Base/Axis/IAxis.h
+++ b/Base/Axis/IAxis.h
@@ -56,6 +56,9 @@ public:
//! Returns distance from first to last point
double span() const;
+ //! Returns midpoint of axis
+ double center() const;
+
virtual double binCenter(size_t index) const = 0;
//! find bin index which is best match for given value
diff --git a/CHANGELOG b/CHANGELOG
index 4778aa9ea7bf5bf777f1ee67b0c2af1c56e0d06e..fa35811f78963848abfb40e1e60d0c43a1160502 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,10 +1,26 @@
BornAgain-1.18.99, ongoing development
> API changes:
- 1) Lattice has been renamed to Lattice3D, for clearer disambuation from Lattice2D.
- 2) Retain only those interference functions constructors that take a Lattice2D
- or Lattice3D parameter.
+ * Compact constructors like GISASimulation(beam, sample, detector)
+ * Removed "get" from several accessor functions
+ * Class Instrument removed from Python API (instead use simulation.beam() etc)
+ * Lattice has been renamed to Lattice3D, for clearer disambuation from Lattice2D
+ * Removed some interference functions constructors
+ * Remove old R&T computations from API (now in Code/Legacy and Tests)
+ * Python plot API entirely keyword based
> Fixes of unreported bugs:
- * For alpha_i, set scattered intensity to 0 (incorrect, but everything else would be worse)
+ * Several GUI bugs that caused crashes
+ * For alpha_i=0, set scattered intensity to 0
+ > Examples:
+ * Uniform API usage in line with exported Python code
+ > Internal refactoring:
+ * Moved code to break directory include cycles
+ * Renamed a few classes (ISimulation)
+ * Simplified and commented std test machinery
+ * Simplified iteration over INode children
+ * Simplified export of get_sample function
+ * Simplified data read/write wrapper
+ * Replaced boost::filesystem by C++17 std
+ * IComputeFF and children drawn out of IFormFactor inheritance tree
BornAgain-1.18.0, released 2020.10.30
> API changes:
@@ -33,6 +49,7 @@ BornAgain-1.18.0, released 2020.10.30
6) Scalar Fresnel computation unified with polarized implementation
7) Directory Core broken into a hierarchy: Core, Device, Sample, Param, Base
8) Request C++17
+ 9) Error handling: core decoupled from Qt
> Issues from external (GitHub) tracker:
* #918: Specular peak location wrong when using flat detector
* #946: CTest points to broken visualization scripts
diff --git a/Core/Export/SimulationToPython.cpp b/Core/Export/SimulationToPython.cpp
index 9257436cac5a5d5f7acad4059f418bb5fe2a28bd..178fb875ed9c8484d86b323e1af3a6f513f06c94 100644
--- a/Core/Export/SimulationToPython.cpp
+++ b/Core/Export/SimulationToPython.cpp
@@ -28,6 +28,7 @@
#include "Core/Simulation/SpecularSimulation.h"
#include "Device/Beam/FootprintGauss.h"
#include "Device/Beam/FootprintSquare.h"
+#include "Device/Detector/DetectorUtils.h"
#include "Device/Detector/RectangularDetector.h"
#include "Device/Detector/RegionOfInterest.h"
#include "Device/Detector/SphericalDetector.h"
@@ -127,13 +128,22 @@ std::string defineDetector(const ISimulation* simulation) {
result << std::setprecision(12);
if (const auto* const det = dynamic_cast<const SphericalDetector*>(detector)) {
- result << indent() << "detector = ba.SphericalDetector(";
- for (size_t index = 0; index < det->dimension(); ++index) {
- if (index != 0)
- result << ", ";
- result << det->axis(index).size() << ", "
- << pyfmt::printDegrees(det->axis(index).lowerBound()) << ", "
- << pyfmt::printDegrees(det->axis(index).upperBound());
+ ASSERT(det->dimension()==2);
+ if (DetectorUtils::isQuadratic(*det)) {
+ result << indent() << "nbin = " << det->axis(0).size() << "\n";
+ result << indent() << "detector = ba.SphericalDetector(nbin, "
+ << pyfmt::printDegrees(det->axis(0).span()) << ", "
+ << pyfmt::printDegrees(det->axis(0).center()) << ", "
+ << pyfmt::printDegrees(det->axis(1).center());
+ } else {
+ result << indent() << "nx = " << det->axis(0).size() << "\n";
+ result << indent() << "ny = " << det->axis(1).size() << "\n";
+ result << indent() << "detector = ba.SphericalDetector(nx, "
+ << pyfmt::printDegrees(det->axis(0).lowerBound()) << ", "
+ << pyfmt::printDegrees(det->axis(0).upperBound()) << ", "
+ << "ny , "
+ << pyfmt::printDegrees(det->axis(1).lowerBound()) << ", "
+ << pyfmt::printDegrees(det->axis(1).upperBound());
}
result << ")\n";
} else if (const auto* const det = dynamic_cast<const RectangularDetector*>(detector)) {
diff --git a/Core/Simulation/ISimulation.cpp b/Core/Simulation/ISimulation.cpp
index 8ae36f605dfa460e8b4cac55ed942eb0d48dac27..402d1fc08121dbaa13a6435c794caa4008b91bc8 100644
--- a/Core/Simulation/ISimulation.cpp
+++ b/Core/Simulation/ISimulation.cpp
@@ -254,7 +254,6 @@ void ISimulation::addParameterDistribution(const std::string& param_name,
}
void ISimulation::addParameterDistribution(const ParameterDistribution& par_distr) {
- std::cout << "DEBUG ISimulation::addParameterDistribution" << std::endl;
validateParametrization(par_distr);
m_distribution_handler.addParameterDistribution(par_distr);
}
diff --git a/Device/Detector/DetectorUtils.cpp b/Device/Detector/DetectorUtils.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fdf1a5af6fbc0bc76ecef5ff515490e42dbc8797
--- /dev/null
+++ b/Device/Detector/DetectorUtils.cpp
@@ -0,0 +1,26 @@
+// ************************************************************************************************
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file Device/Detector/DetectorUtils.cpp
+//! @brief Implements namespace DetectorUtils.
+//!
+//! @homepage http://www.bornagainproject.org
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2018
+//! @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
+//
+// ************************************************************************************************
+
+#include "Device/Detector/DetectorUtils.h"
+#include "Device/Detector/IDetector2D.h"
+
+bool DetectorUtils::isQuadratic(const IDetector2D& det) {
+ ASSERT(det.dimension()==2);
+ if (det.axis(0).size()!=det.axis(1).size())
+ return false;
+ if (std::abs(det.axis(0).span() - det.axis(1).span()) >
+ 1e-12*(det.axis(0).span() + det.axis(1).span()))
+ return false;
+ return true;
+}
diff --git a/Device/Detector/DetectorUtils.h b/Device/Detector/DetectorUtils.h
new file mode 100644
index 0000000000000000000000000000000000000000..b23aa3b9ad6bf2ef16592d40460666c0b53b9cd3
--- /dev/null
+++ b/Device/Detector/DetectorUtils.h
@@ -0,0 +1,26 @@
+// ************************************************************************************************
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file Device/Detector/DetectorUtils.h
+//! @brief Defines namespace DetectorUtils.
+//!
+//! @homepage http://www.bornagainproject.org
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2018
+//! @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
+//
+// ************************************************************************************************
+
+#ifndef BORNAGAIN_DEVICE_DETECTOR_DETECTORUTILS_H
+#define BORNAGAIN_DEVICE_DETECTOR_DETECTORUTILS_H
+
+class IDetector2D;
+
+namespace DetectorUtils {
+
+bool isQuadratic(const IDetector2D& det);
+
+} // namespace DetectorUtils
+
+#endif // BORNAGAIN_DEVICE_DETECTOR_DETECTORUTILS_H
diff --git a/Device/Detector/SphericalDetector.cpp b/Device/Detector/SphericalDetector.cpp
index 5266e1c3f51215735ccb01b575e674722062fac0..24ddc90549ed201f5c422239cd92392523e5d913 100644
--- a/Device/Detector/SphericalDetector.cpp
+++ b/Device/Detector/SphericalDetector.cpp
@@ -30,6 +30,10 @@ SphericalDetector::SphericalDetector(size_t n_phi, double phi_min, double phi_ma
setDetectorParameters(n_phi, phi_min, phi_max, n_alpha, alpha_min, alpha_max);
}
+SphericalDetector::SphericalDetector(size_t n_bin, double width, double phi, double alpha)
+ : SphericalDetector(n_bin, phi-width/2, phi+width/2, n_bin, alpha-width/2, alpha+width/2) {
+}
+
SphericalDetector::SphericalDetector(const SphericalDetector& other) : IDetector2D(other) {
setName("SphericalDetector");
}
diff --git a/Device/Detector/SphericalDetector.h b/Device/Detector/SphericalDetector.h
index 256034574065c3d87fd621092b07975731e226e8..258180ab0c6da8e05c317fb5fa7a2c8b5d374507 100644
--- a/Device/Detector/SphericalDetector.h
+++ b/Device/Detector/SphericalDetector.h
@@ -37,6 +37,13 @@ public:
SphericalDetector(size_t n_phi, double phi_min, double phi_max, size_t n_alpha,
double alpha_min, double alpha_max);
+ //! Spherical detector constructor with quadratic angle ranges
+ //! @param n_bin number of bins per direction
+ //! @param width angular width
+ //! @param phi central phi angle
+ //! @param alpha central alpha angle
+ SphericalDetector(size_t n_bin, double width, double phi, double alpha);
+
SphericalDetector(const SphericalDetector& other);
SphericalDetector* clone() const override;
diff --git a/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py b/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
index 83a6aac72ee922d771be3204e5cfe3a5c6d93ff8..4871a86cb04063cc6a960c3619afb008658d8eba 100644
--- a/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
+++ b/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
@@ -27,7 +27,7 @@ def get_sample(params):
particle_layout.addParticle(sphere)
interference = ba.InterferenceFunction2DLattice(
- ba.HexagonalLattice2D(lattice_length))
+ ba.HexagonalLattice2D(lattice_length, 0*deg))
pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
interference.setDecayFunction(pdf)
@@ -74,13 +74,13 @@ def create_real_data():
return noisy
-class Plotter:
+class LMFITPlotter:
"""
Adapts standard plotter for lmfit minimizer.
"""
def __init__(self, fit_objective, every_nth=10):
self.fit_objective = fit_objective
- self.plotter_gisas = ba.PlotterGISAS()
+ self.plotter_gisas = ba.fit_monitor.PlotterGISAS()
self.every_nth = every_nth
def __call__(self, params, iter, resid):
@@ -102,7 +102,7 @@ def run_fitting():
params.add('radius', value=7*nm, min=5*nm, max=8*nm)
params.add('length', value=10*nm, min=8*nm, max=14*nm)
- plotter = Plotter(fit_objective)
+ plotter = LMFITPlotter(fit_objective)
result = lmfit.minimize(fit_objective.evaluate_residuals,
params,
iter_cb=plotter)
diff --git a/Examples/Python/fit55_SpecularIntro/FitSpecularBasics.py b/Examples/Python/fit55_SpecularIntro/FitSpecularBasics.py
index 249ee9daf9f730b0463272d5eee7bbd50626efba..4ce6cb3e1793f1199d7e5f57170c4c2a6d2c20ff 100644
--- a/Examples/Python/fit55_SpecularIntro/FitSpecularBasics.py
+++ b/Examples/Python/fit55_SpecularIntro/FitSpecularBasics.py
@@ -110,7 +110,7 @@ def run_fitting():
fit_objective = ba.FitObjective()
fit_objective.addSimulationAndData(get_simulation, real_data, 1.0)
- plot_observer = ba.PlotterSpecular()
+ plot_observer = ba.fit_monitor.PlotterSpecular()
fit_objective.initPrint(10)
fit_objective.initPlot(10, plot_observer)
diff --git a/Examples/Python/fit55_SpecularIntro/FitWithUncertainties.py b/Examples/Python/fit55_SpecularIntro/FitWithUncertainties.py
index c8f8a4ba6719cb9e20c674f2d1f5af8ad68af098..f8eb0d58963922e2bb96675d55d982c7edaa1915 100644
--- a/Examples/Python/fit55_SpecularIntro/FitWithUncertainties.py
+++ b/Examples/Python/fit55_SpecularIntro/FitWithUncertainties.py
@@ -16,7 +16,6 @@ import bornagain as ba
from matplotlib import pyplot as plt
from os import path
-
def get_sample(params):
"""
Creates a sample and returns it
@@ -118,7 +117,7 @@ def run_fitting():
fit_objective = ba.FitObjective()
fit_objective.addSimulationAndData(get_simulation, real_data, uncertainties)
- plot_observer = ba.PlotterSpecular(units=ba.Axes.RQ4)
+ plot_observer = ba.fit_monitor.PlotterSpecular(units=ba.Axes.RQ4)
fit_objective.initPrint(10)
fit_objective.initPlot(10, plot_observer)
fit_objective.setObjectiveMetric("Chi2", "L1")
diff --git a/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py b/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
index 01330432da73abc2645eeb68dcc03de998fe8140..82ce0f5f93d951b5bd5a01ef4f8660ad91d78f42 100644
--- a/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
+++ b/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
@@ -78,7 +78,7 @@ def simulate(ff):
return simulation.result()
-def run_simulation():
+def simulate_and_plot():
"""
Run simulation one by one for every form factor from the list and plot results
on a single canvas
@@ -113,8 +113,8 @@ def run_simulation():
horizontalalignment='center',
verticalalignment='center',
fontsize=9)
+ plt.show()
if __name__ == '__main__':
- run_simulation()
- plt.show()
+ simulate_and_plot()
diff --git a/Examples/Python/sim01_Particles/CylindersAndPrisms.py b/Examples/Python/sim01_Particles/CylindersAndPrisms.py
index cbab1b3b6d47c381c6f2adc6dc66d69f608dbf28..795c4f2f1adfa97b9fb120f57f53beb6c2e6fd13 100644
--- a/Examples/Python/sim01_Particles/CylindersAndPrisms.py
+++ b/Examples/Python/sim01_Particles/CylindersAndPrisms.py
@@ -1,8 +1,9 @@
"""
Mixture of cylinders and prisms without interference
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -48,22 +49,16 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns resulting intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim01_Particles/CylindersInBA.py b/Examples/Python/sim01_Particles/CylindersInBA.py
index 26855e44a93ba0f63acf6bb3e266b453afc3050d..4ff161164ef0215c5dca4e1f6a52f23215042dfe 100644
--- a/Examples/Python/sim01_Particles/CylindersInBA.py
+++ b/Examples/Python/sim01_Particles/CylindersInBA.py
@@ -1,8 +1,9 @@
"""
Cylinder form factor in Born approximation
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -39,22 +40,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim01_Particles/CylindersInDWBA.py b/Examples/Python/sim01_Particles/CylindersInDWBA.py
index 28d884bf62df1e399244fdd48aba86bc76b148d0..73a903eb021ed19559b9200433a9969298bdcdf7 100644
--- a/Examples/Python/sim01_Particles/CylindersInDWBA.py
+++ b/Examples/Python/sim01_Particles/CylindersInDWBA.py
@@ -1,8 +1,9 @@
"""
Cylinder form factor in DWBA
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -41,22 +42,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py b/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
index adc1fd1decbcae25800c687551080346903e08d2..81e115809deace253452a6de7e9d30a74f5dcd2d 100644
--- a/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
+++ b/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
@@ -1,8 +1,9 @@
"""
Cylinders with size distribution
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -45,22 +46,16 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim01_Particles/RotatedPyramids.py b/Examples/Python/sim01_Particles/RotatedPyramids.py
index 0077becb7bfe0fbb2de1ba8ed717227810b81960..7c83b39452ae51fb227d738aa9e72b028473d3ca 100644
--- a/Examples/Python/sim01_Particles/RotatedPyramids.py
+++ b/Examples/Python/sim01_Particles/RotatedPyramids.py
@@ -1,8 +1,9 @@
"""
Rotated pyramids on top of substrate
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -43,22 +44,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py b/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
index 4609d50824a4e035e5a8a960b09a00ec1564754b..6fa2b1f0786120ee50aaf6fa06923ddf39962b0e 100644
--- a/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
+++ b/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
@@ -1,8 +1,9 @@
"""
Mixture cylinder particles with different size distribution
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -54,22 +55,16 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim02_Complexes/BiMaterialCylinders.py b/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
index c99b9de98ba2a6c4bfefebcc54c150e46627ea53..6b4f501baa909f97000aba19f199337fa625f3bd 100644
--- a/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
+++ b/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
@@ -2,30 +2,9 @@
Cylindrical particle made from two materials.
Particle crosses air/substrate interface.
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
-
-
-def get_composition(top_material,
- bottom_material,
- top_height=4.0,
- bottom_height=10.0):
- """
- Returns cylindrical particle made of two different materials.
- """
-
- cylinder_radius = 10*nm
-
- topPart = ba.Particle(top_material,
- ba.FormFactorCylinder(cylinder_radius, top_height))
- bottomPart = ba.Particle(
- bottom_material, ba.FormFactorCylinder(cylinder_radius, bottom_height))
-
- result = ba.ParticleComposition()
- result.addParticle(topPart, ba.kvector_t(0.0, 0.0, bottom_height))
- result.addParticle(bottomPart)
-
- return result
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -79,23 +58,16 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*deg, 1.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- simulation.beam().setIntensity(1.0e+08)
+ beam = ba.Beam(100000000.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns resulting intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py b/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
index 0ff5326cf1f6ba7d591fdfa20063ec2540d3fde2..c6452b607b2fee7671d9b6c15dae326918b202fd 100644
--- a/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
+++ b/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
@@ -1,8 +1,9 @@
"""
Core shell nanoparticles
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -48,22 +49,16 @@ def get_sample():
def get_simulation():
- """
- Returns a 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py b/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
index 860732d97d96c21cdd8a05304edf2b4bc84b9855..4fc0c6d8f666cb69e5254176103c77e7ae08e283 100644
--- a/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
+++ b/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
@@ -1,9 +1,9 @@
"""
Spheres on two hexagonal close packed layers
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -61,22 +61,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, -1.0*deg, 1.0*deg, 200, 0.0*deg,
- 1.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -1.0*deg, 1.0*deg, ny, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py b/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
index 040309946ec011bfd50c7af3fd36c138d0d6880c..2f2e28ab0a91c5b250a2f2df6bb6075eb8237196 100644
--- a/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
+++ b/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
@@ -54,7 +54,7 @@ def get_simulation(integration_flag):
return simulation
-def run_simulation():
+def simulate_and_plot():
"""
Run simulation and plot results 4 times: for small and large cylinders,
with and without integration
@@ -108,8 +108,8 @@ def run_simulation():
zmin = condition['zmin']
zmax = condition['zmax']
ba.plot_colormap(result,
- zmin=zmin,
- zmax=zmax,
+ intensity_min=zmin,
+ intensity_max=zmax,
cmap='jet',
aspect='auto')
@@ -119,8 +119,8 @@ def run_simulation():
horizontalalignment='center',
verticalalignment='center',
fontsize=12)
+ plt.show()
if __name__ == '__main__':
- run_simulation()
- plt.show()
+ simulate_and_plot()
diff --git a/Examples/Python/sim02_Complexes/MesoCrystal.py b/Examples/Python/sim02_Complexes/MesoCrystal.py
index 3bd203daadd04ab6d752e726b4b8dc616ddf2e31..a3b78a2461fa0fca832355d4ac13c5922eb7a281 100644
--- a/Examples/Python/sim02_Complexes/MesoCrystal.py
+++ b/Examples/Python/sim02_Complexes/MesoCrystal.py
@@ -1,8 +1,9 @@
"""
Cylindrical mesocrystal on a substrate
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -53,22 +54,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py b/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
index 4065dbd16b0bebe16f00d52bd210fcf489f372e0..493b78308c09cdfafad51b77a9dc6a5c0d254405 100644
--- a/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
+++ b/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
@@ -16,11 +16,9 @@ adjusts calculations accordingly.
For example, X or Y rotated particles can not yet cross interfaces (exception
will be thrown when trying to simulate such geometries).
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
-
-phi_min, phi_max = -1.0, 1.0
-alpha_min, alpha_max = 0.0, 2.0
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -70,23 +68,16 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, phi_min*deg, phi_max*deg, 100,
- alpha_min*deg, alpha_max*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns resulting intensity map.
- """
- sample = get_sample()
simulation = get_simulation()
- simulation.setSample(sample)
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/ApproximationDA.py b/Examples/Python/sim03_Structures/ApproximationDA.py
index c072968b804ba59f5effe416b447e620af14c038..bdac8aa52541d7ea9192a3687d49ee01fdf613f0 100644
--- a/Examples/Python/sim03_Structures/ApproximationDA.py
+++ b/Examples/Python/sim03_Structures/ApproximationDA.py
@@ -1,8 +1,9 @@
"""
Cylinders of two different sizes in Decoupling Approximation
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -51,22 +52,16 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/ApproximationLMA.py b/Examples/Python/sim03_Structures/ApproximationLMA.py
index 73c8eebb9b3947f23b9da1de47a4608d8b17e872..158032846f186d29d70d70a7d1b1217a312ac908 100644
--- a/Examples/Python/sim03_Structures/ApproximationLMA.py
+++ b/Examples/Python/sim03_Structures/ApproximationLMA.py
@@ -1,8 +1,9 @@
"""
Cylinders of two different sizes in Local Monodisperse Approximation
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -59,22 +60,16 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/ApproximationSSCA.py b/Examples/Python/sim03_Structures/ApproximationSSCA.py
index abc4a8cb83ba6dd9afedf41a54b0aa6ac54e53cf..8530cfe49f7126a8a1a4627bd4f1eb11c71085f1 100644
--- a/Examples/Python/sim03_Structures/ApproximationSSCA.py
+++ b/Examples/Python/sim03_Structures/ApproximationSSCA.py
@@ -1,8 +1,9 @@
"""
Cylinders of two different sizes in Size-Spacing Coupling Approximation
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -52,22 +53,16 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py b/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
index b4ae226890224b83dc62439efe2f945e434d0c20..fc0993f33e756073b3e876780472505ffd71a4b5 100644
--- a/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
+++ b/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
@@ -1,9 +1,9 @@
"""
Cosine ripple on a 2D lattice
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -52,22 +52,17 @@ def get_sample():
def get_simulation():
- """
- characterizing the input beam and output detector
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1.5*deg, 1.5*deg, 100, 0.0*deg,
- 2.5*deg)
- simulation.setBeamParameters(1.6*angstrom, 0.3*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.16*nm, ba.Direction(0.3*deg, 0.0*deg))
+ nx = 100
+ ny = 100
+ detector = ba.SphericalDetector(nx, -1.5*deg, 1.5*deg, ny, 0.0*deg, 2.5*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/FindPeaks.py b/Examples/Python/sim03_Structures/FindPeaks.py
index 73d5d3cc323d699c82bce0a2d72721adc9d43647..2ec3cf1487c105693f9d770eceb3fe3c993c7337 100644
--- a/Examples/Python/sim03_Structures/FindPeaks.py
+++ b/Examples/Python/sim03_Structures/FindPeaks.py
@@ -77,7 +77,7 @@ def run_simulation():
return simulation.result()
-if __name__ == '__main__':
+def simulate_and_plot():
result = run_simulation().histogram2d()
ba.plot_histogram(result, cmap='jet', aspect='auto')
@@ -92,3 +92,7 @@ if __name__ == '__main__':
color='white',
markersize=10)
plt.show()
+
+
+if __name__ == '__main__':
+ simulate_and_plot()
diff --git a/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py b/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
index 12e550a5a155149517eeca0327417769bcc95125..a411314da8651bc490d2d319d1207db2f37b1854 100644
--- a/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
+++ b/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
@@ -1,11 +1,9 @@
"""
radial paracrystal
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
-
-phi_min, phi_max = -2.0, 2.0
-alpha_min, alpha_max = 0.0, 2.0
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -50,22 +48,17 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
index 03049b3fb7b280223d910daf2450e1c90088194a..5b5bb61fbc349340c5e105fe4cec728a9c28f5d7 100644
--- a/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
@@ -1,9 +1,9 @@
"""
2D lattice with disorder, centered square lattice
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -61,23 +61,17 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py b/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
index 1948f822ed174e40c629bbea026678b28806d920..fb5b18b520bc400741edd71f58a918e734826739 100644
--- a/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
+++ b/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
@@ -1,7 +1,6 @@
-# 2D lattice with different disorder (IsGISAXS example #6), sum of rotated lattices
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import deg, angstrom, nm
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -38,32 +37,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- Assigns additional distribution to lattice rotation angle.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
-
- simulation.setSample(get_sample())
-
- xi_min = 0.0*deg
- xi_max = 240.0*deg
- xi_distr = ba.DistributionGate(xi_min, xi_max)
-
- # assigns distribution with 3 equidistant points to lattice rotation angle
- simulation.addParameterDistribution("*/SquareLattice2D/Xi", xi_distr, 3)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
+ distr_1 = ba.DistributionGate(0.0*deg, 240.0*deg)
+ simulation.addParameterDistribution("*/SquareLattice2D/Xi", distr_1, 3, 0.0)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
-
simulation = get_simulation()
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/Interference2DParaCrystal.py b/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
index dfae0d5c546f0ba8c4e51376d145db064bdf33d3..86ad4e6daaa1b431755e70a60b449b0d75d57d0e 100644
--- a/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
+++ b/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
@@ -1,8 +1,9 @@
"""
2D paracrystal
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -53,25 +54,17 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined.
- """
- simulation = ba.GISASSimulation()
- # coarse grid because this simulation takes rather long
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
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()
diff --git a/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
index 33ec3f79809db7ed9ef3666054966b6723863b70..2b1da4c2d661ff728dfd2935238c9171ad91abe6 100644
--- a/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
@@ -1,9 +1,9 @@
"""
Cylinders on a rotated 2D lattice
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -52,23 +52,17 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py b/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
index e018b063c317bb9935640c8dce3f10b1fd4ffff5..99a9af46b441b04bd759bedac75df846fb75936d 100644
--- a/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
@@ -1,9 +1,9 @@
"""
Cylinders on a 2D square lattice
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -50,22 +50,17 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/Interference2DSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
index affd7715ec59e66c594c4acf5a22332d0da8d990..e7968d38fde37fbabf5b2cb8d9e68f073be7f20d 100644
--- a/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
@@ -1,9 +1,9 @@
"""
Cylinders on a 2D square lattice
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -51,22 +51,17 @@ def get_sample():
def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- 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)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/RectangularGrating.py b/Examples/Python/sim03_Structures/RectangularGrating.py
index da5b67337499317af369d351c39d7c99a1c57af4..b720c9981dbfdd86dfd67314475bf804fccdde90 100644
--- a/Examples/Python/sim03_Structures/RectangularGrating.py
+++ b/Examples/Python/sim03_Structures/RectangularGrating.py
@@ -3,8 +3,9 @@ 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, sys
import bornagain as ba
-from bornagain import deg, angstrom, nm, micrometer
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample(lattice_rotation_angle=0.0*deg):
@@ -52,26 +53,18 @@ def get_sample(lattice_rotation_angle=0.0*deg):
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.beam().setIntensity(1e+08)
+ beam = ba.Beam(100000000.0, 0.134*nm, ba.Direction(0.4*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -0.5*deg, 0.5*deg, ny, 0.0*deg, 0.6*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
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()
diff --git a/Examples/Python/sim03_Structures/SpheresAtHexLattice.py b/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
index 7f3c49d042b4f7e05fa5b942c17900b3816cb40e..cfff1d0eefef5a98e2e95b6f4629b64b43c88be1 100644
--- a/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
+++ b/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
@@ -1,8 +1,9 @@
"""
Spheres on a hexagonal lattice
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -51,22 +52,17 @@ def get_sample():
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,
- 1.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -1.0*deg, 1.0*deg, ny, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim03_Structures/TriangularRipple.py b/Examples/Python/sim03_Structures/TriangularRipple.py
index 2815287042a10a22f4e7cb04849b1132650fd8b9..4082acffcbb507268762d67d7fa7980939360a81 100644
--- a/Examples/Python/sim03_Structures/TriangularRipple.py
+++ b/Examples/Python/sim03_Structures/TriangularRipple.py
@@ -1,9 +1,9 @@
"""
Sample from the article D. Babonneau et. al., Phys. Rev. B 85, 235415, 2012 (Fig.3)
"""
-import numpy
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -53,22 +53,17 @@ def get_sample():
def get_simulation():
- """
- characterizing the input beam and output detector
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, -1.5*deg, 1.5*deg, 200, 0.0*deg,
- 2.5*deg)
- simulation.setBeamParameters(1.6*angstrom, 0.3*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.16*nm, ba.Direction(0.3*deg, 0.0*deg))
+ nx = 200
+ ny = 200
+ detector = ba.SphericalDetector(nx, -1.5*deg, 1.5*deg, ny, 0.0*deg, 2.5*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim04_Multilayers/BuriedParticles.py b/Examples/Python/sim04_Multilayers/BuriedParticles.py
index d543571da20b84d28b480c3c3dcc2cec353c3d3c..db574d201f13144ac46ebab2715c3575c6283af8 100644
--- a/Examples/Python/sim04_Multilayers/BuriedParticles.py
+++ b/Examples/Python/sim04_Multilayers/BuriedParticles.py
@@ -1,8 +1,9 @@
"""
Spherical particles embedded in the middle of the layer on top of substrate.
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -48,22 +49,16 @@ def get_sample():
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)
+ beam = ba.Beam(1.0, 0.15*nm, ba.Direction(0.15*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 0.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py b/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
index a32410384e7c997082411d3a6dbf060feee46284..f968871ae5b3ff1fc5792df6b6679ec0641bc6ad 100644
--- a/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
+++ b/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
@@ -1,8 +1,9 @@
"""
MultiLayer with correlated roughness
"""
+import numpy, sys
import bornagain as ba
-from bornagain import deg, angstrom, nm
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -45,23 +46,16 @@ def get_sample():
def get_simulation():
- """
- Characterizing the input beam and output detector
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, -0.5*deg, 0.5*deg, 200, 0.0*deg,
- 1.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- simulation.beam().setIntensity(5e11)
+ beam = ba.Beam(500000000000.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 1.0*deg, 0.0*deg, 0.5*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py b/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
index bfbe4d269e5e858c40f11980d172608c49d41ac1..dcbca06bfa726862b80c00ce790004f56d8deb34 100644
--- a/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
+++ b/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
@@ -1,8 +1,9 @@
"""
Square lattice of cylinders inside finite layer with usage of average material
"""
+import numpy, sys
import bornagain as ba
-from bornagain import deg, angstrom, nm
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample(cyl_height=5*nm):
@@ -42,23 +43,18 @@ def get_sample(cyl_height=5*nm):
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -2.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 100
+ ny = 100
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
simulation.getOptions().setUseAvgMaterials(True)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim04_Multilayers/GratingMC.py b/Examples/Python/sim04_Multilayers/GratingMC.py
index 91cb58dfa3f6c1264b57abec931f3bc151e8ae57..8e1a89e89f7f2644940cc15419410cab96a34dd0 100644
--- a/Examples/Python/sim04_Multilayers/GratingMC.py
+++ b/Examples/Python/sim04_Multilayers/GratingMC.py
@@ -77,7 +77,7 @@ def run_simulation():
return simulation.result()
-if __name__ == '__main__':
+def simulate_and_plot():
interactive = True
result = run_simulation().histogram2d()
ba.plot_histogram(result, cmap='jet', aspect='auto')
@@ -93,3 +93,7 @@ if __name__ == '__main__':
color='white',
markersize=10)
plt.show()
+
+
+if __name__ == '__main__':
+ simulate_and_plot()
diff --git a/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py b/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
index a691fbab52d14a78ea9c97b1a90129aade4781e1..5c5544d3d3a8ef7dd4d708d0d173f1d318f184db 100644
--- a/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
+++ b/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
@@ -2,11 +2,9 @@
Square lattice of half spheres on substrate with usage of average material
and slicing
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
-
-sphere_radius = 5*nm
-n_slices = 10
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -55,24 +53,18 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -2.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 100
+ ny = 100
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
simulation.getOptions().setUseAvgMaterials(True)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
- sample = get_sample()
simulation = get_simulation()
- simulation.setSample(sample)
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim05_Magnetism/MagneticSpheres.py b/Examples/Python/sim05_Magnetism/MagneticSpheres.py
index 171baed9ac7d00e256b8d063e3e2bed67e150fad..6d1e01bbaca188f25b3c16db0e28a4293dacc4c5 100644
--- a/Examples/Python/sim05_Magnetism/MagneticSpheres.py
+++ b/Examples/Python/sim05_Magnetism/MagneticSpheres.py
@@ -1,11 +1,9 @@
"""
Simulation demo: magnetic spheres in substrate
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
-
-# Magnetization of the particle's material (A/m)
-magnetization_particle = ba.kvector_t(0.0, 0.0, 1e7)
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -48,29 +46,20 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(200, -3.0*deg, 3.0*deg, 200, 0.0*deg,
- 6.0*deg)
- simulation.setBeamParameters(1.*angstrom, 0.5*deg, 0.0*deg)
- simulation.beam().setIntensity(1e12)
-
- analyzer_dir = ba.kvector_t(0.0, 0.0, -1.0)
- beampol = ba.kvector_t(0.0, 0.0, 1.0)
- simulation.setBeamPolarization(beampol)
- simulation.setAnalyzerProperties(analyzer_dir, 1.0, 0.5)
-
+ beam = ba.Beam(1e+12, 0.1*nm, ba.Direction(0.5*deg, 0.0*deg))
+ beam_polarization = kvector_t(0.0, 0.0, 1.0)
+ beam.setPolarization(beam_polarization)
+ nbin = 200
+ detector = ba.SphericalDetector(nbin, 6.0*deg, 0.0*deg, 3.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
+ analyzer_direction = kvector_t(0.0, 0.0, -1.0)
+ simulation.setAnalyzerProperties(analyzer_direction, 1.0, 0.5)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim11_Device/BeamDivergence.py b/Examples/Python/sim11_Device/BeamDivergence.py
index 9fdc00c06f875932142dd7e433719193725f30e0..088a9ab3e45c52bca19022ca76c3090183c25240 100644
--- a/Examples/Python/sim11_Device/BeamDivergence.py
+++ b/Examples/Python/sim11_Device/BeamDivergence.py
@@ -1,8 +1,9 @@
"""
Cylinder form factor in DWBA with beam divergence
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -41,32 +42,24 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam (+ divergence) and detector defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- wavelength_distr = ba.DistributionLogNormal(1.0*angstrom, 0.1)
- alpha_distr = ba.DistributionGaussian(0.2*deg, 0.1*deg)
- phi_distr = ba.DistributionGaussian(0.0*deg, 0.1*deg)
- simulation.addParameterDistribution("*/Beam/Wavelength", wavelength_distr,
- 5)
- simulation.addParameterDistribution("*/Beam/InclinationAngle", alpha_distr,
- 5)
- simulation.addParameterDistribution("*/Beam/AzimuthalAngle", phi_distr, 5)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
+ distr_1 = ba.DistributionLogNormal(0.1*nm, 0.1)
+ simulation.addParameterDistribution("*/Beam/Wavelength", distr_1, 5, 0.0)
+ distr_2 = ba.DistributionGaussian(0.2*deg, 0.1*deg)
+ simulation.addParameterDistribution("*/Beam/InclinationAngle", distr_2, 5,
+ 0.0)
+ distr_3 = ba.DistributionGaussian(0.0*deg, 0.1*deg)
+ simulation.addParameterDistribution("*/Beam/AzimuthalAngle", distr_3, 5,
+ 0.0)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
- print(simulation.treeToString())
- print(simulation.parametersToString())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim11_Device/ConstantBackground.py b/Examples/Python/sim11_Device/ConstantBackground.py
index a1e5e980907b73953ac9a142f39ef471663e25ad..0ca4ccd72eb3085323578b0bbfc5179ebc12d43e 100644
--- a/Examples/Python/sim11_Device/ConstantBackground.py
+++ b/Examples/Python/sim11_Device/ConstantBackground.py
@@ -1,8 +1,9 @@
"""
Cylinder form factor in DWBA with constant background
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -41,26 +42,18 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with a constant backround.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- simulation.beam().setIntensity(1e6)
- bg = ba.ConstantBackground(1e3)
- simulation.setBackground(bg)
+ beam = ba.Beam(1000000.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
+ background = ba.ConstantBackground(1.0e+03)
+ simulation.setBackground(background)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
- print(simulation.parametersToString())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim11_Device/DetectorResolutionFunction.py b/Examples/Python/sim11_Device/DetectorResolutionFunction.py
index 5add835f7998d4aad0f4c544aee6734061adfb37..739ca5512b4303f4798ba39309705904001023b0 100644
--- a/Examples/Python/sim11_Device/DetectorResolutionFunction.py
+++ b/Examples/Python/sim11_Device/DetectorResolutionFunction.py
@@ -1,8 +1,9 @@
"""
Cylinder form factor in DWBA with detector resolution function applied
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -41,24 +42,18 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with detector resolution function defined.
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nbin = 100
+ detector = ba.SphericalDetector(nbin, 2.0*deg, 1.0*deg, 1.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
simulation.setDetectorResolutionFunction(
ba.ResolutionFunction2DGaussian(0.02*deg, 0.02*deg))
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
simulation = get_simulation()
- simulation.setSample(get_sample())
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py b/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
index e5d58ff02734e888aacc75f51f14792d2d29278d..6845d03748d0ce08a107df721957e1438bfca0ff 100644
--- a/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
+++ b/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
@@ -1,8 +1,9 @@
"""
Square lattice of boxes on substrate (including the specular peak)
"""
+import numpy, sys
import bornagain as ba
-from bornagain import angstrom, deg, nm, nm2, kvector_t
+from bornagain import angstrom, deg, micrometer, nm, nm2, kvector_t
def get_sample():
@@ -50,25 +51,19 @@ def get_sample():
def get_simulation():
- """
- Returns a GISAXS simulation with beam and detector defined
- """
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(101, -2.0*deg, 2.0*deg, 101, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ beam = ba.Beam(1.0, 0.1*nm, ba.Direction(0.2*deg, 0.0*deg))
+ nx = 101
+ ny = 101
+ detector = ba.SphericalDetector(nx, -2.0*deg, 2.0*deg, ny, 0.0*deg, 2.0*deg)
+
+ simulation = ba.GISASSimulation(beam, get_sample(), detector)
simulation.getOptions().setUseAvgMaterials(True)
simulation.getOptions().setIncludeSpecular(True)
return simulation
def run_simulation():
- """
- Runs simulation and returns intensity map.
- """
- sample = get_sample()
simulation = get_simulation()
- simulation.setSample(sample)
simulation.runSimulation()
return simulation.result()
diff --git a/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py b/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
index b1e8ad350cd202d2ba4f521599eaecff9ff941ad..4f77425a76831646a8b284da1b91842ec1635b21 100644
--- a/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
+++ b/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
@@ -71,15 +71,13 @@ def get_noisy_image(hist):
return result
-def plot_histogram(hist, zmin=None, zmax=None):
+def plot_histogram(hist, **kwargs):
ba.plot_histogram(hist,
xlabel=r'$\varphi_f ^{\circ}$',
ylabel=r'$\alpha_f ^{\circ}$',
zlabel="",
- zmin=zmin,
- zmax=zmax,
cmap='jet',
- aspect='auto')
+ aspect='auto', **kwargs)
def get_relative_difference(hist):
@@ -140,7 +138,7 @@ def plot(hist):
plt.subplot(2, 2, 3)
reldiff = get_relative_difference(hist)
- plot_histogram(reldiff, zmin=1e-03, zmax=10)
+ plot_histogram(reldiff, intensity_min=1e-03, intensity_max=10)
plt.title("Relative difference")
plt.subplot(2, 2, 4)
diff --git a/Examples/Python/sim29_DepthProbe/DepthProbe.py b/Examples/Python/special40_DepthProbe/DepthProbe.py
similarity index 100%
rename from Examples/Python/sim29_DepthProbe/DepthProbe.py
rename to Examples/Python/special40_DepthProbe/DepthProbe.py
diff --git a/GUI/coregui/Models/GUIDomainSampleVisitor.cpp b/GUI/coregui/Models/GUIDomainSampleVisitor.cpp
index 996aacc2258e04862450ec0f279676dad9e8d476..f1d6434977bd7e9f498b69cf0e7acf7348e5ca00 100644
--- a/GUI/coregui/Models/GUIDomainSampleVisitor.cpp
+++ b/GUI/coregui/Models/GUIDomainSampleVisitor.cpp
@@ -78,7 +78,7 @@ SessionItem* GUIDomainSampleVisitor::populateSampleModel(SampleModel* sampleMode
if (m_topSampleName.isEmpty())
m_topSampleName = sample.getName().c_str();
- for (const auto [child, depth, parent] : NodeUtils::progenyPlus(&sample)) {
+ for (const auto& [child, depth, parent] : NodeUtils::progenyPlus(&sample)) {
setDepth(depth + 1);
child->accept(this);
}
@@ -106,7 +106,7 @@ void GUIDomainSampleVisitor::visit(const Layer* sample) {
SessionItem* parent = m_levelToParentItem[depth() - 1];
ASSERT(parent);
- auto multilayer = dynamic_cast<const MultiLayer*>(m_itemToSample[parent]);
+ const auto* multilayer = dynamic_cast<const MultiLayer*>(m_itemToSample[parent]);
ASSERT(multilayer);
size_t layer_index = MultiLayerUtils::IndexOfLayer(*multilayer, sample);
const LayerInterface* top_interface =
diff --git a/Param/Node/NodeUtils.cpp b/Param/Node/NodeUtils.cpp
index 40e8adc60590e2385670e8512ac2e42c930d9f09..efac25fa51986a9d2f0cb0f133a1685e47cbd91a 100644
--- a/Param/Node/NodeUtils.cpp
+++ b/Param/Node/NodeUtils.cpp
@@ -59,12 +59,16 @@ std::string nodeString(const INode& node, int depth) {
}
} // namespace
+// ************************************************************************************************
+// namespace NodeUtils
+// ************************************************************************************************
+
std::vector<std::tuple<const INode*, int, const INode*>> NodeUtils::progenyPlus(const INode* node,
int level) {
std::vector<std::tuple<const INode*, int, const INode*>> result;
result.push_back({node, level, nullptr});
for (const auto* child : node->getChildren()) {
- for (const auto [subchild, sublevel, subparent] : progenyPlus(child, level + 1))
+ for (const auto& [subchild, sublevel, subparent] : progenyPlus(child, level + 1))
result.push_back({subchild, sublevel, child});
}
return result;
@@ -72,7 +76,7 @@ std::vector<std::tuple<const INode*, int, const INode*>> NodeUtils::progenyPlus(
std::string NodeUtils::nodeToString(const INode* node) {
std::ostringstream result;
- for (const auto [child, depth, parent] : progenyPlus(node))
+ for (const auto& [child, depth, parent] : progenyPlus(node))
result << nodeString(*child, depth);
return result.str();
}
diff --git a/Tests/Functional/Python/PyCore/CMakeLists.txt b/Tests/Functional/Python/PyCore/CMakeLists.txt
index 9d195c49ec556d2b9f26b5c25a5f7fb7dd0c69a6..ed485d869195f64871f6b7fbb27ed88ec86b39b1 100644
--- a/Tests/Functional/Python/PyCore/CMakeLists.txt
+++ b/Tests/Functional/Python/PyCore/CMakeLists.txt
@@ -5,18 +5,17 @@
set(OUTPUT_DIR ${TEST_OUTPUT_DIR_PY_CORE})
file(MAKE_DIRECTORY ${OUTPUT_DIR})
-file(GLOB sources RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*.py")
+file(GLOB tests RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*.py")
+list(REMOVE_ITEM tests utils.py)
if(NOT BORNAGAIN_TIFF_SUPPORT)
- list(REMOVE_ITEM sources "intensitydata_io_tiff.py")
+ list(REMOVE_ITEM tests "intensitydata_io_tiff.py")
endif()
-foreach(_src ${sources})
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${_src} ${OUTPUT_DIR}/${_src} @ONLY)
-endforeach()
-
-set(tests ${sources})
-list(REMOVE_ITEM tests utils.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/utils.py ${OUTPUT_DIR}/utils.py @ONLY)
foreach(_test ${tests})
- add_test(PyCore.${_test} ${Python3_EXECUTABLE} ${OUTPUT_DIR}/${_test})
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${_test} ${OUTPUT_DIR}/${_test} COPYONLY)
+ add_test(PyCore.${_test}
+ env PYTHONPATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
+ ${Python3_EXECUTABLE} ${OUTPUT_DIR}/${_test})
endforeach()
diff --git a/Tests/Functional/Python/PyCore/histogram2d.py b/Tests/Functional/Python/PyCore/histogram2d.py
index 84c639fe60acd65fa1b97763f04045b5aac12b9d..c9df823fc106c1d7ae2f36d2d6c95e1131af61fb 100644
--- a/Tests/Functional/Python/PyCore/histogram2d.py
+++ b/Tests/Functional/Python/PyCore/histogram2d.py
@@ -1,6 +1,4 @@
import numpy, os, sys, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyCore/intensitydata.py b/Tests/Functional/Python/PyCore/intensitydata.py
index bb6befd4d55f1ca540f9947c51480f6d899e7a58..e32620b5761b4456c2321d1fef2327618f7427ef 100644
--- a/Tests/Functional/Python/PyCore/intensitydata.py
+++ b/Tests/Functional/Python/PyCore/intensitydata.py
@@ -1,8 +1,6 @@
# Functional test: tests of IntensityData object
import numpy, os, sys, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyCore/intensitydata_io.py b/Tests/Functional/Python/PyCore/intensitydata_io.py
index f45b73ce23ba2440a47d18f09631a78a36d858c4..d11811068d2c1daa1e9d61dcc9abfda6fb6dba38 100644
--- a/Tests/Functional/Python/PyCore/intensitydata_io.py
+++ b/Tests/Functional/Python/PyCore/intensitydata_io.py
@@ -1,8 +1,6 @@
# Functional test: tests of IO operations with the IntensityData object
import math, numpy, os, sys, time, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
from bornagain import deg, deg2rad, rad2deg
diff --git a/Tests/Functional/Python/PyCore/intensitydata_io_tiff.py b/Tests/Functional/Python/PyCore/intensitydata_io_tiff.py
index 8ae1ad26bb573b3d8aa2cc250fc558bde0d78fa8..4b6e0f29ea8276f31dca5e720182f4d7b66aad09 100644
--- a/Tests/Functional/Python/PyCore/intensitydata_io_tiff.py
+++ b/Tests/Functional/Python/PyCore/intensitydata_io_tiff.py
@@ -1,8 +1,6 @@
# Functional test: tests of IO operations with the IntensityData object
import math, numpy, os, sys, time, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyCore/parameterpool.py b/Tests/Functional/Python/PyCore/parameterpool.py
index ca8d9d0252d1e16996bf01be127de90483996458..d61107d8fa06697b54d28a9354fbd02cf84b40db 100644
--- a/Tests/Functional/Python/PyCore/parameterpool.py
+++ b/Tests/Functional/Python/PyCore/parameterpool.py
@@ -1,6 +1,4 @@
import numpy, os, sys, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
from bornagain import nm
diff --git a/Tests/Functional/Python/PyCore/samplebuilder.py b/Tests/Functional/Python/PyCore/samplebuilder.py
index 35dd5ab702679a4a61ab97a7fb1deafd29efbe3d..a8628a3f00297a5e1b1a6eb86271849546ba1c85 100644
--- a/Tests/Functional/Python/PyCore/samplebuilder.py
+++ b/Tests/Functional/Python/PyCore/samplebuilder.py
@@ -1,7 +1,5 @@
import sys, unittest, ctypes
import inspect
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
initial_width = 42
diff --git a/Tests/Functional/Python/PyCore/shape2d.py b/Tests/Functional/Python/PyCore/shape2d.py
index ad92c8211c84231b1c32cead1c399fa953c1e4cf..794763c866023c585212b9d63a17d86795ad9937 100644
--- a/Tests/Functional/Python/PyCore/shape2d.py
+++ b/Tests/Functional/Python/PyCore/shape2d.py
@@ -1,6 +1,4 @@
import numpy, os, sys, unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyCore/utils.py b/Tests/Functional/Python/PyCore/utils.py
index e17bba8b0543e96a73f88200e09b3111cdee0d36..ab4ff98bd51404693bee29f870da72e4fd25e783 100644
--- a/Tests/Functional/Python/PyCore/utils.py
+++ b/Tests/Functional/Python/PyCore/utils.py
@@ -3,8 +3,6 @@ Collection of utils for testing
"""
import gzip, numpy, sys, os
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
from bornagain import deg, angstrom
@@ -42,39 +40,7 @@ def get_reference_data(filename):
os.path.join(REFERENCE_DIR, filename))
-def get_simulation_MiniGISAS(sample=None):
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(25, -2.0*deg, 2.0*deg, 25, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- if sample:
- simulation.setSample(sample)
- return simulation
-
-
-def get_simulation_BasicGISAS(sample=None):
- simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0.0*deg, 2.0*deg, 100, 0.0*deg,
- 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- if sample:
- simulation.setSample(sample)
- return simulation
-
-
-def plot_int(intensity):
- import matplotlib, pylab
- data = intensity.getArray() + 1
- # data = numpy.abs(intensity.getArray())
- phi_min = rad2deg(intensity.axis(0).lowerBound())
- phi_max = rad2deg(intensity.axis(0).upperBound())
- alpha_min = rad2deg(intensity.axis(1).lowerBound())
- alpha_max = rad2deg(intensity.axis(1).upperBound())
- im = pylab.imshow(data,
- norm=matplotlib.colors.LogNorm(),
- extent=[phi_min, phi_max, alpha_min, alpha_max])
- cb = pylab.colorbar(im)
- cb.set_label(r'Intensity (arb. u.)', size=16)
- pylab.xlabel(r'$\phi_f (^{\circ})$', fontsize=16)
- pylab.ylabel(r'$\alpha_f (^{\circ})$', fontsize=16)
- pylab.show()
+def get_simulation_MiniGISAS(sample):
+ detector = ba.SphericalDetector(25, -2*deg, 2*deg, 25, 0*deg, 2*deg)
+ beam = ba.Beam(1., 1*angstrom, ba.Direction(0.2*deg, 0))
+ return ba.GISASSimulation(beam, sample, detector)
diff --git a/Tests/Functional/Python/PyExamples/CMakeLists.txt b/Tests/Functional/Python/PyExamples/CMakeLists.txt
index d7ca6675cf1ce5092063db38b89be494bd52a20d..4b3c7629b4306187be94bbc3534dfdd47f5ed557 100644
--- a/Tests/Functional/Python/PyExamples/CMakeLists.txt
+++ b/Tests/Functional/Python/PyExamples/CMakeLists.txt
@@ -9,17 +9,21 @@ set(output_dir ${TEST_OUTPUT_DIR_PY_EXAMPLES})
file(MAKE_DIRECTORY ${output_dir})
file(GLOB sim_examples ${PY_EXAMPLES_DIR}/sim*/*.py)
-file(GLOB fit_examples
- ${PY_EXAMPLES_DIR}/fit55_Specular/FitSpecularBasics.py)
+if (WIN32)
+ # Convergence problem in Gauss-Kronrod integration
+ list(REMOVE_ITEM sim_examples ${PY_EXAMPLES_DIR}/sim03_Structures/Interference2DParaCrystal.py)
+endif()
+
+
+file(GLOB fit_examples ${PY_EXAMPLES_DIR}/fit55_Specular/FitSpecularBasics.py)
set(examples ${sim_examples} ${fit_examples})
-set(test_script ${output_dir}/check_functionality.py)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/check_functionality.in.py ${test_script} @ONLY)
+set(test_script ${TOOL_DIR}/code-tools/batch-plot.py)
foreach(example_path ${examples})
get_filename_component(example_name ${example_path} NAME_WE)
set(test_name PyExamples.${example_name})
-
- add_test(${test_name} ${Python3_EXECUTABLE} ${test_script} ${example_path})
- set_tests_properties(${test_name} PROPERTIES LABELS Fullcheck)
+ add_test(${test_name}
+ env PYTHONPATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
+ ${Python3_EXECUTABLE} ${test_script} -s ${example_path} ${output_dir})
endforeach()
diff --git a/Tests/Functional/Python/PyExamples/check_functionality.in.py b/Tests/Functional/Python/PyExamples/check_functionality.in.py
deleted file mode 100644
index c885bd9275a6d62f4e8a408c6449a5a44854217d..0000000000000000000000000000000000000000
--- a/Tests/Functional/Python/PyExamples/check_functionality.in.py
+++ /dev/null
@@ -1,83 +0,0 @@
-"""
-Usage: python check_functionality.py <path-to-example>/<example>.py
-
-Checks functionality of BornAgain Python example by running it in 'embedded' way.
-
-The check passes successfully if the example runs without exceptions thrown and
-generates non-zero-size intensity image.
-"""
-
-import sys
-import os
-import matplotlib
-matplotlib.use('Agg')
-from matplotlib import pyplot as plt
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
-
-output_dir = "@output_dir@"
-
-
-def get_figure(filename):
- """
- Returns pyplot figure of appropriate size
- """
- if "AllFormFactorsAvailable" in filename:
- xsize, ysize = 1024, 768
- else:
- xsize, ysize = 640, 480
-
- dpi = 72.
- return plt.figure(figsize=(xsize/dpi, ysize/dpi))
-
-
-def exec_full(filepath):
- """
- Executes embedded python script.
- http://stackoverflow.com/questions/436198/what-is-an-alternative-to-execfile-in-python-3
- """
- import os
- global_namespace = {
- "__file__": filepath,
- "__name__": "__main__",
- "__no_terminal__": True
- }
- sys.argv = [] # TODO: FIXME after cleanup in plot_utils
- with open(filepath, 'rb') as file:
- exec(compile(file.read(), filepath, 'exec'), global_namespace)
-
-
-def run_example(filename):
- """
- Tries to run python example and produce a *.png image
- """
- if not os.path.exists(filename):
- raise Exception("Example script '" + filename + "' not found")
-
- 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,
- os.path.splitext(os.path.basename(filename))[0] + ".png")
- print("Output image: " + plot_file_name)
- plt.savefig(plot_file_name, bbox_inches='tight')
- plt.close(fig)
-
- imgSize = os.path.getsize(plot_file_name)
- if imgSize == 0:
- raise Exception("Image file is empty")
- if imgSize < 20000:
- raise Exception("Image file is unplausibly small")
-
-
-if __name__ == '__main__':
-
- if len(sys.argv) != 2:
- exit("check_functionality called with wrong number of arguments")
-
- run_example(sys.argv[1])
diff --git a/Tests/Functional/Python/PyFit/CMakeLists.txt b/Tests/Functional/Python/PyFit/CMakeLists.txt
index 81bed49f6c36ba321380085defc919750db1ee14..133fcae57fa9671cad5d9c457779428153694d90 100644
--- a/Tests/Functional/Python/PyFit/CMakeLists.txt
+++ b/Tests/Functional/Python/PyFit/CMakeLists.txt
@@ -5,18 +5,11 @@
set(output_dir ${TEST_OUTPUT_DIR_PY_FIT})
file(MAKE_DIRECTORY ${output_dir})
-file(GLOB sources RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*.py")
-foreach(_src ${sources})
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${_src}
- ${output_dir}/${_src} @ONLY)
-endforeach()
-
-set(tests
- "minimizer_api.py"
- "standalone_fits.py"
- "fitobjective_api.py"
-)
+file(GLOB tests RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*.py")
foreach(_test ${tests})
- add_test(PyFit.${_test} ${Python3_EXECUTABLE} ${output_dir}/${_test})
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${_test} ${output_dir}/${_test} COPYONLY)
+ add_test(PyFit.${_test}
+ env PYTHONPATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
+ ${Python3_EXECUTABLE} ${output_dir}/${_test})
endforeach()
diff --git a/Tests/Functional/Python/PyFit/README.md b/Tests/Functional/Python/PyFit/README.md
index 4221b4ca37838d42966e620b79ff078351be72bc..003cc60e8a4647cc10ded63f04bfe8ca8b62b7fb 100644
--- a/Tests/Functional/Python/PyFit/README.md
+++ b/Tests/Functional/Python/PyFit/README.md
@@ -1,4 +1,4 @@
-Collection of functional tests (Python)
+## Functional tests of libBornAgainFit
Collection of fitting tests for libBornAgainFit library.
Different geometries, number of fit parameters, variety
diff --git a/Tests/Functional/Python/PyFit/fitobjective_api.py b/Tests/Functional/Python/PyFit/fitobjective_api.py
index bdd91ddca2e7ec69241060340d955282abd73ecf..27ebf571de6cc73fdfd4f2e160efe1f58c15cf39 100644
--- a/Tests/Functional/Python/PyFit/fitobjective_api.py
+++ b/Tests/Functional/Python/PyFit/fitobjective_api.py
@@ -5,8 +5,6 @@ import sys
import os
import unittest
import numpy as np
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyFit/minimizer_api.py b/Tests/Functional/Python/PyFit/minimizer_api.py
index 8eabce41be48ae779115c228a7f641801afda22e..ee5bbe4d0136bfb16bf6743e7823bd24317a4f6b 100644
--- a/Tests/Functional/Python/PyFit/minimizer_api.py
+++ b/Tests/Functional/Python/PyFit/minimizer_api.py
@@ -4,8 +4,6 @@ Testing python specific API for Minimizer related classes.
import sys
import os
import unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
diff --git a/Tests/Functional/Python/PyFit/standalone_fits.py b/Tests/Functional/Python/PyFit/standalone_fits.py
index 53f8ff1b39c06af1a76c29189d69cd6ac411e301..e3518b757cac750dc8047eafa1643a1f736fccd8 100644
--- a/Tests/Functional/Python/PyFit/standalone_fits.py
+++ b/Tests/Functional/Python/PyFit/standalone_fits.py
@@ -4,8 +4,6 @@ Fitting scalar and residual based objective functions
import sys
import os
import unittest
-
-sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
import numpy as np
diff --git a/Tests/Functional/Python/PyPersistence/CMakeLists.txt b/Tests/Functional/Python/PyPersistence/CMakeLists.txt
index c1960ad2c3ccd6d2911a54c5d0c6ccb4df7eef34..00a6defb321078447d52915d3704023abf0c6e5e 100644
--- a/Tests/Functional/Python/PyPersistence/CMakeLists.txt
+++ b/Tests/Functional/Python/PyPersistence/CMakeLists.txt
@@ -66,6 +66,6 @@ test_example(sim21_Reflectometry/BeamFullDivergence 2e-10)
test_example(sim21_Reflectometry/TimeOfFlightReflectometry 2e-10)
test_example(sim21_Reflectometry/TOFRWithResolution 2e-10)
-test_example(sim29_DepthProbe/DepthProbe 2e-10)
+test_example(special40_DepthProbe/DepthProbe 2e-10)
test_example(sim31_Parameterization/SimulationParameters 2e-10)
diff --git a/Wrap/Python/__init__.py.in b/Wrap/Python/__init__.py.in
index 8f8981f68c44978a9ad9aeb6d45f71a0be7fb53b..4e140ee7f8c7afa03e057ed91f5e803c016525fe 100644
--- a/Wrap/Python/__init__.py.in
+++ b/Wrap/Python/__init__.py.in
@@ -26,3 +26,4 @@ from libBornAgainCore import *
# To prevent inclusion of plotting tools during functional tests:
if not "NOPLOT" in os.environ:
from .plot_utils import *
+ import fit_monitor
diff --git a/Wrap/Python/fit_monitor.py b/Wrap/Python/fit_monitor.py
new file mode 100644
index 0000000000000000000000000000000000000000..3496dced8aee3257f470ace6f90663669ccef2bb
--- /dev/null
+++ b/Wrap/Python/fit_monitor.py
@@ -0,0 +1,258 @@
+# ************************************************************************** #
+"""
+# BornAgain: simulate and fit scattering at grazing incidence
+#
+# @file Wrap/Python/fit_monitor.py
+# @brief Plotter classes for monitoring fit progress.
+#
+# @homepage http://apps.jcns.fz-juelich.de/BornAgain
+# @license GNU General Public License v3 or higher (see COPYING)
+# @copyright Forschungszentrum Juelich GmbH 2019
+# @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
+"""
+# ************************************************************************** #
+
+import bornagain as ba
+try: # workaround for build servers
+ import numpy as np
+ from matplotlib import pyplot as plt
+ from matplotlib import gridspec, colors
+except Exception as e:
+ print("In plot_utils.py: {:s}".format(str(e)))
+
+label_fontsize = 16
+
+class Plotter:
+ """
+ Draws fit progress. Base class for simulation-specific classes (PlotterGISAS etc).
+ """
+ def __init__(self,
+ zmin=None,
+ zmax=None,
+ xlabel=None,
+ ylabel=None,
+ units=ba.Axes.DEFAULT,
+ aspect=None):
+
+ self._fig = plt.figure(figsize=(10.25, 7.69))
+ self._fig.canvas.draw()
+ self._zmin = zmin
+ self._zmax = zmax
+ self._xlabel = xlabel
+ self._ylabel = ylabel
+ self._units = units
+ self._aspect = aspect
+
+ def reset(self):
+ self._fig.clf()
+
+ def plot(self):
+ self._fig.tight_layout()
+ plt.pause(0.03)
+
+
+class PlotterGISAS(Plotter):
+ """
+ Draws fit progress, for GISAS simulation.
+ """
+ def __init__(self,
+ zmin=None,
+ zmax=None,
+ xlabel=None,
+ ylabel=None,
+ units=ba.Axes.DEFAULT,
+ aspect=None):
+ Plotter.__init__(self, zmin, zmax, xlabel, ylabel, units, aspect)
+
+ @staticmethod
+ def make_subplot(nplot):
+ plt.subplot(2, 2, nplot)
+ plt.subplots_adjust(wspace=0.2, hspace=0.2)
+
+ def plot(self, fit_objective):
+ Plotter.reset(self)
+
+ real_data = fit_objective.experimentalData()
+ sim_data = fit_objective.simulationResult()
+ diff = fit_objective.absoluteDifference()
+
+ self.make_subplot(1)
+
+ # same limits for both plots
+ arr = real_data.array()
+ zmax = np.amax(arr) if self._zmax is None else self._zmax
+ zmin = zmax*1e-6 if self._zmin is None else self._zmin
+
+ ba.plot_colormap(real_data,
+ title="Experimental data",
+ zmin=zmin,
+ zmax=zmax,
+ units=self._units,
+ xlabel=self._xlabel,
+ ylabel=self._ylabel,
+ zlabel='',
+ aspect=self._aspect)
+
+ self.make_subplot(2)
+ ba.plot_colormap(sim_data,
+ title="Simulated data",
+ zmin=zmin,
+ zmax=zmax,
+ units=self._units,
+ xlabel=self._xlabel,
+ ylabel=self._ylabel,
+ zlabel='',
+ aspect=self._aspect)
+
+ self.make_subplot(3)
+ ba.plot_colormap(diff,
+ title="Difference",
+ zmin=zmin,
+ zmax=zmax,
+ units=self._units,
+ xlabel=self._xlabel,
+ ylabel=self._ylabel,
+ zlabel='',
+ aspect=self._aspect)
+
+ self.make_subplot(4)
+ plt.title('Parameters')
+ plt.axis('off')
+
+ iteration_info = fit_objective.iterationInfo()
+
+ plt.text(
+ 0.01, 0.85,
+ "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
+ plt.text(0.01, 0.75,
+ "Chi2 " + '{:8.4f}'.format(iteration_info.chi2()))
+ index = 0
+ params = iteration_info.parameterMap()
+ for key in params:
+ plt.text(0.01, 0.55 - index*0.1,
+ '{:30.30s}: {:6.3f}'.format(key, params[key]))
+ index = index + 1
+
+ Plotter.plot(self)
+
+
+class PlotterSpecular(Plotter):
+ """
+ Draws fit progress, for specular simulation.
+ """
+ def __init__(self, units=ba.Axes.DEFAULT):
+ Plotter.__init__(self)
+ self.gs = gridspec.GridSpec(1, 2, width_ratios=[2.5, 1], wspace=0)
+ self.units = units
+
+ def __call__(self, fit_objective):
+ self.plot(fit_objective)
+
+ @staticmethod
+ def as_si(val, ndp):
+ """
+ Fancy print of scientific-formatted values
+ :param val: numeric value
+ :param ndp: number of decimal digits to print
+ :return: a string corresponding to the _val_
+ """
+ s = '{x:0.{ndp:d}e}'.format(x=val, ndp=ndp)
+ m, e = s.split('e')
+ return r'{m:s}\times 10^{{{e:d}}}'.format(m=m, e=int(e))
+
+ @staticmethod
+ def trunc_str(token, length):
+ """
+ Truncates token if it is longer than length.
+
+ Example:
+ trunc_str("123456789", 8) returns "123456.."
+
+ trunc_str("123456789", 9) returns "123456789"
+
+ :param token: input string
+ :param length: max non-truncated length
+ :return:
+ """
+ return (token[:length - 2] + '..') if len(token) > length else token
+
+ def plot_table(self, fit_objective):
+
+ iteration_info = fit_objective.iterationInfo()
+
+ trunc_length = 9 # max string field width in the table
+ n_digits = 1 # number of decimal digits to print
+
+ n_iterations = iteration_info.iterationCount(
+ ) # current number of iterations passed
+ rel_dif = fit_objective.relativeDifference().array().max(
+ ) # maximum relative difference
+ fitted_parameters = iteration_info.parameterMap()
+
+ # creating table content
+ labels = ("Parameter", "Value")
+ table_data = [["Iteration", '${:d}$'.format(n_iterations)],
+ [
+ "$d_{r, max}$",
+ '${:s}$'.format(self.as_si(rel_dif, n_digits))
+ ]]
+ for key, value in fitted_parameters.iteritems():
+ table_data.append([
+ '{:s}'.format(self.trunc_str(key, trunc_length)),
+ '${:s}$'.format(self.as_si(value, n_digits))
+ ])
+
+ # creating table
+ axs = plt.subplot(self.gs[1])
+ axs.axis('tight')
+ axs.axis('off')
+ table = plt.table(cellText=table_data,
+ colLabels=labels,
+ cellLoc='center',
+ loc='bottom left',
+ bbox=[0.0, 0.0, 1.0, 1.0])
+
+ def plot_graph(self, fit_objective):
+ # retrieving data from fit suite
+ real_data = fit_objective.experimentalData()
+ sim_data = fit_objective.simulationResult()
+ unc_data = fit_objective.uncertaintyData()
+
+ # data values
+ sim_values = sim_data.array(self.units)
+ real_values = real_data.array(self.units)
+ unc_values = None if unc_data is None else unc_data.array(self.units)
+
+ # default font properties dictionary to use
+ font = {'family': 'serif', 'weight': 'normal', 'size': label_fontsize}
+
+ plt.subplot(self.gs[0])
+ plt.semilogy(sim_data.axis(), sim_values, 'b', real_data.axis(),
+ real_values, 'k--')
+ if unc_values is not None:
+ plt.semilogy(real_data.axis(),
+ real_values - unc_values,
+ 'xkcd:grey',
+ alpha=0.6)
+ plt.semilogy(real_data.axis(),
+ real_values + unc_values,
+ 'xkcd:grey',
+ alpha=0.6)
+ plt.ylim((0.5*np.min(real_values), 5*np.max(real_values)))
+
+ xlabel = ba.plot_utils.get_axes_labels(real_data, self.units)[0]
+ legend = ['BornAgain', 'Data']
+ if unc_values is not None:
+ legend = ['BornAgain', 'Data', r'Data $\pm \sigma$']
+ plt.legend(legend, loc='upper right', prop=font)
+ plt.xlabel(xlabel, fontdict=font)
+ plt.ylabel("Intensity", fontdict=font)
+ plt.title("Specular data fitting", fontdict=font)
+
+ def plot(self, fit_objective):
+ Plotter.reset(self)
+
+ self.plot_graph(fit_objective)
+ self.plot_table(fit_objective)
+
+ Plotter.plot(self)
diff --git a/Wrap/Python/plot_utils.py b/Wrap/Python/plot_utils.py
index a19327dd31162e29775f5b03ccab21356e61d642..6b569d757f72ee5de8ad7934d57b9876cfc1a151 100644
--- a/Wrap/Python/plot_utils.py
+++ b/Wrap/Python/plot_utils.py
@@ -2,14 +2,13 @@
"""
# BornAgain: simulate and fit scattering at grazing incidence
#
-# @file Wrap/Python.plot_utils
+# @file Wrap/Python/plot_utils.py
# @brief Python extensions of the SWIG-generated Python module bornagain.
#
# @homepage http://apps.jcns.fz-juelich.de/BornAgain
# @license GNU General Public License v3 or higher (see COPYING)
# @copyright Forschungszentrum Juelich GmbH 2016
-# @authors Scientific Computing Group at MLZ Garching
-# @authors J. Fisher, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+# @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
"""
# ************************************************************************** #
@@ -48,19 +47,19 @@ def translate_axis_label(label):
"""
label_dict = {
'X [nbins]': r'$X \; $(bins)',
+ 'X [mm]': r'$X \; $(mm)',
+ 'Y [nbins]': r'$Y \; $(bins)',
+ 'Y [mm]': r'$Y \; $(mm)',
'phi_f [rad]': r'$\varphi_f \; $(rad)',
'phi_f [deg]': r'$\varphi_f \; $(deg)',
'alpha_i [rad]': r'$\alpha_i \; $(rad)',
'alpha_i [deg]': r'$\alpha_i \; $(deg)',
- 'X [mm]': r'$X \; $(mm)',
- 'Qx [1/nm]': r'$Q_x \; $(nm$^{-1}$)',
- 'Qy [1/nm]': r'$Q_y \; $(nm$^{-1}$)',
- 'Q [1/nm]': r'$Q \; $(nm$^{-1}$)',
- 'Y [nbins]': r'$Y \; $(bins)',
'alpha_f [rad]': r'$\alpha_f \; $(rad)',
'alpha_f [deg]': r'$\alpha_f \; $(deg)',
- 'Y [mm]': r'$Y \; $(mm)',
+ 'Qx [1/nm]': r'$Q_x \; $(nm$^{-1}$)',
+ 'Qy [1/nm]': r'$Q_y \; $(nm$^{-1}$)',
'Qz [1/nm]': r'$Q_z \; $(nm$^{-1}$)',
+ 'Q [1/nm]': r'$Q \; $(nm$^{-1}$)',
'Position [nm]': r'$Position \; $(nm)'
}
if label in label_dict.keys():
@@ -85,38 +84,32 @@ def get_axes_labels(result, units):
return labels
-def plot_array(array,
- zmin=None,
- zmax=None,
- xlabel=None,
- ylabel=None,
- zlabel=None,
- title=None,
- axes_limits=None,
- **kwargs):
+def plot_array(array, axes_limits=None, **kwargs):
"""
Plots numpy array as a colormap in log scale.
"""
- zlabel = "Intensity" if zlabel is None else zlabel
-
- zmax = np.amax(array) if zmax is None else zmax
- zmin = 1e-6*zmax if zmin is None else zmin
+ zmax = kwargs.pop('intensity_max', np.amax(array))
+ zmin = kwargs.pop('intensity_min', 1e-6*zmax)
if zmin == zmax == 0.0:
norm = colors.Normalize(0, 1)
else:
norm = colors.LogNorm(zmin, zmax)
+ xlabel = kwargs.pop('xlabel', None)
+ ylabel = kwargs.pop('ylabel', None)
+ zlabel = kwargs.pop('zlabel', "Intensity")
+
+ title = kwargs.pop('title', None)
+
im = plt.imshow(array, norm=norm, extent=axes_limits, **kwargs)
cb = plt.colorbar(im, pad=0.025)
if xlabel:
plt.xlabel(xlabel, fontsize=label_fontsize)
-
if ylabel:
plt.ylabel(ylabel, fontsize=label_fontsize)
-
if zlabel:
cb.set_label(zlabel, size=label_fontsize)
@@ -124,14 +117,7 @@ def plot_array(array,
plt.title(title)
-def plot_histogram(hist,
- zmin=None,
- zmax=None,
- xlabel=None,
- ylabel=None,
- zlabel=None,
- title=None,
- **kwargs):
+def plot_histogram(hist, **kwargs):
"""
Plots intensity data as color map
:param intensity: Histogram2D object obtained from GISASSimulation
@@ -139,11 +125,10 @@ def plot_histogram(hist,
:param zmax: Max value on amplitude's color bar
"""
- if not xlabel:
- xlabel = translate_axis_label(hist.xAxis().getName())
-
- if not ylabel:
- ylabel = translate_axis_label(hist.yAxis().getName())
+ if not 'xlabel' in kwargs:
+ kwargs['xlabel'] = translate_axis_label(hist.xAxis().getName())
+ if not 'ylabel' in kwargs:
+ kwargs['ylabel'] = translate_axis_label(hist.yAxis().getName())
axes_limits = [
hist.getXmin(),
@@ -152,26 +137,12 @@ def plot_histogram(hist,
hist.getYmax()
]
- plot_array(hist.array(),
- zmin=zmin,
- zmax=zmax,
- xlabel=xlabel,
- ylabel=ylabel,
- zlabel=zlabel,
- title=title,
- axes_limits=axes_limits,
- **kwargs)
-
-
-def plot_colormap(result,
- zmin=None,
- zmax=None,
- units=ba.Axes.DEFAULT,
- xlabel=None,
- ylabel=None,
- zlabel=None,
- title=None,
- **kwargs):
+ title = kwargs.pop('title', None)
+
+ plot_array(hist.array(), title=title, axes_limits=axes_limits, **kwargs)
+
+
+def plot_colormap(result, **kwargs):
"""
Plots intensity data as color map
:param result: SimulationResult from GISAS/OffSpecSimulation
@@ -179,30 +150,19 @@ def plot_colormap(result,
:param zmax: Max value on amplitude's color bar
"""
+ units = kwargs.pop('units', ba.Axes.DEFAULT)
axes_limits = get_axes_limits(result, units)
axes_labels = get_axes_labels(result, units)
- xlabel = axes_labels[0] if xlabel is None else xlabel
- ylabel = axes_labels[1] if ylabel is None else ylabel
-
- plot_array(result.array(),
- zmin=zmin,
- zmax=zmax,
- xlabel=xlabel,
- ylabel=ylabel,
- zlabel=zlabel,
- title=title,
- axes_limits=axes_limits,
- **kwargs)
-
-
-def plot_specular_simulation_result(result,
- ymin=None,
- ymax=None,
- units=ba.Axes.DEFAULT,
- xlabel=None,
- ylabel=None,
- title=None,
- **kwargs):
+
+ if not 'xlabel' in kwargs:
+ kwargs['xlabel'] = axes_labels[0]
+ if not 'ylabel' in kwargs:
+ kwargs['ylabel'] = axes_labels[1]
+
+ plot_array(result.array(), axes_limits=axes_limits, **kwargs)
+
+
+def plot_specular_simulation_result(result, **kwargs):
"""
Plots intensity data for specular simulation result
:param result: SimulationResult from SpecularSimulation
@@ -211,13 +171,16 @@ def plot_specular_simulation_result(result,
:param units: units on the x-axis
"""
+ units = kwargs.pop('units', ba.Axes.DEFAULT)
intensity = result.array(units)
x_axis = result.axis(units)
- ymax = np.amax(intensity)*2.0 if ymax is None else ymax
- ymin = max(np.amin(intensity)*0.5, 1e-18*ymax) if ymin is None else ymin
- xlabel = get_axes_labels(result, units)[0] if xlabel is None else xlabel
- ylabel = "Intensity" if ylabel is None else ylabel
+ ymax = kwargs.pop('intensity_max', np.amax(np.amax(intensity)*2))
+ ymin = kwargs.pop('intensity_min', max(np.amin(intensity)*0.5, 1e-18*ymax))
+
+ xlabel = kwargs.pop('xlabel', get_axes_labels(result, units)[0])
+ ylabel = kwargs.pop('ylabel', "Intensity")
+ title = kwargs.pop('title', None)
plt.semilogy(x_axis, intensity, **kwargs)
@@ -225,7 +188,6 @@ def plot_specular_simulation_result(result,
if xlabel:
plt.xlabel(xlabel, fontsize=label_fontsize)
-
if ylabel:
plt.ylabel(ylabel, fontsize=label_fontsize)
@@ -233,15 +195,7 @@ def plot_specular_simulation_result(result,
plt.title(title)
-def plot_simulation_result(result,
- intensity_min=None,
- intensity_max=None,
- units=ba.Axes.DEFAULT,
- xlabel=None,
- ylabel=None,
- postpone_show=False,
- title=None,
- **kwargs):
+def plot_simulation_result(result, **kwargs):
"""
Draws simulation result and (optionally) shows the plot.
:param result_: SimulationResult object obtained from GISAS/OffSpec/SpecularSimulation
@@ -250,249 +204,12 @@ def plot_simulation_result(result,
:param units: units for plot axes
:param postpone_show: postpone showing the plot for later tuning (False by default)
"""
+ postpone_show = kwargs.pop('postpone_show', False)
+
if len(result.array().shape) == 1: # 1D data, specular simulation assumed
- plot_specular_simulation_result(result, intensity_min, intensity_max,
- units, **kwargs)
+ plot_specular_simulation_result(result, **kwargs)
else:
- plot_colormap(result,
- intensity_min,
- intensity_max,
- units,
- xlabel,
- ylabel,
- title=title,
- **kwargs)
+ plot_colormap(result, **kwargs)
plt.tight_layout()
- if not postpone_show:
+ if not (postpone_show):
plt.show()
-
-
-class Plotter:
- def __init__(self,
- zmin=None,
- zmax=None,
- xlabel=None,
- ylabel=None,
- units=ba.Axes.DEFAULT,
- aspect=None):
-
- self._fig = plt.figure(figsize=(10.25, 7.69))
- self._fig.canvas.draw()
- self._zmin = zmin
- self._zmax = zmax
- self._xlabel = xlabel
- self._ylabel = ylabel
- self._units = units
- self._aspect = aspect
-
- def reset(self):
- self._fig.clf()
-
- def plot(self):
- self._fig.tight_layout()
- plt.pause(0.03)
-
-
-class PlotterGISAS(Plotter):
- def __init__(self,
- zmin=None,
- zmax=None,
- xlabel=None,
- ylabel=None,
- units=ba.Axes.DEFAULT,
- aspect=None):
- Plotter.__init__(self, zmin, zmax, xlabel, ylabel, units, aspect)
-
- @staticmethod
- def make_subplot(nplot):
- plt.subplot(2, 2, nplot)
- plt.subplots_adjust(wspace=0.2, hspace=0.2)
-
- def plot(self, fit_objective):
- Plotter.reset(self)
-
- real_data = fit_objective.experimentalData()
- sim_data = fit_objective.simulationResult()
- diff = fit_objective.absoluteDifference()
-
- self.make_subplot(1)
-
- # same limits for both plots
- arr = real_data.array()
- zmax = np.amax(arr) if self._zmax is None else self._zmax
- zmin = zmax*1e-6 if self._zmin is None else self._zmin
-
- ba.plot_colormap(real_data,
- title="Experimental data",
- zmin=zmin,
- zmax=zmax,
- units=self._units,
- xlabel=self._xlabel,
- ylabel=self._ylabel,
- zlabel='',
- aspect=self._aspect)
-
- self.make_subplot(2)
- ba.plot_colormap(sim_data,
- title="Simulated data",
- zmin=zmin,
- zmax=zmax,
- units=self._units,
- xlabel=self._xlabel,
- ylabel=self._ylabel,
- zlabel='',
- aspect=self._aspect)
-
- self.make_subplot(3)
- ba.plot_colormap(diff,
- title="Difference",
- zmin=zmin,
- zmax=zmax,
- units=self._units,
- xlabel=self._xlabel,
- ylabel=self._ylabel,
- zlabel='',
- aspect=self._aspect)
-
- self.make_subplot(4)
- plt.title('Parameters')
- plt.axis('off')
-
- iteration_info = fit_objective.iterationInfo()
-
- plt.text(
- 0.01, 0.85,
- "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
- plt.text(0.01, 0.75,
- "Chi2 " + '{:8.4f}'.format(iteration_info.chi2()))
- index = 0
- params = iteration_info.parameterMap()
- for key in params:
- plt.text(0.01, 0.55 - index*0.1,
- '{:30.30s}: {:6.3f}'.format(key, params[key]))
- index = index + 1
-
- Plotter.plot(self)
-
-
-class PlotterSpecular(Plotter):
- """
- Draws fit progress. Intended specifically for observing
- specular data fit.
- """
- def __init__(self, units=ba.Axes.DEFAULT):
- Plotter.__init__(self)
- self.gs = gridspec.GridSpec(1, 2, width_ratios=[2.5, 1], wspace=0)
- self.units = units
-
- def __call__(self, fit_objective):
- self.plot(fit_objective)
-
- @staticmethod
- def as_si(val, ndp):
- """
- Fancy print of scientific-formatted values
- :param val: numeric value
- :param ndp: number of decimal digits to print
- :return: a string corresponding to the _val_
- """
- s = '{x:0.{ndp:d}e}'.format(x=val, ndp=ndp)
- m, e = s.split('e')
- return r'{m:s}\times 10^{{{e:d}}}'.format(m=m, e=int(e))
-
- @staticmethod
- def trunc_str(token, length):
- """
- Truncates token if it is longer than length.
-
- Example:
- trunc_str("123456789", 8) returns "123456.."
-
- trunc_str("123456789", 9) returns "123456789"
-
- :param token: input string
- :param length: max non-truncated length
- :return:
- """
- return (token[:length - 2] + '..') if len(token) > length else token
-
- def plot_table(self, fit_objective):
-
- iteration_info = fit_objective.iterationInfo()
-
- trunc_length = 9 # max string field width in the table
- n_digits = 1 # number of decimal digits to print
-
- n_iterations = iteration_info.iterationCount(
- ) # current number of iterations passed
- rel_dif = fit_objective.relativeDifference().array().max(
- ) # maximum relative difference
- fitted_parameters = iteration_info.parameterMap()
-
- # creating table content
- labels = ("Parameter", "Value")
- table_data = [["Iteration", '${:d}$'.format(n_iterations)],
- [
- "$d_{r, max}$",
- '${:s}$'.format(self.as_si(rel_dif, n_digits))
- ]]
- for key, value in fitted_parameters.iteritems():
- table_data.append([
- '{:s}'.format(self.trunc_str(key, trunc_length)),
- '${:s}$'.format(self.as_si(value, n_digits))
- ])
-
- # creating table
- axs = plt.subplot(self.gs[1])
- axs.axis('tight')
- axs.axis('off')
- table = plt.table(cellText=table_data,
- colLabels=labels,
- cellLoc='center',
- loc='bottom left',
- bbox=[0.0, 0.0, 1.0, 1.0])
-
- def plot_graph(self, fit_objective):
- # retrieving data from fit suite
- real_data = fit_objective.experimentalData()
- sim_data = fit_objective.simulationResult()
- unc_data = fit_objective.uncertaintyData()
-
- # data values
- sim_values = sim_data.array(self.units)
- real_values = real_data.array(self.units)
- unc_values = None if unc_data is None else unc_data.array(self.units)
-
- # default font properties dictionary to use
- font = {'family': 'serif', 'weight': 'normal', 'size': label_fontsize}
-
- plt.subplot(self.gs[0])
- plt.semilogy(sim_data.axis(), sim_values, 'b', real_data.axis(),
- real_values, 'k--')
- if unc_values is not None:
- plt.semilogy(real_data.axis(),
- real_values - unc_values,
- 'xkcd:grey',
- alpha=0.6)
- plt.semilogy(real_data.axis(),
- real_values + unc_values,
- 'xkcd:grey',
- alpha=0.6)
- plt.ylim((0.5*np.min(real_values), 5*np.max(real_values)))
-
- xlabel = get_axes_labels(real_data, self.units)[0]
- legend = ['BornAgain', 'Data']
- if unc_values is not None:
- legend = ['BornAgain', 'Data', r'Data $\pm \sigma$']
- plt.legend(legend, loc='upper right', prop=font)
- plt.xlabel(xlabel, fontdict=font)
- plt.ylabel("Intensity", fontdict=font)
- plt.title("Specular data fitting", fontdict=font)
-
- def plot(self, fit_objective):
- Plotter.reset(self)
-
- self.plot_graph(fit_objective)
- self.plot_table(fit_objective)
-
- Plotter.plot(self)
diff --git a/Wrap/Swig/libBornAgainCore.i b/Wrap/Swig/libBornAgainCore.i
index e3c40850623c75f4a0758465c2c0df1a6036f1a1..69114fd852ee5a329f8089a88f44df97c4548639 100644
--- a/Wrap/Swig/libBornAgainCore.i
+++ b/Wrap/Swig/libBornAgainCore.i
@@ -26,6 +26,8 @@
%ignore ISpecularScan;
+%import(module="libBornAgainFit") ""
+
%rename(setSampleBuilderCpp) ISimulation::setSampleBuilder;
%rename(setSampleBuilderCpp) SpecularSimulation::setSampleBuilder;
%rename(addSimulationAndData_cpp) FitObjective::addSimulationAndData;
diff --git a/auto/Wrap/doxygenBase.i b/auto/Wrap/doxygenBase.i
index a28a5913a953f0be27a10e9cce37c1cd665433e3..b9bb4d6f0f66217816bb62387d10017d5bda3046 100644
--- a/auto/Wrap/doxygenBase.i
+++ b/auto/Wrap/doxygenBase.i
@@ -550,6 +550,11 @@ Returns value of last point of axis.
Returns distance from first to last point.
";
+%feature("docstring") IAxis::center "double IAxis::center() const
+
+Returns midpoint of axis.
+";
+
%feature("docstring") IAxis::binCenter "virtual double IAxis::binCenter(size_t index) const =0
";
diff --git a/auto/Wrap/doxygenDevice.i b/auto/Wrap/doxygenDevice.i
index 4d751daeffaf49b8043aa92fd57989ff7c7316f2..c1a20b8f1ca65a87e951a4fdea27fb9a59aaf111 100644
--- a/auto/Wrap/doxygenDevice.i
+++ b/auto/Wrap/doxygenDevice.i
@@ -2850,6 +2850,26 @@ alpha_max:
upper edge of last alpha-bin
";
+%feature("docstring") SphericalDetector::SphericalDetector "SphericalDetector::SphericalDetector(size_t n_bin, double width, double phi, double alpha)
+
+Spherical detector constructor with quadratic angle ranges
+
+Parameters:
+-----------
+
+n_bin:
+number of bins per direction
+
+width:
+angular width
+
+phi:
+central phi angle
+
+alpha:
+central alpha angle
+";
+
%feature("docstring") SphericalDetector::SphericalDetector "SphericalDetector::SphericalDetector(const SphericalDetector &other)
";
@@ -3003,16 +3023,16 @@ Returns true if area defined by two bins is inside or on border of polygon (more
// File: classConvolve_1_1Workspace.xml
-// File: namespace_0d105.xml
+// File: namespace_0d107.xml
-// File: namespace_0d33.xml
+// File: namespace_0d35.xml
-// File: namespace_0d56.xml
+// File: namespace_0d58.xml
-// File: namespace_0d62.xml
+// File: namespace_0d64.xml
// File: namespaceArrayUtils.xml
@@ -3126,6 +3146,11 @@ Parse double values from string to vector of double.
";
+// File: namespaceDetectorUtils.xml
+%feature("docstring") DetectorUtils::isQuadratic "bool DetectorUtils::isQuadratic(const IDetector2D &det)
+";
+
+
// File: namespaceIntensityDataFunctions.xml
%feature("docstring") IntensityDataFunctions::RelativeDifference "double IntensityDataFunctions::RelativeDifference(const SimulationResult &dat, const SimulationResult &ref)
@@ -3287,6 +3312,12 @@ make Swappable
// File: DetectorMask_8h.xml
+// File: DetectorUtils_8cpp.xml
+
+
+// File: DetectorUtils_8h.xml
+
+
// File: IDetector_8cpp.xml
diff --git a/auto/Wrap/libBornAgainBase.py b/auto/Wrap/libBornAgainBase.py
index 4248754550195b1ef42c9afee34922900443535d..42bc36a22441656ddad66f52c1772fc53170097f 100644
--- a/auto/Wrap/libBornAgainBase.py
+++ b/auto/Wrap/libBornAgainBase.py
@@ -2109,6 +2109,16 @@ class IAxis(object):
"""
return _libBornAgainBase.IAxis_span(self)
+ def center(self):
+ r"""
+ center(IAxis self) -> double
+ double IAxis::center() const
+
+ Returns midpoint of axis.
+
+ """
+ return _libBornAgainBase.IAxis_center(self)
+
def binCenter(self, index):
r"""
binCenter(IAxis self, size_t index) -> double
diff --git a/auto/Wrap/libBornAgainBase_wrap.cpp b/auto/Wrap/libBornAgainBase_wrap.cpp
index 20b8fd3b0156933b34560c4c169551c396535577..c0aa71b944b19ac95bc887ea291f25d177a4c9c5 100644
--- a/auto/Wrap/libBornAgainBase_wrap.cpp
+++ b/auto/Wrap/libBornAgainBase_wrap.cpp
@@ -26004,6 +26004,29 @@ fail:
}
+SWIGINTERN PyObject *_wrap_IAxis_center(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
+ PyObject *resultobj = 0;
+ IAxis *arg1 = (IAxis *) 0 ;
+ void *argp1 = 0 ;
+ int res1 = 0 ;
+ PyObject *swig_obj[1] ;
+ double result;
+
+ if (!args) SWIG_fail;
+ swig_obj[0] = args;
+ res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_IAxis, 0 | 0 );
+ if (!SWIG_IsOK(res1)) {
+ SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "IAxis_center" "', argument " "1"" of type '" "IAxis const *""'");
+ }
+ arg1 = reinterpret_cast< IAxis * >(argp1);
+ result = (double)((IAxis const *)arg1)->center();
+ resultobj = SWIG_From_double(static_cast< double >(result));
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
SWIGINTERN PyObject *_wrap_IAxis_binCenter(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
PyObject *resultobj = 0;
IAxis *arg1 = (IAxis *) 0 ;
@@ -33303,6 +33326,13 @@ static PyMethodDef SwigMethods[] = {
"Returns distance from first to last point. \n"
"\n"
""},
+ { "IAxis_center", _wrap_IAxis_center, METH_O, "\n"
+ "IAxis_center(IAxis self) -> double\n"
+ "double IAxis::center() const\n"
+ "\n"
+ "Returns midpoint of axis. \n"
+ "\n"
+ ""},
{ "IAxis_binCenter", _wrap_IAxis_binCenter, METH_VARARGS, "\n"
"IAxis_binCenter(IAxis self, size_t index) -> double\n"
"virtual double IAxis::binCenter(size_t index) const =0\n"
diff --git a/auto/Wrap/libBornAgainCore.py b/auto/Wrap/libBornAgainCore.py
index f2636b40ee8b12804d84bbc1f946ff217738f66d..b29772e589413c6221be05902c337aa03a72b949 100644
--- a/auto/Wrap/libBornAgainCore.py
+++ b/auto/Wrap/libBornAgainCore.py
@@ -1678,6 +1678,7 @@ class vector_pvacuum_double_t(object):
# Register vector_pvacuum_double_t in _libBornAgainCore:
_libBornAgainCore.vector_pvacuum_double_t_swigregister(vector_pvacuum_double_t)
+import libBornAgainFit
import libBornAgainBase
class kvector_t(object):
r"""Proxy of C++ BasicVector3D< double > class."""
diff --git a/auto/Wrap/libBornAgainDevice.py b/auto/Wrap/libBornAgainDevice.py
index 476eb2340edadc07de5eab51045a5a0a2744400e..15bb81134b2bff3b13dce40d6c6ce168aea6fa74 100644
--- a/auto/Wrap/libBornAgainDevice.py
+++ b/auto/Wrap/libBornAgainDevice.py
@@ -4919,6 +4919,7 @@ class SphericalDetector(IDetector2D):
r"""
__init__(SphericalDetector self) -> SphericalDetector
__init__(SphericalDetector self, size_t n_phi, double phi_min, double phi_max, size_t n_alpha, double alpha_min, double alpha_max) -> SphericalDetector
+ __init__(SphericalDetector self, size_t n_bin, double width, double phi, double alpha) -> SphericalDetector
__init__(SphericalDetector self, SphericalDetector other) -> SphericalDetector
SphericalDetector::SphericalDetector(const SphericalDetector &other)
diff --git a/auto/Wrap/libBornAgainDevice_wrap.cpp b/auto/Wrap/libBornAgainDevice_wrap.cpp
index 4a781d0bf52a2d09bc608c072e06df875479dd73..bfa18e94307cadf43cddd59109f8a8298dcaa4ac 100644
--- a/auto/Wrap/libBornAgainDevice_wrap.cpp
+++ b/auto/Wrap/libBornAgainDevice_wrap.cpp
@@ -39530,6 +39530,51 @@ fail:
SWIGINTERN PyObject *_wrap_new_SphericalDetector__SWIG_2(PyObject *SWIGUNUSEDPARM(self), Py_ssize_t nobjs, PyObject **swig_obj) {
+ PyObject *resultobj = 0;
+ size_t arg1 ;
+ double arg2 ;
+ double arg3 ;
+ double arg4 ;
+ size_t val1 ;
+ int ecode1 = 0 ;
+ double val2 ;
+ int ecode2 = 0 ;
+ double val3 ;
+ int ecode3 = 0 ;
+ double val4 ;
+ int ecode4 = 0 ;
+ SphericalDetector *result = 0 ;
+
+ if ((nobjs < 4) || (nobjs > 4)) SWIG_fail;
+ ecode1 = SWIG_AsVal_size_t(swig_obj[0], &val1);
+ if (!SWIG_IsOK(ecode1)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode1), "in method '" "new_SphericalDetector" "', argument " "1"" of type '" "size_t""'");
+ }
+ arg1 = static_cast< size_t >(val1);
+ ecode2 = SWIG_AsVal_double(swig_obj[1], &val2);
+ if (!SWIG_IsOK(ecode2)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "new_SphericalDetector" "', argument " "2"" of type '" "double""'");
+ }
+ arg2 = static_cast< double >(val2);
+ ecode3 = SWIG_AsVal_double(swig_obj[2], &val3);
+ if (!SWIG_IsOK(ecode3)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode3), "in method '" "new_SphericalDetector" "', argument " "3"" of type '" "double""'");
+ }
+ arg3 = static_cast< double >(val3);
+ ecode4 = SWIG_AsVal_double(swig_obj[3], &val4);
+ if (!SWIG_IsOK(ecode4)) {
+ SWIG_exception_fail(SWIG_ArgError(ecode4), "in method '" "new_SphericalDetector" "', argument " "4"" of type '" "double""'");
+ }
+ arg4 = static_cast< double >(val4);
+ result = (SphericalDetector *)new SphericalDetector(arg1,arg2,arg3,arg4);
+ resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_SphericalDetector, SWIG_POINTER_NEW | 0 );
+ return resultobj;
+fail:
+ return NULL;
+}
+
+
+SWIGINTERN PyObject *_wrap_new_SphericalDetector__SWIG_3(PyObject *SWIGUNUSEDPARM(self), Py_ssize_t nobjs, PyObject **swig_obj) {
PyObject *resultobj = 0;
SphericalDetector *arg1 = 0 ;
void *argp1 = 0 ;
@@ -39569,7 +39614,35 @@ SWIGINTERN PyObject *_wrap_new_SphericalDetector(PyObject *self, PyObject *args)
int res = SWIG_ConvertPtr(argv[0], 0, SWIGTYPE_p_SphericalDetector, SWIG_POINTER_NO_NULL | 0);
_v = SWIG_CheckState(res);
if (_v) {
- return _wrap_new_SphericalDetector__SWIG_2(self, argc, argv);
+ return _wrap_new_SphericalDetector__SWIG_3(self, argc, argv);
+ }
+ }
+ if (argc == 4) {
+ int _v;
+ {
+ int res = SWIG_AsVal_size_t(argv[0], NULL);
+ _v = SWIG_CheckState(res);
+ }
+ if (_v) {
+ {
+ int res = SWIG_AsVal_double(argv[1], NULL);
+ _v = SWIG_CheckState(res);
+ }
+ if (_v) {
+ {
+ int res = SWIG_AsVal_double(argv[2], NULL);
+ _v = SWIG_CheckState(res);
+ }
+ if (_v) {
+ {
+ int res = SWIG_AsVal_double(argv[3], NULL);
+ _v = SWIG_CheckState(res);
+ }
+ if (_v) {
+ return _wrap_new_SphericalDetector__SWIG_2(self, argc, argv);
+ }
+ }
+ }
}
}
if (argc == 6) {
@@ -39618,6 +39691,7 @@ fail:
" Possible C/C++ prototypes are:\n"
" SphericalDetector::SphericalDetector()\n"
" SphericalDetector::SphericalDetector(size_t,double,double,size_t,double,double)\n"
+ " SphericalDetector::SphericalDetector(size_t,double,double,double)\n"
" SphericalDetector::SphericalDetector(SphericalDetector const &)\n");
return 0;
}
@@ -47082,6 +47156,7 @@ static PyMethodDef SwigMethods[] = {
{ "new_SphericalDetector", _wrap_new_SphericalDetector, METH_VARARGS, "\n"
"SphericalDetector()\n"
"SphericalDetector(size_t n_phi, double phi_min, double phi_max, size_t n_alpha, double alpha_min, double alpha_max)\n"
+ "SphericalDetector(size_t n_bin, double width, double phi, double alpha)\n"
"new_SphericalDetector(SphericalDetector other) -> SphericalDetector\n"
"SphericalDetector::SphericalDetector(const SphericalDetector &other)\n"
"\n"
diff --git a/cmake/BornAgain/Directories.cmake b/cmake/BornAgain/Directories.cmake
index bc51aee1ac7b5e6402f5d24a561f18837b737bec..03eb4f793603304ead0e2e6b71d7e27107af2b26 100644
--- a/cmake/BornAgain/Directories.cmake
+++ b/cmake/BornAgain/Directories.cmake
@@ -2,6 +2,7 @@
# source directories
# -----------------------------------------------------------------------------
+set(TOOL_DIR ${CMAKE_SOURCE_DIR}/devtools)
set(WRAP_DIR ${CMAKE_SOURCE_DIR}/Wrap)
set(SWIG_DIR ${WRAP_DIR}/Swig)
set(PY_EXAMPLES_DIR ${CMAKE_SOURCE_DIR}/Examples/Python)
diff --git a/cmake/BornAgain/LineLength.cmake b/cmake/BornAgain/LineLength.cmake
index 311637cedbd93d009f65c27dcf393e8ff2228970..c5025e90e94ab60ca713668e509dce0b285c89e2 100644
--- a/cmake/BornAgain/LineLength.cmake
+++ b/cmake/BornAgain/LineLength.cmake
@@ -4,7 +4,7 @@ set(WEB_LEN_LIM 85) # maximum line length of code for display in web docs
if(NOT MSVC)
set(LINECOUNT
- ${Python3_EXECUTABLE} ${CMAKE_SOURCE_DIR}/devtools/line-count/check-line-length.py)
+ ${Python3_EXECUTABLE} ${TOOL_DIR}/line-count/check-line-length.py)
foreach(dir ${AllComponents})
file(GLOB_RECURSE src1 ${dir}/*.cpp)
diff --git a/cmake/BornAgain/PythonAPI.cmake b/cmake/BornAgain/PythonAPI.cmake
index fd9c0bb25900a15f978e87b43345aaa69f04effb..fd1fb7d8a6e9acde0a9cc8323603265e030f6e55 100644
--- a/cmake/BornAgain/PythonAPI.cmake
+++ b/cmake/BornAgain/PythonAPI.cmake
@@ -4,9 +4,6 @@ if(NOT BORNAGAIN_PYTHON)
message(FATAL_ERROR PythonAPI included though BORNAGAIN_PYTHON=false)
endif()
-configure_file(${WRAP_DIR}/Python/plot_utils.py
- ${CMAKE_BINARY_DIR}/lib/bornagain/plot_utils.py COPYONLY)
-
if(WIN32)
set(BA_MODULES_IMPORT_PATH ../../bin)
else()
@@ -16,8 +13,12 @@ if(BORNAGAIN_APPLE_BUNDLE)
set(BA_MODULES_IMPORT_PATH
lib/BornAgain-${BornAgain_VERSION_MAJOR}.${BornAgain_VERSION_MINOR})
endif()
+
configure_file(${WRAP_DIR}/Python/__init__.py.in
${CMAKE_BINARY_DIR}/lib/bornagain/__init__.py @ONLY)
+foreach(mod plot_utils.py fit_monitor.py)
+ configure_file(${WRAP_DIR}/Python/${mod} ${CMAKE_BINARY_DIR}/lib/bornagain/${mod} COPYONLY)
+endforeach()
if(CONFIGURE_BINDINGS)
add_custom_command(
diff --git a/devtools/code-tools/batch-plot.py b/devtools/code-tools/batch-plot.py
new file mode 100755
index 0000000000000000000000000000000000000000..1059d28d19a3f5f14d6d39b4b17f2eccf38f4e7b
--- /dev/null
+++ b/devtools/code-tools/batch-plot.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+"""
+Run plotting code in batch mode: generate figure, but don't plot to terminal.
+
+This script is used in BornAgain:
+- with option -s in PyExamples tests, to check functionality of Python examples;
+- with option -l to remake full-size images.
+"""
+
+import matplotlib, os, re, sys
+matplotlib.use('Agg')
+from matplotlib import pyplot as plt
+
+
+def exec_full(script, filename):
+ """
+ Executes embedded python script.
+ http://stackoverflow.com/questions/436198/what-is-an-alternative-to-execfile-in-python-3
+ """
+ import os
+ global_namespace = {
+ "__file__": filename,
+ "__name__": "__main__",
+ "__no_terminal__": True
+ }
+ sys.argv = []
+ exec(compile(script, filename, 'exec'), global_namespace)
+
+def reduce_nbin(t):
+ """
+ Overwrites script lines that set nbin, nx, ny
+ """
+ pat = re.compile(r'(^\s+(nbin|nx|ny) = )(\d+)$')
+ ret = []
+ for l in t.split('\n'):
+ m = re.match(pat, l)
+ if m:
+ oldsize = int(m.group(3))
+ newsize = min(10, oldsize)
+ lout = re.sub(pat, m.group(1)+f'{newsize}', l)
+ else:
+ lout = l
+ ret.append(lout)
+ return '\n'.join(ret)
+
+
+def run_example(mode_short, filename, output_dir):
+ """
+ Tries to run python example and produce a *.png image
+ """
+ # Read script from file.
+ if not os.path.exists(filename):
+ raise Exception("Example script '" + filename + "' not found")
+ print("Input script: " + filename, flush=True)
+ with open(filename, 'r') as file:
+ script = file.read()
+
+ # Detect or impose figure size.
+ m = re.search(r'plt\.figure\(.+?figsize=\((.+?),(.+?)\)', script)
+ if m: # set figure size as in script
+ figsize = (float(m.group(1)), float(m.group(2)))
+ else: # script does not specify figure size
+ figsize = (640/72, 480/72)
+ fig = plt.figure(figsize=(figsize[0], figsize[1]))
+
+ if mode_short:
+ script = reduce_nbin(script)
+
+ # Run modified script.
+ exec_full(script, filename)
+ print("Input script completed.", flush=True)
+
+ # Generate output figure.
+ plot_file_name = os.path.join(
+ output_dir,
+ os.path.splitext(os.path.basename(filename))[0] + ".png")
+ print("Output image: " + plot_file_name)
+ plt.savefig(plot_file_name, bbox_inches='tight')
+ plt.close(fig)
+
+ # Check obtained figure.
+ imgSize = os.path.getsize(plot_file_name)
+ if imgSize == 0:
+ raise Exception("Image file is empty")
+ if imgSize < 20000:
+ raise Exception("Image file is unplausibly small")
+
+
+if __name__ == '__main__':
+
+ if len(sys.argv) != 4:
+ exit("Usage: check_functionality -s|-f <script_to_test> <output_dir>")
+ if sys.argv[1]=='-s':
+ mode_short = True
+ elif sys.argv[1]=='-f':
+ mode_short = False
+ else:
+ exit("Use flag -s|-f for short or long runs")
+
+ run_example(mode_short, sys.argv[2], sys.argv[3])
diff --git a/devtools/code-tools/normalize-usercode.py b/devtools/code-tools/normalize-usercode.py
index c427a89801fe1296ef2e20c71a4c86a676f3a95b..10a0435382c65c525acc2026ac6b5b85c71d903d 100755
--- a/devtools/code-tools/normalize-usercode.py
+++ b/devtools/code-tools/normalize-usercode.py
@@ -69,6 +69,14 @@ def normalize_text(ti, fname):
f'.. cycled through BA, {len(ti.split())} -> {len(tc.split())} lines'
)
tf = restitute_sample(ti, tc)
+
+ # restitute main
+ tf = re.sub(r"if __name__ == '__main__':.+",
+ """if __name__ == '__main__':
+ result = run_simulation()
+ ba.plot_simulation_result(result, cmap='jet', aspect='auto')""",
+ tf, flags=re.S)
+
if verbose:
print(f'.. normalized, {len(ti.split())} -> {len(tf.split())} lines')
# YAPF formatting
@@ -88,6 +96,12 @@ def normalize_file(fname, inplace):
if verbose:
print(f'.. read {len(ti.split())} lines')
+ m = re.search(r"""if __name__ == '__main__':
+ result = run_simulation\(\)
+ ba.plot_simulation_result\(result, cmap='jet', aspect='auto'\)""", ti)
+ if not m:
+ return 3
+
# normalize
tf = normalize_text(ti, fname)
if verbose:
@@ -156,7 +170,7 @@ if __name__ == '__main__':
verbose = args.verbose
files = args.input_files
- count = [0, 0, 0]
+ count = [0, 0, 0, 0]
for f in files:
ret = normalize_file(f, args.in_place)
count[ret] += 1
@@ -171,4 +185,6 @@ if __name__ == '__main__':
out.append(f'{count[1]} normalized')
if count[2] > 0:
out.append(f'{count[2]} failed')
+ if count[2] > 0:
+ out.append(f'{count[3]} skipped')
print(f'TOTAL of {len(args.input_files)} files: {", ".join(out)}')