diff --git a/.style.yapf b/.style.yapf
index 1c9f7a913b1e117a75821ef5cd1af9bca2a58ea7..01194835fd81ee6300e82f398503619ffd9e1f04 100644
--- a/.style.yapf
+++ b/.style.yapf
@@ -1,4 +1,4 @@
[style]
based_on_style = pep8
-column_limit = 80
+column_limit = 75
no_spaces_around_selected_binary_operators = "*,/"
\ No newline at end of file
diff --git a/Doc/FFCatalog/fig/ff2/bornplot.py b/Doc/FFCatalog/fig/ff2/bornplot.py
index 27f3c1838a1db6aaa0e14c3e2cbfcd0d760c04eb..a48f916c362bc189a656456588fee108a325b3b1 100644
--- a/Doc/FFCatalog/fig/ff2/bornplot.py
+++ b/Doc/FFCatalog/fig/ff2/bornplot.py
@@ -19,10 +19,12 @@ class Result:
self.data = data
self.title = title
+
def rectangle(det):
return (det.axis(0).lowerBound(), det.axis(0).upperBound(),
det.axis(1).lowerBound(), det.axis(1).upperBound())
+
def make_plot(results, det, name, nrow=1):
"""
Make a plot consisting of one detector image for each Result in results,
@@ -66,13 +68,19 @@ def make_plot(results, det, name, nrow=1):
# Plot the subfigures.
for res in results:
ax = axes[res.idx]
- im = ax.imshow(res.data, norm=norm, extent=rectangle(det), aspect=1)
+ im = ax.imshow(res.data,
+ norm=norm,
+ extent=rectangle(det),
+ aspect=1)
ax.set_xlabel(r'$\phi_{\rm f} (^{\circ})$', fontsize=fontsize)
if res.idx % ncol == 0:
- ax.set_ylabel(r'$\alpha_{\rm f} (^{\circ})$', fontsize=fontsize)
+ ax.set_ylabel(r'$\alpha_{\rm f} (^{\circ})$',
+ fontsize=fontsize)
if res.title != "":
ax.set_title(res.title, fontsize=fontsize)
- ax.tick_params(axis='both', which='major', labelsize=fontsize*21/24)
+ ax.tick_params(axis='both',
+ which='major',
+ labelsize=fontsize*21/24)
# Adjust whitespace around and between subfigures.
plt.subplots_adjust(wspace=xskip,
hspace=yskip,
diff --git a/Doc/PhysicsManual/fig/drawing/Green.py b/Doc/PhysicsManual/fig/drawing/Green.py
index c6ec918e20909f8a2ba3665ccaee7c939c64cd28..e2dd0ffd549719c591a4dca1f17575425a59d4de 100755
--- a/Doc/PhysicsManual/fig/drawing/Green.py
+++ b/Doc/PhysicsManual/fig/drawing/Green.py
@@ -59,8 +59,8 @@ for P in PP:
DeltaPath.append(0)
elif inside(y, -T[0], 0) and inside(yold, -T[0], 0):
DeltaPath.append(DeltaLayer[0])
- elif inside(y, -T[0] - T[1], -T[0]) and inside(yold, -T[0] - T[1],
- -T[0]):
+ elif inside(y, -T[0] - T[1], -T[0]) and inside(
+ yold, -T[0] - T[1], -T[0]):
DeltaPath.append(DeltaLayer[1])
else:
sys.stderr.write("Invalid input => layer ill defined\n")
@@ -89,8 +89,10 @@ for P in PP:
cmd1 += "st\n"
cmd2 += "st\n"
len1 = math.sqrt((xtot + x0 - x1)**2 + yd**2) - 8
- cmd1 += "%6.3g %6.3g %7.3g .8 %6.3g pfeiL\n" % (x1, y, 180*a0/math.pi, len1)
- cmd2 += "%6.3g %6.3g %7.3g .8 %6.3g pfeiL\n" % (x2, y, 180*b0/math.pi, 7)
+ cmd1 += "%6.3g %6.3g %7.3g .8 %6.3g pfeiL\n" % (x1, y, 180*a0/math.pi,
+ len1)
+ cmd2 += "%6.3g %6.3g %7.3g .8 %6.3g pfeiL\n" % (x2, y, 180*b0/math.pi,
+ 7)
cmd1 += "\n"
cmd2 += "\n"
#/pfeiL { % (arrow anchored at base) x y rot siz len
diff --git a/Examples/fit52_Advanced/find_background.py b/Examples/fit52_Advanced/find_background.py
index 05fe2b589dcd44e569aafcad15edd652de511550..b14487241e2d657bb92096551ea5b79e2743d2c8 100644
--- a/Examples/fit52_Advanced/find_background.py
+++ b/Examples/fit52_Advanced/find_background.py
@@ -48,8 +48,7 @@ def get_simulation(params):
scale = params["scale"]
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e12*scale)
simulation.setBackground(ba.ConstantBackground(background))
diff --git a/Examples/fit52_Advanced/fit_along_slices.py b/Examples/fit52_Advanced/fit_along_slices.py
index 78242d985812101a164f3c50ec86eb6a2d99fb03..373f64ff46482bd01ebc77b1b16af3c808bbed12 100644
--- a/Examples/fit52_Advanced/fit_along_slices.py
+++ b/Examples/fit52_Advanced/fit_along_slices.py
@@ -43,8 +43,7 @@ def get_simulation(params, add_masks=True):
Create and return GISAXS simulation with beam and detector defined
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
@@ -115,7 +114,9 @@ class PlotObserver:
"""
plt.subplots_adjust(wspace=0.2, hspace=0.3)
for label, slice in slices:
- plt.semilogy(slice.binCenters(), slice.binValues(), label=label)
+ plt.semilogy(slice.binCenters(),
+ slice.binValues(),
+ label=label)
plt.xlim(slice.getXmin(), slice.getXmax())
plt.ylim(1, slice.getMaximum()*10)
plt.legend(loc='upper right')
@@ -132,13 +133,14 @@ class PlotObserver:
iteration_info = fit_objective.iterationInfo()
plt.text(
- 0.01, 0.85,
- "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
+ 0.01, 0.85, "Iterations " +
+ '{:d}'.format(iteration_info.iterationCount()))
plt.text(0.01, 0.75,
"Chi2 " + '{:8.4f}'.format(iteration_info.chi2()))
for index, params in enumerate(iteration_info.parameters()):
- plt.text(0.01, 0.55 - index*0.1,
- '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
+ plt.text(
+ 0.01, 0.55 - index*0.1,
+ '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
plt.tight_layout()
plt.draw()
@@ -168,7 +170,8 @@ class PlotObserver:
# vertical slices
slices = [("real", real_data.projectionY(phi_slice_value)),
("simul", simul_data.projectionY(phi_slice_value))]
- title = "Vertical slice at phi =" + '{:3.1f}'.format(phi_slice_value)
+ title = "Vertical slice at phi =" + '{:3.1f}'.format(
+ phi_slice_value)
plt.subplot(2, 2, 3)
self.plot_slices(slices, title)
diff --git a/Examples/fit52_Advanced/fit_with_masks.py b/Examples/fit52_Advanced/fit_with_masks.py
index b8191e23801caebd3a55fe074aa09f5b76f08067..c9ec3794b9ffb3b0aeaa0f1c2823ed1e1ec53655 100644
--- a/Examples/fit52_Advanced/fit_with_masks.py
+++ b/Examples/fit52_Advanced/fit_with_masks.py
@@ -42,8 +42,7 @@ def get_simulation(params, add_masks=True):
Create and return GISAXS simulation with beam and detector defined
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
@@ -93,7 +92,8 @@ def add_mask_to_simulation(simulation):
simulation.addMask(ba.Ellipse(0, 1*deg, 0.5*deg, 0.5*deg), False)
# set mask for pacman's eye
- simulation.addMask(ba.Ellipse(0.11*deg, 1.25*deg, 0.05*deg, 0.05*deg), True)
+ simulation.addMask(ba.Ellipse(0.11*deg, 1.25*deg, 0.05*deg, 0.05*deg),
+ True)
# set mask for pacman's mouth
points = [[0*deg, 1*deg], [0.5*deg, 1.2*deg], [0.5*deg, 0.8*deg],
@@ -101,12 +101,12 @@ def add_mask_to_simulation(simulation):
simulation.addMask(ba.Polygon(points), True)
# giving pacman something to eat
- simulation.addMask(ba.Rectangle(0.45*deg, 0.95*deg, 0.55*deg, 1.05*deg),
- False)
- simulation.addMask(ba.Rectangle(0.61*deg, 0.95*deg, 0.71*deg, 1.05*deg),
- False)
- simulation.addMask(ba.Rectangle(0.75*deg, 0.95*deg, 0.85*deg, 1.05*deg),
- False)
+ simulation.addMask(
+ ba.Rectangle(0.45*deg, 0.95*deg, 0.55*deg, 1.05*deg), False)
+ simulation.addMask(
+ ba.Rectangle(0.61*deg, 0.95*deg, 0.71*deg, 1.05*deg), False)
+ simulation.addMask(
+ ba.Rectangle(0.75*deg, 0.95*deg, 0.85*deg, 1.05*deg), False)
def run_fitting():
diff --git a/Examples/fit52_Advanced/multiple_datasets.py b/Examples/fit52_Advanced/multiple_datasets.py
index 7180fce19a56bf0118e1cee93d736bcebd72db8c..1d73f5e95c4351473038fe87c7f7d4dceb1c11ce 100644
--- a/Examples/fit52_Advanced/multiple_datasets.py
+++ b/Examples/fit52_Advanced/multiple_datasets.py
@@ -45,8 +45,7 @@ def get_simulation(params):
incident_angle = params["incident_angle"]
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(50, -1.5*deg, 1.5*deg, 50, 0,
- 2*deg)
+ simulation.setDetectorParameters(50, -1.5*deg, 1.5*deg, 50, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, incident_angle, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
@@ -110,13 +109,15 @@ class PlotObserver():
plt.subplot(canvas[i_dataset*3])
ba.plot_colormap(real_data,
- title="\"Real\" data - #" + str(i_dataset + 1),
+ title="\"Real\" data - #" +
+ str(i_dataset + 1),
zmin=1,
zmax=zmax,
zlabel="")
plt.subplot(canvas[1 + i_dataset*3])
ba.plot_colormap(simul_data,
- title="Simulated data - #" + str(i_dataset + 1),
+ title="Simulated data - #" +
+ str(i_dataset + 1),
zmin=1,
zmax=zmax,
zlabel="")
@@ -138,13 +139,14 @@ class PlotObserver():
iteration_info = fit_objective.iterationInfo()
plt.text(
- 0.01, 0.85,
- "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
+ 0.01, 0.85, "Iterations " +
+ '{:d}'.format(iteration_info.iterationCount()))
plt.text(0.01, 0.75,
"Chi2 " + '{:8.4f}'.format(iteration_info.chi2()))
for index, params in enumerate(iteration_info.parameters()):
- plt.text(0.01, 0.55 - index*0.1,
- '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
+ plt.text(
+ 0.01, 0.55 - index*0.1,
+ '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
@staticmethod
def plot_fit_parameters(fit_objective):
@@ -156,13 +158,14 @@ class PlotObserver():
iteration_info = fit_objective.iterationInfo()
plt.text(
- 0.01, 0.95,
- "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
+ 0.01, 0.95, "Iterations " +
+ '{:d}'.format(iteration_info.iterationCount()))
plt.text(0.01, 0.70,
"Chi2 " + '{:8.4f}'.format(iteration_info.chi2()))
for index, params in enumerate(iteration_info.parameters()):
- plt.text(0.01, 0.30 - index*0.3,
- '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
+ plt.text(
+ 0.01, 0.30 - index*0.3,
+ '{:30.30s}: {:6.3f}'.format(params.name(), params.value))
def update(self, fit_objective):
self.fig.clf()
diff --git a/Examples/fit53_CustomObjective/custom_objective_function.py b/Examples/fit53_CustomObjective/custom_objective_function.py
index 35179a58aec1040b30283e562b4a1df221976755..fdd53ac2324eb93f8b3d86bdb7f3fc38487b8f34 100644
--- a/Examples/fit53_CustomObjective/custom_objective_function.py
+++ b/Examples/fit53_CustomObjective/custom_objective_function.py
@@ -73,8 +73,7 @@ def get_simulation(params):
Create and return GISAXS simulation with beam and detector defined.
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
diff --git a/Examples/fit54_ExternalMinimizer/lmfit_basics.py b/Examples/fit54_ExternalMinimizer/lmfit_basics.py
index 3a4c3a13f857e55af2b9bed6928f158754e6c8d0..db43da508518f774c6af3479b7b3682e5e6de0e4 100644
--- a/Examples/fit54_ExternalMinimizer/lmfit_basics.py
+++ b/Examples/fit54_ExternalMinimizer/lmfit_basics.py
@@ -47,8 +47,7 @@ def get_simulation(params):
Create and return GISAXS simulation with beam and detector defined
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
diff --git a/Examples/fit54_ExternalMinimizer/lmfit_with_plotting.py b/Examples/fit54_ExternalMinimizer/lmfit_with_plotting.py
index 73d680d14af5aa2028d4a9f716c3a89d0074ba5b..a68e67899c9c03a5d0413732378e5f0c8642f951 100644
--- a/Examples/fit54_ExternalMinimizer/lmfit_with_plotting.py
+++ b/Examples/fit54_ExternalMinimizer/lmfit_with_plotting.py
@@ -48,8 +48,7 @@ def get_simulation(params):
Create and return GISAXS simulation with beam and detector defined
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0,
- 2*deg)
+ simulation.setDetectorParameters(100, -1*deg, 1*deg, 100, 0, 2*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
simulation.beam().setIntensity(1e+08)
simulation.setSample(get_sample(params))
diff --git a/Examples/fit55_SpecularIntro/FitSpecularBasics.py b/Examples/fit55_SpecularIntro/FitSpecularBasics.py
index 0d4f94f7e7856359bfa0d704d3b96758c0972fd8..54bb986cd05abb9167c02904b1db08538416ab2f 100644
--- a/Examples/fit55_SpecularIntro/FitSpecularBasics.py
+++ b/Examples/fit55_SpecularIntro/FitSpecularBasics.py
@@ -63,7 +63,8 @@ def get_real_data():
"""
if not hasattr(get_real_data, "data"):
filename = "genx_interchanging_layers.dat.gz"
- filepath = path.join(path.dirname(path.realpath(__file__)), filename)
+ filepath = path.join(path.dirname(path.realpath(__file__)),
+ filename)
real_data = np.loadtxt(filepath, usecols=(0, 1), skiprows=3)
# translating axis values from double incident angle (degs)
diff --git a/Examples/fit55_SpecularIntro/FitWithUncertainties.py b/Examples/fit55_SpecularIntro/FitWithUncertainties.py
index 4d3142f2752bc415da01d1c16cea2e31f4347324..186bf12ccaa459ddf2fcdaf3e595f506ef69feba 100644
--- a/Examples/fit55_SpecularIntro/FitWithUncertainties.py
+++ b/Examples/fit55_SpecularIntro/FitWithUncertainties.py
@@ -67,7 +67,8 @@ def get_real_data():
"""
if not hasattr(get_real_data, "data"):
filename = "genx_interchanging_layers.dat.gz"
- filepath = path.join(path.dirname(path.realpath(__file__)), filename)
+ filepath = path.join(path.dirname(path.realpath(__file__)),
+ filename)
real_data = np.loadtxt(filepath, usecols=(0, 1), skiprows=3)
# translating axis values from double incident angle (degs)
@@ -117,7 +118,8 @@ def run_fitting():
uncertainties = real_data*0.5
fit_objective = ba.FitObjective()
- fit_objective.addSimulationAndData(get_simulation, real_data, uncertainties)
+ fit_objective.addSimulationAndData(get_simulation, real_data,
+ uncertainties)
plot_observer = ba_fitmonitor.PlotterSpecular(units=ba.Axes.RQ4)
fit_objective.initPrint(10)
diff --git a/Examples/fit55_SpecularIntro/PolarizedSpinAsymmetryFit.py b/Examples/fit55_SpecularIntro/PolarizedSpinAsymmetryFit.py
index 4f60c1f3e5a9f4c28940cf32073ff50c995f278d..66330a72344f513f5040d4b36635cb0f89015f5c 100644
--- a/Examples/fit55_SpecularIntro/PolarizedSpinAsymmetryFit.py
+++ b/Examples/fit55_SpecularIntro/PolarizedSpinAsymmetryFit.py
@@ -53,8 +53,8 @@ def get_sample(params):
magnetizationMagnitude*numpy.cos(angle*deg), 0)
mat_vacuum = ba.MaterialBySLD("Vacuum", 0, 0)
- mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4", params["rho_Mafo"]*1e-6, 0,
- magnetizationVector)
+ mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4", params["rho_Mafo"]*1e-6,
+ 0, magnetizationVector)
mat_substrate = ba.MaterialBySLD("MgAl2O4", *sldMao)
ambient_layer = ba.Layer(mat_vacuum)
@@ -174,7 +174,8 @@ def plotSpinAsymmetry(data_pp, data_mm, q, r_pp, r_mm, filename):
fig = plt.figure()
ax = fig.add_subplot(111)
- ax.errorbar(data_pp[0], (data_pp[1] - data_mm[1])/(data_pp[1] + data_mm[1]),
+ ax.errorbar(data_pp[0],
+ (data_pp[1] - data_mm[1])/(data_pp[1] + data_mm[1]),
xerr=data_pp[3],
yerr=delta,
fmt='.',
@@ -232,7 +233,8 @@ def get_Experimental_data(qmin, qmax):
data_pp = normalizeData(input_Data[0])
data_mm = normalizeData(input_Data[1])
- return (filterData(data_pp, qmin, qmax), filterData(data_mm, qmin, qmax))
+ return (filterData(data_pp, qmin,
+ qmax), filterData(data_mm, qmin, qmax))
def downloadAndExtractData():
@@ -248,11 +250,11 @@ def downloadAndExtractData():
rawdata = zipfile.open("MAFO_Saturated.refl").read().decode("utf-8")
table_pp = match(
- r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*', rawdata,
- DOTALL).group(1)
+ r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
table_mm = match(
- r'.*# "polarization": "\-\-"\n#.*?\n# "units".*?\n(.*?)#.*', rawdata,
- DOTALL).group(1)
+ r'.*# "polarization": "\-\-"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
data_pp = numpy.genfromtxt(BytesIO(table_pp.encode()), unpack=True)
data_mm = numpy.genfromtxt(BytesIO(table_mm.encode()), unpack=True)
@@ -265,7 +267,8 @@ def downloadAndExtractData():
####################################################################
-def run_fit_ba(q_axis, r_data, r_uncertainty, simulationFactory, startParams):
+def run_fit_ba(q_axis, r_data, r_uncertainty, simulationFactory,
+ startParams):
fit_objective = ba.FitObjective()
fit_objective.setObjectiveMetric("chi2")
@@ -368,8 +371,8 @@ if __name__ == '__main__':
q_pp, r_pp = qr(run_Simulation_pp(qzs, fitResult))
q_mm, r_mm = qr(run_Simulation_mm(qzs, fitResult))
- plot([q_pp, q_mm], [r_pp, r_mm], [data_pp, data_mm], ["$++$", "$--$"],
- f'MAFO_Saturated_fit.pdf')
+ plot([q_pp, q_mm], [r_pp, r_mm], [data_pp, data_mm],
+ ["$++$", "$--$"], f'MAFO_Saturated_fit.pdf')
plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
"MAFO_Saturated_spin_asymmetry_fit.pdf")
diff --git a/Examples/fit55_SpecularIntro/RealLifeReflectometryFitting.py b/Examples/fit55_SpecularIntro/RealLifeReflectometryFitting.py
index a96af5188c52c2bb4426319d977b56760e83bb61..e1ec8a7bde2d8bae719a97a53a595c2faaf1d499 100644
--- a/Examples/fit55_SpecularIntro/RealLifeReflectometryFitting.py
+++ b/Examples/fit55_SpecularIntro/RealLifeReflectometryFitting.py
@@ -46,7 +46,8 @@ def get_real_data(filename="mg6a_Merged.txt.gz"):
and the third one being weights to restore intensity values from experiment
"""
if not hasattr(get_real_data, "data"):
- filepath = path.join(path.dirname(path.realpath(__file__)), filename)
+ filepath = path.join(path.dirname(path.realpath(__file__)),
+ filename)
real_data = np.loadtxt(filepath, usecols=(0, 1, 3), skiprows=1)
# translating axis values from double incident angle (degs)
@@ -111,9 +112,9 @@ def buildSample(arg_dict):
"""
# defining materials
m_vacuum = ba.HomogeneousMaterial("Vacuum", 0, 0)
- m_si_o2 = ba.HomogeneousMaterial("SiO2",
- 8.57040868e-06*arg_dict["concentration"],
- 1.11016654e-07*arg_dict["concentration"])
+ m_si_o2 = ba.HomogeneousMaterial(
+ "SiO2", 8.57040868e-06*arg_dict["concentration"],
+ 1.11016654e-07*arg_dict["concentration"])
m_si = ba.HomogeneousMaterial("Si", 7.57211137e-06, 1.72728178e-07)
# roughness
@@ -193,7 +194,8 @@ def objective_fine(args, intensity, footprint_factor, divergence):
bin_start = 404 # first bin in the experimental data to calculate
bin_end = -1 # last bin in the experimental data to calculate
- arg_dict = create_par_dict(intensity, footprint_factor, divergence, *args)
+ arg_dict = create_par_dict(intensity, footprint_factor, divergence,
+ *args)
sim_result = run_simulation(arg_dict, bin_start, bin_end)
sim_data = sim_result.array()
@@ -237,7 +239,8 @@ def run_fitting():
preliminary_result.x[2] # beam divergence
)
- print("\nStart fitting big incident angle part of experimental data:\n")
+ print(
+ "\nStart fitting big incident angle part of experimental data:\n")
fine_tuning_result = differential_evolution(objective_fine,
bounds,
@@ -264,8 +267,8 @@ def plot_result(sim_result, ref_result, bin_start=0, bin_end=-1):
plt.semilogy(
get_real_data_axis(bin_start, bin_end)*180/np.pi,
- get_real_data_values(bin_start, bin_end), sim_result.axis(), sim_data,
- ref_result.axis(), ref_data)
+ get_real_data_values(bin_start, bin_end), sim_result.axis(),
+ sim_data, ref_result.axis(), ref_data)
xlabel = ba.get_axes_labels(sim_result, ba.Axes.DEFAULT)[0]
ylabel = "Intensity"
diff --git a/Examples/fit56_SpecularAdvanced/Honeycomb_fit.py b/Examples/fit56_SpecularAdvanced/Honeycomb_fit.py
index ac1a55b222523ef4a167faf14085ce702b518266..de7bc5854462dc87dc3583fee733dd837b3cc7c6 100644
--- a/Examples/fit56_SpecularAdvanced/Honeycomb_fit.py
+++ b/Examples/fit56_SpecularAdvanced/Honeycomb_fit.py
@@ -225,9 +225,10 @@ def get_Experimental_data(filename, qmin, qmax):
if not hasattr(get_Experimental_data, "zipfile"):
get_Experimental_data.zipfile = ZipFile("honeycomb_data.zip")
- input_Data = numpy.genfromtxt(get_Experimental_data.zipfile.open(filename),
- unpack=True,
- usecols=(0, 2, 3))
+ input_Data = numpy.genfromtxt(
+ get_Experimental_data.zipfile.open(filename),
+ unpack=True,
+ usecols=(0, 2, 3))
data = normalizeData(input_Data)
minIndex = numpy.argmin(numpy.abs(data[0] - qmin))
@@ -270,7 +271,8 @@ class FitObjective:
self._parameterNames = parameterNames
def __call__(self, *args):
- fitParameters = create_Parameter_dictionary(self._parameterNames, *args)
+ fitParameters = create_Parameter_dictionary(self._parameterNames,
+ *args)
print(f"FitParamters = {fitParameters}")
result_metric = 0
@@ -290,7 +292,8 @@ def run_fit_differential_evolution(q_axis, rdata, simulationFactory,
parameterNames = [n for n, par in startParams.items()]
print(f"Bounds = {bounds}")
- objective = FitObjective(q_axis, rdata, simulationFactory, parameterNames)
+ objective = FitObjective(q_axis, rdata, simulationFactory,
+ parameterNames)
chi2_initial = objective(parameters)
@@ -302,7 +305,8 @@ def run_fit_differential_evolution(q_axis, rdata, simulationFactory,
disp=True,
tol=1e-2)
- resultParameters = create_Parameter_dictionary(parameterNames, result.x)
+ resultParameters = create_Parameter_dictionary(parameterNames,
+ result.x)
chi2_final = objective(resultParameters.values())
print(f"Initial chi2: {chi2_initial}")
@@ -405,7 +409,8 @@ if __name__ == '__main__':
data_150_p = get_Experimental_data("honeycomb_150_p.dat", qmin, qmax)
data_150_m = get_Experimental_data("honeycomb_150_m.dat", qmin, qmax)
- plot_sld_profile(paramsInitial, f"Honeycomb_Fit_sld_profile_initial.pdf")
+ plot_sld_profile(paramsInitial,
+ f"Honeycomb_Fit_sld_profile_initial.pdf")
plot([q_300_p, q_300_m, q_150_p, q_150_m],
[r_300_p, r_300_m, r_150_p, r_150_m],
[data_300_p, data_300_m, data_150_p, data_150_m], [1, 1, 10, 10],
@@ -422,7 +427,8 @@ if __name__ == '__main__':
run_Simulation_150_p, run_Simulation_150_m
]]
- fitResult = run_fit_differential_evolution(*dataSimTuple, startParams)
+ fitResult = run_fit_differential_evolution(*dataSimTuple,
+ startParams)
print("Fit Result:")
print(fitResult)
@@ -435,7 +441,8 @@ if __name__ == '__main__':
plot([q_300_p, q_300_m, q_150_p, q_150_m],
[r_300_p, r_300_m, r_150_p, r_150_m],
- [data_300_p, data_300_m, data_150_p, data_150_m], [1, 1, 10, 10],
+ [data_300_p, data_300_m, data_150_p, data_150_m],
+ [1, 1, 10, 10],
["300K $+$", "300K $-$", "150K $+$", "150K $-$"],
f"Honeycomb_Fit_reflectivity_fit.pdf")
diff --git a/Examples/fit56_SpecularAdvanced/Pt_layer_fit.py b/Examples/fit56_SpecularAdvanced/Pt_layer_fit.py
index b2d0232e3f56fd53606968bad9e9cda4ccd03a66..a82dc971a4550e7d84293f51ee010710943065ae 100644
--- a/Examples/fit56_SpecularAdvanced/Pt_layer_fit.py
+++ b/Examples/fit56_SpecularAdvanced/Pt_layer_fit.py
@@ -171,14 +171,15 @@ def get_Experimental_data(qmin, qmax):
####################################################################
-def run_fit_ba(q_axis, r_data, r_uncertainty, simulationFactory, startParams):
+def run_fit_ba(q_axis, r_data, r_uncertainty, simulationFactory,
+ startParams):
fit_objective = ba.FitObjective()
fit_objective.setObjectiveMetric("chi2")
fit_objective.addSimulationAndData(
- lambda params: simulationFactory(q_axis, params), r_data, r_uncertainty,
- 1)
+ lambda params: simulationFactory(q_axis, params), r_data,
+ r_uncertainty, 1)
fit_objective.initPrint(10)
@@ -247,4 +248,5 @@ if __name__ == '__main__':
print(fitResult)
q, r = qr(run_simulation(qzs, fitParams=fitResult))
- plot(q, r, data, f'PtLayerFit_fit.pdf', dict(fitResult, **fixedParams))
+ plot(q, r, data, f'PtLayerFit_fit.pdf',
+ dict(fitResult, **fixedParams))
diff --git a/Examples/fit61_Galaxi/fit_galaxi_data.py b/Examples/fit61_Galaxi/fit_galaxi_data.py
index 257eb0520e5bbd6ec1225fc806c1d7becda739c5..0cee8f191100526b53c567e6581d10755e0586f3 100644
--- a/Examples/fit61_Galaxi/fit_galaxi_data.py
+++ b/Examples/fit61_Galaxi/fit_galaxi_data.py
@@ -40,7 +40,8 @@ def create_simulation(params):
simulation.setBeamParameters(wavelength, alpha_i, 0)
simulation.beam().setIntensity(1.2e7)
simulation.setRegionOfInterest(85, 70, 120, 92.)
- simulation.addMask(ba.Rectangle(101.9, 82.1, 103.7, 85.2), True) # beamstop
+ simulation.addMask(ba.Rectangle(101.9, 82.1, 103.7, 85.2),
+ True) # beamstop
sample_builder = SampleBuilder()
sample = sample_builder.create_sample(params)
diff --git a/Examples/fit61_Galaxi/sample_builder.py b/Examples/fit61_Galaxi/sample_builder.py
index d9fe9b45b6407735fe5607275f2d7dc53ff8422f..6a18bfa9e94e5cfca4ea19be7cd5af1736e2521b 100755
--- a/Examples/fit61_Galaxi/sample_builder.py
+++ b/Examples/fit61_Galaxi/sample_builder.py
@@ -46,8 +46,10 @@ class SampleBuilder:
m_vacuum = ba.HomogeneousMaterial("Vacuum", 0, 0)
m_Si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7)
m_Ag = ba.HomogeneousMaterial("Ag", 2.24749529E-5, 1.61528396E-6)
- m_PTFE = ba.HomogeneousMaterial("PTFE", 5.20508729E-6, 1.96944292E-8)
- m_HMDSO = ba.HomogeneousMaterial("HMDSO", 2.0888308E-6, 1.32605651E-8)
+ m_PTFE = ba.HomogeneousMaterial("PTFE", 5.20508729E-6,
+ 1.96944292E-8)
+ m_HMDSO = ba.HomogeneousMaterial("HMDSO", 2.0888308E-6,
+ 1.32605651E-8)
# collection of particles with size distribution
nparticles = 20
diff --git a/Examples/scatter2d/BeamDivergence.py b/Examples/scatter2d/BeamDivergence.py
index 0e9fed1d8bd54f03c96fe0ffdbc506333d1bf57a..18a6713cabd3484788eaf23addcf1e8f5755abcd 100644
--- a/Examples/scatter2d/BeamDivergence.py
+++ b/Examples/scatter2d/BeamDivergence.py
@@ -48,11 +48,11 @@ def get_simulation(sample):
distr_1 = ba.DistributionLogNormal(0.1*nm, 0.1)
simulation.addParameterDistribution("*/Beam/Wavelength", distr_1, 5, 0)
distr_2 = ba.DistributionGaussian(0.2*deg, 0.1*deg)
- simulation.addParameterDistribution("*/Beam/InclinationAngle", distr_2, 5,
- 0)
+ simulation.addParameterDistribution("*/Beam/InclinationAngle", distr_2,
+ 5, 0)
distr_3 = ba.DistributionGaussian(0, 0.1*deg)
- simulation.addParameterDistribution("*/Beam/AzimuthalAngle", distr_3, 5,
- 0)
+ simulation.addParameterDistribution("*/Beam/AzimuthalAngle", distr_3,
+ 5, 0)
return simulation
diff --git a/Examples/scatter2d/BuriedParticles.py b/Examples/scatter2d/BuriedParticles.py
index 85ee794af1de9cd832b54a9db25c456fa59a1974..61908f5152542fab82107f581bc4655771633f74 100644
--- a/Examples/scatter2d/BuriedParticles.py
+++ b/Examples/scatter2d/BuriedParticles.py
@@ -16,7 +16,8 @@ def get_sample():
material_IntermLayer = ba.HomogeneousMaterial("IntermLayer", 3.45e-06,
5.24e-09)
material_Particle = ba.HomogeneousMaterial("Particle", 0, 0)
- material_Substrate = ba.HomogeneousMaterial("Substrate", 7.43e-06, 1.72e-07)
+ material_Substrate = ba.HomogeneousMaterial("Substrate", 7.43e-06,
+ 1.72e-07)
material_Vacuum = ba.HomogeneousMaterial("Vacuum", 0, 0)
# Define form factors
diff --git a/Examples/scatter2d/CosineRipplesAtRectLattice.py b/Examples/scatter2d/CosineRipplesAtRectLattice.py
index 3a7d251956f9eeb264a518842151ffb0b4087862..3beaea3123fafd0a43c3ffaee6ee53de0228b665 100644
--- a/Examples/scatter2d/CosineRipplesAtRectLattice.py
+++ b/Examples/scatter2d/CosineRipplesAtRectLattice.py
@@ -53,7 +53,8 @@ def get_sample():
def get_simulation(sample):
beam = ba.Beam(1, 0.16*nm, ba.Direction(0.3*deg, 0))
- detector = ba.SphericalDetector(100, -1.5*deg, 1.5*deg, 100, 0, 2.5*deg)
+ detector = ba.SphericalDetector(100, -1.5*deg, 1.5*deg, 100, 0,
+ 2.5*deg)
simulation = ba.GISASSimulation(beam, sample, detector)
return simulation
diff --git a/Examples/scatter2d/Cylinders.py b/Examples/scatter2d/Cylinders.py
index 6006762bdfbe134271864af887ed36efc40e49a0..4ebc23eadc386cc8dba31470a41ed47d96def09d 100755
--- a/Examples/scatter2d/Cylinders.py
+++ b/Examples/scatter2d/Cylinders.py
@@ -42,7 +42,7 @@ def get_simulation(sample):
beam = ba.Beam(1, wavelength, ba.Direction(alpha_i, 0))
# Define detector
- nPix = 200 # pixels per direction
+ nPix = 200 # pixels per direction
detector = ba.SphericalDetector(nPix, -2*deg, 2*deg, nPix, 0, 3*deg)
return ba.GISASSimulation(beam, sample, detector)
diff --git a/Examples/scatter2d/CylindersWithSizeDistribution.py b/Examples/scatter2d/CylindersWithSizeDistribution.py
index ebf733b3f34a8f24da4ab0e8d46f0bd93dced5a9..976c0572e1bde5fccc90e91f24b83a6e38e9d783 100644
--- a/Examples/scatter2d/CylindersWithSizeDistribution.py
+++ b/Examples/scatter2d/CylindersWithSizeDistribution.py
@@ -24,8 +24,8 @@ def get_sample():
# Define particles with parameter following a distribution
distr_1 = ba.DistributionGaussian(5*nm, 1*nm)
- par_distr_1 = ba.ParameterDistribution("/Particle/Cylinder/Radius", distr_1,
- 100, 2)
+ par_distr_1 = ba.ParameterDistribution("/Particle/Cylinder/Radius",
+ distr_1, 100, 2)
particle_distrib = ba.ParticleDistribution(particle, par_distr_1)
# Define particle layouts
diff --git a/Examples/scatter2d/DodecahedraSAS.py b/Examples/scatter2d/DodecahedraSAS.py
index d95abd1ff1a092a3531c1d9aad09a7ed60cf9e8f..da5cc69801a42b24599c6d8a2840a02ba81ea7c4 100755
--- a/Examples/scatter2d/DodecahedraSAS.py
+++ b/Examples/scatter2d/DodecahedraSAS.py
@@ -19,8 +19,8 @@ def get_sample():
layout = ba.ParticleLayout()
layout.addParticle(particle)
solution_layer = ba.Layer(m_solution, 1000*nm)
- # TODO: make intensity proportional to thickness,
- # https://github.com/scgmlz/BornAgain/issues/1222
+ # TODO: make intensity proportional to thickness,
+ # https://github.com/scgmlz/BornAgain/issues/1222
solution_layer.addLayout(layout)
# Flat sample layer sandwiched between semi-infinite vacuum layers:
@@ -36,9 +36,9 @@ def get_simulation(sample):
beam = ba.Beam(1, 0.4*nm, ba.Direction(90*deg, 0))
# Detector opposite to source:
- detPos = 2000 # distance from sample center to detector in mm
- detWid = 500 # detector width in mm
- detPix = 200 # number of pixels per direction
+ detPos = 2000 # distance from sample center to detector in mm
+ detWid = 500 # detector width in mm
+ detPix = 200 # number of pixels per direction
det = ba.RectangularDetector(detPix, detWid, detPix, detWid)
det.setPerpendicularToDirectBeam(detPos, detWid/2, detWid/2)
diff --git a/Examples/scatter2d/Interference2DLatticeSumOfRotated.py b/Examples/scatter2d/Interference2DLatticeSumOfRotated.py
index 7b087346fc5e10ecf07d47908b4619b81645bfb7..c6dda65aa8875daefb406ccda6c70b50cb5a7370 100644
--- a/Examples/scatter2d/Interference2DLatticeSumOfRotated.py
+++ b/Examples/scatter2d/Interference2DLatticeSumOfRotated.py
@@ -41,7 +41,8 @@ def get_simulation(sample):
detector = ba.SphericalDetector(100, 2*deg, 1*deg, 1*deg)
simulation = ba.GISASSimulation(beam, sample, detector)
distr_1 = ba.DistributionGate(0, 240*deg)
- simulation.addParameterDistribution("*/SquareLattice2D/Xi", distr_1, 3, 0)
+ simulation.addParameterDistribution("*/SquareLattice2D/Xi", distr_1, 3,
+ 0)
return simulation
diff --git a/Examples/scatter2d/Interference2DRotatedSquareLattice.py b/Examples/scatter2d/Interference2DRotatedSquareLattice.py
index 6e83cae2931801c0cdf3f15b795b12bbe9d74703..860438958963aab69b0a6f48ecd1ea839829fed4 100644
--- a/Examples/scatter2d/Interference2DRotatedSquareLattice.py
+++ b/Examples/scatter2d/Interference2DRotatedSquareLattice.py
@@ -27,8 +27,8 @@ def get_sample():
# Define interference functions
iff = ba.InterferenceFunction2DLattice(lattice)
- iff_pdf = ba.FTDecayFunction2DCauchy(47.7464829276*nm, 15.9154943092*nm,
- 30*deg)
+ iff_pdf = ba.FTDecayFunction2DCauchy(47.7464829276*nm,
+ 15.9154943092*nm, 30*deg)
iff.setDecayFunction(iff_pdf)
# Define particle layouts
diff --git a/Examples/scatter2d/MagneticSpheres.py b/Examples/scatter2d/MagneticSpheres.py
index ac09edd7e0f897e2d051710b6f7879f1eb680667..47270df3829b5f92ba6806396bac22fc3d33e6b4 100644
--- a/Examples/scatter2d/MagneticSpheres.py
+++ b/Examples/scatter2d/MagneticSpheres.py
@@ -15,7 +15,8 @@ def get_sample():
magnetic_field = kvector_t(0, 0, 10000000)
material_Particle = ba.HomogeneousMaterial("Particle", 2e-05, 4e-07,
magnetic_field)
- material_Substrate = ba.HomogeneousMaterial("Substrate", 7e-06, 1.8e-07)
+ material_Substrate = ba.HomogeneousMaterial("Substrate", 7e-06,
+ 1.8e-07)
material_Vacuum = ba.HomogeneousMaterial("Vacuum", 0, 0)
# Define form factors
diff --git a/Examples/scatter2d/RectangularGrating.py b/Examples/scatter2d/RectangularGrating.py
index 9fbe9f5a263704ffa08b8e562b24029aa341ff23..93693afebbb3f15812c6f4d521f1f0cc24eba337 100644
--- a/Examples/scatter2d/RectangularGrating.py
+++ b/Examples/scatter2d/RectangularGrating.py
@@ -55,7 +55,8 @@ def get_sample(lattice_rotation_angle=0*deg):
def get_simulation(sample):
beam = ba.Beam(100000000, 0.134*nm, ba.Direction(0.4*deg, 0))
- detector = ba.SphericalDetector(200, -0.5*deg, 0.5*deg, 200, 0, 0.6*deg)
+ detector = ba.SphericalDetector(200, -0.5*deg, 0.5*deg, 200, 0,
+ 0.6*deg)
simulation = ba.GISASSimulation(beam, sample, detector)
simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
diff --git a/Examples/scatter2d/TriangularRipple.py b/Examples/scatter2d/TriangularRipple.py
index dbc832090f50895854048a4cca4ab372b59a61be..3087b065b6d9debc0a225beac10f24f4e91c3e0c 100644
--- a/Examples/scatter2d/TriangularRipple.py
+++ b/Examples/scatter2d/TriangularRipple.py
@@ -54,7 +54,8 @@ def get_sample():
def get_simulation(sample):
beam = ba.Beam(1, 0.16*nm, ba.Direction(0.3*deg, 0))
- detector = ba.SphericalDetector(200, -1.5*deg, 1.5*deg, 200, 0, 2.5*deg)
+ detector = ba.SphericalDetector(200, -1.5*deg, 1.5*deg, 200, 0,
+ 2.5*deg)
simulation = ba.GISASSimulation(beam, sample, detector)
return simulation
diff --git a/Examples/specular/BeamAngularDivergence.py b/Examples/specular/BeamAngularDivergence.py
index 8c6a75c04b01758559eeb8e05b3b4324c1cb5598..41190fd742fb89729428e14e16e04e09bb70436c 100755
--- a/Examples/specular/BeamAngularDivergence.py
+++ b/Examples/specular/BeamAngularDivergence.py
@@ -11,7 +11,7 @@ from matplotlib import pyplot as plt
# input parameters
wavelength = 1.54*angstrom
-alpha_i_min = 0 # min incident angle, deg
+alpha_i_min = 0 # min incident angle, deg
alpha_i_max = 2*deg # max incident angle, rad
beam_sample_ratio = 0.01 # beam-to-sample size ratio
@@ -76,7 +76,8 @@ def get_simulation(sample, scan_size=500):
footprint = ba.FootprintSquare(beam_sample_ratio)
alpha_distr = ba.RangedDistributionGaussian(n_points, n_sig)
- scan = ba.AngularSpecScan(wavelength, scan_size, alpha_i_min, alpha_i_max)
+ scan = ba.AngularSpecScan(wavelength, scan_size, alpha_i_min,
+ alpha_i_max)
scan.setFootprintFactor(footprint)
scan.setAbsoluteAngularResolution(alpha_distr, d_ang)
diff --git a/Examples/specular/BeamFullDivergence.py b/Examples/specular/BeamFullDivergence.py
index 382342164b215be0c67ecae95da3a6bd939c8068..79a342412cc2e4f4c64d5cb3932f3036203a6ac7 100755
--- a/Examples/specular/BeamFullDivergence.py
+++ b/Examples/specular/BeamFullDivergence.py
@@ -8,8 +8,8 @@ from bornagain import angstrom, deg
# input parameters
wavelength = 1.54*angstrom
-alpha_i_min = 0 # min incident angle, deg
-alpha_i_max = 2*deg # max incident angle, rad
+alpha_i_min = 0 # min incident angle, deg
+alpha_i_max = 2*deg # max incident angle, rad
# convolution parameters
d_wl = 0.01*wavelength # spread width for wavelength
@@ -59,7 +59,8 @@ def get_simulation(sample, scan_size=500):
alpha_distr = ba.RangedDistributionGaussian(n_points, n_sig)
wavelength_distr = ba.RangedDistributionGaussian(n_points, n_sig)
- scan = ba.AngularSpecScan(wavelength, scan_size, alpha_i_min, alpha_i_max)
+ scan = ba.AngularSpecScan(wavelength, scan_size, alpha_i_min,
+ alpha_i_max)
scan.setAbsoluteAngularResolution(alpha_distr, d_ang)
scan.setAbsoluteWavelengthResolution(wavelength_distr, d_wl)
diff --git a/Examples/varia/AxesInDifferentUnits.py b/Examples/varia/AxesInDifferentUnits.py
index b6ea0eb5ab69f377f640b19ad6a78379abea23f5..db767965c5d82541bb95bfb62a06560a72c048e7 100644
--- a/Examples/varia/AxesInDifferentUnits.py
+++ b/Examples/varia/AxesInDifferentUnits.py
@@ -54,7 +54,8 @@ def get_simulation(sample):
pilatus_npx, pilatus_npy = 981, 1043 # number of pixels
width = pilatus_npx*pilatus_pixel_size
height = pilatus_npy*pilatus_pixel_size
- detector = ba.RectangularDetector(pilatus_npx, width, pilatus_npy, height)
+ detector = ba.RectangularDetector(pilatus_npx, width, pilatus_npy,
+ height)
detector.setPerpendicularToSampleX(detector_distance, width/2., 0)
simulation = ba.GISASSimulation(beam, sample, detector)
@@ -110,7 +111,11 @@ def plot(result):
ylabel=r'$Q_{z} [1/nm]$',
zlabel=None)
- plt.subplots_adjust(left=0.07, right=0.97, top=0.9, bottom=0.1, hspace=0.25)
+ plt.subplots_adjust(left=0.07,
+ right=0.97,
+ top=0.9,
+ bottom=0.1,
+ hspace=0.25)
plt.show()
diff --git a/Examples/varia/BasicPolarizedReflectometry.py b/Examples/varia/BasicPolarizedReflectometry.py
index 7c40e593ac065044382a10f9c549ce6669edecc2..db9ea9c179a4aaceed08650f3f73a87f4ff5d665 100644
--- a/Examples/varia/BasicPolarizedReflectometry.py
+++ b/Examples/varia/BasicPolarizedReflectometry.py
@@ -18,7 +18,8 @@ def get_sample():
# Define materials
material_Ambient = ba.MaterialBySLD("Ambient", 0, 0)
magnetic_field = kvector_t(0, 100000000, 0)
- material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08, magnetic_field)
+ material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08,
+ magnetic_field)
material_Substrate = ba.MaterialBySLD("Substrate", 7e-05, 2e-06)
# Define layers
@@ -80,6 +81,8 @@ def plot(data, labels):
if __name__ == '__main__':
- results_pp = run_simulation(ba.kvector_t(0, 1, 0), ba.kvector_t(0, 1, 0))
- results_mm = run_simulation(ba.kvector_t(0, -1, 0), ba.kvector_t(0, -1, 0))
+ results_pp = run_simulation(ba.kvector_t(0, 1, 0),
+ ba.kvector_t(0, 1, 0))
+ results_mm = run_simulation(ba.kvector_t(0, -1, 0),
+ ba.kvector_t(0, -1, 0))
plot([results_pp, results_mm], ["$++$", "$--$"])
diff --git a/Examples/varia/DepthProbe.py b/Examples/varia/DepthProbe.py
index bc6224776f0231e4b614254ea47b07ef3823815a..3b2914bea93ff30df19f8d18b1c398a5c15dd711 100644
--- a/Examples/varia/DepthProbe.py
+++ b/Examples/varia/DepthProbe.py
@@ -92,8 +92,8 @@ def get_simulation(sample):
simulation = ba.DepthProbeSimulation()
simulation.setBeamParameters(wl, n_ai_bins, ai_min, ai_max, footprint)
simulation.setZSpan(n_z_bins, z_min, z_max)
- simulation.addParameterDistribution("*/Beam/InclinationAngle", alpha_distr,
- n_points, n_sig)
+ simulation.addParameterDistribution("*/Beam/InclinationAngle",
+ alpha_distr, n_points, n_sig)
simulation.setSample(sample)
return simulation
diff --git a/Examples/varia/LargeParticlesFormFactor.py b/Examples/varia/LargeParticlesFormFactor.py
index da2d80b000eaa9a2d359a4c1328bcf9a63858bdc..7604ec12bd41ae4e06a0c54c605d3863170042ae 100644
--- a/Examples/varia/LargeParticlesFormFactor.py
+++ b/Examples/varia/LargeParticlesFormFactor.py
@@ -107,7 +107,9 @@ def simulate_and_plot():
zmin = condition['zmin']
zmax = condition['zmax']
- ba_plot.plot_colormap(result, intensity_min=zmin, intensity_max=zmax)
+ ba_plot.plot_colormap(result,
+ intensity_min=zmin,
+ intensity_max=zmax)
plt.text(0,
2.1,
diff --git a/Examples/varia/PolarizedNoAnalyzer.py b/Examples/varia/PolarizedNoAnalyzer.py
index 143518cca37d97ec0fcb2f7339d6f4b42b45c5ef..ea19f15aad87d00ba808f3a712595127b501ce01 100644
--- a/Examples/varia/PolarizedNoAnalyzer.py
+++ b/Examples/varia/PolarizedNoAnalyzer.py
@@ -18,7 +18,8 @@ def get_sample():
# Define materials
material_Ambient = ba.MaterialBySLD("Ambient", 0, 0)
magnetic_field = kvector_t(50000000, 86602540.3784, 0)
- material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08, magnetic_field)
+ material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08,
+ magnetic_field)
material_Substrate = ba.MaterialBySLD("Substrate", 7e-05, 2e-06)
# Define layers
@@ -80,7 +81,8 @@ def plot(axis, data, labels):
if __name__ == '__main__':
- q, results_pp = run_simulation(ba.kvector_t(0, 1, 0), ba.kvector_t(0, 1, 0))
+ q, results_pp = run_simulation(ba.kvector_t(0, 1, 0),
+ ba.kvector_t(0, 1, 0))
q, results_mm = run_simulation(ba.kvector_t(0, -1, 0),
ba.kvector_t(0, -1, 0))
diff --git a/Examples/varia/PolarizedNonperfectAnalyzerPolarizer.py b/Examples/varia/PolarizedNonperfectAnalyzerPolarizer.py
index a22a3f0cca7ab141d8881c721564012e0d366247..8a9c670e8a5ec5b9a8f3f3ea4a4f512854782f6a 100644
--- a/Examples/varia/PolarizedNonperfectAnalyzerPolarizer.py
+++ b/Examples/varia/PolarizedNonperfectAnalyzerPolarizer.py
@@ -16,9 +16,9 @@ sldMgO = (5.9803e-06, 9.3996e-12)
magnetizationMagnitude = 1.6e6
angle = 0
-magnetizationVector = ba.kvector_t(magnetizationMagnitude*numpy.sin(angle*deg),
- magnetizationMagnitude*numpy.cos(angle*deg),
- 0)
+magnetizationVector = ba.kvector_t(
+ magnetizationMagnitude*numpy.sin(angle*deg),
+ magnetizationMagnitude*numpy.cos(angle*deg), 0)
def get_sample(*, magnetization=magnetizationVector):
@@ -83,8 +83,8 @@ def run_simulation(*,
simulation = get_simulation(sample)
simulation.beam().setPolarization(polarization*polarizer_efficiency)
- simulation.detector().setAnalyzerProperties(analyzer, analyzer_efficiency,
- 0.5)
+ simulation.detector().setAnalyzerProperties(analyzer,
+ analyzer_efficiency, 0.5)
simulation.setBackground(ba.ConstantBackground(1e-7))
diff --git a/Examples/varia/PolarizedSANS.py b/Examples/varia/PolarizedSANS.py
index 0dfbdbfdf0e452a687f163f093461a52a3593039..f4ad3defd97c68a4ac5be2e92ff3c711beb69570 100644
--- a/Examples/varia/PolarizedSANS.py
+++ b/Examples/varia/PolarizedSANS.py
@@ -18,7 +18,8 @@ def get_sample():
# Define materials
magnetic_field = kvector_t(0, 0, 10000000)
- material_Core = ba.HomogeneousMaterial("Core", 6e-06, 2e-08, magnetic_field)
+ material_Core = ba.HomogeneousMaterial("Core", 6e-06, 2e-08,
+ magnetic_field)
material_Shell = ba.HomogeneousMaterial("Shell", 1e-07, 2e-08)
material_Solvent = ba.HomogeneousMaterial("Solvent", 5e-06, 0)
@@ -59,7 +60,8 @@ def get_simulation(sample):
simulation = ba.GISASSimulation()
# Defining detector
- simulation.setDetectorParameters(200, -3*deg, 3*deg, 200, -3*deg, 3*deg)
+ simulation.setDetectorParameters(200, -3*deg, 3*deg, 200, -3*deg,
+ 3*deg)
# Defining beam parameters
simulation.setBeamParameters(0.5*nm, 0, 0)
diff --git a/Examples/varia/PolarizedSpinAsymmetry.py b/Examples/varia/PolarizedSpinAsymmetry.py
index 5caeac35afbc5c8ac8b3f253dcdd3dcf58432ddd..0b5a89dcf3451eedcbbc4e88565d2ec597b65c5a 100644
--- a/Examples/varia/PolarizedSpinAsymmetry.py
+++ b/Examples/varia/PolarizedSpinAsymmetry.py
@@ -53,8 +53,8 @@ def get_sample(params):
magnetizationMagnitude*numpy.cos(angle*deg), 0)
mat_vacuum = ba.MaterialBySLD("Vacuum", 0, 0)
- mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4", params["rho_Mafo"]*1e-6, 0,
- magnetizationVector)
+ mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4", params["rho_Mafo"]*1e-6,
+ 0, magnetizationVector)
mat_substrate = ba.MaterialBySLD("MgAl2O4", *sldMao)
ambient_layer = ba.Layer(mat_vacuum)
@@ -174,7 +174,8 @@ def plotSpinAsymmetry(data_pp, data_mm, q, r_pp, r_mm, filename):
fig = plt.figure()
ax = fig.add_subplot(111)
- ax.errorbar(data_pp[0], (data_pp[1] - data_mm[1])/(data_pp[1] + data_mm[1]),
+ ax.errorbar(data_pp[0],
+ (data_pp[1] - data_mm[1])/(data_pp[1] + data_mm[1]),
xerr=data_pp[3],
yerr=delta,
fmt='.',
@@ -241,7 +242,8 @@ def get_Experimental_data(qmin, qmax):
get_Experimental_data.data_mm = data_mm
get_Experimental_data.raw_data = True
- return (filterData(data_pp, qmin, qmax), filterData(data_mm, qmin, qmax))
+ return (filterData(data_pp, qmin,
+ qmax), filterData(data_mm, qmin, qmax))
def downloadAndExtractData():
@@ -257,11 +259,11 @@ def downloadAndExtractData():
read().decode("utf-8")
table_pp = match(
- r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*', rawdata,
- DOTALL).group(1)
+ r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
table_mm = match(
- r'.*# "polarization": "\-\-"\n#.*?\n# "units".*?\n(.*?)#.*', rawdata,
- DOTALL).group(1)
+ r'.*# "polarization": "\-\-"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
data_pp = numpy.genfromtxt(BytesIO(table_pp.encode()), unpack=True)
data_mm = numpy.genfromtxt(BytesIO(table_mm.encode()), unpack=True)
diff --git a/Examples/varia/PolarizedSpinFlip.py b/Examples/varia/PolarizedSpinFlip.py
index b86334c0fa5fa6d33c8d253bff1dd40a682483b9..203c91145aa7888e87bfb79900cf1ae740c46114 100644
--- a/Examples/varia/PolarizedSpinFlip.py
+++ b/Examples/varia/PolarizedSpinFlip.py
@@ -17,7 +17,8 @@ def get_sample():
# Define materials
material_Ambient = ba.MaterialBySLD("Ambient", 0, 0)
magnetic_field = kvector_t(50000000, 86602540.3784, 0)
- material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08, magnetic_field)
+ material_Layer = ba.MaterialBySLD("Layer", 0.0001, 1e-08,
+ magnetic_field)
material_Substrate = ba.MaterialBySLD("Substrate", 7e-05, 2e-06)
# Define layers
@@ -79,11 +80,15 @@ def plot(data, labels):
if __name__ == '__main__':
- results_pp = run_simulation(ba.kvector_t(0, 1, 0), ba.kvector_t(0, 1, 0))
- results_mm = run_simulation(ba.kvector_t(0, -1, 0), ba.kvector_t(0, -1, 0))
-
- results_pm = run_simulation(ba.kvector_t(0, 1, 0), ba.kvector_t(0, -1, 0))
- results_mp = run_simulation(ba.kvector_t(0, -1, 0), ba.kvector_t(0, 1, 0))
+ results_pp = run_simulation(ba.kvector_t(0, 1, 0),
+ ba.kvector_t(0, 1, 0))
+ results_mm = run_simulation(ba.kvector_t(0, -1, 0),
+ ba.kvector_t(0, -1, 0))
+
+ results_pm = run_simulation(ba.kvector_t(0, 1, 0),
+ ba.kvector_t(0, -1, 0))
+ results_mp = run_simulation(ba.kvector_t(0, -1, 0),
+ ba.kvector_t(0, 1, 0))
plot([results_pp, results_mm, results_pm, results_mp],
["$++$", "$--$", "$+-$", "$-+$"])
diff --git a/Tests/Functional/PyCore/histogram2d.py b/Tests/Functional/PyCore/histogram2d.py
index 54cf54b97f8b90047714c61a0c4ca7e0ead4f50a..060ee3d0f7f8fb903c193340b1b53b39fda1bcc3 100644
--- a/Tests/Functional/PyCore/histogram2d.py
+++ b/Tests/Functional/PyCore/histogram2d.py
@@ -34,9 +34,9 @@ class Histogram2DTest(unittest.TestCase):
"""
Testing construction of 2D histogram from numpy array
"""
- arr = numpy.array(
- [[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0], [11, 12, 13, 14, 15.0]],
- dtype=numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0],
+ [11, 12, 13, 14, 15.0]],
+ dtype=numpy.float64)
hist = ba.Histogram2D(arr)
self.assertEqual(hist.getNbinsX(), 5)
@@ -76,9 +76,9 @@ class Histogram2DTest(unittest.TestCase):
"""
Adding to the histogram content from numpy array
"""
- arr = numpy.array(
- [[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0], [11, 12, 13, 14, 15.0]],
- dtype=numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0],
+ [11, 12, 13, 14, 15.0]],
+ dtype=numpy.float64)
hist = ba.Histogram2D(arr)
# adding same content once again
hist.addContent(arr)
@@ -110,9 +110,9 @@ class Histogram2DTest(unittest.TestCase):
"""
Testing newly create object
"""
- arr = numpy.array(
- [[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0], [11, 12, 13, 14, 15.0]],
- dtype=numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5.0], [6, 7, 8, 9, 10.0],
+ [11, 12, 13, 14, 15.0]],
+ dtype=numpy.float64)
hist = self.create_histogram(arr)
arr_from_hist = hist.getArray()
diff --git a/Tests/Functional/PyCore/intensitydata_io.py b/Tests/Functional/PyCore/intensitydata_io.py
index a58b9a5344117a18655243648bc30a305b5f384b..922fea8ea79e122e6d07d7e466e7ec34e9cbb72a 100644
--- a/Tests/Functional/PyCore/intensitydata_io.py
+++ b/Tests/Functional/PyCore/intensitydata_io.py
@@ -77,8 +77,9 @@ class OutputDataIOTest(unittest.TestCase):
def test_04_VariableBinAxis_1D(self):
data = ba.IntensityData()
data.addAxis(
- ba.VariableBinAxis("axis0", 10,
- get_boundaries_flat_in_sin(10, -5*deg, 5*deg)))
+ ba.VariableBinAxis(
+ "axis0", 10, get_boundaries_flat_in_sin(10, -5*deg,
+ 5*deg)))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -87,8 +88,9 @@ class OutputDataIOTest(unittest.TestCase):
def test_05_VariableBinAxis_2D(self):
data = ba.IntensityData()
data.addAxis(
- ba.VariableBinAxis("axis0", 10,
- get_boundaries_flat_in_sin(10, -5*deg, 5*deg)))
+ ba.VariableBinAxis(
+ "axis0", 10, get_boundaries_flat_in_sin(10, -5*deg,
+ 5*deg)))
data.addAxis(
ba.VariableBinAxis("axis1", 3,
get_boundaries_flat_in_sin(3, 0, 2*deg)))
@@ -155,13 +157,15 @@ class OutputDataIOTest(unittest.TestCase):
self.assertTrue(is_the_same_data(data, newdata))
def test_SaveNumpyArray_ReadOutputData(self):
- arr = numpy.array([[0, 1, 2, 3.0], [4, 5, 6, 7.0], [8, 9, 10, 11.0]])
+ arr = numpy.array([[0, 1, 2, 3.0], [4, 5, 6, 7.0],
+ [8, 9, 10, 11.0]])
numpy.savetxt('tmp.txt', arr)
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.txt")
self.assertTrue(numpy.array_equal(newdata.getArray(), arr))
def test_SaveNumpyArray_ReadRawDataVector(self):
- arr = numpy.array([[0, 1, 2, 3.0], [4, 5, 6, 7.0], [8, 9, 10, 11.0]])
+ arr = numpy.array([[0, 1, 2, 3.0], [4, 5, 6, 7.0],
+ [8, 9, 10, 11.0]])
numpy.savetxt('tmp.txt', arr)
newdata = numpy.array(
ba.IntensityDataIOFactory.readOutputData(
diff --git a/Tests/Functional/PyCore/mesocrystal1.py b/Tests/Functional/PyCore/mesocrystal1.py
index f59d36e8b3879513dd78cb2397ba9627e15f4838..68fc2d2824bb34f14d8562580ef05fe15bf1f961 100644
--- a/Tests/Functional/PyCore/mesocrystal1.py
+++ b/Tests/Functional/PyCore/mesocrystal1.py
@@ -33,20 +33,23 @@ class MySampleBuilder(ISampleBuilder):
"lattice_length_c", ctypes.addressof(
self.lattice_length_c)).setUnit("nm").setNonnegative()
self.registerParameter(
- "nanoparticle_radius", ctypes.addressof(
+ "nanoparticle_radius",
+ ctypes.addressof(
self.nanoparticle_radius)).setUnit("nm").setNonnegative()
self.registerParameter(
"sigma_nanoparticle_radius",
- ctypes.addressof(
- self.sigma_nanoparticle_radius)).setUnit("nm").setNonnegative()
- self.registerParameter("meso_height", ctypes.addressof(
- self.meso_height)).setUnit("nm").setNonnegative()
- self.registerParameter("meso_radius", ctypes.addressof(
- self.meso_radius)).setUnit("nm").setNonnegative()
+ ctypes.addressof(self.sigma_nanoparticle_radius)).setUnit(
+ "nm").setNonnegative()
+ self.registerParameter(
+ "meso_height", ctypes.addressof(
+ self.meso_height)).setUnit("nm").setNonnegative()
+ self.registerParameter(
+ "meso_radius", ctypes.addressof(
+ self.meso_radius)).setUnit("nm").setNonnegative()
self.registerParameter(
"sigma_lattice_length_a",
- ctypes.addressof(
- self.sigma_lattice_length_a)).setUnit("nm").setNonnegative()
+ ctypes.addressof(self.sigma_lattice_length_a)).setUnit(
+ "nm").setNonnegative()
self.registerParameter(
"surface_filling_ratio",
ctypes.addressof(self.surface_filling_ratio)).setNonnegative()
@@ -61,11 +64,13 @@ class MySampleBuilder(ISampleBuilder):
n_particle = complex(1.0 - 2.84e-5, 4.7e-7)
avg_n_squared_meso = complex(0.7886*n_particle*n_particle + 0.2114)
n_avg = complex(
- numpy.sqrt(self.surface_filling_ratio.value*avg_n_squared_meso +
- 1.0 - self.surface_filling_ratio.value))
+ numpy.sqrt(self.surface_filling_ratio.value*
+ avg_n_squared_meso + 1.0 -
+ self.surface_filling_ratio.value))
n_particle_adapted = complex(
numpy.sqrt(n_avg*n_avg + n_particle*n_particle - 1))
- ff = FormFactorCylinder(self.meso_radius.value, self.meso_height.value)
+ ff = FormFactorCylinder(self.meso_radius.value,
+ self.meso_height.value)
# Create multilayer
p_multi_layer = MultiLayer()
@@ -73,8 +78,10 @@ class MySampleBuilder(ISampleBuilder):
n_substrate = complex(1.0 - 7.57e-6, 1.73e-7)
p_vacuum_material = HomogeneousMaterial("Vacuum", n_air)
- p_average_layer_material = HomogeneousMaterial("Averagelayer", n_avg)
- p_substrate_material = HomogeneousMaterial("Substrate", n_substrate)
+ p_average_layer_material = HomogeneousMaterial(
+ "Averagelayer", n_avg)
+ p_substrate_material = HomogeneousMaterial("Substrate",
+ n_substrate)
vacuum_layer = Layer(p_vacuum_material)
avg_layer = Layer(p_average_layer_material, self.meso_height.value)
substrate_layer = Layer(p_substrate_material)
@@ -144,7 +151,8 @@ class MySampleBuilder(ISampleBuilder):
# create lattice
# -------------------------------------------------------------------------
def createLattice(self, stacking_radius_a, stacking_radius_c):
- result = HexagonalLattice(stacking_radius_a*2, stacking_radius_c*2*2.3)
+ result = HexagonalLattice(stacking_radius_a*2,
+ stacking_radius_c*2*2.3)
result.setSelectionRule(SimpleSelectionRule(-1, 1, 1, 3))
return result
diff --git a/Tests/Functional/PyCore/parameterpool.py b/Tests/Functional/PyCore/parameterpool.py
index b85d3851c0748581b3041461ebc72dbb5b5953ec..c49ab84b92032711cc1d9cfe8f0f8bb6d93d9577 100644
--- a/Tests/Functional/PyCore/parameterpool.py
+++ b/Tests/Functional/PyCore/parameterpool.py
@@ -18,8 +18,9 @@ class ParameterPoolTest(unittest.TestCase):
pool = particle.parameterPool()
self.assertEqual(pool.size(), 4)
- self.assertEqual(pool.parameterNames(),
- ('Abundance', 'PositionX', 'PositionY', 'PositionZ'))
+ self.assertEqual(
+ pool.parameterNames(),
+ ('Abundance', 'PositionX', 'PositionY', 'PositionZ'))
expected = {
'Abundance': 1,
diff --git a/Tests/Functional/PyCore/polmagcylinders1.py b/Tests/Functional/PyCore/polmagcylinders1.py
index f86c25e9a99b77d62c715778a9e115e8e00aa1c3..c5c9fb0746786239ad8148b50bb8b6702ba31fad 100644
--- a/Tests/Functional/PyCore/polmagcylinders1.py
+++ b/Tests/Functional/PyCore/polmagcylinders1.py
@@ -53,7 +53,8 @@ def run_test():
result = runSimulation()
# ba.IntensityDataIOFactory.writeIntensityData(result, 'polmagcylinders1_reference.int')
- reference = utils.get_reference_data('polmagcylinders1_reference.int.gz')
+ reference = utils.get_reference_data(
+ 'polmagcylinders1_reference.int.gz')
diff = utils.get_difference(result.array(), reference.getArray())
diff --git a/Tests/Functional/PyCore/polmagcylinders2.py b/Tests/Functional/PyCore/polmagcylinders2.py
index 454870959e829d6207c3b81fd28274e81a7e32e0..9a94fd39dce7f8acb788608b155e34cf3f503acd 100644
--- a/Tests/Functional/PyCore/polmagcylinders2.py
+++ b/Tests/Functional/PyCore/polmagcylinders2.py
@@ -20,7 +20,8 @@ def getSimulationIntensity(rho_beam, efficiency):
magnetization = kvector_t(0, 1e6, 0)
- magParticle = HomogeneousMaterial("magParticle", 5e-6, 0, magnetization)
+ magParticle = HomogeneousMaterial("magParticle", 5e-6, 0,
+ magnetization)
# collection of particles
cylinder_ff = FormFactorCylinder(5*nm, 5*nm)
cylinder = Particle(magParticle, cylinder_ff)
@@ -79,16 +80,20 @@ def run_test():
diff = 0.0
diff += get_difference(
getSimulationIntensity(zplus, 1).array(),
- get_reference_data('polmagcylinders2_reference_00.int.gz').getArray())
+ get_reference_data(
+ 'polmagcylinders2_reference_00.int.gz').getArray())
diff += get_difference(
getSimulationIntensity(zplus, -1).array(),
- get_reference_data('polmagcylinders2_reference_01.int.gz').getArray())
+ get_reference_data(
+ 'polmagcylinders2_reference_01.int.gz').getArray())
diff += get_difference(
getSimulationIntensity(zmin, 1).array(),
- get_reference_data('polmagcylinders2_reference_10.int.gz').getArray())
+ get_reference_data(
+ 'polmagcylinders2_reference_10.int.gz').getArray())
diff += get_difference(
getSimulationIntensity(zmin, -1).array(),
- get_reference_data('polmagcylinders2_reference_11.int.gz').getArray())
+ get_reference_data(
+ 'polmagcylinders2_reference_11.int.gz').getArray())
diff /= 4.0
status = "OK"
diff --git a/Tests/Functional/PyCore/samplebuilder.py b/Tests/Functional/PyCore/samplebuilder.py
index 104516a04fb92b33b0405fdfe4de54614e9890d2..e2be45ea8c3fcd1385278b2bb6bbef5d4fd3323f 100644
--- a/Tests/Functional/PyCore/samplebuilder.py
+++ b/Tests/Functional/PyCore/samplebuilder.py
@@ -49,10 +49,11 @@ class BuilderPrototype(ba.ISampleBuilder):
" in given class")
# defining the name for new ctype variable and creating dynamic attribute
wrapper_key = "wrapper_" + var_key
- setattr(self, wrapper_key, ctypes.c_double(self.__dict__.get(var_key)))
+ setattr(self, wrapper_key,
+ ctypes.c_double(self.__dict__.get(var_key)))
# registering new attribute in BornAgain
- self.registerParameter(par_name,
- ctypes.addressof(getattr(self, wrapper_key)))
+ self.registerParameter(
+ par_name, ctypes.addressof(getattr(self, wrapper_key)))
class SampleBuilderTest(unittest.TestCase):
diff --git a/Tests/Functional/PyCore/sliced_composition.py b/Tests/Functional/PyCore/sliced_composition.py
index a6e1055ced71aab33ae84e7f9d93d8456d3f2aad..a882b1378f264aedd037f67e58cd02941b435a88 100644
--- a/Tests/Functional/PyCore/sliced_composition.py
+++ b/Tests/Functional/PyCore/sliced_composition.py
@@ -55,13 +55,13 @@ class SlicedSpheresTest(unittest.TestCase):
topCup = ba.Particle(
top_material,
- ba.FormFactorTruncatedSphere(sphere_radius,
- sphere_radius*2 - bottom_cup_height,
- 0))
+ ba.FormFactorTruncatedSphere(
+ sphere_radius, sphere_radius*2 - bottom_cup_height, 0))
bottomCup = ba.Particle(
bottom_material,
- ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius*2,
- sphere_radius*2 - bottom_cup_height))
+ ba.FormFactorTruncatedSphere(
+ sphere_radius, sphere_radius*2,
+ sphere_radius*2 - bottom_cup_height))
# origin of resulting sphere will be at the bottom
result = ba.ParticleComposition()
@@ -79,12 +79,12 @@ class SlicedSpheresTest(unittest.TestCase):
topCup = ba.Particle(
top_material,
- ba.FormFactorTruncatedSphere(sphere_radius,
- sphere_radius*2 - bottom_cup_height,
- 0))
+ ba.FormFactorTruncatedSphere(
+ sphere_radius, sphere_radius*2 - bottom_cup_height, 0))
bottomCup = ba.Particle(
bottom_material,
- ba.FormFactorTruncatedSphere(sphere_radius, bottom_cup_height, 0))
+ ba.FormFactorTruncatedSphere(sphere_radius, bottom_cup_height,
+ 0))
bottomCup.setRotation(ba.RotationX(180*deg))
# origin of resulting sphere will be at the bottom
@@ -102,7 +102,8 @@ class SlicedSpheresTest(unittest.TestCase):
"""
# spherical particle
- sphere = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
+ sphere = ba.Particle(mParticle,
+ ba.FormFactorFullSphere(sphere_radius))
reference = self.get_result(sphere)
# spherical composition
@@ -164,7 +165,8 @@ class SlicedSpheresTest(unittest.TestCase):
shift = 3*nm
# spherical particle
- sphere = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
+ sphere = ba.Particle(mParticle,
+ ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -shift)
reference = self.get_result(sphere)
@@ -189,9 +191,8 @@ class SlicedSpheresTest(unittest.TestCase):
# truncated sphere on top of substrate with height 16nm
truncatedSphere = ba.Particle(
mParticle,
- ba.FormFactorTruncatedSphere(sphere_radius,
- sphere_radius*2 - bottom_cup_height,
- 0))
+ ba.FormFactorTruncatedSphere(
+ sphere_radius, sphere_radius*2 - bottom_cup_height, 0))
reference = self.get_result(truncatedSphere)
# Particle composition, top part made of same material, as particle. Bottom part made of same material as substrate.
diff --git a/Tests/Functional/PyCore/sliced_spheres.py b/Tests/Functional/PyCore/sliced_spheres.py
index 1e51b8d561ee886749c02b625f4111c771df0f5f..2116b4093636274e3f4c744809c4d3710195ab12 100644
--- a/Tests/Functional/PyCore/sliced_spheres.py
+++ b/Tests/Functional/PyCore/sliced_spheres.py
@@ -60,11 +60,13 @@ class SlicedSpheresTest(unittest.TestCase):
truncatedSphere = ba.Particle(
mSubstrate,
ba.FormFactorTruncatedSphere(sphere_radius,
- sphere_radius*2 - sphere_shift, 0))
+ sphere_radius*2 - sphere_shift,
+ 0))
reference = self.get_result(truncatedSphere)
# sphere crossing interface to look like truncated sphere above
- sphere = ba.Particle(mSubstrate, ba.FormFactorFullSphere(sphere_radius))
+ sphere = ba.Particle(mSubstrate,
+ ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -sphere_shift)
data = self.get_result(sphere)
@@ -90,7 +92,8 @@ class SlicedSpheresTest(unittest.TestCase):
reference = self.get_result(truncatedSphere)
# sphere crossing interface to look like truncated sphere above
- sphere = ba.Particle(mAmbience, ba.FormFactorFullSphere(sphere_radius))
+ sphere = ba.Particle(mAmbience,
+ ba.FormFactorFullSphere(sphere_radius))
sphere.setPosition(0, 0, -sphere_shift)
data = self.get_result(sphere)
@@ -111,12 +114,14 @@ class SlicedSpheresTest(unittest.TestCase):
sphere_shift = 4.0 # shift beneath interface in absolute units
# Sphere intended for vacuum layer and crossing interface
- sphere1 = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
+ sphere1 = ba.Particle(mParticle,
+ ba.FormFactorFullSphere(sphere_radius))
sphere1.setPosition(0, 0, -sphere_shift)
reference = self.get_result(particle_to_air=sphere1)
# Sphere intended for substrate layer and crossing interface
- sphere2 = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
+ sphere2 = ba.Particle(mParticle,
+ ba.FormFactorFullSphere(sphere_radius))
sphere2.setPosition(0, 0, -sphere_shift)
data = self.get_result(particle_to_substrate=sphere2)
diff --git a/Tests/Functional/PyCore/transform_BoxComposition.py b/Tests/Functional/PyCore/transform_BoxComposition.py
index fc40e1d89954834ed31de07f800dfc7dfaac0e92..d9e528cc0a26b01e970bc3c68d0b4e25b81101ed 100644
--- a/Tests/Functional/PyCore/transform_BoxComposition.py
+++ b/Tests/Functional/PyCore/transform_BoxComposition.py
@@ -57,7 +57,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 10.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxComposition.int")
@@ -89,7 +90,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 20.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateX.int")
@@ -120,7 +122,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 50.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateY.int")
@@ -152,7 +155,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 10.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateZ.int")
@@ -184,7 +188,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 20.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateZandY.int")
@@ -216,7 +221,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
height = 50.0
particle = Particle(particle_material,
FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2))
+ particle.setPosition(
+ kvector_t(0, 0, -layer_thickness/2.0 - height/2))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxStackComposition.int")
@@ -227,16 +233,18 @@ class TransformBoxCompositionTest(unittest.TestCase):
box1_length = 20.0
box1_width = 50.0
box1_height = 5.0
- box1 = Particle(particle_material,
- FormFactorBox(box1_length, box1_width, box1_height))
+ box1 = Particle(
+ particle_material,
+ FormFactorBox(box1_length, box1_width, box1_height))
box1.setRotation(RotationZ(90*deg))
# box2 (5,20,50), rotatedY
box2_length = 5.0
box2_width = 20.0
box2_height = 50.0
- box2 = Particle(particle_material,
- FormFactorBox(box2_length, box2_width, box2_height))
+ box2 = Particle(
+ particle_material,
+ FormFactorBox(box2_length, box2_width, box2_height))
box2.setRotation(RotationY(90*deg))
box2.setPosition(kvector_t(-box2_height/2, 0, box2_length/2))
diff --git a/Tests/Functional/PyCore/transform_CoreShellBox.py b/Tests/Functional/PyCore/transform_CoreShellBox.py
index 3bc46c3e25d8c056255bab2a2a9bd68578bcdcd2..dc37f876a40ed37b7629deb149e2ccf209e65e41 100644
--- a/Tests/Functional/PyCore/transform_CoreShellBox.py
+++ b/Tests/Functional/PyCore/transform_CoreShellBox.py
@@ -61,10 +61,10 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_length = shell_length/2.0
core_width = shell_width/2.0
core_height = shell_height/2.0
- shell = Particle(mCore,
- FormFactorBox(shell_length, shell_width, shell_height))
- core = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
+ shell = Particle(
+ mCore, FormFactorBox(shell_length, shell_width, shell_height))
+ core = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
coreshell = ParticleCoreShell(
shell, core, kvector_t(0, 0, (shell_height - core_height)/2))
coreshell.setPosition(
@@ -93,17 +93,16 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core_ref = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
+ core_ref = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
shell_ref = Particle(
mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell_ref = ParticleCoreShell(
- shell_ref, core_ref, kvector_t(0, 0,
- (shell_height - core_height)/2))
+ shell_ref, core_ref,
+ kvector_t(0, 0, (shell_height - core_height)/2))
coreshell_ref.setPosition(
- kvector_t(
- 0, 0, -layer_thickness/2.0 -
- shell_height/2)) # center of coreshell in center of the layer
+ kvector_t(0, 0, -layer_thickness/2.0 - shell_height/
+ 2)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
@@ -115,17 +114,16 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
- shell = Particle(mShell,
- FormFactorBox(shell_length, shell_width, shell_height))
+ core = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
+ shell = Particle(
+ mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell = ParticleCoreShell(
shell, core, kvector_t(0, 0, (shell_height - core_height)/2))
coreshell.setRotation(RotationZ(90*deg))
coreshell.setPosition(
- kvector_t(
- 0, 0, -layer_thickness/2.0 -
- shell_height/2)) # center of coreshell in center of the layer
+ kvector_t(0, 0, -layer_thickness/2.0 - shell_height/
+ 2)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
@@ -150,17 +148,16 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core_ref = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
+ core_ref = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
shell_ref = Particle(
mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell_ref = ParticleCoreShell(
- shell_ref, core_ref, kvector_t(0, 0,
- (shell_height - core_height)/2))
+ shell_ref, core_ref,
+ kvector_t(0, 0, (shell_height - core_height)/2))
coreshell_ref.setPosition(
- kvector_t(
- 0, 0, -layer_thickness/2.0 -
- shell_height/2)) # center of coreshell in center of the layer
+ kvector_t(0, 0, -layer_thickness/2.0 - shell_height/
+ 2)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
@@ -172,16 +169,16 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
- shell = Particle(mShell,
- FormFactorBox(shell_length, shell_width, shell_height))
+ core = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
+ shell = Particle(
+ mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell = ParticleCoreShell(
shell, core, kvector_t(0, 0, (shell_height - core_height)/2))
coreshell.setRotation(RotationY(90.*deg))
- coreshell.setPosition(kvector_t(
- 0, 0,
- -layer_thickness/2)) # center of coreshell in center of the layer
+ coreshell.setPosition(
+ kvector_t(0, 0, -layer_thickness/
+ 2)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
@@ -206,17 +203,16 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core_ref = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
+ core_ref = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
shell_ref = Particle(
mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell_ref = ParticleCoreShell(
- shell_ref, core_ref, kvector_t(0, 0,
- (shell_height - core_height)/2))
+ shell_ref, core_ref,
+ kvector_t(0, 0, (shell_height - core_height)/2))
coreshell_ref.setPosition(
- kvector_t(
- 0, 0, -layer_thickness/2.0 -
- shell_height/2)) # center of coreshell in center of the layer
+ kvector_t(0, 0, -layer_thickness/2.0 - shell_height/
+ 2)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_CoreShellBoxRotateZandY.int")
@@ -229,18 +225,18 @@ class TransformCoreShellBoxTest(unittest.TestCase):
core_width = shell_width/2.0
core_height = shell_height/2.0
- core = Particle(mCore,
- FormFactorBox(core_length, core_width, core_height))
- shell = Particle(mShell,
- FormFactorBox(shell_length, shell_width, shell_height))
+ core = Particle(
+ mCore, FormFactorBox(core_length, core_width, core_height))
+ shell = Particle(
+ mShell, FormFactorBox(shell_length, shell_width, shell_height))
coreshell = ParticleCoreShell(
shell, core, kvector_t(0, 0, (shell_height - core_height)/2))
coreshell.setRotation(RotationZ(90*deg))
coreshell.rotate(RotationY(90*deg))
# rotation changes reference point, which now coincide with center of the volume
- coreshell.setPosition(kvector_t(
- 0, 0,
- -layer_thickness/2)) # center of coreshell in center of the layer
+ coreshell.setPosition(
+ kvector_t(0, 0, -layer_thickness/
+ 2)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
diff --git a/Tests/Functional/PyCore/transform_box.py b/Tests/Functional/PyCore/transform_box.py
index 8f15e4b2cf905e7ba736b7cfe3f45d4cec795b64..655ee5a3f3b6cba37473ddfb06c9bccd40fe197a 100644
--- a/Tests/Functional/PyCore/transform_box.py
+++ b/Tests/Functional/PyCore/transform_box.py
@@ -18,7 +18,8 @@ class BoxTransformationsTest(unittest.TestCase):
def get_sample(self, particle):
mAmbience = ba.HomogeneousMaterial("Vacuum", 0, 0)
mMiddle = ba.HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
- mSubstrate = ba.HomogeneousMaterial("Substrate", 3.212e-6, 3.244e-8)
+ mSubstrate = ba.HomogeneousMaterial("Substrate", 3.212e-6,
+ 3.244e-8)
layout = ba.ParticleLayout()
layout.addParticle(particle)
@@ -52,7 +53,8 @@ class BoxTransformationsTest(unittest.TestCase):
width = 50
height = 20
- box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
+ box = ba.Particle(mParticle,
+ ba.FormFactorBox(length, width, height))
box.setPosition(kvector_t(0, 0, -layer_thickness/2 - height/2))
reference_data = self.get_result(box)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_TransformBox.int")
@@ -61,7 +63,8 @@ class BoxTransformationsTest(unittest.TestCase):
length = 50
width = 20
height = 10
- box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
+ box = ba.Particle(mParticle,
+ ba.FormFactorBox(length, width, height))
box.setRotation(ba.RotationZ(90*deg))
box.rotate(ba.RotationY(90*deg))
box.setPosition(kvector_t(0, 0, -layer_thickness/2))
diff --git a/Tests/Functional/PyCore/transform_cube.py b/Tests/Functional/PyCore/transform_cube.py
index 73e9cb63c375c1592ee3489feaaec488f6f2dd80..df719a07b6137d4cea1591c090ad0ea5c3482bee 100644
--- a/Tests/Functional/PyCore/transform_cube.py
+++ b/Tests/Functional/PyCore/transform_cube.py
@@ -62,7 +62,8 @@ class RotationsCubeTest(unittest.TestCase):
pos = data[2]
layout_rot = data[3]
layout_pos = data[4]
- sample = self.get_sample(ff, rot, pos, layout_rot, layout_pos, add_to)
+ sample = self.get_sample(ff, rot, pos, layout_rot, layout_pos,
+ add_to)
# simulation = self.get_simulation(sample)
simulation = utils.get_simulation_MiniGISAS(sample)
simulation.runSimulation()
@@ -82,7 +83,8 @@ class RotationsCubeTest(unittest.TestCase):
data_to_test = [
# ff rot pos layout_rot layout_pos
(box, None, None, None, None), # reference
- (box, RotationZ(90.*deg), None, None, None), # rotating particle
+ (box, RotationZ(90.*deg), None, None,
+ None), # rotating particle
(box, RotationZ(-90.*deg), None, None, None),
(box, RotationZ(180.*deg), None, None, None),
(box, None, None, RotationZ(90.*deg),
@@ -118,7 +120,8 @@ class RotationsCubeTest(unittest.TestCase):
kvector_t(0, 0, 5)), # rotating and translating
(box, RotationY(90.*deg), None, None,
kvector_t(0, 0, 5)), # rotating and translating
- (box, RotationY(45.*deg), kvector_t(0, 0, 0), RotationY(45.*deg),
+ (box, RotationY(45.*deg), kvector_t(0, 0,
+ 0), RotationY(45.*deg),
kvector_t(0, 0, 5)), # rotating and translating
]
@@ -149,7 +152,8 @@ class RotationsCubeTest(unittest.TestCase):
kvector_t(0, 0, 5)), # rotating and translating
(box, RotationX(90.*deg), None, None,
kvector_t(0, 0, 5)), # rotating and translating
- (box, RotationX(45.*deg), kvector_t(0, 0, 0), RotationX(45.*deg),
+ (box, RotationX(45.*deg), kvector_t(0, 0,
+ 0), RotationX(45.*deg),
kvector_t(0, 0, 5)), # rotating and translating
]
diff --git a/Tests/Functional/PyFit/fitobjective_api.py b/Tests/Functional/PyFit/fitobjective_api.py
index 4526a6185c0de25a5353beb44d42f15b8b6a11c1..b3f2bbe5fd82d6b006e540905c041201145b4056 100644
--- a/Tests/Functional/PyFit/fitobjective_api.py
+++ b/Tests/Functional/PyFit/fitobjective_api.py
@@ -29,7 +29,8 @@ class SimulationBuilder:
simulation = ba.GISASSimulation()
simulation.setSample(ml)
- simulation.setDetectorParameters(self.m_ncol, 0, 1, self.m_nrow, 0, 1)
+ simulation.setDetectorParameters(self.m_ncol, 0, 1, self.m_nrow, 0,
+ 1)
return simulation
def create_data(self):
@@ -43,7 +44,8 @@ class FitObserver:
def update(self, fit_objective):
self.m_ncalls += 1
- self.m_iterations.append(fit_objective.iterationInfo().iterationCount())
+ self.m_iterations.append(
+ fit_objective.iterationInfo().iterationCount())
class FitObjectiveAPITest(unittest.TestCase):
@@ -78,7 +80,8 @@ class FitObjectiveAPITest(unittest.TestCase):
expected_sim.append(0)
expected_data.append(1)
self.assertEqual(expected_sim, list(objective.simulation_array()))
- self.assertEqual(expected_data, list(objective.experimental_array()))
+ self.assertEqual(expected_data,
+ list(objective.experimental_array()))
def test_FittingObserver(self):
"""
diff --git a/Tests/Functional/PyFit/standalone_fits.py b/Tests/Functional/PyFit/standalone_fits.py
index 33b8458b9c699ccc2918f4d6b9432250f5860cae..52c400f79657a9321964835b649424a085d5afa5 100644
--- a/Tests/Functional/PyFit/standalone_fits.py
+++ b/Tests/Functional/PyFit/standalone_fits.py
@@ -56,7 +56,8 @@ class StandaloneFitTest(unittest.TestCase):
Testing fit of rosenbrock function
"""
params = ba.Parameters()
- params.add(ba.Parameter("x", -1.2, ba.AttLimits.limited(-5, 5), 0.01))
+ params.add(
+ ba.Parameter("x", -1.2, ba.AttLimits.limited(-5, 5), 0.01))
params.add(ba.Parameter("y", 1, ba.AttLimits.limited(-5, 5), 0.01))
model = Rosenbrock()
@@ -77,7 +78,8 @@ class StandaloneFitTest(unittest.TestCase):
params = ba.Parameters()
params.add(ba.Parameter('amp', 1, ba.AttLimits.positive()))
params.add(ba.Parameter('decay', 0.1, ba.AttLimits.positive()))
- params.add(ba.Parameter('phase', 0.1, ba.AttLimits.limited(0, 3.1)))
+ params.add(ba.Parameter('phase', 0.1, ba.AttLimits.limited(0,
+ 3.1)))
params.add(ba.Parameter('frequency', 1, ba.AttLimits.positive()))
model = DecayingSin()
diff --git a/Tests/Performance/Python/test_performance.py b/Tests/Performance/Python/test_performance.py
index 1878642eeaada7a6e09f9a595c6f3416fe15dd6c..bcac6348ff4286ef8500b8ce8efeb22532405dbb 100755
--- a/Tests/Performance/Python/test_performance.py
+++ b/Tests/Performance/Python/test_performance.py
@@ -76,7 +76,8 @@ class CustomFormFactor(IBornFF):
# class for performance test, constructed using sample factories
class FactoryTest:
- def __init__(self, name, simulation_name, sample_builder, nrepetitions):
+ def __init__(self, name, simulation_name, sample_builder,
+ nrepetitions):
self.m_test_name = name
self.m_simulation_name = simulation_name
self.m_sample_builder_name = sample_builder
@@ -185,8 +186,8 @@ class CustomTest(FactoryTest):
"""
simulation = GISASSimulation()
simulation.getOptions().setNumberOfThreads(-1)
- simulation.setDetectorParameters(100, phi_min*deg, phi_max*deg, 100,
- alpha_min*deg, alpha_max*deg)
+ simulation.setDetectorParameters(100, phi_min*deg, phi_max*deg,
+ 100, alpha_min*deg, alpha_max*deg)
simulation.setBeamParameters(1*angstrom, 0.2*deg, 0)
return simulation
@@ -201,17 +202,24 @@ class PerformanceTests:
self.m_pyversion = ""
self.m_filename = filename
- self.add("MultiLayer", "MaxiGISAS", "MultiLayerWithRoughnessBuilder", 1)
- self.add("CylindersInDWBA", "MaxiGISAS", "CylindersInDWBABuilder", 10)
- self.add("RotatedPyramids", "MaxiGISAS", "RotatedPyramidsBuilder", 10)
+ self.add("MultiLayer", "MaxiGISAS",
+ "MultiLayerWithRoughnessBuilder", 1)
+ self.add("CylindersInDWBA", "MaxiGISAS", "CylindersInDWBABuilder",
+ 10)
+ self.add("RotatedPyramids", "MaxiGISAS", "RotatedPyramidsBuilder",
+ 10)
self.add("CoreShell", "MaxiGISAS", "CoreShellParticleBuilder", 10)
- self.add("SquareLattice2D", "MaxiGISAS", "SquareLattice2DBuilder", 10)
- self.add("RadialParaCrystal", "MaxiGISAS", "RadialParaCrystalBuilder",
+ self.add("SquareLattice2D", "MaxiGISAS", "SquareLattice2DBuilder",
+ 10)
+ self.add("RadialParaCrystal", "MaxiGISAS",
+ "RadialParaCrystalBuilder", 10)
+ self.add("HexParaCrystal", "BasicGISAS", "HexParaCrystalBuilder",
+ 1)
+ self.add("SSCA", "MaxiGISAS", "SizeDistributionSSCAModelBuilder",
10)
- self.add("HexParaCrystal", "BasicGISAS", "HexParaCrystalBuilder", 1)
- self.add("SSCA", "MaxiGISAS", "SizeDistributionSSCAModelBuilder", 10)
self.add("Mesocrystal", "MaxiGISAS", "MesoCrystalBuilder", 2)
- self.add("PolMagCyl", "MaxiGISAS00", "MagneticCylindersBuilder", 10)
+ self.add("PolMagCyl", "MaxiGISAS00", "MagneticCylindersBuilder",
+ 10)
# custom form factor is a special case since it's not in the registry
self.m_tests.append(CustomTest("Custom FF", 10))
@@ -221,7 +229,8 @@ class PerformanceTests:
def add(self, name, simulation_name, sample_builder, nrepetitions):
self.m_tests.append(
- FactoryTest(name, simulation_name, sample_builder, nrepetitions))
+ FactoryTest(name, simulation_name, sample_builder,
+ nrepetitions))
# execute all performance tests
def execute(self):
@@ -279,7 +288,8 @@ class PerformanceTests:
# determine platform, architecture, python version, etc.
def init_sysinfo(self):
- system, node, release, version, machine, processor = platform.uname()
+ system, node, release, version, machine, processor = platform.uname(
+ )
self.m_datime = datetime.datetime.strftime(datetime.datetime.now(),
'%Y-%m-%d %H:%M:%S')
self.m_hostname = node
diff --git a/Wrap/Python/ba_fitmonitor.py b/Wrap/Python/ba_fitmonitor.py
index 4b01ec3c56624c4d38625df552002930e9be4042..6b5b11ad1ab18549689bbf875c275dd9ce8fedff 100644
--- a/Wrap/Python/ba_fitmonitor.py
+++ b/Wrap/Python/ba_fitmonitor.py
@@ -23,6 +23,7 @@ except Exception as e:
label_fontsize = 16
+
class Plotter:
"""
Draws fit progress. Base class for simulation-specific classes (PlotterGISAS etc).
@@ -123,8 +124,8 @@ class PlotterGISAS(Plotter):
iteration_info = fit_objective.iterationInfo()
plt.text(
- 0.01, 0.85,
- "Iterations " + '{:d}'.format(iteration_info.iterationCount()))
+ 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
@@ -175,7 +176,8 @@ class PlotterSpecular(Plotter):
:param length: max non-truncated length
:return:
"""
- return (token[:length - 2] + '..') if len(token) > length else token
+ return (token[:length - 2] +
+ '..') if len(token) > length else token
def plot_table(self, fit_objective):
@@ -222,10 +224,15 @@ class PlotterSpecular(Plotter):
# 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)
+ 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}
+ font = {
+ 'family': 'serif',
+ 'weight': 'normal',
+ 'size': label_fontsize
+ }
plt.subplot(self.gs[0])
plt.semilogy(sim_data.axis(), sim_values, 'b', real_data.axis(),
diff --git a/Wrap/Python/ba_plot.py b/Wrap/Python/ba_plot.py
index 7f884bd8c01456726ed7043d209a57df8edf2ec4..aae62b12463fc2a77f1a751a36d2f35a518cb0f4 100644
--- a/Wrap/Python/ba_plot.py
+++ b/Wrap/Python/ba_plot.py
@@ -108,7 +108,12 @@ def plot_array(array, axes_limits=None, **kwargs):
aspect = kwargs.pop('aspect', 'equal')
cmap = kwargs.pop('cmap', CMAP)
- im = plt.imshow(array, cmap=cmap, norm=norm, aspect=aspect, extent=axes_limits, **kwargs)
+ im = plt.imshow(array,
+ cmap=cmap,
+ norm=norm,
+ aspect=aspect,
+ extent=axes_limits,
+ **kwargs)
cb = plt.colorbar(im, pad=0.025)
if xlabel:
@@ -144,7 +149,10 @@ def plot_histogram(hist, **kwargs):
title = kwargs.pop('title', None)
- plot_array(hist.array(), title=title, axes_limits=axes_limits, **kwargs)
+ plot_array(hist.array(),
+ title=title,
+ axes_limits=axes_limits,
+ **kwargs)
def plot_colormap(result, **kwargs):
@@ -181,7 +189,8 @@ def plot_specular_simulation_result(result, **kwargs):
x_axis = result.axis(units)
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))
+ 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")
@@ -211,7 +220,8 @@ def plot_simulation_result(result, **kwargs):
"""
noshow = kwargs.pop('noshow', NOSHOW)
- if len(result.array().shape) == 1: # 1D data, specular simulation assumed
+ if len(result.array().shape
+ ) == 1: # 1D data, specular simulation assumed
plot_specular_simulation_result(result, **kwargs)
else:
plot_colormap(result, **kwargs)
@@ -221,6 +231,7 @@ def plot_simulation_result(result, **kwargs):
else:
print("plot_simulation_result: noshow")
+
def run_and_plot(simulation, **kwargs):
simulation.runSimulation()
plot_simulation_result(simulation.result(), **kwargs)
diff --git a/Wrap/Python/bornagain_python_install.py b/Wrap/Python/bornagain_python_install.py
index 7743517fe3483a83cb0993f3d1671695a7542abd..6479f0cb6814a912844fdf9b6464c81fafbad64f 100644
--- a/Wrap/Python/bornagain_python_install.py
+++ b/Wrap/Python/bornagain_python_install.py
@@ -47,8 +47,9 @@ def python_version_string():
def add_rpath(newpath, filename):
print("add_rpath ", newpath, filename)
- p = subprocess.Popen(['install_name_tool', '-add_rpath', newpath, filename],
- stdout=subprocess.PIPE)
+ p = subprocess.Popen(
+ ['install_name_tool', '-add_rpath', newpath, filename],
+ stdout=subprocess.PIPE)
p.communicate()
return
@@ -90,8 +91,8 @@ def get_python_shared_library():
Returns full path to the python shared library on which current interpreter is relying
"""
prefix = sys.prefix
- suffix = sysconfig.get_config_var('LDVERSION') or sysconfig.get_config_var(
- 'VERSION')
+ suffix = sysconfig.get_config_var(
+ 'LDVERSION') or sysconfig.get_config_var('VERSION')
result = sys.prefix + "/lib/libpython" + suffix + ".dylib"
return result
@@ -113,10 +114,12 @@ def get_application_dir():
app_dir = sys.argv[1]
else:
script_dir = get_script_path()
- app_dir = os.path.abspath(os.path.join(script_dir, "..", "..", ".."))
+ app_dir = os.path.abspath(
+ os.path.join(script_dir, "..", "..", ".."))
# getting version number
- lib_dir = glob.glob(os.path.join(app_dir, "Contents", "lib", "BornAgain-*"))
+ lib_dir = glob.glob(
+ os.path.join(app_dir, "Contents", "lib", "BornAgain-*"))
if len(lib_dir) != 1:
exit("Can't find BornAgain libraries in " + app_dir)
@@ -192,7 +195,8 @@ setup(name='bornagain',
def prepare_init_module(app_dir, bundle_dir):
source_dir = os.path.join(app_dir, "Contents", "libexec")
- libexec_dir = os.path.join(source_dir, "BornAgain-" + BORNAGAIN_VERSION,
+ libexec_dir = os.path.join(source_dir,
+ "BornAgain-" + BORNAGAIN_VERSION,
"bornagain")
package_dir = os.path.join(bundle_dir, "bornagain")
print("--> Copying modules from '{0}' to '{1}'".format(
@@ -216,7 +220,8 @@ def copy_libraries(app_dir, destination_dir):
os.path.join(destination_dir, "BornAgain-" + BORNAGAIN_VERSION))
# cleaning unnecessary files
- libfiles = glob.glob(os.path.join(destination_dir, '*/libBornAgainGUI*'))
+ libfiles = glob.glob(
+ os.path.join(destination_dir, '*/libBornAgainGUI*'))
for f in libfiles:
os.remove(f)
pass
@@ -227,8 +232,8 @@ def copy_libraries(app_dir, destination_dir):
if not os.path.exists(frameworks_dest):
os.makedirs(frameworks_dest)
for lib in frameworks_libs:
- shutil.copyfile(lib, os.path.join(frameworks_dest,
- os.path.basename(lib)))
+ shutil.copyfile(
+ lib, os.path.join(frameworks_dest, os.path.basename(lib)))
def patch_libraries(dir_name):
@@ -296,8 +301,8 @@ def install_bundle(dir_name):
os.chdir(bundle_dir)
sys.argv = ['setup.py', 'install']
exec_full('setup.py')
- print("\nBornAgain Python bundle is successfully installed in '{0}'".format(
- get_python_lib()))
+ print("\nBornAgain Python bundle is successfully installed in '{0}'".
+ format(get_python_lib()))
print("Congratulations!")
@@ -316,7 +321,9 @@ if __name__ == '__main__':
print("To :", get_python_lib())
print(" ")
print("Possible options:")
- print("[0] - Generate bundle with BornAgain libraries, do not install it.")
+ print(
+ "[0] - Generate bundle with BornAgain libraries, do not install it."
+ )
print(
"[1] - Generate bundle and install it into site-packages of your Python."
)
diff --git a/Wrap/Swig/doxy2swig.py b/Wrap/Swig/doxy2swig.py
index 93c2aa5b175022d338203267c6c85102898fa96c..e2044194d4661263f101da3ca74bb5394375ad96 100755
--- a/Wrap/Swig/doxy2swig.py
+++ b/Wrap/Swig/doxy2swig.py
@@ -69,8 +69,9 @@ class Doxy2SWIG:
'innerclass', 'name', 'declname', 'incdepgraph',
'invincdepgraph', 'programlisting', 'type',
'references', 'referencedby', 'location',
- 'collaborationgraph', 'reimplements', 'reimplementedby',
- 'derivedcompoundref', 'basecompoundref')
+ 'collaborationgraph', 'reimplements',
+ 'reimplementedby', 'derivedcompoundref',
+ 'basecompoundref')
#self.generics = []
def generate(self):
@@ -188,8 +189,8 @@ class Doxy2SWIG:
prot = node.attributes['prot'].value
if prot != 'public':
return
- names = ('compoundname', 'briefdescription', 'detaileddescription',
- 'includes')
+ names = ('compoundname', 'briefdescription',
+ 'detaileddescription', 'includes')
first = self.get_specific_nodes(node, names)
for n in names:
#if first.has_key(n):
diff --git a/cmake/pack/fix_apple_bundle.py b/cmake/pack/fix_apple_bundle.py
index 7c5749866215da53a949eca43608032462deaa7f..9eb35f4edb7cca9c8b799b9df460ddcc3b85880d 100644
--- a/cmake/pack/fix_apple_bundle.py
+++ b/cmake/pack/fix_apple_bundle.py
@@ -53,8 +53,8 @@ def bundle_main_executables():
def bundle_python_library():
- return os.path.join("Python.framework", "Versions", python_version_string(),
- "Python")
+ return os.path.join("Python.framework", "Versions",
+ python_version_string(), "Python")
def qtlibs_path():
@@ -75,7 +75,8 @@ def bundle_plugins():
def bornagain_binaries():
- return bundle_main_executables() + bundle_libraries() + bundle_plugins()
+ return bundle_main_executables() + bundle_libraries() + bundle_plugins(
+ )
def get_list_of_files(dirname):
@@ -121,7 +122,8 @@ def otool(filename):
"""
Parses dependencies of given binary file
"""
- p = subprocess.Popen(['otool', '-XL', filename], stdout=subprocess.PIPE)
+ p = subprocess.Popen(['otool', '-XL', filename],
+ stdout=subprocess.PIPE)
# return iter(p.stdout.readline, b'')
for line in iter(p.stdout.readline, b''):
if is_python3():
@@ -145,8 +147,9 @@ def fixDependency(filename, old, new):
Replaces old dependency with new one for given binary file
"""
print(" fixDependency(filename, old, new)", filename, old, new)
- p = subprocess.Popen(['install_name_tool', '-change', old, new, filename],
- stdout=subprocess.PIPE)
+ p = subprocess.Popen(
+ ['install_name_tool', '-change', old, new, filename],
+ stdout=subprocess.PIPE)
p.communicate()
return
@@ -253,7 +256,8 @@ def get_dependency_dest_location(dependency):
libname = os.path.basename(dependency)
if is_python_framework_dependency(dependency):
- return os.path.join(bundle_frameworks_path(), bundle_python_library())
+ return os.path.join(bundle_frameworks_path(),
+ bundle_python_library())
if is_qt_framework_dependency(dependency):
libpath = os.path.join(libname + ".framework", "Versions", "5")
@@ -269,7 +273,8 @@ def get_special_dependency_id(dependency):
if is_python_framework_dependency(dependency):
return "@rpath/" + bundle_python_library()
- if is_qt_framework_dependency(dependency) and not "@rpath" in dependency:
+ if is_qt_framework_dependency(
+ dependency) and not "@rpath" in dependency:
libname = os.path.basename(dependency)
return "@rpath/" + libname + ".framework/Versions/5/" + libname
return None
@@ -288,8 +293,8 @@ def get_python_library_location():
# Let's try to find library directly
prefix = sys.prefix
- suffix = sysconfig.get_config_var('LDVERSION') or sysconfig.get_config_var(
- 'VERSION')
+ suffix = sysconfig.get_config_var(
+ 'LDVERSION') or sysconfig.get_config_var('VERSION')
result = sys.prefix + "/lib/libpython" + suffix + ".dylib"
if os.path.exists(result):
return result
@@ -308,7 +313,8 @@ def copy_python_framework():
"""
print("--> Copying Python framework")
python_lib = get_python_library_location()
- destfile = os.path.join(bundle_frameworks_path(), bundle_python_library())
+ destfile = os.path.join(bundle_frameworks_path(),
+ bundle_python_library())
make_dir(os.path.dirname(destfile))
print(" From '{0}'\n To '{1}'".format(python_lib, destfile))
if not os.path.exists(destfile):