diff --git a/.style.yapf b/.style.yapf
new file mode 100644
index 0000000000000000000000000000000000000000..31c66473c6435a92ab0a0d2774aa138dcfeff9a9
--- /dev/null
+++ b/.style.yapf
@@ -0,0 +1,3 @@
+[style]
+based_on_style = pep8
+column_limit = 85
diff --git a/Doc/FFCatalog/fig/ff2/bornplot.py b/Doc/FFCatalog/fig/ff2/bornplot.py
index b5bd7d63d8d6f31934ac4976827bc071f17b6cd6..cecb5a8ac858410f822f25fce42ff2b6b6fa4318 100644
--- a/Doc/FFCatalog/fig/ff2/bornplot.py
+++ b/Doc/FFCatalog/fig/ff2/bornplot.py
@@ -5,7 +5,7 @@ import math, numpy
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib import rc
-rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
+rc('font', **{'family': 'sans-serif', 'sans-serif': ['Helvetica']})
rc('text', usetex=True)
rc('image', cmap='inferno')
@@ -20,7 +20,7 @@ class BinRange:
self.n = n
def central_index(self):
- return int((0.-self.vmin)/(self.vmax-self.vmin)*self.n)
+ return int((0. - self.vmin) / (self.vmax - self.vmin) * self.n)
class Detector:
@@ -51,16 +51,16 @@ def make_plot(results, det, name, nrow=1):
"""
mpl.rcParams['image.interpolation'] = 'none'
n = len(results)
- ncol = 1+(n-1)//nrow
+ ncol = 1 + (n - 1) // nrow
# Parameters as fraction of subfig size.
yskip = 0.2 # +ncol*0.02
bottomskip = yskip
- topskip = yskip/2
+ topskip = yskip / 2
xskip = 0.18
leftskip = xskip
- rightskip = 0.28+ncol*0.03
- xtot = ncol*1.0 + (ncol-1)*xskip + leftskip + rightskip
- ytot = nrow*1.0 + (nrow-1)*yskip + bottomskip + topskip
+ rightskip = 0.28 + ncol * 0.03
+ xtot = ncol * 1.0 + (ncol - 1) * xskip + leftskip + rightskip
+ ytot = nrow * 1.0 + (nrow - 1) * yskip + bottomskip + topskip
# We need parameters as fraction of total fig size.
xskip /= xtot
leftskip /= xtot
@@ -70,9 +70,9 @@ def make_plot(results, det, name, nrow=1):
topskip /= ytot
# Set total figure dimensions.
ftot = 5
- fontsize = 18+36.0/(ncol+2)
+ fontsize = 18 + 36.0 / (ncol + 2)
# Create the figure 'fig' and its subplots axes ('tmp'->'axes').
- fig, tmp = plt.subplots(nrow, ncol, figsize=(ftot*xtot, ftot*ytot))
+ fig, tmp = plt.subplots(nrow, ncol, figsize=(ftot * xtot, ftot * ytot))
if n > 1:
axes = tmp.flat
else:
@@ -82,33 +82,35 @@ 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=det.rectangle(),
- aspect=1)
+ im = ax.imshow(res.data, norm=norm, extent=det.rectangle(), 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)
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,
- left=leftskip, right=1-rightskip,
- bottom=bottomskip, top=1-topskip)
+ plt.subplots_adjust(wspace=xskip,
+ hspace=yskip,
+ left=leftskip,
+ right=1 - rightskip,
+ bottom=bottomskip,
+ top=1 - topskip)
# Plot the color scale.
- cbar_ax = fig.add_axes([1-rightskip+0.4*xskip, bottomskip,
- 0.25*xskip, 1-bottomskip-topskip])
+ cbar_ax = fig.add_axes([
+ 1 - rightskip + 0.4 * xskip, bottomskip, 0.25 * xskip,
+ 1 - bottomskip - topskip
+ ])
cb = fig.colorbar(im, cax=cbar_ax)
cb.set_label(r'$\left|F(q)\right|^2/V^{\,2}$', fontsize=fontsize)
# Output to data file, image file, and display.
- nDigits = int(math.log10(len(results)))+1
+ nDigits = int(math.log10(len(results))) + 1
formatN = "%" + str(nDigits) + "i"
for i in range(len(results)):
- fname = name+"."+(formatN % i)+".int"
+ fname = name + "." + (formatN % i) + ".int"
print(fname)
numpy.savetxt(fname, results[i].data)
- plt.savefig(name+".pdf", format="pdf", bbox_inches='tight')
+ plt.savefig(name + ".pdf", format="pdf", bbox_inches='tight')
# plt.show()
@@ -146,10 +148,11 @@ def get_simulation(det):
:param det: Detector limits
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(
- det.phi.n, det.phi.vmin*degree, det.phi.vmax*degree,
- det.alpha.n, det.alpha.vmin*degree, det.alpha.vmax*degree )
- simulation.setBeamParameters(1.0*angstrom, 0, 0)
+ simulation.setDetectorParameters(det.phi.n, det.phi.vmin * degree,
+ det.phi.vmax * degree, det.alpha.n,
+ det.alpha.vmin * degree,
+ det.alpha.vmax * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0, 0)
return simulation
diff --git a/Doc/FFCatalog/fig/ff2/sim_AnisoPyramid.py b/Doc/FFCatalog/fig/ff2/sim_AnisoPyramid.py
index 6f2619451017a32cf009c55c22691244e9e78bcf..b7865ffdf71a7609db8dce75fe349f44c594c83c 100644
--- a/Doc/FFCatalog/fig/ff2/sim_AnisoPyramid.py
+++ b/Doc/FFCatalog/fig/ff2/sim_AnisoPyramid.py
@@ -2,18 +2,19 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorAnisoPyramid(13*nanometer, 8*nanometer, 4.2*nanometer, 60.0*degree)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_AnisoPyramid" )
+ ff = ba.FormFactorAnisoPyramid(13 * nanometer, 8 * nanometer, 4.2 * nanometer,
+ 60.0 * degree)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_AnisoPyramid")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Box.py b/Doc/FFCatalog/fig/ff2/sim_Box.py
index 4390624dc1e42b280094f21081d099f4a417c34a..96e3b61d31d2705518ebd421ddcd515ade5ed997 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Box.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Box.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
det = bp.Detector(200, 0, 5, 0, 5)
n = 4
results = []
for i in range(n):
- omega = 90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorBox(18*nanometer, 4.6*nanometer, 3*nanometer)
- trafo = ba.RotationZ(omega*degree)
+ ff = ba.FormFactorBox(18 * nanometer, 4.6 * nanometer, 3 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
data = bp.run_simulation(det, ff, trafo)
results.append(bp.Result(i, data, title))
-
+
bp.make_plot(results, det, "ff_Box")
diff --git a/Doc/FFCatalog/fig/ff2/sim_CantellatedCube.py b/Doc/FFCatalog/fig/ff2/sim_CantellatedCube.py
index e50cf83ff4d2683f90fd85580c25b2d7d751c4d7..8dbd6cad41751f01b094e2b9e3e853ca3df0a867 100644
--- a/Doc/FFCatalog/fig/ff2/sim_CantellatedCube.py
+++ b/Doc/FFCatalog/fig/ff2/sim_CantellatedCube.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=45*i/(n-1)
+ omega = 45 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorTruncatedCube(6.4*nanometer, 1.5*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_TruncatedCube" )
+ ff = ba.FormFactorTruncatedCube(6.4 * nanometer, 1.5 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_TruncatedCube")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Cone.py b/Doc/FFCatalog/fig/ff2/sim_Cone.py
index 1ba5f1c7f6a38ffe6069ece8020c416e8c364b64..7c3c343ad52023143cdca0819f413ae49ef5429f 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Cone.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Cone.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- theta=30*i/(n-1)
+ theta = 30 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorCone(4*nanometer, 11*nanometer, 75*degree)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Cone" )
+ ff = ba.FormFactorCone(4 * nanometer, 11 * nanometer, 75 * degree)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Cone")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Cone6.py b/Doc/FFCatalog/fig/ff2/sim_Cone6.py
index d9ef435c72576bedab3eeac41ccf815d729c0908..2dd0071693bbe47a1a4a8a9bbcdf2095c2d32929 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Cone6.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Cone6.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=30*i/(n-1)
+ omega = 30 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorCone6(6*nanometer, 5*nanometer, 60*degree)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Cone6" )
+ ff = ba.FormFactorCone6(6 * nanometer, 5 * nanometer, 60 * degree)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Cone6")
diff --git a/Doc/FFCatalog/fig/ff2/sim_CosineRipple.py b/Doc/FFCatalog/fig/ff2/sim_CosineRipple.py
index 885213f9d095ca09386424c553f71eb52237512f..db0c740db8f01c1fdfbcf0b6f7174196ffe67de4 100644
--- a/Doc/FFCatalog/fig/ff2/sim_CosineRipple.py
+++ b/Doc/FFCatalog/fig/ff2/sim_CosineRipple.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorCosineRipple(25*nanometer, 10*nanometer, 8*nanometer )
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_CosineRipple" )
+ ff = ba.FormFactorCosineRipple(25 * nanometer, 10 * nanometer, 8 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_CosineRipple")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Cuboctahedron.py b/Doc/FFCatalog/fig/ff2/sim_Cuboctahedron.py
index 5e75058386573fefbbed501a91c54ffa5e1f0bf6..58956e6c827a69a4186bd8c41adb6d80d8464492 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Cuboctahedron.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Cuboctahedron.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=45*i/(n-1)
+ omega = 45 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorCuboctahedron(8*nanometer, 5*nanometer, 0.5, 60.0*degree)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Cuboctahedron" )
+ ff = ba.FormFactorCuboctahedron(8 * nanometer, 5 * nanometer, 0.5, 60.0 * degree)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Cuboctahedron")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Cylinder.py b/Doc/FFCatalog/fig/ff2/sim_Cylinder.py
index f122da5c01e8e4c3dd7744f2caa3baf9c383e435..3ba3c824766f480d676a654de81b9151b871cab6 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Cylinder.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Cylinder.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 4
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 4
results = []
for i in range(n):
- theta=135*i/(n-1)
+ theta = 135 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorCylinder(3*nanometer, 8.8*nanometer)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
+ ff = ba.FormFactorCylinder(3 * nanometer, 8.8 * nanometer)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
-bp.make_plot( results, det, "ff_Cylinder" )
+bp.make_plot(results, det, "ff_Cylinder")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_asy.py b/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_asy.py
index f5f07dd1afcd67931447e85c2deceafd408dc69c..47fba21ca170ec04044a6712975a29e197460a38 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_asy.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_asy.py
@@ -2,30 +2,30 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
import math
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 3
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 3
results = []
edge = 3.2
title = 'default'
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff)
-results.append( bp.Result(0, data, title) )
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff)
+results.append(bp.Result(0, data, title))
title = 'rotated'
-trafo = ba.RotationZ(13*degree)
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(1, data, title) )
+trafo = ba.RotationZ(13 * degree)
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(1, data, title))
title = 'rotated, tilted'
-trafo = ba.createProduct( ba.RotationX(9*degree), ba.RotationZ(13*degree))
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(2, data, title) )
+trafo = ba.createProduct(ba.RotationX(9 * degree), ba.RotationZ(13 * degree))
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(2, data, title))
-bp.make_plot( results, det, "ff_Dodecahedron_asy" )
+bp.make_plot(results, det, "ff_Dodecahedron_asy")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_sym.py b/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_sym.py
index 159141f7a2a2fc838e6e574581d140c0242ad2b3..71b0a95565f729ae6a7dff4d1e0420bc12c91724 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_sym.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Dodecahedron_sym.py
@@ -2,31 +2,31 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
import math
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 3
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 3
results = []
edge = 3.2
title = 'face normal'
-trafo = ba.RotationY(26.5651*degree)
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(0, data, title) )
+trafo = ba.RotationY(26.5651 * degree)
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(0, data, title))
title = 'vertex normal'
-trafo = ba.RotationY(-52.6226*degree)
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(1, data, title) )
+trafo = ba.RotationY(-52.6226 * degree)
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(1, data, title))
title = 'edge normal'
-trafo = ba.RotationY(58.2825*degree)
-ff = ba.FormFactorDodecahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(2, data, title) )
+trafo = ba.RotationY(58.2825 * degree)
+ff = ba.FormFactorDodecahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(2, data, title))
-bp.make_plot( results, det, "ff_Dodecahedron_sym" )
+bp.make_plot(results, det, "ff_Dodecahedron_sym")
diff --git a/Doc/FFCatalog/fig/ff2/sim_EllipsoidalCylinder.py b/Doc/FFCatalog/fig/ff2/sim_EllipsoidalCylinder.py
index 24864d5d32e4d3b96a426ab91a8b055ebfb1abdf..b55eeccbb944c80d6f02b1e03ba87cefadb31379 100644
--- a/Doc/FFCatalog/fig/ff2/sim_EllipsoidalCylinder.py
+++ b/Doc/FFCatalog/fig/ff2/sim_EllipsoidalCylinder.py
@@ -2,18 +2,19 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorEllipsoidalCylinder(6.3*nanometer, 4.2*nanometer, 3*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_EllipsoidalCylinder" )
+ ff = ba.FormFactorEllipsoidalCylinder(6.3 * nanometer, 4.2 * nanometer,
+ 3 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_EllipsoidalCylinder")
diff --git a/Doc/FFCatalog/fig/ff2/sim_FullSphere.py b/Doc/FFCatalog/fig/ff2/sim_FullSphere.py
index cbef53a72d9eaf0db63b51061d87ecd4b38225df..33644736202b1e00c67cdd8c2b9fba66d5298833 100644
--- a/Doc/FFCatalog/fig/ff2/sim_FullSphere.py
+++ b/Doc/FFCatalog/fig/ff2/sim_FullSphere.py
@@ -2,15 +2,15 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 1
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 1
results = []
for i in range(n):
- ff = ba.FormFactorFullSphere(3.9*nanometer)
- data = bp.run_simulation(det,ff)
- results.append( bp.Result(i, data) )
-
-bp.make_plot( results, det, "ff_FullSphere" )
+ ff = ba.FormFactorFullSphere(3.9 * nanometer)
+ data = bp.run_simulation(det, ff)
+ results.append(bp.Result(i, data))
+
+bp.make_plot(results, det, "ff_FullSphere")
diff --git a/Doc/FFCatalog/fig/ff2/sim_FullSpheroid.py b/Doc/FFCatalog/fig/ff2/sim_FullSpheroid.py
index e67f9e7c649248036e910099d3078293d28855b7..c4ce6b75da1a11b15683984b1ab3136996dc550c 100644
--- a/Doc/FFCatalog/fig/ff2/sim_FullSpheroid.py
+++ b/Doc/FFCatalog/fig/ff2/sim_FullSpheroid.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- theta=90*i/(n-1)
+ theta = 90 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorFullSpheroid(3*nanometer, 13*nanometer)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
+ ff = ba.FormFactorFullSpheroid(3 * nanometer, 13 * nanometer)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
-bp.make_plot( results, det, "ff_FullSpheroid" )
+bp.make_plot(results, det, "ff_FullSpheroid")
diff --git a/Doc/FFCatalog/fig/ff2/sim_HemiEllipsoid.py b/Doc/FFCatalog/fig/ff2/sim_HemiEllipsoid.py
index 18d03a49b5b35d3a3669675fbb85563e1d13cfeb..a51ba9cfeaa38fa018448049a31382b52150cbd3 100644
--- a/Doc/FFCatalog/fig/ff2/sim_HemiEllipsoid.py
+++ b/Doc/FFCatalog/fig/ff2/sim_HemiEllipsoid.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorHemiEllipsoid(10*nanometer, 3.8*nanometer, 3.2*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_HemiEllipsoid" )
+ ff = ba.FormFactorHemiEllipsoid(10 * nanometer, 3.8 * nanometer, 3.2 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_HemiEllipsoid")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Icosahedron_asy.py b/Doc/FFCatalog/fig/ff2/sim_Icosahedron_asy.py
index fb68b7009058f9d66231b3cb89a1018a36d38ad9..38a72e6556ce0d09a1ff4bf52e5ce5d596b15fef 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Icosahedron_asy.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Icosahedron_asy.py
@@ -2,30 +2,30 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
import math
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 3
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 3
results = []
edge = 4.8
title = 'default'
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff)
-results.append( bp.Result(0, data, title) )
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff)
+results.append(bp.Result(0, data, title))
title = 'rotated'
-trafo = ba.RotationZ(13*degree)
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(1, data, title) )
+trafo = ba.RotationZ(13 * degree)
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(1, data, title))
title = 'rotated, tilted'
-trafo = ba.createProduct( ba.RotationX(9*degree), ba.RotationZ(13*degree))
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(2, data, title) )
+trafo = ba.createProduct(ba.RotationX(9 * degree), ba.RotationZ(13 * degree))
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(2, data, title))
-bp.make_plot( results, det, "ff_Icosahedron_asy" )
+bp.make_plot(results, det, "ff_Icosahedron_asy")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Icosahedron_sym.py b/Doc/FFCatalog/fig/ff2/sim_Icosahedron_sym.py
index b8c908404c7edafaf9b6cd9a567ea5b4445142bb..035b8dba17b379365711bfbf5172f811e20a4dad 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Icosahedron_sym.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Icosahedron_sym.py
@@ -2,31 +2,31 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
import math
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 3
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 3
results = []
edge = 4.8
title = 'face normal'
-trafo = ba.RotationY(48.1897*degree)
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(0, data, title) )
+trafo = ba.RotationY(48.1897 * degree)
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(0, data, title))
title = 'vertex normal'
-trafo = ba.RotationY(-52.6226*degree)
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(1, data, title) )
+trafo = ba.RotationY(-52.6226 * degree)
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(1, data, title))
title = 'edge normal'
-trafo = ba.RotationY(69.0948*degree)
-ff = ba.FormFactorIcosahedron(edge*nanometer)
-data = bp.run_simulation(det,ff,trafo)
-results.append( bp.Result(2, data, title) )
+trafo = ba.RotationY(69.0948 * degree)
+ff = ba.FormFactorIcosahedron(edge * nanometer)
+data = bp.run_simulation(det, ff, trafo)
+results.append(bp.Result(2, data, title))
-bp.make_plot( results, det, "ff_Icosahedron_sym" )
+bp.make_plot(results, det, "ff_Icosahedron_sym")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Prism3.py b/Doc/FFCatalog/fig/ff2/sim_Prism3.py
index e55217d8cc003985db281ab78bf7af65d706ec0a..3096f0c35dbe4c5c438ed04550eddb10722b49af 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Prism3.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Prism3.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=30*i/(n-1)
+ omega = 30 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorPrism3(13.8*nanometer, 3*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Prism3" )
+ ff = ba.FormFactorPrism3(13.8 * nanometer, 3 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Prism3")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Prism6.py b/Doc/FFCatalog/fig/ff2/sim_Prism6.py
index 02997b725b9b4cabfaf074ec277d924fa803a63a..c63e4e5a5733a729c64f09b7b2c1cfa0da6b925c 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Prism6.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Prism6.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=30*i/(n-1)
+ omega = 30 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorPrism6(5.7*nanometer, 3*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Prism6" )
+ ff = ba.FormFactorPrism6(5.7 * nanometer, 3 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Prism6")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Pyramid.py b/Doc/FFCatalog/fig/ff2/sim_Pyramid.py
index 79b0a128373e367b05138f1ba710caac37356969..99580c57f4b727c576b638aa5ae358fe7a0309a4 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Pyramid.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Pyramid.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=45*i/(n-1)
+ omega = 45 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorPyramid(10*nanometer, 4.2*nanometer, 60.0*degree)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Pyramid" )
+ ff = ba.FormFactorPyramid(10 * nanometer, 4.2 * nanometer, 60.0 * degree)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Pyramid")
diff --git a/Doc/FFCatalog/fig/ff2/sim_SawtoothRipple.py b/Doc/FFCatalog/fig/ff2/sim_SawtoothRipple.py
index c255993694b34b30488afef40c609622275ba043..f682952aa82e0274a34358ed997621aacd4bac3e 100644
--- a/Doc/FFCatalog/fig/ff2/sim_SawtoothRipple.py
+++ b/Doc/FFCatalog/fig/ff2/sim_SawtoothRipple.py
@@ -2,18 +2,19 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 4
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 4
results = []
for i in range(n):
- omega=90*i/(n-1)
+ omega = 90 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorSawtoothRippleBox(25*nanometer, 10*nanometer, 8*nanometer, 5*nanometer )
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
+ ff = ba.FormFactorSawtoothRippleBox(25 * nanometer, 10 * nanometer,
+ 8 * nanometer, 5 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
-bp.make_plot( results, det, "ff_SawtoothRipple" )
+bp.make_plot(results, det, "ff_SawtoothRipple")
diff --git a/Doc/FFCatalog/fig/ff2/sim_Tetrahedron.py b/Doc/FFCatalog/fig/ff2/sim_Tetrahedron.py
index 197819ca024bc3019dd42b8603a0d3986e498cac..593c2bf47414b0933280e4fb03dcb2e8213f75a1 100644
--- a/Doc/FFCatalog/fig/ff2/sim_Tetrahedron.py
+++ b/Doc/FFCatalog/fig/ff2/sim_Tetrahedron.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, -5, 5, -5, 5 )
-n = 4
+det = bp.Detector(200, -5, 5, -5, 5)
+n = 4
results = []
for i in range(n):
- omega=60*i/(n-1)
+ omega = 60 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorTetrahedron(12*nanometer, 8*nanometer, 75*degree)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_Tetrahedron" )
+ ff = ba.FormFactorTetrahedron(12 * nanometer, 8 * nanometer, 75 * degree)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_Tetrahedron")
diff --git a/Doc/FFCatalog/fig/ff2/sim_TruncatedCube.py b/Doc/FFCatalog/fig/ff2/sim_TruncatedCube.py
index e50cf83ff4d2683f90fd85580c25b2d7d751c4d7..8dbd6cad41751f01b094e2b9e3e853ca3df0a867 100644
--- a/Doc/FFCatalog/fig/ff2/sim_TruncatedCube.py
+++ b/Doc/FFCatalog/fig/ff2/sim_TruncatedCube.py
@@ -2,18 +2,18 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- omega=45*i/(n-1)
+ omega = 45 * i / (n - 1)
title = r'$\omega=%d^\circ$' % omega
- ff = ba.FormFactorTruncatedCube(6.4*nanometer, 1.5*nanometer)
- trafo = ba.RotationZ(omega*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_TruncatedCube" )
+ ff = ba.FormFactorTruncatedCube(6.4 * nanometer, 1.5 * nanometer)
+ trafo = ba.RotationZ(omega * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_TruncatedCube")
diff --git a/Doc/FFCatalog/fig/ff2/sim_TruncatedSphere.py b/Doc/FFCatalog/fig/ff2/sim_TruncatedSphere.py
index d71e08a99a02af21f304e3f4702220889d305b20..17a4c33469cdd41362ad2c92a0bc4be6ec7d9473 100644
--- a/Doc/FFCatalog/fig/ff2/sim_TruncatedSphere.py
+++ b/Doc/FFCatalog/fig/ff2/sim_TruncatedSphere.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- theta=30*i/(n-1)
+ theta = 30 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorTruncatedSphere(4.2*nanometer, 6.1*nanometer, 0)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_TruncatedSphere" )
+ ff = ba.FormFactorTruncatedSphere(4.2 * nanometer, 6.1 * nanometer, 0)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_TruncatedSphere")
diff --git a/Doc/FFCatalog/fig/ff2/sim_TruncatedSpheroid.py b/Doc/FFCatalog/fig/ff2/sim_TruncatedSpheroid.py
index d5bcc1ad053ddcdf424c964846295329f1969424..5d872ac4f55543294d37b09d7b82091ed87654de 100644
--- a/Doc/FFCatalog/fig/ff2/sim_TruncatedSpheroid.py
+++ b/Doc/FFCatalog/fig/ff2/sim_TruncatedSpheroid.py
@@ -2,18 +2,18 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-n = 4
+det = bp.Detector(200, 0, 5, 0, 5)
+n = 4
results = []
for i in range(n):
- theta=30*i/(n-1)
+ theta = 30 * i / (n - 1)
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorTruncatedSpheroid(3.3*nanometer, 9.6*nanometer, 1.8, 0)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_TruncatedSpheroid" )
+ ff = ba.FormFactorTruncatedSpheroid(3.3 * nanometer, 9.6 * nanometer, 1.8, 0)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_TruncatedSpheroid")
diff --git a/Doc/FFCatalog/fig/ff2/sim_demo_1quadrants.py b/Doc/FFCatalog/fig/ff2/sim_demo_1quadrants.py
index f441c201010fb255e66244595fe1a47c61afa72a..61cafe14d66089a57c123c2ef2d589f00b379ad7 100644
--- a/Doc/FFCatalog/fig/ff2/sim_demo_1quadrants.py
+++ b/Doc/FFCatalog/fig/ff2/sim_demo_1quadrants.py
@@ -2,19 +2,19 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, 0, 5, 0, 5 )
-pars = [0,5,10,20]
+det = bp.Detector(200, 0, 5, 0, 5)
+pars = [0, 5, 10, 20]
n = len(pars)
results = []
for i in range(n):
- theta=pars[i]
+ theta = pars[i]
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorTruncatedSphere(4.2*nanometer, 6.1*nanometer, 0)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_demo_1quadrants" )
+ ff = ba.FormFactorTruncatedSphere(4.2 * nanometer, 6.1 * nanometer, 0)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_demo_1quadrants")
diff --git a/Doc/FFCatalog/fig/ff2/sim_demo_4quadrants.py b/Doc/FFCatalog/fig/ff2/sim_demo_4quadrants.py
index 9214797e1be0cd7576cdff07b25dbf163db1c8d0..6663250d29c79fd9abecd85c32e3e5f95af3d9bc 100644
--- a/Doc/FFCatalog/fig/ff2/sim_demo_4quadrants.py
+++ b/Doc/FFCatalog/fig/ff2/sim_demo_4quadrants.py
@@ -2,19 +2,19 @@
Plot form factor.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
-det = bp.Detector( 200, -5, 5, -5, 5 )
-pars = [0,5,10,20]
+det = bp.Detector(200, -5, 5, -5, 5)
+pars = [0, 5, 10, 20]
n = len(pars)
results = []
for i in range(n):
- theta=pars[i]
+ theta = pars[i]
title = r'$\vartheta=%d^\circ$' % theta
- ff = ba.FormFactorTruncatedSphere(4.2*nanometer, 6.1*nanometer, 0)
- trafo = ba.RotationY(theta*degree)
- data = bp.run_simulation(det,ff,trafo)
- results.append( bp.Result(i, data, title) )
-
-bp.make_plot( results, det, "ff_demo_4quadrants" )
+ ff = ba.FormFactorTruncatedSphere(4.2 * nanometer, 6.1 * nanometer, 0)
+ trafo = ba.RotationY(theta * degree)
+ data = bp.run_simulation(det, ff, trafo)
+ results.append(bp.Result(i, data, title))
+
+bp.make_plot(results, det, "ff_demo_4quadrants")
diff --git a/Doc/FFCatalog/fig/ff2/sim_det_box.py b/Doc/FFCatalog/fig/ff2/sim_det_box.py
index c32ba4232160e336d0de88748844b96cfe6024c8..69698aa9605187020d00405d2aef65edcf4a46e5 100644
--- a/Doc/FFCatalog/fig/ff2/sim_det_box.py
+++ b/Doc/FFCatalog/fig/ff2/sim_det_box.py
@@ -2,14 +2,14 @@
Plot form factors.
"""
import bornagain as ba
-from bornagain import nanometer, degree
+from bornagain import nanometer, degree
import bornplot as bp
det = bp.Detector(1000, 0, 5, 0, 5)
n = 3
results = []
for i in range(n):
- siz = [10,100,1000][i]
+ siz = [10, 100, 1000][i]
title = r'$L_x = %d~nm$' % siz
ff = ba.FormFactorBox(siz, 10, 10)
data = bp.run_simulation(det, ff)
diff --git a/Doc/PhysicsManual/fig/drawing/Green.py b/Doc/PhysicsManual/fig/drawing/Green.py
index 0026ebed5c9a5c979476bd6c4d24968b736b67df..b3d5887da82c77869e445b8fb02df2f14a119176 100755
--- a/Doc/PhysicsManual/fig/drawing/Green.py
+++ b/Doc/PhysicsManual/fig/drawing/Green.py
@@ -1,44 +1,46 @@
#!/usr/bin/env python3
-
'''
Compute radiation trajectories through multilayer sample
for use in figure that explains the Green function.
'''
xd = 52
-yd = 10 # detector
-s = 3 # source located at -s
-T = [ 6, 6 ] # layer thickness
-sd = T[0]-s # distance from source to lower interface
-DeltaLayer = [ .05, .1 ] # refractive index parameter delta, per layer
-x0 = 4
-xtot = xd - x0 # determine angles so that sum dx matches this
+yd = 10 # detector
+s = 3 # source located at -s
+T = [6, 6] # layer thickness
+sd = T[0] - s # distance from source to lower interface
+DeltaLayer = [.05, .1] # refractive index parameter delta, per layer
+x0 = 4
+xtot = xd - x0 # determine angles so that sum dx matches this
PP = [
- [ s, yd ],
- [ -sd, T[0], yd ],
- [ s, -T[0], T[0], yd ],
- [ -sd, T[0], -T[0], T[0], yd ],
- [ -sd, -T[1], T[1], T[0], yd ],
- [ -sd, -T[1], T[1], -T[1], T[1], T[0], yd ],
- [ -sd, -T[1], T[1], T[0], -T[0], T[0], yd ],
+ [s, yd],
+ [-sd, T[0], yd],
+ [s, -T[0], T[0], yd],
+ [-sd, T[0], -T[0], T[0], yd],
+ [-sd, -T[1], T[1], T[0], yd],
+ [-sd, -T[1], T[1], -T[1], T[1], T[0], yd],
+ [-sd, -T[1], T[1], T[0], -T[0], T[0], yd],
]
import math, re, scipy.optimize, sys
-def inside( y, mi, ma ):
- return mi<=y and y<=ma
-def xsum( a0, P, D ):
+def inside(y, mi, ma):
+ return mi <= y and y <= ma
+
+
+def xsum(a0, P, D):
n = len(P)
if len(D) != n:
- sys.stderr.write( "Bug: inconsistent array lengths\n" )
+ sys.stderr.write("Bug: inconsistent array lengths\n")
exit(1)
ret = 0
for i in range(n):
- a = math.acos( min( .99, math.cos(a0) / (1-D[i]) ) )
- ret += abs(P[i])/math.tan(a)
- return ret-xtot
+ a = math.acos(min(.99, math.cos(a0) / (1 - D[i])))
+ ret += abs(P[i]) / math.tan(a)
+ return ret - xtot
+
cmd0 = ""
cmd0 += "/xd %6.3g def\n" % xd
@@ -53,55 +55,56 @@ for P in PP:
for dy in P:
yold = y
y += dy
- if yold>=0 and y>=0:
- 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]) :
- DeltaPath.append( DeltaLayer[1] )
+ if yold >= 0 and y >= 0:
+ 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]):
+ DeltaPath.append(DeltaLayer[1])
else:
- sys.stderr.write( "Invalid input => layer ill defined\n" )
- if y!=yd:
- sys.stderr.write( "Invalid input => detector not hit\n" )
+ sys.stderr.write("Invalid input => layer ill defined\n")
+ if y != yd:
+ sys.stderr.write("Invalid input => detector not hit\n")
exit(1)
- a0 = scipy.optimize.newton( xsum, .5, args = ( P, DeltaPath ) )
- print( a0 )
+ a0 = scipy.optimize.newton(xsum, .5, args=(P, DeltaPath))
+ print(a0)
y = -s
- x1 = x0
- x2 = x0
- wgt = 5 - len(P)/2
+ x1 = x0
+ x2 = x0
+ wgt = 5 - len(P) / 2
cmd1 += "%1i [] lset\n" % (wgt)
cmd2 += "%1i [] lset\n" % (wgt)
- cmd1 += "%6.3g %6.3g np mv\n" % ( x1, y )
- cmd2 += "%6.3g %6.3g np mv\n" % ( x2, y )
- for i in range(len(P)-1):
- a = math.acos( math.cos(a0) / (1-DeltaPath[i]) )
- x1 += abs(P[i])/math.tan(a)
- b = math.acos( math.cos(b0) / (1-DeltaPath[i]) )
- x2 += abs(P[i])/math.tan(b)
+ cmd1 += "%6.3g %6.3g np mv\n" % (x1, y)
+ cmd2 += "%6.3g %6.3g np mv\n" % (x2, y)
+ for i in range(len(P) - 1):
+ a = math.acos(math.cos(a0) / (1 - DeltaPath[i]))
+ x1 += abs(P[i]) / math.tan(a)
+ b = math.acos(math.cos(b0) / (1 - DeltaPath[i]))
+ x2 += abs(P[i]) / math.tan(b)
y += P[i]
- cmd1 += "%6.3g %6.3g li\n" % ( x1, y )
- cmd2 += "%6.3g %6.3g li\n" % ( x2, y )
+ cmd1 += "%6.3g %6.3g li\n" % (x1, y)
+ cmd2 += "%6.3g %6.3g li\n" % (x2, y)
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 )
+ 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 += "\n"
cmd2 += "\n"
#/pfeiL { % (arrow anchored at base) x y rot siz len
-t = "% This file is automatically generated by script " + sys.argv[0] + "\n% DO NOT EDIT!\n\n"
-fd = open( "Green1.ps.in", 'r' )
+t = "% This file is automatically generated by script " + sys.argv[
+ 0] + "\n% DO NOT EDIT!\n\n"
+fd = open("Green1.ps.in", 'r')
t += fd.read()
fd.close
-cmd0 += "/b0 %7.3g def\n" % (180*b0/math.pi)
-t = re.sub( r'%#0', cmd0, t )
-t = re.sub( r'%#1', cmd1, t )
-t = re.sub( r'%#2', cmd2, t )
+cmd0 += "/b0 %7.3g def\n" % (180 * b0 / math.pi)
+t = re.sub(r'%#0', cmd0, t)
+t = re.sub(r'%#1', cmd1, t)
+t = re.sub(r'%#2', cmd2, t)
-fd = open( "Green1.ps", 'w' )
-fd.write( t )
+fd = open("Green1.ps", 'w')
+fd.write(t)
fd.close
diff --git a/Examples/Demos/FitCylindersPrisms_movie.py b/Examples/Demos/FitCylindersPrisms_movie.py
index acd255944a14c87d47c1da59b92ebf5fff7945c7..c438217f09435c6fd3380589d5facacbecc22b29 100644
--- a/Examples/Demos/FitCylindersPrisms_movie.py
+++ b/Examples/Demos/FitCylindersPrisms_movie.py
@@ -21,7 +21,6 @@ minimization engine, with starting values cylinder_height = prism3_height = 4nm,
cylinder_radius = prism3_length/2 = 6nm as initial fit parameter values.
"""
-
import numpy
import matplotlib
import matplotlib.pyplot as plt
@@ -35,10 +34,10 @@ fig = plt.figure(1)
max_line_length = 30
-def get_sample(cylinder_height=1.0*nanometer,
- cylinder_radius=1.0*nanometer,
- prism_length=2.0*nanometer,
- prism_height=1.0*nanometer):
+def get_sample(cylinder_height=1.0 * nanometer,
+ cylinder_radius=1.0 * nanometer,
+ prism_length=2.0 * nanometer,
+ prism_height=1.0 * nanometer):
"""
Build the sample representing cylinders and pyramids on top of
substrate without interference.
@@ -75,7 +74,8 @@ def create_real_data():
This function has been used once to generate refdata_fitcylinderprisms.int
"""
# creating sample with set of parameters we will later try to find during the fit
- sample = get_sample(5.0*nanometer, 5.0*nanometer, 5.0*nanometer, 5.0*nanometer)
+ sample = get_sample(5.0 * nanometer, 5.0 * nanometer, 5.0 * nanometer,
+ 5.0 * nanometer)
simulation = get_simulation()
simulation.setSample(sample)
simulation.runSimulation()
@@ -85,7 +85,7 @@ def create_real_data():
# random seed made as in FitSPheresInHexLattice_builder.py example
np.random.seed(0)
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
IntensityDataIOFactory.writeIntensityData(ba.Histogram2D(noisy),
'refdata_fitcylinderprisms.int')
@@ -96,8 +96,9 @@ def get_simulation():
Create GISAXS simulation with beam and detector defined
"""
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, 100, 0.0*degree, 2.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setDetectorParameters(100, -1.0 * degree, 1.0 * degree, 100,
+ 0.0 * degree, 2.0 * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
return simulation
@@ -119,12 +120,16 @@ class DrawObserver(IFitObserver):
real_data = fit_suite.getFitObjects().getRealData().getArray()
simulated_data = fit_suite.getFitObjects().getSimulationData().getArray()
plt.subplot(2, 2, 1)
- im = plt.imshow(real_data + 1, norm=matplotlib.colors.LogNorm(),extent=[-1.0, 1.0, 0, 2.0])
+ im = plt.imshow(real_data + 1,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-1.0, 1.0, 0, 2.0])
plt.colorbar(im)
plt.title('\"Real\" data')
# plotting real data
plt.subplot(2, 2, 2)
- im = plt.imshow(simulated_data + 1, norm=matplotlib.colors.LogNorm(),extent=[-1.0, 1.0, 0, 2.0])
+ im = plt.imshow(simulated_data + 1,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-1.0, 1.0, 0, 2.0])
plt.colorbar(im)
plt.title('Simulated data')
# plotting parameter space
@@ -185,7 +190,8 @@ def run_fitting():
simulation = get_simulation()
simulation.setSample(sample)
- real_data = IntensityDataIOFactory.readIntensityData('refdata_fitcylinderprisms.int.gz')
+ real_data = IntensityDataIOFactory.readIntensityData(
+ 'refdata_fitcylinderprisms.int.gz')
fit_suite = FitSuite()
fit_suite.addSimulationAndRealData(simulation, real_data)
@@ -195,10 +201,14 @@ def run_fitting():
fit_suite.attachObserver(draw_observer)
# setting fitting parameters with starting values
- fit_suite.addFitParameter("*Cylinder/Height", 2.*nanometer, Limits.limited(0.01, 10.0))
- fit_suite.addFitParameter("*Cylinder/Radius", 2.*nanometer, Limits.limited(0.01, 10.0))
- fit_suite.addFitParameter("*Prism3/Height", 2.*nanometer, Limits.limited(0.01, 10.0))
- fit_suite.addFitParameter("*Prism3/Length", 2.*nanometer, Limits.limited(0.01, 10.0))
+ fit_suite.addFitParameter("*Cylinder/Height", 2. * nanometer,
+ Limits.limited(0.01, 10.0))
+ fit_suite.addFitParameter("*Cylinder/Radius", 2. * nanometer,
+ Limits.limited(0.01, 10.0))
+ fit_suite.addFitParameter("*Prism3/Height", 2. * nanometer,
+ Limits.limited(0.01, 10.0))
+ fit_suite.addFitParameter("*Prism3/Length", 2. * nanometer,
+ Limits.limited(0.01, 10.0))
# # Now we create first fig strategy which will run first minimization round using Genetic minimizer.
# # Genetic minimizer is able to explore large parameter space without being trapped by some local minima.
@@ -220,7 +230,9 @@ def run_fitting():
fitpars = fit_suite.getFitParameters()
for i in range(0, fitpars.size()):
print fitpars[i].getName(), fitpars[i].getValue(), fitpars[i].getError()
- os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o fit_movie.mpg")
+ os.system(
+ "mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o fit_movie.mpg"
+ )
print 'Removing temporary files'
os.system("rm _tmp*")
diff --git a/Examples/Demos/simul_demo_cyl_SSCA.py b/Examples/Demos/simul_demo_cyl_SSCA.py
index e469a40df3d7a1ca65df3be7abd8453930cfc2ac..f35435d2708797987ff8baff4412947f912dcfa1 100644
--- a/Examples/Demos/simul_demo_cyl_SSCA.py
+++ b/Examples/Demos/simul_demo_cyl_SSCA.py
@@ -7,6 +7,7 @@ import matplotlib
import math
from bornagain import *
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -14,7 +15,7 @@ def RunSimulation():
# defining materials
mVacuum = HomogeneousMaterial("Vacuum", 0.0, 0.0)
mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- mParticle =HomogeneousMaterial("Particle", 6e-4, 2e-8)
+ mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
mLayer = HomogeneousMaterial("Layer", 2e-5, 2e-8)
# collection of particles
@@ -46,7 +47,8 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100, 0.0 * degree, 8.0 * degree)
+ simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100,
+ 0.0 * degree, 8.0 * degree)
simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.runSimulation()
@@ -58,9 +60,10 @@ def RunSimulation():
# main()
#-------------------------------------------------------------
if __name__ == '__main__':
- result = RunSimulation() + 1 # for log scale
- im = plt.imshow(result, norm=matplotlib.colors.LogNorm(),
- extent=[-4.0, 4.0, 0, 8.0])
+ result = RunSimulation() + 1 # for log scale
+ im = plt.imshow(result,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-4.0, 4.0, 0, 8.0])
plt.colorbar(im)
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
diff --git a/Examples/Demos/simul_demo_cylsphere.py b/Examples/Demos/simul_demo_cylsphere.py
index 1b7f60f258aa464c60d38ec027dae0aa15e1ee6c..ad458a483b32e70523e266f01a2a50ab00296bd4 100644
--- a/Examples/Demos/simul_demo_cylsphere.py
+++ b/Examples/Demos/simul_demo_cylsphere.py
@@ -7,6 +7,7 @@ import matplotlib
import math
from bornagain import *
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -39,7 +40,8 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100, 0.0 * degree, 8.0 * degree)
+ simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100,
+ 0.0 * degree, 8.0 * degree)
simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.runSimulation()
@@ -51,10 +53,10 @@ def RunSimulation():
# main()
#-------------------------------------------------------------
if __name__ == '__main__':
- result = RunSimulation() + 1 # for log scale
+ result = RunSimulation() + 1 # for log scale
im = plt.imshow(result,
- norm=matplotlib.colors.LogNorm(),
- extent=[-4.0, 4.0, 0, 8.0])
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-4.0, 4.0, 0, 8.0])
plt.colorbar(im)
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
diff --git a/Examples/Demos/simul_demo_lattice1.py b/Examples/Demos/simul_demo_lattice1.py
index 2fc3a58d21ab56a8cd94674105bb837d010806f5..e44f4337356ecd23a43df86f6bff950b9e48c5fb 100644
--- a/Examples/Demos/simul_demo_lattice1.py
+++ b/Examples/Demos/simul_demo_lattice1.py
@@ -9,17 +9,18 @@ from bornagain import *
M_PI = numpy.pi
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
def RunSimulation():
# defining materials
- mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0 )
- mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8 )
- mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8 )
+ mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0)
+ mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
+ mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
# particle
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder_ff = FormFactorCylinder(5 * nanometer, 5 * nanometer)
cylinder = Particle(mParticle, cylinder_ff.clone())
position = kvector_t(0.0, 0.0, 0.0)
cylinder.setPosition(position)
@@ -27,8 +28,10 @@ def RunSimulation():
particle_layout.addParticle(cylinder, 1.0)
# interference function
- interference = InterferenceFunction2DLattice(ba.SquareLattice2D(10.0*nanometer))
- pdf = FTDecayFunction2DCauchy(300.0*nanometer/2.0/M_PI, 100.0*nanometer/2.0/M_PI, 0)
+ interference = InterferenceFunction2DLattice(ba.SquareLattice2D(10.0 *
+ nanometer))
+ pdf = FTDecayFunction2DCauchy(300.0 * nanometer / 2.0 / M_PI,
+ 100.0 * nanometer / 2.0 / M_PI, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -46,8 +49,9 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -2.0*degree, 2.0*degree, 100, 0.0*degree, 4.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setDetectorParameters(100, -2.0 * degree, 2.0 * degree, 100,
+ 0.0 * degree, 4.0 * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
# run simulation
simulation.setSample(multi_layer)
@@ -60,9 +64,9 @@ def RunSimulation():
#-------------------------------------------------------------
if __name__ == '__main__':
result = RunSimulation()
- im = plt.imshow(result+1,
- norm=matplotlib.colors.LogNorm(),
- extent=[-2.0, 2.0, 0, 4.0])
+ im = plt.imshow(result + 1,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-2.0, 2.0, 0, 4.0])
plt.colorbar(im)
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
diff --git a/Examples/Demos/simul_demo_lattice2.py b/Examples/Demos/simul_demo_lattice2.py
index b7dc1f7d1042aec7e1e27884135475123ff3ecde..22b369c5b9c214b96b2e8f5c1fa3c018b60cf771 100644
--- a/Examples/Demos/simul_demo_lattice2.py
+++ b/Examples/Demos/simul_demo_lattice2.py
@@ -9,31 +9,34 @@ from bornagain import *
M_PI = numpy.pi
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
def RunSimulation():
# defining materials
- mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0 )
- mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8 )
- mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8 )
+ mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0)
+ mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
+ mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
# particle 1
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder_ff = FormFactorCylinder(5 * nanometer, 5 * nanometer)
cylinder = Particle(mParticle, cylinder_ff)
position = kvector_t(0.0, 0.0, 0.0)
cylinder.setPosition(position)
particle_layout1 = ParticleLayout()
particle_layout1.addParticle(cylinder, 1.0)
# particle 2
- position_2 = kvector_t(5.0*nanometer, 5.0*nanometer, 0.0)
+ position_2 = kvector_t(5.0 * nanometer, 5.0 * nanometer, 0.0)
cylinder.setPosition(position_2)
particle_layout2 = ParticleLayout()
particle_layout2.addParticle(cylinder, 1.0)
# interference function
- interference = InterferenceFunction2DLattice(ba.SquareLattice2D(10.0*nanometer))
- pdf = FTDecayFunction2DCauchy(300.0*nanometer/2.0/M_PI, 100.0*nanometer/2.0/M_PI, 0)
+ interference = InterferenceFunction2DLattice(ba.SquareLattice2D(10.0 *
+ nanometer))
+ pdf = FTDecayFunction2DCauchy(300.0 * nanometer / 2.0 / M_PI,
+ 100.0 * nanometer / 2.0 / M_PI, 0)
interference.setDecayFunction(pdf)
particle_layout1.setInterferenceFunction(interference)
particle_layout2.setInterferenceFunction(interference)
@@ -53,8 +56,9 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -2.0*degree, 2.0*degree, 100, 0.0*degree, 4.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setDetectorParameters(100, -2.0 * degree, 2.0 * degree, 100,
+ 0.0 * degree, 4.0 * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
# run simulation
simulation.setSample(multi_layer)
@@ -67,9 +71,9 @@ def RunSimulation():
#-------------------------------------------------------------
if __name__ == '__main__':
result = RunSimulation()
- im = plt.imshow(result+1,
- norm=matplotlib.colors.LogNorm(),
- extent=[-2.0, 2.0, 0, 4.0])
+ im = plt.imshow(result + 1,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-2.0, 2.0, 0, 4.0])
plt.colorbar(im)
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
diff --git a/Examples/Demos/simul_demo_movie.py b/Examples/Demos/simul_demo_movie.py
index dfb7de2e43d6de760e40bb5df3ff1bd33f0a081e..de1a31f701ee55bdc92efd73da1be7fe8e459b5b 100644
--- a/Examples/Demos/simul_demo_movie.py
+++ b/Examples/Demos/simul_demo_movie.py
@@ -14,6 +14,7 @@ radius = 1
height = 4
distance = 5
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -45,46 +46,50 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100, 0.0 * degree, 8.0 * degree)
+ simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100,
+ 0.0 * degree, 8.0 * degree)
simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.runSimulation()
# intensity data
return simulation.result().array()
-
+
def SetParameters(i):
global radius
global height
global distance
- radius = (1. + (3.0/Nframes)*i) * nanometer
- height = (1. + (4.0/Nframes)*i) * nanometer
- distance = (10. - (1.0/Nframes)*i) * nanometer
+ radius = (1. + (3.0 / Nframes) * i) * nanometer
+ height = (1. + (4.0 / Nframes) * i) * nanometer
+ distance = (10. - (1.0 / Nframes) * i) * nanometer
+
#-------------------------------------------------------------
# main()
#-------------------------------------------------------------
if __name__ == '__main__':
files = []
- fig = plt.figure(figsize=(5,5))
+ fig = plt.figure(figsize=(5, 5))
ax = fig.add_subplot(111)
for i in range(Nframes):
SetParameters(i)
result = RunSimulation() + 1 # for log scale
ax.cla()
- im = ax.imshow(result, vmax=1e3,
- norm=matplotlib.colors.LogNorm(),
- extent=[-4.0, 4.0, 0, 8.0])
+ im = ax.imshow(result,
+ vmax=1e3,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-4.0, 4.0, 0, 8.0])
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
- if i==0:
+ if i == 0:
plt.colorbar(im)
- fname = '_tmp%03d.png'%i
+ fname = '_tmp%03d.png' % i
print 'Saving frame', fname
try:
fig.savefig(fname)
except IOError as e:
- print "Frame cannot be saved. I/O error({0}): {1}".format(e.errno, e.strerror)
+ print "Frame cannot be saved. I/O error({0}): {1}".format(
+ e.errno, e.strerror)
print "Copy these examples to the directory where you have a write permission and enough free space to save the movie."
sys.exit()
except:
@@ -94,10 +99,11 @@ if __name__ == '__main__':
files.append(fname)
try:
- os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation.mpg")
+ os.system(
+ "mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation.mpg"
+ )
print 'Removing temporary files'
os.system("rm _tmp*")
except:
print "Movie cannot be saved. Error:", sys.exc_info()[0]
sys.exit()
-
diff --git a/Examples/Demos/simul_demo_movie2.py b/Examples/Demos/simul_demo_movie2.py
index 72b73ae6537c23914c12b09ff4e64321fba7f3c8..5662269b8a9b5ce9483c4fb859db85ab8971d2de 100644
--- a/Examples/Demos/simul_demo_movie2.py
+++ b/Examples/Demos/simul_demo_movie2.py
@@ -13,6 +13,7 @@ layer_thickness = 1
Nframes = 100
Ngrowframes = 30
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -46,7 +47,8 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100, 0.0 * degree, 8.0 * degree)
+ simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100,
+ 0.0 * degree, 8.0 * degree)
simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.runSimulation()
@@ -57,37 +59,41 @@ def RunSimulation():
def SetParameters(i):
global radius
global layer_thickness
- if i<Ngrowframes:
- radius = (1. + (3.0/Ngrowframes)*i) * nanometer
+ if i < Ngrowframes:
+ radius = (1. + (3.0 / Ngrowframes) * i) * nanometer
layer_thickness = 0.01 * nanometer
else:
radius = 4. * nanometer
- layer_thickness = (0.01 + (0.5/(Nframes-Ngrowframes))*(i-Ngrowframes)) * nanometer
+ layer_thickness = (0.01 + (0.5 / (Nframes - Ngrowframes)) *
+ (i - Ngrowframes)) * nanometer
+
#-------------------------------------------------------------
# main()
#-------------------------------------------------------------
if __name__ == '__main__':
files = []
- fig = plt.figure(figsize=(5,5))
+ fig = plt.figure(figsize=(5, 5))
ax = fig.add_subplot(111)
for i in range(Nframes):
SetParameters(i)
- result = RunSimulation() + 1 # for log scale
+ result = RunSimulation() + 1 # for log scale
ax.cla()
- im = ax.imshow(result, vmax=1e3,
- norm=matplotlib.colors.LogNorm(),
- extent=[-4.0, 4.0, 0, 8.0])
+ im = ax.imshow(result,
+ vmax=1e3,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-4.0, 4.0, 0, 8.0])
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
- if i==0:
+ if i == 0:
plt.colorbar(im)
- fname = '_tmp%03d.png'%i
+ fname = '_tmp%03d.png' % i
print 'Saving frame', fname
try:
fig.savefig(fname)
except IOError as e:
- print "Frame cannot be saved. I/O error({0}): {1}".format(e.errno, e.strerror)
+ print "Frame cannot be saved. I/O error({0}): {1}".format(
+ e.errno, e.strerror)
print "Copy these examples to the directory where you have a write permission and enough free space to save the movie."
sys.exit()
except:
@@ -96,10 +102,11 @@ if __name__ == '__main__':
else:
files.append(fname)
try:
- os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation2.mpg")
+ os.system(
+ "mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation2.mpg"
+ )
print 'Removing temporary files'
os.system("rm _tmp*")
except:
print "Movie cannot be saved. Error:", sys.exc_info()[0]
sys.exit()
-
diff --git a/Examples/Demos/simul_demo_movie3.py b/Examples/Demos/simul_demo_movie3.py
index 0037480b61ed8e0b5de18e734746005381e4d40b..b6983fd1bceec13db3e03ed36e099e1725ad6ada 100644
--- a/Examples/Demos/simul_demo_movie3.py
+++ b/Examples/Demos/simul_demo_movie3.py
@@ -12,6 +12,7 @@ Nframes = 50
kappa = 0.
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -51,7 +52,8 @@ def RunSimulation():
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100, 0.0 * degree, 8.0 * degree)
+ simulation.setDetectorParameters(100, -4.0 * degree, 4.0 * degree, 100,
+ 0.0 * degree, 8.0 * degree)
simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.runSimulation()
@@ -61,32 +63,35 @@ def RunSimulation():
def SetParameters(i):
global kappa
- kappa = 0.01 + (2.0/Nframes)*i
+ kappa = 0.01 + (2.0 / Nframes) * i
+
#-------------------------------------------------------------
# main()
#-------------------------------------------------------------
if __name__ == '__main__':
files = []
- fig = plt.figure(figsize=(5,5))
+ fig = plt.figure(figsize=(5, 5))
ax = fig.add_subplot(111)
for i in range(Nframes):
SetParameters(i)
result = RunSimulation() + 1 # for log scale
ax.cla()
- im = ax.imshow(result, vmax=1e3,
- norm=matplotlib.colors.LogNorm(),
- extent=[-4.0, 4.0, 0, 8.0])
+ im = ax.imshow(result,
+ vmax=1e3,
+ norm=matplotlib.colors.LogNorm(),
+ extent=[-4.0, 4.0, 0, 8.0])
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
- if i==0:
+ if i == 0:
plt.colorbar(im)
- fname = '_tmp%03d.png'%i
+ fname = '_tmp%03d.png' % i
print 'Saving frame', fname
try:
fig.savefig(fname)
except IOError as e:
- print "Frame cannot be saved. I/O error({0}): {1}".format(e.errno, e.strerror)
+ print "Frame cannot be saved. I/O error({0}): {1}".format(
+ e.errno, e.strerror)
print "Copy these examples to the directory where you have a write permission and enough free space to save the movie."
sys.exit()
except:
@@ -96,10 +101,11 @@ if __name__ == '__main__':
files.append(fname)
try:
- os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation3.mpg")
+ os.system(
+ "mencoder 'mf://_tmp*.png' -mf type=png:fps=10 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o animation3.mpg"
+ )
print 'Removing temporary files'
os.system("rm _tmp*")
except:
print "Movie cannot be saved. Error:", sys.exc_info()[0]
sys.exit()
-
diff --git a/Examples/Python/fit51_Basic/basic_fitting_tutorial.py b/Examples/Python/fit51_Basic/basic_fitting_tutorial.py
index 14b06998c3c902e665ef552fc568fa845fc1cff7..7cf45a418885f86a30ea47ff23c880b9d7102c03 100644
--- a/Examples/Python/fit51_Basic/basic_fitting_tutorial.py
+++ b/Examples/Python/fit51_Basic/basic_fitting_tutorial.py
@@ -47,9 +47,9 @@ def get_simulation(params):
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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -62,8 +62,12 @@ def create_real_data():
"""
# default sample parameters
- params = {'cylinder_height': 5.0*nm, 'cylinder_radius': 5.0*nm,
- 'prism_height': 5.0*nm, 'prism_base_edge': 5.0*nm}
+ params = {
+ 'cylinder_height': 5.0 * nm,
+ 'cylinder_radius': 5.0 * nm,
+ 'prism_height': 5.0 * nm,
+ 'prism_base_edge': 5.0 * nm
+ }
# retrieving simulated data in the form of numpy array
simulation = get_simulation(params)
@@ -73,7 +77,7 @@ def create_real_data():
# spoiling simulated data with noise to produce "real" data
np.random.seed(0)
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
np.savetxt("basic_fitting_tutorial_data.txt.gz", real_data)
@@ -103,10 +107,10 @@ def run_fitting():
fit_objective.initPlot(10)
params = ba.Parameters()
- params.add("cylinder_height", 4.*nm, min=0.01)
- params.add("cylinder_radius", 6.*nm, min=0.01)
- params.add("prism_height", 4.*nm, min=0.01)
- params.add("prism_base_edge", 6.*nm, min=0.01)
+ params.add("cylinder_height", 4. * nm, min=0.01)
+ params.add("cylinder_radius", 6. * nm, min=0.01)
+ params.add("prism_height", 4. * nm, min=0.01)
+ params.add("prism_base_edge", 6. * nm, min=0.01)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit51_Basic/consecutive_fitting.py b/Examples/Python/fit51_Basic/consecutive_fitting.py
index 56d5dc25bae9a3237717aa9901ea2de92ab93ed2..fa54e2100aabd7bad49c2e5ea0ba1d20bfbc53b8 100644
--- a/Examples/Python/fit51_Basic/consecutive_fitting.py
+++ b/Examples/Python/fit51_Basic/consecutive_fitting.py
@@ -44,9 +44,9 @@ def get_simulation(params):
Returns a GISAXS simulation with beam 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)
+ 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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -56,7 +56,7 @@ def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius': 5.0*nm, 'height': 5.0*nm}
+ params = {'radius': 5.0 * nm, 'height': 5.0 * nm}
simulation = get_simulation(params)
simulation.runSimulation()
@@ -66,7 +66,7 @@ def create_real_data():
# spoiling simulated data with the noise to produce "real" data
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -81,16 +81,14 @@ def run_fitting():
fit_objective.addSimulationAndData(get_simulation, real_data, 1.0)
fit_objective.initPrint(10)
fit_objective.initPlot(10)
-
"""
Setting fitting parameters with starting values.
Here we select starting values being quite far from true values
to puzzle our minimizer's as much as possible.
"""
params = ba.Parameters()
- params.add("height", 1.*nm, min=0.01, max=30.0, step=0.05*nm)
- params.add("radius", 20.*nm, min=0.01, max=30.0, step=0.05*nm)
-
+ params.add("height", 1. * nm, min=0.01, max=30.0, step=0.05 * nm)
+ params.add("radius", 20. * nm, min=0.01, max=30.0, step=0.05 * nm)
"""
Now we run first minimization round using the Genetic minimizer.
The Genetic minimizer is able to explore large parameter space
@@ -102,7 +100,6 @@ def run_fitting():
fit_objective.finalize(result)
best_params_so_far = result.parameters()
-
"""
Second fit will use another minimizer.
It starts from best parameters found in previous minimization
diff --git a/Examples/Python/fit51_Basic/minimal_fit_example.py b/Examples/Python/fit51_Basic/minimal_fit_example.py
index bc71decbb208f1a0ca7113f4848a33a3dc84c397..e5c68e14c5ef7e61a5f91eb0df0484185f44b7c2 100644
--- a/Examples/Python/fit51_Basic/minimal_fit_example.py
+++ b/Examples/Python/fit51_Basic/minimal_fit_example.py
@@ -20,9 +20,9 @@ def get_simulation(params):
multi_layer.addLayer(layer)
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.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.setSample(multi_layer)
return simulation
@@ -32,7 +32,7 @@ def real_data():
"""
Generating "experimental" data by running simulation with default parameters.
"""
- simulation = get_simulation({'radius': 5.0*nm})
+ simulation = get_simulation({'radius': 5.0 * nm})
simulation.runSimulation()
return simulation.result().array()
@@ -46,7 +46,7 @@ def run_fitting():
fit_objective.initPrint(10)
params = ba.Parameters()
- params.add("radius", 4.*nm, min=0.01)
+ params.add("radius", 4. * nm, min=0.01)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit51_Basic/minimizer_settings.py b/Examples/Python/fit51_Basic/minimizer_settings.py
index 871368b4efcd5fbf1f9e65d75b9ae8d093a811fe..0b48597356b0caeef05f7e301ccde2936edd4718 100644
--- a/Examples/Python/fit51_Basic/minimizer_settings.py
+++ b/Examples/Python/fit51_Basic/minimizer_settings.py
@@ -45,9 +45,9 @@ def get_simulation(params):
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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -58,8 +58,12 @@ def create_real_data():
Generating "real" data from simulated image with default parameters.
"""
- params = {'cylinder_height': 5.0*nm, 'cylinder_radius': 5.0*nm,
- 'prism_height': 5.0*nm, 'prism_base_edge': 5.0*nm}
+ params = {
+ 'cylinder_height': 5.0 * nm,
+ 'cylinder_radius': 5.0 * nm,
+ 'prism_height': 5.0 * nm,
+ 'prism_base_edge': 5.0 * nm
+ }
simulation = get_simulation(params)
simulation.runSimulation()
@@ -85,32 +89,28 @@ def run_fitting():
fit_objective.initPrint(10)
params = ba.Parameters()
- params.add("cylinder_height", 4.*nm, min=0.01)
- params.add("cylinder_radius", 6.*nm, min=0.01)
- params.add("prism_height", 4.*nm, min=0.01)
- params.add("prism_base_edge", 12.*nm, min=0.01)
+ params.add("cylinder_height", 4. * nm, min=0.01)
+ params.add("cylinder_radius", 6. * nm, min=0.01)
+ params.add("prism_height", 4. * nm, min=0.01)
+ params.add("prism_base_edge", 12. * nm, min=0.01)
minimizer = ba.Minimizer()
# Uncomment one of the line below to adjust minimizer settings
-
"""
Setting Minuit2 minimizer with Migrad algorithm, limiting number of iterations.
Minimization will try to respect MaxFunctionCalls value.
"""
# minimizer.setMinimizer("Minuit2", "Migrad", "MaxFunctionCalls=50")
-
"""
Setting two options at once.
Strategy=2 promises more accurate fit.
"""
# minimizer.setMinimizer("Minuit2", "Migrad", "MaxFunctionCalls=500;Strategy=2")
-
"""
Setting Minuit2 minimizer with Fumili algorithm.
"""
# minimizer.setMinimizer("Minuit2", "Fumili")
-
"""
Setting Levenberg-Marquardt algorithm.
"""
diff --git a/Examples/Python/fit52_Advanced/find_background.py b/Examples/Python/fit52_Advanced/find_background.py
index 7c40fe97c105ee577baabc203ad4588346018a11..8a0b1f4442da19fef6d4fac52bc55f5d517556de 100644
--- a/Examples/Python/fit52_Advanced/find_background.py
+++ b/Examples/Python/fit52_Advanced/find_background.py
@@ -47,10 +47,10 @@ def get_simulation(params):
scale = params["scale"]
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.setBeamIntensity(1e12*scale)
+ 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.setBeamIntensity(1e12 * scale)
simulation.setBackground(ba.ConstantBackground(background))
simulation.setSample(get_sample(params))
@@ -66,7 +66,12 @@ def create_real_data():
scale, background factors.
"""
- params = {'radius': 5.0*nm, 'height': 10.0*nm, 'scale': 2.0, 'background': 1000}
+ params = {
+ 'radius': 5.0 * nm,
+ 'height': 10.0 * nm,
+ 'scale': 2.0,
+ 'background': 1000
+ }
simulation = get_simulation(params)
simulation.runSimulation()
@@ -88,8 +93,8 @@ def run_fitting():
fit_objective.initPlot(10)
params = ba.Parameters()
- params.add("radius", 5.*nm, vary=False)
- params.add("height", 9.*nm, min=8.*nm, max=12.*nm)
+ params.add("radius", 5. * nm, vary=False)
+ params.add("height", 9. * nm, min=8. * nm, max=12. * nm)
params.add("scale", 1.5, min=1.0, max=3.0)
params.add("background", 200, min=100.0, max=2000.0, step=100.0)
diff --git a/Examples/Python/fit52_Advanced/fit_along_slices.py b/Examples/Python/fit52_Advanced/fit_along_slices.py
index 9124e731d9fa667b52a29a6adb1bc4fb1b81ba2d..9c22611daefaa5c5bcd4db20f5220e10970522c7 100644
--- a/Examples/Python/fit52_Advanced/fit_along_slices.py
+++ b/Examples/Python/fit52_Advanced/fit_along_slices.py
@@ -42,8 +42,9 @@ def get_simulation(params, add_masks=True):
Create and return 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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
if add_masks:
@@ -53,8 +54,8 @@ def get_simulation(params, add_masks=True):
simulation/fitting to be performed along slices only.
"""
simulation.maskAll()
- simulation.addMask(ba.HorizontalLine(alpha_slice_value*deg), False)
- simulation.addMask(ba.VerticalLine(phi_slice_value*deg), False)
+ simulation.addMask(ba.HorizontalLine(alpha_slice_value * deg), False)
+ simulation.addMask(ba.VerticalLine(phi_slice_value * deg), False)
return simulation
@@ -63,7 +64,7 @@ def create_real_data():
Generating "real" data by adding noise to the simulated data.
"""
# initial values which we will have to find later during the fit
- params = {'radius': 5.0*nm, 'height': 10.0*nm}
+ params = {'radius': 5.0 * nm, 'height': 10.0 * nm}
# retrieving simulated data in the form of numpy array
simulation = get_simulation(params, add_masks=False)
@@ -78,7 +79,6 @@ class PlotObserver:
Draws fit progress every nth iteration. Here we plot slices along real
and simulated images to see fit progress.
"""
-
def __init__(self):
self.fig = plt.figure(figsize=(10.25, 7.69))
self.fig.canvas.draw()
@@ -97,11 +97,15 @@ class PlotObserver:
# line representing vertical slice
plt.plot([phi_slice_value, phi_slice_value],
[data.getYmin(), data.getYmax()],
- color='gray', linestyle='-', linewidth=1)
+ color='gray',
+ linestyle='-',
+ linewidth=1)
# line representing horizontal slice
plt.plot([data.getXmin(), data.getXmax()],
[alpha_slice_value, alpha_slice_value],
- color='gray', linestyle='-', linewidth=1)
+ color='gray',
+ linestyle='-',
+ linewidth=1)
@staticmethod
def plot_slices(slices, title):
@@ -110,10 +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(1.0, slice.getMaximum()*10.0)
+ plt.ylim(1.0, slice.getMaximum() * 10.0)
plt.legend(loc='upper right')
plt.title(title)
@@ -127,14 +130,13 @@ class PlotObserver:
iteration_info = fit_objective.iterationInfo()
- plt.text(0.01, 0.85, "Iterations " + '{:d}'.
- format(iteration_info.iterationCount()))
+ 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()))
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.tight_layout()
plt.draw()
plt.pause(0.01)
@@ -153,19 +155,15 @@ class PlotObserver:
self.plot_real_data(real_data)
# horizontal slices
- slices = [
- ("real", real_data.projectionX(alpha_slice_value)),
- ("simul", simul_data.projectionX(alpha_slice_value))
- ]
+ slices = [("real", real_data.projectionX(alpha_slice_value)),
+ ("simul", simul_data.projectionX(alpha_slice_value))]
title = ("Horizontal slice at alpha =" + '{:3.1f}'.format(alpha_slice_value))
plt.subplot(2, 2, 2)
self.plot_slices(slices, title)
# vertical slices
- slices = [
- ("real", real_data.projectionY(phi_slice_value)),
- ("simul", simul_data.projectionY(phi_slice_value))
- ]
+ 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)
plt.subplot(2, 2, 3)
self.plot_slices(slices, title)
@@ -191,8 +189,8 @@ def run_fitting():
fit_objective.initPlot(10, plotter)
params = ba.Parameters()
- params.add("radius", 6.*nm, min=4.0, max=8.0)
- params.add("height", 9.*nm, min=8.0, max=12.0)
+ params.add("radius", 6. * nm, min=4.0, max=8.0)
+ params.add("height", 9. * nm, min=8.0, max=12.0)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit52_Advanced/fit_with_masks.py b/Examples/Python/fit52_Advanced/fit_with_masks.py
index 2306038950cec5ce99564304cab6865adacf8268..8226014c5551e145616b39d2dbd363a48b0114f9 100644
--- a/Examples/Python/fit52_Advanced/fit_with_masks.py
+++ b/Examples/Python/fit52_Advanced/fit_with_masks.py
@@ -41,9 +41,9 @@ def get_simulation(params, add_masks=True):
Create and return 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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
@@ -57,7 +57,7 @@ def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius': 5.0*nm, 'height': 10.0*nm}
+ params = {'radius': 5.0 * nm, 'height': 10.0 * nm}
# retrieving simulated data in the form of numpy array
simulation = get_simulation(params, add_masks=False)
@@ -66,7 +66,7 @@ def create_real_data():
# spoiling simulated data with the noise to produce "real" data
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -89,25 +89,24 @@ def add_mask_to_simulation(simulation):
simulation.maskAll()
# set mask to simulate pacman's head
- simulation.addMask(
- ba.Ellipse(0.0*deg, 1.0*deg, 0.5*deg, 0.5*deg), False)
+ simulation.addMask(ba.Ellipse(0.0 * deg, 1.0 * 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 = [[0.0*deg, 1.0*deg], [0.5*deg, 1.2*deg],
- [0.5*deg, 0.8*deg], [0.0*deg, 1.0*deg]]
+ points = [[0.0 * deg, 1.0 * deg], [0.5 * deg, 1.2 * deg], [0.5 * deg, 0.8 * deg],
+ [0.0 * deg, 1.0 * deg]]
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)
# other mask's shapes are possible too
# simulation.removeMasks()
@@ -131,8 +130,8 @@ def run_fitting():
fit_objective.initPlot(10)
params = ba.Parameters()
- params.add("radius", 6.*nm, min=4.0, max=8.0)
- params.add("height", 9.*nm, min=8.0, max=12.0)
+ params.add("radius", 6. * nm, min=4.0, max=8.0)
+ params.add("height", 9. * nm, min=8.0, max=12.0)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit52_Advanced/multiple_datasets.py b/Examples/Python/fit52_Advanced/multiple_datasets.py
index ae0cb86e846ed5551ea168ba98e4a5d4a9571a6b..5ce7f94d250e20fd0df6706593b36f82a365e078 100644
--- a/Examples/Python/fit52_Advanced/multiple_datasets.py
+++ b/Examples/Python/fit52_Advanced/multiple_datasets.py
@@ -44,21 +44,21 @@ def get_simulation(params):
incident_angle = params["incident_angle"]
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(50, -1.5*deg, 1.5*deg,
- 50, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, incident_angle, 0.0*deg)
+ simulation.setDetectorParameters(50, -1.5 * deg, 1.5 * deg, 50, 0.0 * deg,
+ 2.0 * deg)
+ simulation.setBeamParameters(1.0 * angstrom, incident_angle, 0.0 * deg)
simulation.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
def simulation1(params):
- params["incident_angle"] = 0.1*deg
+ params["incident_angle"] = 0.1 * deg
return get_simulation(params)
def simulation2(params):
- params["incident_angle"] = 0.4*deg
+ params["incident_angle"] = 0.4 * deg
return get_simulation(params)
@@ -66,8 +66,12 @@ def create_real_data(incident_alpha):
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius_a': 5.0*nm, 'radius_b': 6.0*nm,
- 'height': 8.0*nm, "incident_angle": incident_alpha}
+ params = {
+ 'radius_a': 5.0 * nm,
+ 'radius_b': 6.0 * nm,
+ 'height': 8.0 * nm,
+ "incident_angle": incident_alpha
+ }
simulation = get_simulation(params)
simulation.runSimulation()
@@ -77,7 +81,7 @@ def create_real_data(incident_alpha):
# spoiling simulated data with the noise to produce "real" data
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -103,15 +107,24 @@ class PlotObserver():
zmax = real_data.histogram2d().getMaximum()
- plt.subplot(canvas[i_dataset*3])
- ba.plot_colormap(real_data, title="\"Real\" data - #"+str(i_dataset+1),
- zmin=1.0, zmax=zmax, zlabel="")
- plt.subplot(canvas[1+i_dataset*3])
- ba.plot_colormap(simul_data, title="Simulated data - #"+str(i_dataset+1),
- zmin=1.0, zmax=zmax, zlabel="")
- plt.subplot(canvas[2+i_dataset*3])
- ba.plot_colormap(chi2_map, title="Chi2 map - #"+str(i_dataset+1),
- zmin=0.001, zmax=10.0, zlabel="")
+ plt.subplot(canvas[i_dataset * 3])
+ ba.plot_colormap(real_data,
+ title="\"Real\" data - #" + str(i_dataset + 1),
+ zmin=1.0,
+ zmax=zmax,
+ zlabel="")
+ plt.subplot(canvas[1 + i_dataset * 3])
+ ba.plot_colormap(simul_data,
+ title="Simulated data - #" + str(i_dataset + 1),
+ zmin=1.0,
+ zmax=zmax,
+ zlabel="")
+ plt.subplot(canvas[2 + i_dataset * 3])
+ ba.plot_colormap(chi2_map,
+ title="Chi2 map - #" + str(i_dataset + 1),
+ zmin=0.001,
+ zmax=10.0,
+ zlabel="")
@staticmethod
def display_fit_parameters(fit_objective):
@@ -123,8 +136,8 @@ class PlotObserver():
iteration_info = fit_objective.iterationInfo()
- plt.text(0.01, 0.85, "Iterations " + '{:d}'.
- format(iteration_info.iterationCount()))
+ 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()))
for index, params in enumerate(iteration_info.parameters()):
plt.text(0.01, 0.55 - index * 0.1,
@@ -139,8 +152,8 @@ class PlotObserver():
iteration_info = fit_objective.iterationInfo()
- plt.text(0.01, 0.95, "Iterations " + '{:d}'.
- format(iteration_info.iterationCount()))
+ plt.text(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,
@@ -151,8 +164,10 @@ class PlotObserver():
# we divide figure to have 3x3 subplots, with two first rows occupying
# most of the space
- canvas = matplotlib.gridspec.GridSpec(
- 3, 3, width_ratios=[1, 1, 1], height_ratios=[4, 4, 1])
+ canvas = matplotlib.gridspec.GridSpec(3,
+ 3,
+ width_ratios=[1, 1, 1],
+ height_ratios=[4, 4, 1])
canvas.update(left=0.05, right=0.95, hspace=0.5, wspace=0.2)
self.plot_dataset(fit_objective, canvas)
@@ -181,9 +196,9 @@ def run_fitting():
fit_objective.initPlot(10, plotter.update)
params = ba.Parameters()
- params.add("radius_a", 4.*nm, min=2.0, max=10.0)
- params.add("radius_b", 6.*nm, vary=False)
- params.add("height", 4.*nm, min=2.0, max=10.0)
+ params.add("radius_a", 4. * nm, min=2.0, max=10.0)
+ params.add("radius_b", 6. * nm, vary=False)
+ params.add("height", 4. * nm, min=2.0, max=10.0)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit53_CustomObjective/custom_objective_function.py b/Examples/Python/fit53_CustomObjective/custom_objective_function.py
index a72521bdb979627c0b206a9c81270a7e43a19b32..75d783e2f3942b116f153f870ed5e68414cf35a2 100644
--- a/Examples/Python/fit53_CustomObjective/custom_objective_function.py
+++ b/Examples/Python/fit53_CustomObjective/custom_objective_function.py
@@ -53,7 +53,7 @@ def get_sample(params):
interference = ba.InterferenceFunction2DLattice(
ba.HexagonalLattice2D(lattice_length))
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
+ pdf = ba.FTDecayFunction2DCauchy(10 * nm, 10 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -72,9 +72,9 @@ def get_simulation(params):
Create and return 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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -84,7 +84,7 @@ def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius': 6*nm, 'length': 12*nm}
+ params = {'radius': 6 * nm, 'length': 12 * nm}
simulation = get_simulation(params)
simulation.runSimulation()
@@ -94,7 +94,7 @@ def create_real_data():
# spoiling simulated data with noise to produce "real" data
np.random.seed(0)
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -110,8 +110,8 @@ def run_fitting():
objective.initPrint(10)
params = ba.Parameters()
- params.add('radius', value=7*nm, min=5*nm, max=8*nm)
- params.add('length', value=10*nm, min=8*nm, max=14*nm)
+ params.add('radius', value=7 * nm, min=5 * nm, max=8 * nm)
+ params.add('length', value=10 * nm, min=8 * nm, max=14 * nm)
minimizer = ba.Minimizer()
result = minimizer.minimize(objective.evaluate_residuals, params)
diff --git a/Examples/Python/fit54_ExternalMinimizer/lmfit_basics.py b/Examples/Python/fit54_ExternalMinimizer/lmfit_basics.py
index f0a22f72c68fe5f16ec536a4f92a4e1463514c0d..8933a0c99e97170b1b2f2b82a85a78ab170f03e1 100644
--- a/Examples/Python/fit54_ExternalMinimizer/lmfit_basics.py
+++ b/Examples/Python/fit54_ExternalMinimizer/lmfit_basics.py
@@ -27,7 +27,7 @@ def get_sample(params):
interference = ba.InterferenceFunction2DLattice(
ba.HexagonalLattice2D(lattice_length))
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
+ pdf = ba.FTDecayFunction2DCauchy(10 * nm, 10 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -46,9 +46,9 @@ def get_simulation(params):
Create and return 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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -58,7 +58,7 @@ def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius': 6*nm, 'length': 12*nm}
+ params = {'radius': 6 * nm, 'length': 12 * nm}
simulation = get_simulation(params)
simulation.runSimulation()
@@ -68,7 +68,7 @@ def create_real_data():
# spoiling simulated data with noise to produce "real" data
np.random.seed(0)
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -84,8 +84,8 @@ def run_fitting():
fit_objective.initPrint(10)
params = lmfit.Parameters()
- params.add('radius', value=7*nm, min=5*nm, max=8*nm)
- params.add('length', value=10*nm, min=8*nm, max=14*nm)
+ params.add('radius', value=7 * nm, min=5 * nm, max=8 * nm)
+ params.add('length', value=10 * nm, min=8 * nm, max=14 * nm)
result = lmfit.minimize(fit_objective.evaluate_residuals, params)
fit_objective.finalize(result)
diff --git a/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py b/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
index fc9514b085ea35b899a796d52848023f89f36223..18ed4558c932577aa1ad62044b1e8c5460d94673 100644
--- a/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
+++ b/Examples/Python/fit54_ExternalMinimizer/lmfit_with_plotting.py
@@ -28,7 +28,7 @@ def get_sample(params):
interference = ba.InterferenceFunction2DLattice(
ba.HexagonalLattice2D(lattice_length))
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
+ pdf = ba.FTDecayFunction2DCauchy(10 * nm, 10 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -47,9 +47,9 @@ def get_simulation(params):
Create and return 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.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.setBeamIntensity(1e+08)
simulation.setSample(get_sample(params))
return simulation
@@ -59,7 +59,7 @@ def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
"""
- params = {'radius': 6*nm, 'length': 12*nm}
+ params = {'radius': 6 * nm, 'length': 12 * nm}
simulation = get_simulation(params)
simulation.runSimulation()
@@ -69,7 +69,7 @@ def create_real_data():
# spoiling simulated data with noise to produce "real" data
np.random.seed(0)
noise_factor = 0.1
- noisy = np.random.normal(real_data, noise_factor*np.sqrt(real_data))
+ noisy = np.random.normal(real_data, noise_factor * np.sqrt(real_data))
noisy[noisy < 0.1] = 0.1
return noisy
@@ -78,13 +78,13 @@ class Plotter:
"""
Adapts standard plotter for lmfit minimizer.
"""
- def __init__(self, fit_objective, every_nth = 10):
+ def __init__(self, fit_objective, every_nth=10):
self.fit_objective = fit_objective
self.plotter_gisas = ba.PlotterGISAS()
self.every_nth = every_nth
def __call__(self, params, iter, resid):
- if iter%self.every_nth == 0:
+ if iter % self.every_nth == 0:
self.plotter_gisas.plot(self.fit_objective)
@@ -99,17 +99,19 @@ def run_fitting():
fit_objective.initPrint(10)
params = lmfit.Parameters()
- params.add('radius', value=7*nm, min=5*nm, max=8*nm)
- params.add('length', value=10*nm, min=8*nm, max=14*nm)
+ 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)
- result = lmfit.minimize(
- fit_objective.evaluate_residuals, params, iter_cb=plotter)
+ result = lmfit.minimize(fit_objective.evaluate_residuals,
+ params,
+ iter_cb=plotter)
fit_objective.finalize(result)
result.params.pretty_print()
print(lmfit.fit_report(result))
+
if __name__ == '__main__':
run_fitting()
plt.show()
diff --git a/Examples/Python/fit55_Specular/FitSpecularBasics.py b/Examples/Python/fit55_Specular/FitSpecularBasics.py
index d74b5ef0b1578898e5983253be64a2bea3ec0335..6dc55480be733db8a9683af4e395e2b098aaa8f4 100644
--- a/Examples/Python/fit55_Specular/FitSpecularBasics.py
+++ b/Examples/Python/fit55_Specular/FitSpecularBasics.py
@@ -21,7 +21,7 @@ def get_sample(params):
# substrate (Si)
si_sld_real = 2.0704e-06 # \AA^{-2}
- density_si = 0.0499 / ba.angstrom ** 3 # Si atomic number density
+ density_si = 0.0499 / ba.angstrom**3 # Si atomic number density
# layers' parameters
n_repetitions = 10
@@ -115,8 +115,10 @@ def run_fitting():
fit_objective.initPlot(10, plot_observer)
params = ba.Parameters()
- params.add("ti_thickness", 50 * ba.angstrom,
- min=10 * ba.angstrom, max=60 * ba.angstrom)
+ params.add("ti_thickness",
+ 50 * ba.angstrom,
+ min=10 * ba.angstrom,
+ max=60 * ba.angstrom)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit55_Specular/FitWithUncertainties.py b/Examples/Python/fit55_Specular/FitWithUncertainties.py
index a03e63688548dac9cedcfab75d6e051d80f7136e..41f9322f5e083403e4c31d0a04801e5f69f49a43 100644
--- a/Examples/Python/fit55_Specular/FitWithUncertainties.py
+++ b/Examples/Python/fit55_Specular/FitWithUncertainties.py
@@ -26,7 +26,7 @@ def get_sample(params):
# substrate (Si)
si_sld_real = 2.0704e-06 # \AA^{-2}
- density_si = 0.0499 / ba.angstrom ** 3 # Si atomic number density
+ density_si = 0.0499 / ba.angstrom**3 # Si atomic number density
# layers' parameters
n_repetitions = 10
@@ -124,8 +124,10 @@ def run_fitting():
fit_objective.setObjectiveMetric("Chi2", "L1")
params = ba.Parameters()
- params.add("ti_thickness", 50 * ba.angstrom,
- min=10 * ba.angstrom, max=60 * ba.angstrom)
+ params.add("ti_thickness",
+ 50 * ba.angstrom,
+ min=10 * ba.angstrom,
+ max=60 * ba.angstrom)
minimizer = ba.Minimizer()
minimizer.setMinimizer("Genetic", "", "MaxIterations=40;PopSize=10")
diff --git a/Examples/Python/fit55_Specular/RealLifeReflectometryFitting.py b/Examples/Python/fit55_Specular/RealLifeReflectometryFitting.py
index 5ac85e84fd6f10383fa96e01117f031c0f58b436..a9e942166a439228383b00483f99255afbeeac06 100644
--- a/Examples/Python/fit55_Specular/RealLifeReflectometryFitting.py
+++ b/Examples/Python/fit55_Specular/RealLifeReflectometryFitting.py
@@ -93,8 +93,7 @@ def create_simulation(arg_dict, bin_start, bin_end):
alpha_distr = ba.RangedDistributionGaussian(30, 3)
footprint = ba.FootprintGauss(arg_dict["footprint_factor"])
- scan = ba.AngularSpecScan(wavelength,
- get_real_data_axis(bin_start, bin_end))
+ scan = ba.AngularSpecScan(wavelength, get_real_data_axis(bin_start, bin_end))
scan.setAbsoluteAngularResolution(alpha_distr, arg_dict["divergence"])
scan.setFootprintFactor(footprint)
@@ -111,8 +110,8 @@ def buildSample(arg_dict):
# defining materials
m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
m_si_o2 = ba.HomogeneousMaterial("SiO2",
- 8.57040868e-06 * arg_dict["concentration"],
- 1.11016654e-07 * arg_dict["concentration"])
+ 8.57040868e-06 * arg_dict["concentration"],
+ 1.11016654e-07 * arg_dict["concentration"])
m_si = ba.HomogeneousMaterial("Si", 7.57211137e-06, 1.72728178e-07)
# roughness
@@ -152,7 +151,7 @@ def chi_2(real_data, sim_data, weights):
sim_data_upsc[sim_data_upsc is 0] = 1e-30
real_data_upsc = np.multiply(weights, real_data)
diff = real_data_upsc - sim_data_upsc
- return np.sum(np.divide(np.multiply(diff,diff), sim_data_upsc))
+ return np.sum(np.divide(np.multiply(diff, diff), sim_data_upsc))
def create_par_dict(*arg):
@@ -160,13 +159,14 @@ def create_par_dict(*arg):
Creates a dictionary with parameter names and values
and returns it
"""
- return {'intensity': arg[0],
- 'footprint_factor': arg[1],
- 'divergence':arg[2],
- 'concentration': arg[3],
- 'thickness': arg[4],
- 'roughness': arg[5]
- }
+ return {
+ 'intensity': arg[0],
+ 'footprint_factor': arg[1],
+ 'divergence': arg[2],
+ 'concentration': arg[3],
+ 'thickness': arg[4],
+ 'roughness': arg[5]
+ }
def objective_primary(args):
@@ -180,8 +180,8 @@ def objective_primary(args):
sim_result = run_simulation(arg_dict, bin_start, bin_end)
sim_data = sim_result.array()
- return chi_2(get_real_data_values(bin_start, bin_end),
- sim_data, get_weights(bin_start, bin_end))
+ return chi_2(get_real_data_values(bin_start, bin_end), sim_data,
+ get_weights(bin_start, bin_end))
def objective_fine(args, intensity, footprint_factor, divergence):
@@ -195,8 +195,8 @@ def objective_fine(args, intensity, footprint_factor, divergence):
sim_result = run_simulation(arg_dict, bin_start, bin_end)
sim_data = sim_result.array()
- return chi_2(get_real_data_values(bin_start, bin_end),
- sim_data, get_weights(bin_start, bin_end))
+ return chi_2(get_real_data_values(bin_start, bin_end), sim_data,
+ get_weights(bin_start, bin_end))
def run_fitting():
@@ -204,39 +204,51 @@ def run_fitting():
Runs fitting and returns its result
"""
# running preliminary optimization on the total range of experimental data.
- bounds = [(1e6, 1e8), # beam intensity
- (0.0, 0.1), # beam-to-sample width ratio
- (0.0, 0.08 * ba.deg), # beam_divergence
- (0.0, 1.0), # oxide_concentration
- (0.0, 2.0 * ba.nm), # oxide_thickness
- (0.0, 2.0 * ba.nm)] # roughness
+ bounds = [
+ (1e6, 1e8), # beam intensity
+ (0.0, 0.1), # beam-to-sample width ratio
+ (0.0, 0.08 * ba.deg), # beam_divergence
+ (0.0, 1.0), # oxide_concentration
+ (0.0, 2.0 * ba.nm), # oxide_thickness
+ (0.0, 2.0 * ba.nm)
+ ] # roughness
print("Start preliminary fitting of experimental data:\n")
- preliminary_result = differential_evolution(objective_primary, bounds,
- maxiter=20, popsize=60,
+ preliminary_result = differential_evolution(objective_primary,
+ bounds,
+ maxiter=20,
+ popsize=60,
mutation=(0.5, 1.5),
- disp=True, tol=1e-5)
+ disp=True,
+ tol=1e-5)
- bounds = [(0.0, 1.0), # oxide_concentration
- (0.0, 2.0 * ba.nm), # oxide_thickness
- (0.0, 2.0 * ba.nm)] # roughness
+ bounds = [
+ (0.0, 1.0), # oxide_concentration
+ (0.0, 2.0 * ba.nm), # oxide_thickness
+ (0.0, 2.0 * ba.nm)
+ ] # roughness
- fixed_args = (preliminary_result.x[0], # beam intensity
- preliminary_result.x[1], # beam-to-sample width ratio
- preliminary_result.x[2] # beam divergence
- )
+ fixed_args = (
+ preliminary_result.x[0], # beam intensity
+ preliminary_result.x[1], # beam-to-sample width ratio
+ preliminary_result.x[2] # beam divergence
+ )
print("\nStart fitting big incident angle part of experimental data:\n")
- fine_tuning_result = differential_evolution(objective_fine, bounds,
- fixed_args, maxiter=20,
- popsize=40, mutation=(0.5, 1.5),
- disp=True, tol=1e-5)
+ fine_tuning_result = differential_evolution(objective_fine,
+ bounds,
+ fixed_args,
+ maxiter=20,
+ popsize=40,
+ mutation=(0.5, 1.5),
+ disp=True,
+ tol=1e-5)
result = create_par_dict(*fixed_args, *fine_tuning_result.x)
print("\nFitting result:")
- print(result,"\n")
+ print(result, "\n")
return result
@@ -248,27 +260,29 @@ def plot_result(sim_result, ref_result, bin_start=0, bin_end=-1):
sim_data = sim_result.array()
ref_data = ref_result.array()
- 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)
+ 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)
xlabel = ba.get_axes_labels(sim_result, ba.Axes.DEFAULT)[0]
ylabel = "Intensity"
plt.xlabel(xlabel, fontsize=16)
plt.ylabel(ylabel, fontsize=16)
plt.legend(['Experimental data', 'Simulation', 'Reference'],
- loc='upper right', fontsize=16)
+ loc='upper right',
+ fontsize=16)
plt.show()
if __name__ == '__main__':
fit_data = run_fitting()
- ref_data = create_par_dict(3.78271438e+06, # beam intensity
- 9.58009763e-04, # beam-to-sample width ratio
- 2.30471294e-04, # beam angular divergence
- 0.58721753, # oxide concentration
- 1.25559347, # oxide thickness
- 0.19281863) # roughness
+ ref_data = create_par_dict(
+ 3.78271438e+06, # beam intensity
+ 9.58009763e-04, # beam-to-sample width ratio
+ 2.30471294e-04, # beam angular divergence
+ 0.58721753, # oxide concentration
+ 1.25559347, # oxide thickness
+ 0.19281863) # roughness
plot_result(run_simulation(fit_data), run_simulation(ref_data))
diff --git a/Examples/Python/fit61_Galaxi/fit_galaxi_data.py b/Examples/Python/fit61_Galaxi/fit_galaxi_data.py
index f02b85a638485e91e4887371c57feb71990ab2ee..b50694c0ea77761723f2fdbaeff363b4469f7993 100644
--- a/Examples/Python/fit61_Galaxi/fit_galaxi_data.py
+++ b/Examples/Python/fit61_Galaxi/fit_galaxi_data.py
@@ -6,8 +6,8 @@ import bornagain as ba
from bornagain import nm as nm
from sample_builder import SampleBuilder
-wavelength = 1.34*ba.angstrom
-alpha_i = 0.463*ba.deg
+wavelength = 1.34 * ba.angstrom
+alpha_i = 0.463 * ba.deg
# detector setup as given from instrument responsible
pilatus_npx, pilatus_npy = 981, 1043
@@ -20,10 +20,10 @@ def create_detector():
"""
Returns a model of the GALAXY detector
"""
- u0 = beam_xpos*pilatus_pixel_size # in mm
- v0 = beam_ypos*pilatus_pixel_size # in mm
- detector = ba.RectangularDetector(pilatus_npx, pilatus_npx*pilatus_pixel_size,
- pilatus_npy, pilatus_npy*pilatus_pixel_size)
+ u0 = beam_xpos * pilatus_pixel_size # in mm
+ v0 = beam_ypos * pilatus_pixel_size # in mm
+ detector = ba.RectangularDetector(pilatus_npx, pilatus_npx * pilatus_pixel_size,
+ pilatus_npy, pilatus_npy * pilatus_pixel_size)
detector.setPerpendicularToDirectBeam(detector_distance, u0, v0)
return detector
@@ -62,9 +62,9 @@ def run_fitting():
fit_objective.initPlot(10)
params = ba.Parameters()
- params.add("radius", 5.*nm, min=4.0, max=6.0, step=0.1*nm)
+ params.add("radius", 5. * nm, min=4.0, max=6.0, step=0.1 * nm)
params.add("sigma", 0.55, min=0.2, max=0.8, step=0.01)
- params.add("distance", 27.*nm, min=20.0, max=70.0)
+ params.add("distance", 27. * nm, min=20.0, max=70.0)
minimizer = ba.Minimizer()
result = minimizer.minimize(fit_objective.evaluate, params)
diff --git a/Examples/Python/fit61_Galaxi/sample_builder.py b/Examples/Python/fit61_Galaxi/sample_builder.py
index dffe9da447901f9a5ba9984e288e3ffb3eafde5f..9189516d30fe2fe2332b82e74d42b1bc44d4a8b4 100644
--- a/Examples/Python/fit61_Galaxi/sample_builder.py
+++ b/Examples/Python/fit61_Galaxi/sample_builder.py
@@ -13,13 +13,13 @@ class SampleBuilder:
"""
Init SampleBuilder with default sample parameters.
"""
- self.radius = 5.75*ba.nm
+ self.radius = 5.75 * ba.nm
self.sigma = 0.4
- self.distance = 53.6*ba.nm
- self.disorder = 10.5*ba.nm
+ self.distance = 53.6 * ba.nm
+ self.disorder = 10.5 * ba.nm
self.kappa = 17.5
- self.ptfe_thickness = 22.1*ba.nm
- self.hmdso_thickness = 18.5*ba.nm
+ self.ptfe_thickness = 22.1 * ba.nm
+ self.hmdso_thickness = 18.5 * ba.nm
def create_sample(self, params):
"""
@@ -54,17 +54,17 @@ class SampleBuilder:
sphere_ff = ba.FormFactorFullSphere(self.radius)
sphere = ba.Particle(m_Ag, sphere_ff)
- position = ba.kvector_t(0*ba.nm, 0*ba.nm,-1.0*self.hmdso_thickness)
+ position = ba.kvector_t(0 * ba.nm, 0 * ba.nm, -1.0 * self.hmdso_thickness)
sphere.setPosition(position)
ln_distr = ba.DistributionLogNormal(self.radius, self.sigma)
par_distr = ba.ParameterDistribution(
"/Particle/FullSphere/Radius", ln_distr, nparticles, nfwhm,
- ba.RealLimits.limited(0.0, self.hmdso_thickness/2.0))
+ ba.RealLimits.limited(0.0, self.hmdso_thickness / 2.0))
part_coll = ba.ParticleDistribution(sphere, par_distr)
# interference function
interference = ba.InterferenceFunctionRadialParaCrystal(
- self.distance, 1e6*ba.nm)
+ self.distance, 1e6 * ba.nm)
interference.setKappa(self.kappa)
interference.setDomainSize(20000.0)
pdf = ba.FTDistribution1DGauss(self.disorder)
@@ -77,8 +77,8 @@ class SampleBuilder:
layout.setTotalParticleSurfaceDensity(1)
# roughness
- r_ptfe = ba.LayerRoughness(2.3*ba.nm, 0.3, 5.0*ba.nm)
- r_hmdso = ba.LayerRoughness(1.1*ba.nm, 0.3, 5.0*ba.nm)
+ r_ptfe = ba.LayerRoughness(2.3 * ba.nm, 0.3, 5.0 * ba.nm)
+ r_hmdso = ba.LayerRoughness(1.1 * ba.nm, 0.3, 5.0 * ba.nm)
# layers
vacuum_layer = ba.Layer(m_vacuum)
diff --git a/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py b/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
index 43a6df116f31a5ebf7894753243cdd6b2ea31f27..d6bf4e26d945112025886cd900564efd6ea65335 100644
--- a/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
+++ b/Examples/Python/sim01_Particles/AllFormFactorsAvailable.py
@@ -9,14 +9,13 @@ from matplotlib import pyplot as plt
phi_min, phi_max = -2.0, 2.0
alpha_min, alpha_max = 0.0, 2.0
-
formfactors = [
- ba.FormFactorAnisoPyramid(20.0, 16.0, 13.0, 60.0*deg),
+ ba.FormFactorAnisoPyramid(20.0, 16.0, 13.0, 60.0 * deg),
ba.FormFactorBox(20.0, 16.0, 13.0),
ba.FormFactorCantellatedCube(15.0, 6.0),
- ba.FormFactorCone(10.0, 13.0, 60.0*deg),
- ba.FormFactorCone6(10.0, 13.0, 60.0*deg),
- ba.FormFactorCuboctahedron(20.0, 13.0, 0.7, 60.0*deg),
+ ba.FormFactorCone(10.0, 13.0, 60.0 * deg),
+ ba.FormFactorCone6(10.0, 13.0, 60.0 * deg),
+ ba.FormFactorCuboctahedron(20.0, 13.0, 0.7, 60.0 * deg),
ba.FormFactorCylinder(8.0, 16.0),
ba.FormFactorDodecahedron(5.0),
ba.FormFactorEllipsoidalCylinder(8.0, 13.0, 16.0),
@@ -26,10 +25,10 @@ formfactors = [
ba.FormFactorIcosahedron(8.0),
ba.FormFactorPrism3(10.0, 13.0),
ba.FormFactorPrism6(5.0, 11.0),
- ba.FormFactorPyramid(18.0, 13.0, 60.0*deg),
+ ba.FormFactorPyramid(18.0, 13.0, 60.0 * deg),
ba.FormFactorCosineRippleBox(27.0, 20.0, 14.0),
ba.FormFactorSawtoothRippleBox(36.0, 25.0, 14.0, 3.0),
- ba.FormFactorTetrahedron(15.0, 6.0, 60.0*deg),
+ ba.FormFactorTetrahedron(15.0, 6.0, 60.0 * deg),
ba.FormFactorTruncatedCube(15.0, 6.0),
ba.FormFactorTruncatedSphere(5.0, 7.0, 0),
ba.FormFactorTruncatedSpheroid(7.5, 9.0, 1.2, 0),
@@ -62,9 +61,9 @@ def get_simulation():
Returns GISAXS simulation with standard beam and detector.
"""
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)
+ 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)
return simulation
@@ -95,17 +94,25 @@ def run_simulation():
result = simulate(ff)
# showing the result
- plt.subplot(5, 5, nplot+1)
+ plt.subplot(5, 5, nplot + 1)
plt.subplots_adjust(wspace=0.3, hspace=0.3)
- ba.plot_colormap(result, xlabel="", ylabel="", zlabel="",
- cmap='jet', aspect='auto')
+ ba.plot_colormap(result,
+ xlabel="",
+ ylabel="",
+ zlabel="",
+ cmap='jet',
+ aspect='auto')
plt.tick_params(axis='both', which='major', labelsize=8)
plt.tick_params(axis='both', which='minor', labelsize=6)
- plt.xticks(numpy.arange(phi_min, phi_max+0.0001, 1.0))
- plt.text(-0.1, 2.15, name, horizontalalignment='center',
- verticalalignment='center', fontsize=9)
+ plt.xticks(numpy.arange(phi_min, phi_max + 0.0001, 1.0))
+ plt.text(-0.1,
+ 2.15,
+ name,
+ horizontalalignment='center',
+ verticalalignment='center',
+ fontsize=9)
if __name__ == '__main__':
diff --git a/Examples/Python/sim01_Particles/CylindersAndPrisms.py b/Examples/Python/sim01_Particles/CylindersAndPrisms.py
index 15acb9b6aec9e54fd902f4526406bd29eeef9b83..32cd6d2c3d72f9c3f64e4f582edb32ecdaac5e36 100644
--- a/Examples/Python/sim01_Particles/CylindersAndPrisms.py
+++ b/Examples/Python/sim01_Particles/CylindersAndPrisms.py
@@ -15,9 +15,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
- prism_ff = ba.FormFactorPrism3(10*nm, 5*nm)
+ prism_ff = ba.FormFactorPrism3(10 * nm, 5 * nm)
prism = ba.Particle(m_particle, prism_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 0.5)
@@ -41,9 +41,9 @@ 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.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)
return simulation
diff --git a/Examples/Python/sim01_Particles/CylindersInBA.py b/Examples/Python/sim01_Particles/CylindersInBA.py
index 9c43f4c7d73085fed32363bc94f9f7e313c24be9..0eda8e8d66a9c7b0a51181f304034f3a50a38cd0 100644
--- a/Examples/Python/sim01_Particles/CylindersInBA.py
+++ b/Examples/Python/sim01_Particles/CylindersInBA.py
@@ -15,7 +15,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -33,9 +33,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim01_Particles/CylindersInDWBA.py b/Examples/Python/sim01_Particles/CylindersInDWBA.py
index 1563aef2afe9de3c00b88b4ed2498d64e76c4157..e0c8d7aa79acab20f29ba32edf3a9392dd3d429e 100644
--- a/Examples/Python/sim01_Particles/CylindersInDWBA.py
+++ b/Examples/Python/sim01_Particles/CylindersInDWBA.py
@@ -15,7 +15,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -35,9 +35,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py b/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
index c268ad94e0be3a9b1e71595a65f0209ce7ba4e27..76dd916f3f7c7ed27a8b1498d0d50e98257071b1 100644
--- a/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
+++ b/Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py
@@ -14,20 +14,20 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# cylindrical particle
- radius = 5*nm
+ radius = 5 * nm
height = radius
cylinder_ff = ba.FormFactorCylinder(radius, height)
cylinder = ba.Particle(m_particle, cylinder_ff)
# collection of particles with size distribution
nparticles = 100
- sigma = 0.2*radius
+ sigma = 0.2 * radius
gauss_distr = ba.DistributionGaussian(radius, sigma)
sigma_factor = 2.0
- par_distr = ba.ParameterDistribution(
- "/Particle/Cylinder/Radius", gauss_distr, nparticles, sigma_factor)
+ par_distr = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr,
+ nparticles, sigma_factor)
# by uncommenting the line below, the height of the cylinders
# can be scaled proportionally to the radius:
# par_distr.linkParameter("/Particle/Cylinder/Height")
@@ -49,9 +49,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim01_Particles/RotatedPyramids.py b/Examples/Python/sim01_Particles/RotatedPyramids.py
index 11e878ad70505259d9e7430598f2797b5aa2595c..ddfa36b47b009226fb7dd3180694ff712d490d2c 100644
--- a/Examples/Python/sim01_Particles/RotatedPyramids.py
+++ b/Examples/Python/sim01_Particles/RotatedPyramids.py
@@ -15,12 +15,11 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- pyramid_ff = ba.FormFactorPyramid(10*nm, 5*nm, 54.73*deg)
+ pyramid_ff = ba.FormFactorPyramid(10 * nm, 5 * nm, 54.73 * deg)
pyramid = ba.Particle(m_particle, pyramid_ff)
- transform = ba.RotationZ(45.*deg)
+ transform = ba.RotationZ(45. * deg)
particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(
- pyramid, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform)
+ particle_layout.addParticle(pyramid, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform)
vacuum_layer = ba.Layer(m_vacuum)
vacuum_layer.addLayout(particle_layout)
@@ -37,9 +36,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py b/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
index ca9c7f0aa246435212550ba4b9a7c6ebbc2896fc..dc02c404264251f910a5af060ab8231c14e192bb 100644
--- a/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
+++ b/Examples/Python/sim01_Particles/TwoTypesOfCylindersWithSizeDistribution.py
@@ -15,9 +15,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles #1
- radius1 = 5.0*nm
+ radius1 = 5.0 * nm
height1 = radius1
- sigma1 = radius1*0.2
+ sigma1 = radius1 * 0.2
cylinder_ff1 = ba.FormFactorCylinder(radius1, height1)
cylinder1 = ba.Particle(m_particle, cylinder_ff1)
@@ -30,22 +30,22 @@ def get_sample():
# limits will assure, that generated Radius'es are >=0
limits = ba.RealLimits.nonnegative()
- par_distr1 = ba.ParameterDistribution(
- "/Particle/Cylinder/Radius", gauss_distr1, nparticles, sigma_factor, limits)
+ par_distr1 = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr1,
+ nparticles, sigma_factor, limits)
part_coll1 = ba.ParticleDistribution(cylinder1, par_distr1)
# collection of particles #2
- radius2 = 10.0*nm
+ radius2 = 10.0 * nm
height2 = radius2
- sigma2 = radius2*0.02
+ sigma2 = radius2 * 0.02
cylinder_ff2 = ba.FormFactorCylinder(radius2, height2)
cylinder2 = ba.Particle(m_particle, cylinder_ff2)
gauss_distr2 = ba.DistributionGaussian(radius2, sigma2)
- par_distr2 = ba.ParameterDistribution(
- "/Particle/Cylinder/Radius", gauss_distr2, nparticles, sigma_factor, limits)
+ par_distr2 = ba.ParameterDistribution("/Particle/Cylinder/Radius", gauss_distr2,
+ nparticles, sigma_factor, limits)
part_coll2 = ba.ParticleDistribution(cylinder2, par_distr2)
# assembling the sample
@@ -66,9 +66,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim02_Complexes/BiMaterialCylinders.py b/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
index 63e44dee9a2e9a8430dd1aa124f9f6a26fcbf2dc..38979c0ceaea9b15ecff6f33eea94de465bd857b 100644
--- a/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
+++ b/Examples/Python/sim02_Complexes/BiMaterialCylinders.py
@@ -6,13 +6,15 @@ import bornagain as ba
from bornagain import deg, angstrom, nm
-def get_composition(top_material, bottom_material,
- top_height=4.0, bottom_height=10.0):
+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
+ cylinder_radius = 10 * nm
topPart = ba.Particle(top_material,
ba.FormFactorCylinder(cylinder_radius, top_height))
@@ -41,7 +43,7 @@ def get_sample():
# collection of particles
composition = get_composition(m_top_part, m_bottom_part)
- shift = 10.0*nm
+ shift = 10.0 * nm
composition.setPosition(0, 0, -shift) # will be shifted below interface
particle_layout = ba.ParticleLayout()
@@ -64,9 +66,9 @@ 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.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.setBeamIntensity(1.0e+08)
return simulation
diff --git a/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py b/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
index 5c62ecb333cf6f4fbee8a497282fdfcdedd2736d..ae1fe3aa5f826b7dc98e1d052b6bb7587e231bb2 100644
--- a/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
+++ b/Examples/Python/sim02_Complexes/CoreShellNanoparticles.py
@@ -10,13 +10,13 @@ def get_sample():
Returns a sample with box-shaped core-shell particles on a substrate.
"""
# defining materials
- m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0 )
- m_shell = ba.HomogeneousMaterial("Shell", 1e-4, 2e-8 )
- m_core = ba.HomogeneousMaterial("Core", 6e-5, 2e-8 )
+ m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
+ m_shell = ba.HomogeneousMaterial("Shell", 1e-4, 2e-8)
+ m_core = ba.HomogeneousMaterial("Core", 6e-5, 2e-8)
# collection of particles
- parallelepiped1_ff = ba.FormFactorBox(16*nm, 16*nm, 8*nm)
- parallelepiped2_ff = ba.FormFactorBox(12*nm, 12*nm, 7*nm)
+ parallelepiped1_ff = ba.FormFactorBox(16 * nm, 16 * nm, 8 * nm)
+ parallelepiped2_ff = ba.FormFactorBox(12 * nm, 12 * nm, 7 * nm)
shell_particle = ba.Particle(m_shell, parallelepiped1_ff)
core_particle = ba.Particle(m_core, parallelepiped2_ff)
core_position = ba.kvector_t(0.0, 0.0, 0.0)
@@ -41,9 +41,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim02_Complexes/CustomFormFactor.py b/Examples/Python/sim02_Complexes/CustomFormFactor.py
index 68e31dff9cb0d59c15c28c4cad8b69c6687c9723..0c9a1cf146d16cc7138b76b9394447a447e44f2d 100644
--- a/Examples/Python/sim02_Complexes/CustomFormFactor.py
+++ b/Examples/Python/sim02_Complexes/CustomFormFactor.py
@@ -10,7 +10,7 @@ def sinc(x):
if abs(x) == 0:
return 1.
else:
- return cmath.sin(x)/x
+ return cmath.sin(x) / x
class CustomFormFactor(ba.IBornFF):
@@ -36,9 +36,9 @@ class CustomFormFactor(ba.IBornFF):
return cloned_ff
def evaluate_for_q(self, q):
- qzhH = 0.5*q.z()*self.H
- qxhL = 0.5*q.x()*self.L
- qyhL = 0.5*q.y()*self.L
+ qzhH = 0.5 * q.z() * self.H
+ qxhL = 0.5 * q.x() * self.L
+ qyhL = 0.5 * q.y() * self.L
return 0.5*self.H*self.L**2*cmath.exp(complex(0., 1.)*qzhH)*\
sinc(qzhH)*(sinc(0.5*qyhL)*(sinc(qxhL)-0.5*sinc(0.5*qxhL))+\
sinc(0.5*qxhL)*sinc(qyhL))
@@ -54,7 +54,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- ff = CustomFormFactor(20.0*nm, 15.0*nm)
+ ff = CustomFormFactor(20.0 * nm, 15.0 * nm)
particle = ba.Particle(m_particle, ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(particle, 1.0)
@@ -77,9 +77,9 @@ def get_simulation():
"""
simulation = ba.GISASSimulation()
simulation.getOptions().setNumberOfThreads(-1)
- 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.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)
return simulation
diff --git a/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py b/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
index 1c2298a929dd8fa9d12de19d36ab40a9ce9e88f0..746b99ec6655113fd14e2ae1dfbecf83da0fe0e9 100644
--- a/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
+++ b/Examples/Python/sim02_Complexes/HexagonalLatticesWithBasis.py
@@ -15,20 +15,20 @@ def get_sample():
m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
- radius = 10.0*nm
+ radius = 10.0 * nm
sphere_ff = ba.FormFactorFullSphere(radius)
sphere = ba.Particle(m_particle, sphere_ff)
particle_layout = ba.ParticleLayout()
pos0 = ba.kvector_t(0.0, 0.0, 0.0)
- pos1 = ba.kvector_t(radius, radius, numpy.sqrt(3.0)*radius)
+ pos1 = ba.kvector_t(radius, radius, numpy.sqrt(3.0) * radius)
basis = ba.ParticleComposition()
basis.addParticles(sphere, [pos0, pos1])
particle_layout.addParticle(basis)
interference = ba.InterferenceFunction2DLattice(
- ba.HexagonalLattice2D(radius*2.0, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
+ ba.HexagonalLattice2D(radius * 2.0, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(10 * nm, 10 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -47,9 +47,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py b/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
index b2bbc6112b9121e670b7f095b8aa6d3d0d072a03..584ad11829d9d474af1ea6940b3c8285ca1873ac 100644
--- a/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
+++ b/Examples/Python/sim02_Complexes/LargeParticlesFormFactor.py
@@ -10,8 +10,8 @@ import bornagain as ba
from bornagain import deg, angstrom, nm
from matplotlib import pyplot as plt
-default_cylinder_radius = 10*nm
-default_cylinder_height = 20*nm
+default_cylinder_radius = 10 * nm
+default_cylinder_height = 20 * nm
def get_sample(cylinder_radius, cylinder_height):
@@ -45,9 +45,9 @@ def get_simulation(integration_flag):
If integration_flag=True, the simulation will integrate over detector bins.
"""
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)
+ simulation.setDetectorParameters(200, -2.0 * deg, 2.0 * deg, 200, 0.0 * deg,
+ 2.0 * deg)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * deg, 0.0 * deg)
simulation.getOptions().setMonteCarloIntegration(integration_flag, 50)
simulation.setTerminalProgressMonitor()
return simulation
@@ -62,42 +62,57 @@ def run_simulation():
fig = plt.figure(figsize=(12.80, 10.24))
# conditions to define cylinders scale factor and integration flag
- conditions = [
- {'title': "Small cylinders, analytical calculations",
- 'scale': 1, 'integration': False, 'zmin': 1e-5, 'zmax': 1e2},
-
- {'title': "Small cylinders, Monte-Carlo integration",
- 'scale': 1, 'integration': True, 'zmin': 1e-5, 'zmax': 1e2},
-
- {'title': "Large cylinders, analytical calculations",
- 'scale': 100, 'integration': False, 'zmin': 1e-5, 'zmax': 1e10},
-
- {'title': "Large cylinders, Monte-Carlo integration",
- 'scale': 100, 'integration': True, 'zmin': 1e-5, 'zmax': 1e10}
- ]
+ conditions = [{
+ 'title': "Small cylinders, analytical calculations",
+ 'scale': 1,
+ 'integration': False,
+ 'zmin': 1e-5,
+ 'zmax': 1e2
+ }, {
+ 'title': "Small cylinders, Monte-Carlo integration",
+ 'scale': 1,
+ 'integration': True,
+ 'zmin': 1e-5,
+ 'zmax': 1e2
+ }, {
+ 'title': "Large cylinders, analytical calculations",
+ 'scale': 100,
+ 'integration': False,
+ 'zmin': 1e-5,
+ 'zmax': 1e10
+ }, {
+ 'title': "Large cylinders, Monte-Carlo integration",
+ 'scale': 100,
+ 'integration': True,
+ 'zmin': 1e-5,
+ 'zmax': 1e10
+ }]
# run simulation 4 times and plot results
for i_plot, condition in enumerate(conditions):
scale = condition['scale']
integration_flag = condition['integration']
- sample = get_sample(default_cylinder_radius*scale,
- default_cylinder_height*scale)
+ sample = get_sample(default_cylinder_radius * scale,
+ default_cylinder_height * scale)
simulation = get_simulation(integration_flag)
simulation.setSample(sample)
simulation.runSimulation()
result = simulation.result()
# plotting results
- plt.subplot(2, 2, i_plot+1)
+ plt.subplot(2, 2, i_plot + 1)
plt.subplots_adjust(wspace=0.3, hspace=0.3)
zmin = condition['zmin']
zmax = condition['zmax']
ba.plot_colormap(result, zmin=zmin, zmax=zmax, cmap='jet', aspect='auto')
- plt.text(0.0, 2.1, conditions[i_plot]['title'],
- horizontalalignment='center', verticalalignment='center',
+ plt.text(0.0,
+ 2.1,
+ conditions[i_plot]['title'],
+ horizontalalignment='center',
+ verticalalignment='center',
fontsize=12)
diff --git a/Examples/Python/sim02_Complexes/MesoCrystal.py b/Examples/Python/sim02_Complexes/MesoCrystal.py
index 857aa322b49142ee77059a220f40cc26790a6617..f7079719c71f02c2d4748077edf8366ad6b2e6d3 100644
--- a/Examples/Python/sim02_Complexes/MesoCrystal.py
+++ b/Examples/Python/sim02_Complexes/MesoCrystal.py
@@ -21,7 +21,7 @@ def get_sample():
lattice = ba.Lattice3D(lattice_basis_1, lattice_basis_2, lattice_basis_3)
# spherical particle that forms the base of the mesocrystal
- sphere_ff = ba.FormFactorFullSphere(2*nm)
+ sphere_ff = ba.FormFactorFullSphere(2 * nm)
sphere = ba.Particle(m_particle, sphere_ff)
# crystal structure
@@ -49,9 +49,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py b/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
index c9cb50390a330e13f640388143418b8ba25a9b1c..26d9abab1829bc81342f434bce1f812d27748487 100644
--- a/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
+++ b/Examples/Python/sim02_Complexes/ParticlesCrossingInterface.py
@@ -32,14 +32,14 @@ def get_sample():
m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
- shift_down = 3*nm
+ shift_down = 3 * nm
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
cylinder.setPosition(0, 0, -shift_down)
- prism_ff = ba.FormFactorPrism3(10*nm, 5*nm)
+ prism_ff = ba.FormFactorPrism3(10 * nm, 5 * nm)
prism = ba.Particle(m_particle, prism_ff)
prism.setPosition(0, 0, -shift_down)
@@ -65,9 +65,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/ApproximationDA.py b/Examples/Python/sim03_Structures/ApproximationDA.py
index 8933892ba41e1bf6ace972bf1e47b7f8c8a3d5c6..86254096993c72371b61efc8f95b3cd8e096e439 100644
--- a/Examples/Python/sim03_Structures/ApproximationDA.py
+++ b/Examples/Python/sim03_Structures/ApproximationDA.py
@@ -15,20 +15,19 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# cylindrical particle 1
- radius1 = 5*nm
+ radius1 = 5 * nm
height1 = radius1
cylinder_ff1 = ba.FormFactorCylinder(radius1, height1)
cylinder1 = ba.Particle(m_particle, cylinder_ff1)
# cylindrical particle 2
- radius2 = 8*nm
+ radius2 = 8 * nm
height2 = radius2
cylinder_ff2 = ba.FormFactorCylinder(radius2, height2)
cylinder2 = ba.Particle(m_particle, cylinder_ff2)
# interference function
- interference = ba.InterferenceFunctionRadialParaCrystal(
- 18.0*nm, 1e3*nm)
+ interference = ba.InterferenceFunctionRadialParaCrystal(18.0 * nm, 1e3 * nm)
pdf = ba.FTDistribution1DGauss(3 * nm)
interference.setProbabilityDistribution(pdf)
@@ -52,9 +51,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/ApproximationLMA.py b/Examples/Python/sim03_Structures/ApproximationLMA.py
index bff8e67d92be2b247326de9c27ca38c4893f1124..e30d648732bd96e02d1c788354154a1f76ede220 100644
--- a/Examples/Python/sim03_Structures/ApproximationLMA.py
+++ b/Examples/Python/sim03_Structures/ApproximationLMA.py
@@ -15,26 +15,24 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# cylindrical particle 1
- radius1 = 5*nm
+ radius1 = 5 * nm
height1 = radius1
cylinder_ff1 = ba.FormFactorCylinder(radius1, height1)
cylinder1 = ba.Particle(m_particle, cylinder_ff1)
# cylindrical particle 2
- radius2 = 8*nm
+ radius2 = 8 * nm
height2 = radius2
cylinder_ff2 = ba.FormFactorCylinder(radius2, height2)
cylinder2 = ba.Particle(m_particle, cylinder_ff2)
# interference function1
- interference1 = ba.InterferenceFunctionRadialParaCrystal(
- 16.8*nm, 1e3*nm)
+ interference1 = ba.InterferenceFunctionRadialParaCrystal(16.8 * nm, 1e3 * nm)
pdf = ba.FTDistribution1DGauss(3 * nm)
interference1.setProbabilityDistribution(pdf)
# interference function2
- interference2 = ba.InterferenceFunctionRadialParaCrystal(
- 22.8*nm, 1e3*nm)
+ interference2 = ba.InterferenceFunctionRadialParaCrystal(22.8 * nm, 1e3 * nm)
interference2.setProbabilityDistribution(pdf)
# assembling the sample
@@ -61,9 +59,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/ApproximationSSCA.py b/Examples/Python/sim03_Structures/ApproximationSSCA.py
index 1d6389d713b400b8156ae489b61c2a72d20fa5e8..9b4111580a80e2faa6e86215bdeb5db861a2521c 100644
--- a/Examples/Python/sim03_Structures/ApproximationSSCA.py
+++ b/Examples/Python/sim03_Structures/ApproximationSSCA.py
@@ -15,19 +15,19 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# cylindrical particle 1
- radius1 = 5*nm
+ radius1 = 5 * nm
height1 = radius1
cylinder_ff1 = ba.FormFactorCylinder(radius1, height1)
cylinder1 = ba.Particle(m_particle, cylinder_ff1)
# cylindrical particle 2
- radius2 = 8*nm
+ radius2 = 8 * nm
height2 = radius2
cylinder_ff2 = ba.FormFactorCylinder(radius2, height2)
cylinder2 = ba.Particle(m_particle, cylinder_ff2)
# interference function
- interference = ba.InterferenceFunctionRadialParaCrystal(18.0*nm, 1e3*nm)
+ interference = ba.InterferenceFunctionRadialParaCrystal(18.0 * nm, 1e3 * nm)
pdf = ba.FTDistribution1DGauss(3 * nm)
interference.setProbabilityDistribution(pdf)
interference.setKappa(1.0)
@@ -52,9 +52,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py b/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
index 5f482c78cae4be965e75378431bf526de6e6ff48..cf9250dff80af6013acd41ac3bc10f145860c98f 100644
--- a/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
+++ b/Examples/Python/sim03_Structures/CosineRipplesAtRectLattice.py
@@ -17,15 +17,16 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- ff = ba.FormFactorCosineRippleBox(100*nm, 20*nm, 4*nm)
+ ff = ba.FormFactorCosineRippleBox(100 * nm, 20 * nm, 4 * nm)
particle = ba.Particle(m_particle, ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(particle, 1.0)
interference = ba.InterferenceFunction2DLattice(
- ba.BasicLattice2D(200.0*nm, 50.0*nm, 90.0*deg, 0.0*deg))
- pdf = ba.FTDecayFunction2DCauchy(1000.*nm/2./numpy.pi, 100.*nm/2./numpy.pi, 0)
+ ba.BasicLattice2D(200.0 * nm, 50.0 * nm, 90.0 * deg, 0.0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(1000. * nm / 2. / numpy.pi,
+ 100. * nm / 2. / numpy.pi, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -45,9 +46,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference1DLattice.py b/Examples/Python/sim03_Structures/Interference1DLattice.py
index 20d98c6b4fdc6287278d2bc48918a24617afd82d..19c4e03e78cdf511bc83b7c2d2a4be14906d6739 100644
--- a/Examples/Python/sim03_Structures/Interference1DLattice.py
+++ b/Examples/Python/sim03_Structures/Interference1DLattice.py
@@ -7,7 +7,7 @@ import bornagain as ba
from bornagain import deg, angstrom, nm
-def get_sample(lattice_rotation_angle=45*deg):
+def get_sample(lattice_rotation_angle=45 * deg):
"""
Returns a sample with a grating on a substrate,
modelled by very long boxes forming a 1D lattice with Cauchy correlations.
@@ -17,12 +17,12 @@ def get_sample(lattice_rotation_angle=45*deg):
m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
- box_length, box_width, box_height = 10*nm, 10000*nm, 10*nm
- lattice_length = 30*nm
+ box_length, box_width, box_height = 10 * nm, 10000 * nm, 10 * nm
+ lattice_length = 30 * nm
# collection of particles
- interference = ba.InterferenceFunction1DLattice(
- lattice_length, lattice_rotation_angle)
+ interference = ba.InterferenceFunction1DLattice(lattice_length,
+ lattice_rotation_angle)
pdf = ba.FTDecayFunction1DCauchy(1000.0)
interference.setDecayFunction(pdf)
@@ -30,8 +30,8 @@ def get_sample(lattice_rotation_angle=45*deg):
box = ba.Particle(m_particle, box_ff)
particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(
- box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), ba.RotationZ(lattice_rotation_angle))
+ particle_layout.addParticle(box, 1.0, ba.kvector_t(0.0, 0.0, 0.0),
+ ba.RotationZ(lattice_rotation_angle))
particle_layout.setInterferenceFunction(interference)
# assembling the sample
@@ -50,9 +50,9 @@ 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, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ 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)
simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py b/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
index 7a38f018a40d82a602a221cc34e8d651d1a1feb8..184727e7e2689abbff06904590addf296e70990c 100644
--- a/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
+++ b/Examples/Python/sim03_Structures/Interference1DRadialParaCrystal.py
@@ -18,11 +18,10 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
- interference = ba.InterferenceFunctionRadialParaCrystal(
- 20.0*nm, 1e3*nm)
+ interference = ba.InterferenceFunctionRadialParaCrystal(20.0 * nm, 1e3 * nm)
pdf = ba.FTDistribution1DGauss(7 * nm)
interference.setProbabilityDistribution(pdf)
@@ -47,9 +46,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
index 7f8399e20aa156732952600b7146855d474568cc..ef88a994f4e5865b885c5c55713063938c2aa4a3 100644
--- a/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DCenteredSquareLattice.py
@@ -17,15 +17,15 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- interference = ba.InterferenceFunction2DLattice(ba.SquareLattice2D(25.0*nm, 0))
- pdf = ba.FTDecayFunction2DCauchy(300.0*nm/2.0/numpy.pi,
- 100.0*nm/2.0/numpy.pi, 0)
+ interference = ba.InterferenceFunction2DLattice(ba.SquareLattice2D(25.0 * nm, 0))
+ pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi,
+ 100.0 * nm / 2.0 / numpy.pi, 0)
interference.setDecayFunction(pdf)
particle_layout = ba.ParticleLayout()
position1 = ba.kvector_t(0.0, 0.0, 0.0)
- position2 = ba.kvector_t(12.5*nm, 12.5*nm, 0.0)
- cylinder_ff = ba.FormFactorCylinder(3.*nm, 3.*nm)
+ position2 = ba.kvector_t(12.5 * nm, 12.5 * nm, 0.0)
+ cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
basis = ba.ParticleComposition()
basis.addParticles(cylinder, [position1, position2])
@@ -50,9 +50,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py b/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
index 6e5f5ba565290c68a090b09cdd06775872bcea65..3eb28944c96279094331aea5818483be2d95b893 100644
--- a/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
+++ b/Examples/Python/sim03_Structures/Interference2DLatticeSumOfRotated.py
@@ -18,12 +18,12 @@ def get_sample():
p_interference_function = \
ba.InterferenceFunction2DLattice(ba.SquareLattice2D(25.0*nm, 0))
- pdf = ba.FTDecayFunction2DCauchy(300.0*nm/2.0/numpy.pi,
- 100.0*nm/2.0/numpy.pi, 0)
+ pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi,
+ 100.0 * nm / 2.0 / numpy.pi, 0)
p_interference_function.setDecayFunction(pdf)
particle_layout = ba.ParticleLayout()
- ff = ba.FormFactorCylinder(3.0*nm, 3.0*nm)
+ ff = ba.FormFactorCylinder(3.0 * nm, 3.0 * nm)
position = ba.kvector_t(0.0, 0.0, 0.0)
cylinder = ba.Particle(m_particle, ff.clone())
cylinder.setPosition(position)
@@ -44,14 +44,14 @@ def get_simulation():
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.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_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
diff --git a/Examples/Python/sim03_Structures/Interference2DParaCrystal.py b/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
index ffee0d01b04cad63b9dc0fc892922634b0cf76fd..ca20c3529e41b51276ef6baf815059e737bf9895 100644
--- a/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
+++ b/Examples/Python/sim03_Structures/Interference2DParaCrystal.py
@@ -14,13 +14,13 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(4*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(4 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
interference = ba.InterferenceFunction2DParaCrystal(
- ba.SquareLattice2D(10.0*nm), 0.0, 20.0*micrometer, 20.0*micrometer)
+ ba.SquareLattice2D(10.0 * nm), 0.0, 20.0 * micrometer, 20.0 * micrometer)
interference.setIntegrationOverXi(True)
- pdf = ba.FTDistribution2DCauchy(1.0*nm, 1.0*nm, 0)
+ pdf = ba.FTDistribution2DCauchy(1.0 * nm, 1.0 * nm, 0)
interference.setProbabilityDistributions(pdf, pdf)
particle_layout = ba.ParticleLayout()
@@ -47,9 +47,9 @@ def get_simulation():
"""
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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
index e0f43a4beef0e44049a922d3c17d3cfe8e670946..e0d6655ed7eb4c6d902772dca6dbf6c1bfa5e0d9 100644
--- a/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DRotatedSquareLattice.py
@@ -17,12 +17,13 @@ def get_sample():
# collection of particles
interference = ba.InterferenceFunction2DLattice(
- ba.SquareLattice2D(25.0*nm, 30.0*deg))
- pdf = ba.FTDecayFunction2DCauchy(300.0*nm/2.0/numpy.pi, 100.0*nm/2.0/numpy.pi, 0)
- pdf.setParameterValue("Gamma", 30.0*deg)
+ ba.SquareLattice2D(25.0 * nm, 30.0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi,
+ 100.0 * nm / 2.0 / numpy.pi, 0)
+ pdf.setParameterValue("Gamma", 30.0 * deg)
interference.setDecayFunction(pdf)
- cylinder_ff = ba.FormFactorCylinder(3.*nm, 3.*nm)
+ cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder)
@@ -44,9 +45,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py b/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
index 5e882bbf4d5c95f0b46dc8aef08afd32f7d42d44..75e4ddff0b9a40f98abcc0746f7f51a0b2529029 100644
--- a/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DSquareFiniteLattice.py
@@ -17,10 +17,10 @@ def get_sample():
# collection of particles
interference = ba.InterferenceFunctionFinite2DLattice(
- ba.SquareLattice2D(25.0*nm, 0.0), 40, 40)
+ ba.SquareLattice2D(25.0 * nm, 0.0), 40, 40)
interference.setPositionVariance(1.0)
- cylinder_ff = ba.FormFactorCylinder(3.*nm, 3.*nm)
+ cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder)
@@ -44,9 +44,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/Interference2DSquareLattice.py b/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
index beee085dcfa8c42f2831c5a775ea28acfddc7217..599b3991ed7ce69037808b52d2856e471e113932 100644
--- a/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
+++ b/Examples/Python/sim03_Structures/Interference2DSquareLattice.py
@@ -17,12 +17,12 @@ def get_sample():
# collection of particles
interference = ba.InterferenceFunction2DLattice(
- ba.SquareLattice2D(25.0*nm, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(300.0*nm/2.0/numpy.pi,
- 100.0*nm/2.0/numpy.pi, 0)
+ ba.SquareLattice2D(25.0 * nm, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(300.0 * nm / 2.0 / numpy.pi,
+ 100.0 * nm / 2.0 / numpy.pi, 0)
interference.setDecayFunction(pdf)
- cylinder_ff = ba.FormFactorCylinder(3.*nm, 3.*nm)
+ cylinder_ff = ba.FormFactorCylinder(3. * nm, 3. * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder)
@@ -46,9 +46,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/RectangularGrating.py b/Examples/Python/sim03_Structures/RectangularGrating.py
index b3765dcbcdede787317c8be2efb1dcdd68132ba2..26793f695f04c1f32caf7bcb19525e37010f33cc 100644
--- a/Examples/Python/sim03_Structures/RectangularGrating.py
+++ b/Examples/Python/sim03_Structures/RectangularGrating.py
@@ -7,7 +7,7 @@ import bornagain as ba
from bornagain import deg, angstrom, nm, micrometer
-def get_sample(lattice_rotation_angle=0.0*deg):
+def get_sample(lattice_rotation_angle=0.0 * deg):
"""
Returns a sample with a grating on a substrate.
lattice_rotation_angle = 0 - beam parallel to grating lines
@@ -17,12 +17,12 @@ def get_sample(lattice_rotation_angle=0.0*deg):
m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
m_si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7)
- box_length, box_width, box_height = 50*micrometer, 70*nm, 50*nm
- lattice_length = 150*nm
+ box_length, box_width, box_height = 50 * micrometer, 70 * nm, 50 * nm
+ lattice_length = 150 * nm
# collection of particles
interference = ba.InterferenceFunction1DLattice(
- lattice_length, 90.0*deg - lattice_rotation_angle)
+ lattice_length, 90.0 * deg - lattice_rotation_angle)
pdf = ba.ba.FTDecayFunction1DGauss(450.0)
interference.setDecayFunction(pdf)
@@ -31,8 +31,8 @@ def get_sample(lattice_rotation_angle=0.0*deg):
box = ba.Particle(m_si, box_ff)
particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(
- box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), ba.RotationZ(lattice_rotation_angle))
+ particle_layout.addParticle(box, 1.0, ba.kvector_t(0.0, 0.0, 0.0),
+ ba.RotationZ(lattice_rotation_angle))
particle_layout.setInterferenceFunction(interference)
# assembling the sample
@@ -56,9 +56,9 @@ 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.setDetectorParameters(200, -0.5 * deg, 0.5 * deg, 200, 0.0 * deg,
+ 0.6 * deg)
+ simulation.setBeamParameters(1.34 * angstrom, 0.4 * deg, 0.0 * deg)
simulation.setBeamIntensity(1e+08)
simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
diff --git a/Examples/Python/sim03_Structures/SpheresAtHexLattice.py b/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
index 3aad9209640967aeeb40f84694b28260bf2c3768..822d8e916909ab9645476a914ac54b7dce1200a5 100644
--- a/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
+++ b/Examples/Python/sim03_Structures/SpheresAtHexLattice.py
@@ -14,14 +14,14 @@ def get_sample():
m_substrate = ba.HomogeneousMaterial("Substrate", 6e-6, 2e-8)
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
- sphere_ff = ba.FormFactorFullSphere(10.0*nm)
+ sphere_ff = ba.FormFactorFullSphere(10.0 * nm)
sphere = ba.Particle(m_particle, sphere_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(sphere)
interference = ba.InterferenceFunction2DLattice(
- ba.HexagonalLattice2D(20.0*nm, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(10*nm, 10*nm, 0)
+ ba.HexagonalLattice2D(20.0 * nm, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(10 * nm, 10 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -40,9 +40,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim03_Structures/TriangularRipple.py b/Examples/Python/sim03_Structures/TriangularRipple.py
index f70859eaa1c1656f5a866a7b63880b91f561c7bd..8798c0171243d1963fd63905a957f0cef1cbd45f 100644
--- a/Examples/Python/sim03_Structures/TriangularRipple.py
+++ b/Examples/Python/sim03_Structures/TriangularRipple.py
@@ -17,16 +17,16 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- ripple2_ff = ba.FormFactorSawtoothRippleBox(
- 100*nm, 20*nm, 4*nm, -3.0*nm)
+ ripple2_ff = ba.FormFactorSawtoothRippleBox(100 * nm, 20 * nm, 4 * nm, -3.0 * nm)
ripple = ba.Particle(m_particle, ripple2_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(ripple, 1.0)
interference = ba.InterferenceFunction2DLattice(
- ba.BasicLattice2D(200.0*nm, 50.0*nm, 90.0*deg, 0.0*deg))
- pdf = ba.FTDecayFunction2DGauss(1000.*nm/2./numpy.pi, 100.*nm/2./numpy.pi, 0)
+ ba.BasicLattice2D(200.0 * nm, 50.0 * nm, 90.0 * deg, 0.0 * deg))
+ pdf = ba.FTDecayFunction2DGauss(1000. * nm / 2. / numpy.pi,
+ 100. * nm / 2. / numpy.pi, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -46,9 +46,9 @@ 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)
+ 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)
return simulation
diff --git a/Examples/Python/sim04_Multilayers/BuriedParticles.py b/Examples/Python/sim04_Multilayers/BuriedParticles.py
index 64a9e3c72b5d035020ee3f7985a579930cc16073..3c636884466797904ba4c856062ea2eaf34bae83 100644
--- a/Examples/Python/sim04_Multilayers/BuriedParticles.py
+++ b/Examples/Python/sim04_Multilayers/BuriedParticles.py
@@ -17,7 +17,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 0.0, 0.0)
# collection of particles
- ff = ba.FormFactorFullSphere(10.2*nm)
+ ff = ba.FormFactorFullSphere(10.2 * nm)
sphere = ba.Particle(m_particle, ff)
sphere.setPosition(0.0, 0.0, -25.2)
particle_layout = ba.ParticleLayout()
@@ -25,7 +25,7 @@ def get_sample():
# assembling the sample
vacuum_layer = ba.Layer(m_vacuum)
- intermediate_layer = ba.Layer(m_interm_layer, 30.*nm)
+ intermediate_layer = ba.Layer(m_interm_layer, 30. * nm)
intermediate_layer.addLayout(particle_layout)
substrate_layer = ba.Layer(m_substrate, 0)
@@ -42,8 +42,8 @@ def get_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)
+ simulation.setDetectorParameters(200, -1 * deg, +1 * deg, 200, 0 * deg, +2 * deg)
+ simulation.setBeamParameters(1.5 * angstrom, 0.15 * deg, 0.0 * deg)
return simulation
diff --git a/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py b/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
index 36b80dd24b5049dc341b228802847522244cc64a..47cec84d5427bf4e4a4c5bdd093c442fdd087de5 100644
--- a/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
+++ b/Examples/Python/sim04_Multilayers/CorrelatedRoughness.py
@@ -17,14 +17,14 @@ def get_sample():
# defining layers
l_ambience = ba.Layer(m_vacuum)
- l_part_a = ba.Layer(m_part_a, 2.5*nm)
- l_part_b = ba.Layer(m_part_b, 5.0*nm)
+ l_part_a = ba.Layer(m_part_a, 2.5 * nm)
+ l_part_b = ba.Layer(m_part_b, 5.0 * nm)
l_substrate = ba.Layer(m_substrate)
roughness = ba.LayerRoughness()
- roughness.setSigma(1.0*nm)
+ roughness.setSigma(1.0 * nm)
roughness.setHurstParameter(0.3)
- roughness.setLatteralCorrLength(5.0*nm)
+ roughness.setLatteralCorrLength(5.0 * nm)
my_sample = ba.MultiLayer()
@@ -37,7 +37,7 @@ def get_sample():
my_sample.addLayerWithTopRoughness(l_part_b, roughness)
my_sample.addLayerWithTopRoughness(l_substrate, roughness)
- my_sample.setCrossCorrLength(10*nm)
+ my_sample.setCrossCorrLength(10 * nm)
print(my_sample.treeToString())
@@ -49,9 +49,9 @@ 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.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.setBeamIntensity(5e11)
return simulation
diff --git a/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py b/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
index 90619a26b8bf62080197f1c51ac52c2a62aa90fb..86ae8b9f2e6ad4c4189f2eea62d910cc67c16fc2 100644
--- a/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
+++ b/Examples/Python/sim04_Multilayers/CylindersInAverageLayer.py
@@ -5,7 +5,7 @@ import bornagain as ba
from bornagain import deg, angstrom, nm
-def get_sample(cyl_height=5*nm):
+def get_sample(cyl_height=5 * nm):
"""
Returns a sample with cylinders on a substrate.
"""
@@ -16,20 +16,21 @@ def get_sample(cyl_height=5*nm):
m_particle = ba.HomogeneousMaterial("Particle", 3e-5, 2e-8)
# cylindrical particle
- cylinder_ff = ba.FormFactorCylinder(5*nm, cyl_height)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, cyl_height)
cylinder = ba.Particle(m_particle, cylinder_ff)
position = ba.kvector_t(0.0, 0.0, -cyl_height)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0, position)
# interference function
- interference = ba.InterferenceFunction2DLattice(ba.SquareLattice2D(15*nm, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(300*nm, 300*nm, 0)
+ interference = ba.InterferenceFunction2DLattice(
+ ba.SquareLattice2D(15 * nm, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(300 * nm, 300 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
vacuum_layer = ba.Layer(m_vacuum)
- intermediate_layer = ba.Layer(m_layer, 5*nm)
+ intermediate_layer = ba.Layer(m_layer, 5 * nm)
intermediate_layer.addLayout(particle_layout)
substrate_layer = ba.Layer(m_substrate)
@@ -45,9 +46,9 @@ 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)
+ 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)
simulation.getOptions().setUseAvgMaterials(True)
return simulation
diff --git a/Examples/Python/sim04_Multilayers/GratingMC.py b/Examples/Python/sim04_Multilayers/GratingMC.py
index 67e819af38a7e163a3ddec33c1b5550762edf7e8..dc988a4171f2028ea8b2e682ca7ad10bf3ed5e1c 100644
--- a/Examples/Python/sim04_Multilayers/GratingMC.py
+++ b/Examples/Python/sim04_Multilayers/GratingMC.py
@@ -8,7 +8,7 @@ from bornagain import deg, angstrom, nm, micrometer
from matplotlib import pyplot as plt
-def get_sample(lattice_rotation_angle=0.0*deg):
+def get_sample(lattice_rotation_angle=0.0 * deg):
"""
Returns a sample with a grating on a substrate.
lattice_rotation_angle = 0 - beam parallel to grating lines
@@ -18,12 +18,12 @@ def get_sample(lattice_rotation_angle=0.0*deg):
m_vacuum = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
m_si = ba.HomogeneousMaterial("Si", 5.78164736e-6, 1.02294578e-7)
- box_length, box_width, box_height = 50*micrometer, 70*nm, 50*nm
- lattice_length = 150*nm
+ box_length, box_width, box_height = 50 * micrometer, 70 * nm, 50 * nm
+ lattice_length = 150 * nm
# collection of particles
interference = ba.InterferenceFunction1DLattice(
- lattice_length, 90.0*deg - lattice_rotation_angle)
+ lattice_length, 90.0 * deg - lattice_rotation_angle)
pdf = ba.ba.FTDecayFunction1DGauss(450.0)
interference.setDecayFunction(pdf)
@@ -32,8 +32,8 @@ def get_sample(lattice_rotation_angle=0.0*deg):
box = ba.Particle(m_si, box_ff)
particle_layout = ba.ParticleLayout()
- particle_layout.addParticle(
- box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), ba.RotationZ(lattice_rotation_angle))
+ particle_layout.addParticle(box, 1.0, ba.kvector_t(0.0, 0.0, 0.0),
+ ba.RotationZ(lattice_rotation_angle))
particle_layout.setInterferenceFunction(interference)
# assembling the sample
@@ -57,9 +57,9 @@ 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.setDetectorParameters(200, -0.5 * deg, 0.5 * deg, 200, 0.0 * deg,
+ 0.6 * deg)
+ simulation.setBeamParameters(1.34 * angstrom, 0.4 * deg, 0.0 * deg)
simulation.setBeamIntensity(1e+08)
simulation.getOptions().setMonteCarloIntegration(True, 100)
return simulation
@@ -84,7 +84,10 @@ if __name__ == '__main__':
xpeaks = [peak[0] for peak in peaks]
ypeaks = [peak[1] for peak in peaks]
print(peaks)
- plt.plot(xpeaks, ypeaks, linestyle='None', marker='x', color='white',
+ plt.plot(xpeaks,
+ ypeaks,
+ linestyle='None',
+ marker='x',
+ color='white',
markersize=10)
plt.show()
-
diff --git a/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py b/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
index a024491a7d5e3688e54195e4881e45d53b9966d9..379a44831b2ae6d490b1ea780b948ffda427ee54 100644
--- a/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
+++ b/Examples/Python/sim04_Multilayers/HalfSpheresInAverageTopLayer.py
@@ -5,7 +5,7 @@ and slicing
import bornagain as ba
from bornagain import deg, angstrom, nm
-sphere_radius = 5*nm
+sphere_radius = 5 * nm
n_slices = 10
@@ -26,8 +26,9 @@ def get_sample():
particle_layout.addParticle(half_sphere)
# interference function
- interference = ba.InterferenceFunction2DLattice(ba.SquareLattice2D(10*nm, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(100*nm, 100*nm, 0)
+ interference = ba.InterferenceFunction2DLattice(
+ ba.SquareLattice2D(10 * nm, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(100 * nm, 100 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -47,9 +48,9 @@ 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)
+ 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)
simulation.getOptions().setUseAvgMaterials(True)
return simulation
diff --git a/Examples/Python/sim05_Magnetism/MagneticSpheres.py b/Examples/Python/sim05_Magnetism/MagneticSpheres.py
index a1a126cb466cdf9d95b32aaa5eacbf9f25932418..a41d49e2e036bd5bd6c73500972d1b2bae02e91f 100644
--- a/Examples/Python/sim05_Magnetism/MagneticSpheres.py
+++ b/Examples/Python/sim05_Magnetism/MagneticSpheres.py
@@ -4,7 +4,6 @@ Simulation demo: magnetic spheres in substrate
import bornagain as ba
from bornagain import deg, angstrom, nm
-
# Magnetization of the particle's material (A/m)
magnetization_particle = ba.kvector_t(0.0, 0.0, 1e7)
@@ -20,9 +19,9 @@ def get_sample():
substrate_material = ba.HomogeneousMaterial("Substrate", 7e-6, 1.8e-7)
# spherical magnetic particle
- sphere_ff = ba.FormFactorFullSphere(5*nm)
+ sphere_ff = ba.FormFactorFullSphere(5 * nm)
sphere = ba.Particle(particle_material, sphere_ff)
- position = ba.kvector_t(0.0, 0.0, -10.0*nm)
+ position = ba.kvector_t(0.0, 0.0, -10.0 * nm)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(sphere, 1.0, position)
@@ -44,8 +43,9 @@ 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.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.setBeamIntensity(1e12)
analyzer_dir = ba.kvector_t(0.0, 0.0, -1.0)
diff --git a/Examples/Python/sim11_Device/AxesInDifferentUnits.py b/Examples/Python/sim11_Device/AxesInDifferentUnits.py
index 9c23535da866b402bd0d70df66ea077ab108b05d..9065945c49ee1dfa0ea2b05676834fc083810b97 100644
--- a/Examples/Python/sim11_Device/AxesInDifferentUnits.py
+++ b/Examples/Python/sim11_Device/AxesInDifferentUnits.py
@@ -18,7 +18,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -42,10 +42,10 @@ def get_rectangular_detector():
pilatus_pixel_size = 0.172 # in mm
pilatus_npx, pilatus_npy = 981, 1043 # number of pixels
- width = pilatus_npx*pilatus_pixel_size
- height = pilatus_npy*pilatus_pixel_size
+ width = pilatus_npx * pilatus_pixel_size
+ height = pilatus_npy * pilatus_pixel_size
detector = ba.RectangularDetector(pilatus_npx, width, pilatus_npy, height)
- detector.setPerpendicularToSampleX(detector_distance, width/2., 0.0)
+ detector.setPerpendicularToSampleX(detector_distance, width / 2., 0.0)
return detector
@@ -54,7 +54,7 @@ def get_simulation():
Returns a GISAXS simulation with beam defined
"""
simulation = ba.GISASSimulation()
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * deg, 0.0 * deg)
simulation.setDetector(get_rectangular_detector())
return simulation
@@ -80,27 +80,41 @@ def plot(result):
# set plotting parameters
rcParams['image.cmap'] = 'jet'
rcParams['image.aspect'] = 'auto'
-
+
fig = plt.figure(figsize=(12.80, 10.24))
plt.subplot(2, 2, 1)
# default units for rectangular detector are millimeters
- ba.plot_colormap(result, title="In default units",
- xlabel=r'$X_{mm}$', ylabel=r'$Y_{mm}$', zlabel=None)
+ ba.plot_colormap(result,
+ title="In default units",
+ xlabel=r'$X_{mm}$',
+ ylabel=r'$Y_{mm}$',
+ zlabel=None)
plt.subplot(2, 2, 2)
- ba.plot_colormap(result, units=ba.Axes.NBINS, title="In number of bins",
- xlabel=r'$X_{nbins}$', ylabel=r'$Y_{nbins}$', zlabel=None)
+ ba.plot_colormap(result,
+ units=ba.Axes.NBINS,
+ title="In number of bins",
+ xlabel=r'$X_{nbins}$',
+ ylabel=r'$Y_{nbins}$',
+ zlabel=None)
plt.subplot(2, 2, 3)
- ba.plot_colormap(result, units=ba.Axes.DEGREES, title="In degs",
- xlabel=r'$\phi_f ^{\circ}$', ylabel=r'$\alpha_f ^{\circ}$',
+ ba.plot_colormap(result,
+ units=ba.Axes.DEGREES,
+ title="In degs",
+ xlabel=r'$\phi_f ^{\circ}$',
+ ylabel=r'$\alpha_f ^{\circ}$',
zlabel=None)
plt.subplot(2, 2, 4)
- ba.plot_colormap(result, units=ba.Axes.QSPACE, title="Q-space",
- xlabel=r'$Q_{y} [1/nm]$', ylabel=r'$Q_{z} [1/nm]$', zlabel=None)
+ ba.plot_colormap(result,
+ units=ba.Axes.QSPACE,
+ title="Q-space",
+ xlabel=r'$Q_{y} [1/nm]$',
+ 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.show()
diff --git a/Examples/Python/sim11_Device/BeamDivergence.py b/Examples/Python/sim11_Device/BeamDivergence.py
index a0f9e73d1aefbb12dcef846b8fedf1c8cc38ad6c..bbbc64e2993498aa51490c743de35bbad376af4c 100644
--- a/Examples/Python/sim11_Device/BeamDivergence.py
+++ b/Examples/Python/sim11_Device/BeamDivergence.py
@@ -15,7 +15,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -36,12 +36,12 @@ 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.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)
diff --git a/Examples/Python/sim11_Device/ConstantBackground.py b/Examples/Python/sim11_Device/ConstantBackground.py
index 5a0484c5b14a90167f7687878fd702d4727b51b8..e7ea35730a913d5bee293e70b95779bac265041e 100644
--- a/Examples/Python/sim11_Device/ConstantBackground.py
+++ b/Examples/Python/sim11_Device/ConstantBackground.py
@@ -15,7 +15,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -36,9 +36,9 @@ 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.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.setBeamIntensity(1e6)
bg = ba.ConstantBackground(1e3)
simulation.setBackground(bg)
diff --git a/Examples/Python/sim11_Device/DetectorResolutionFunction.py b/Examples/Python/sim11_Device/DetectorResolutionFunction.py
index d2735fa4cb4190462fc9eb1b3176fb75d84e06dd..ae9ec0e4be89bb1a04b52d258b9f64f3f343cfdc 100644
--- a/Examples/Python/sim11_Device/DetectorResolutionFunction.py
+++ b/Examples/Python/sim11_Device/DetectorResolutionFunction.py
@@ -15,7 +15,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -36,11 +36,11 @@ 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)
+ 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.setDetectorResolutionFunction(
- ba.ResolutionFunction2DGaussian(0.02*deg, 0.02*deg))
+ ba.ResolutionFunction2DGaussian(0.02 * deg, 0.02 * deg))
return simulation
diff --git a/Examples/Python/sim11_Device/OffSpecularSimulation.py b/Examples/Python/sim11_Device/OffSpecularSimulation.py
index 43fccdc77cb3b9f7d6b8cbe3394705890c6adfb2..a5db46bb3d5d1e0d3b35bdc126e69cab907a6fc3 100644
--- a/Examples/Python/sim11_Device/OffSpecularSimulation.py
+++ b/Examples/Python/sim11_Device/OffSpecularSimulation.py
@@ -20,16 +20,16 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- lattice_length = 100.0*nm
- lattice_rotation_angle = 0.0*deg
- interference = ba.InterferenceFunction1DLattice(
- lattice_length, lattice_rotation_angle)
+ lattice_length = 100.0 * nm
+ lattice_rotation_angle = 0.0 * deg
+ interference = ba.InterferenceFunction1DLattice(lattice_length,
+ lattice_rotation_angle)
pdf = ba.FTDecayFunction1DCauchy(1e+6)
interference.setDecayFunction(pdf)
- box_ff = ba.FormFactorBox(1000*nm, 20*nm, 10.0*nm)
+ box_ff = ba.FormFactorBox(1000 * nm, 20 * nm, 10.0 * nm)
box = ba.Particle(m_particle, box_ff)
- transform = ba.RotationZ(90.0*deg)
+ transform = ba.RotationZ(90.0 * deg)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(box, 1.0, ba.kvector_t(0.0, 0.0, 0.0), transform)
particle_layout.setInterferenceFunction(interference)
@@ -50,12 +50,12 @@ def get_simulation():
Returns an off-specular simulation with beam and detector defined.
"""
simulation = ba.OffSpecSimulation()
- simulation.setDetectorParameters(20, phi_f_min*deg, phi_f_max*deg,
- 200, alpha_f_min*deg, alpha_f_max*deg)
+ simulation.setDetectorParameters(20, phi_f_min * deg, phi_f_max * deg, 200,
+ alpha_f_min * deg, alpha_f_max * deg)
# define the beam with alpha_i varied between alpha_i_min and alpha_i_max
- alpha_i_axis = ba.FixedBinAxis(
- "alpha_i", 200, alpha_i_min*deg, alpha_i_max*deg)
- simulation.setBeamParameters(1.0*angstrom, alpha_i_axis, 0.0*deg)
+ alpha_i_axis = ba.FixedBinAxis("alpha_i", 200, alpha_i_min * deg,
+ alpha_i_max * deg)
+ simulation.setBeamParameters(1.0 * angstrom, alpha_i_axis, 0.0 * deg)
simulation.setBeamIntensity(1e9)
return simulation
diff --git a/Examples/Python/sim11_Device/RectangularDetector.py b/Examples/Python/sim11_Device/RectangularDetector.py
index 7bf9045b8811932c7fe99c611ccec180435f0348..91e683e115680ef969b7b3c3f3ee8362aff4b9d1 100644
--- a/Examples/Python/sim11_Device/RectangularDetector.py
+++ b/Examples/Python/sim11_Device/RectangularDetector.py
@@ -23,7 +23,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- edge = 40*nm
+ edge = 40 * nm
ff = ba.FormFactorBox(edge, edge, edge)
cylinder = ba.Particle(m_particle, ff)
particle_layout = ba.ParticleLayout()
@@ -45,24 +45,24 @@ def get_spherical_detector():
"""
n_phi = pilatus_npx
n_alpha = pilatus_npy
- width = pilatus_npx*pilatus_pixel_size
- height = pilatus_npy*pilatus_pixel_size
- phi_min = numpy.arctan(-width/2./detector_distance)
- phi_max = numpy.arctan(width/2./detector_distance)
+ width = pilatus_npx * pilatus_pixel_size
+ height = pilatus_npy * pilatus_pixel_size
+ phi_min = numpy.arctan(-width / 2. / detector_distance)
+ phi_max = numpy.arctan(width / 2. / detector_distance)
alpha_min = 0.0
- alpha_max = numpy.arctan(height/detector_distance)
- return ba.SphericalDetector(
- n_phi, phi_min, phi_max, n_alpha, alpha_min, alpha_max)
+ alpha_max = numpy.arctan(height / detector_distance)
+ return ba.SphericalDetector(n_phi, phi_min, phi_max, n_alpha, alpha_min,
+ alpha_max)
def get_rectangular_detector():
"""
Returns a rectangular detector representing our PILATUS detector
"""
- width = pilatus_npx*pilatus_pixel_size
- height = pilatus_npy*pilatus_pixel_size
+ width = pilatus_npx * pilatus_pixel_size
+ height = pilatus_npy * pilatus_pixel_size
detector = ba.RectangularDetector(pilatus_npx, width, pilatus_npy, height)
- detector.setPerpendicularToSampleX(detector_distance, width/2., 0.0)
+ detector.setPerpendicularToSampleX(detector_distance, width / 2., 0.0)
return detector
@@ -71,7 +71,7 @@ def get_simulation():
Return a GISAXS simulation with defined beam
"""
simulation = ba.GISASSimulation()
- simulation.setBeamParameters(10*angstrom, 0.2*deg, 0.0*deg)
+ simulation.setBeamParameters(10 * angstrom, 0.2 * deg, 0.0 * deg)
return simulation
@@ -84,24 +84,34 @@ def plot(results):
# showing result of spherical detector simulation
plt.subplot(1, 3, 1)
- ba.plot_colormap(results['spherical'], title="Spherical detector",
- xlabel=r'$\phi_f ^{\circ}$', ylabel=r'$\alpha_f ^{\circ}$',
- zlabel="", cmap='jet', aspect='auto')
+ ba.plot_colormap(results['spherical'],
+ title="Spherical detector",
+ xlabel=r'$\phi_f ^{\circ}$',
+ ylabel=r'$\alpha_f ^{\circ}$',
+ zlabel="",
+ cmap='jet',
+ aspect='auto')
# showing result of rectangular detector simulation
plt.subplot(1, 3, 2)
- ba.plot_colormap(results['rectangular'], title="Rectangular detector",
- xlabel='X, mm', ylabel='Y, mm', zlabel="",
- cmap='jet', aspect='auto')
+ ba.plot_colormap(results['rectangular'],
+ title="Rectangular detector",
+ xlabel='X, mm',
+ ylabel='Y, mm',
+ zlabel="",
+ cmap='jet',
+ aspect='auto')
# show relative difference between two plots (sph[i]-rect[i])/rect[i]
# for every detector pixel
sph_array = results['spherical'].array()
rect_array = results['rectangular'].array()
- rel_diff = 2.0 * numpy.abs(sph_array - rect_array)/(sph_array + rect_array)
+ rel_diff = 2.0 * numpy.abs(sph_array - rect_array) / (sph_array + rect_array)
plt.subplot(1, 3, 3)
- im = plt.imshow(rel_diff, norm=colors.LogNorm(1e-6, 1.0),
- aspect='auto', cmap='jet')
+ im = plt.imshow(rel_diff,
+ norm=colors.LogNorm(1e-6, 1.0),
+ aspect='auto',
+ cmap='jet')
cb = plt.colorbar(im, pad=0.025)
plt.xlabel('X, bins', fontsize=14)
plt.ylabel('Y, bins', fontsize=14)
diff --git a/Examples/Python/sim11_Device/ResonatorOffSpecSetup.py b/Examples/Python/sim11_Device/ResonatorOffSpecSetup.py
index a516764ad7275765450319d5ba7823fe36bd63f5..e9330b6033c025259e0af1e775568f673f171c7d 100644
--- a/Examples/Python/sim11_Device/ResonatorOffSpecSetup.py
+++ b/Examples/Python/sim11_Device/ResonatorOffSpecSetup.py
@@ -5,7 +5,7 @@ import bornagain as ba
from bornagain import deg, nm, micrometer, angstrom
-def get_sample(nlayers = 3):
+def get_sample(nlayers=3):
"""
Construct resonator with given number of Ti/Pt double layers nlayers.
"""
@@ -18,18 +18,18 @@ def get_sample(nlayers = 3):
m_D2O = ba.HomogeneousMaterial("D2O", 2.52897204573e-05, 4.5224432814e-13)
# create layers
- l_TiO2 = ba.Layer(m_TiO2, 3.0*nm)
- l_Ti_top = ba.Layer(m_Ti, 10.0*nm)
- l_Ti = ba.Layer(m_Ti, 13.0*nm)
- l_Si = ba.Layer(m_Si) # consider it as an ambient layer
- l_Pt = ba.Layer(m_Pt, 32.0*nm)
+ l_TiO2 = ba.Layer(m_TiO2, 3.0 * nm)
+ l_Ti_top = ba.Layer(m_Ti, 10.0 * nm)
+ l_Ti = ba.Layer(m_Ti, 13.0 * nm)
+ l_Si = ba.Layer(m_Si) # consider it as an ambient layer
+ l_Pt = ba.Layer(m_Pt, 32.0 * nm)
l_D2O = ba.Layer(m_D2O) # thickness is not given, seems to be like a substrate
# describe layer roughness
roughness = ba.LayerRoughness()
- roughness.setSigma(2.0*nm)
+ roughness.setSigma(2.0 * nm)
roughness.setHurstParameter(0.8)
- roughness.setLatteralCorrLength(10.0*micrometer)
+ roughness.setLatteralCorrLength(10.0 * micrometer)
# assemble multilayer
sample = ba.MultiLayer()
@@ -43,7 +43,7 @@ def get_sample(nlayers = 3):
sample.addLayerWithTopRoughness(l_TiO2, roughness)
sample.addLayerWithTopRoughness(l_D2O, roughness)
- sample.setCrossCorrLength(400*nm)
+ sample.setCrossCorrLength(400 * nm)
return sample
@@ -58,26 +58,27 @@ def get_offspec_simulation():
simulation.setTerminalProgressMonitor()
# define detector parameters
- n_alpha, alpha_min, alpha_max = 300, 0.0*deg, 4.0*deg
- n_phi, phi_min, phi_max = 10, -0.1*deg, 0.1*deg
- simulation.setDetectorParameters(
- n_phi, phi_min, phi_max, n_alpha, alpha_min, alpha_max)
+ n_alpha, alpha_min, alpha_max = 300, 0.0 * deg, 4.0 * deg
+ n_phi, phi_min, phi_max = 10, -0.1 * deg, 0.1 * deg
+ simulation.setDetectorParameters(n_phi, phi_min, phi_max, n_alpha, alpha_min,
+ alpha_max)
# define the beam with alpha_i varied between alpha_i_min and alpha_i_max
n_scan_points, alpha_i_min, alpha_i_max = n_alpha, alpha_min, alpha_max
- alpha_i_axis = ba.FixedBinAxis(
- "alpha_i", n_scan_points, alpha_i_min, alpha_i_max)
- simulation.setBeamParameters(5.0*angstrom, alpha_i_axis, 0.0)
+ alpha_i_axis = ba.FixedBinAxis("alpha_i", n_scan_points, alpha_i_min,
+ alpha_i_max)
+ simulation.setBeamParameters(5.0 * angstrom, alpha_i_axis, 0.0)
simulation.setBeamIntensity(1e9)
simulation.getOptions().setIncludeSpecular(True)
# define detector resolution function with smearing depending on bin size
- d_alpha = (alpha_max - alpha_min)/n_alpha
- d_phi = (phi_max-phi_min)/n_phi
+ d_alpha = (alpha_max - alpha_min) / n_alpha
+ d_phi = (phi_max - phi_min) / n_phi
sigma_factor = 1.0
simulation.setDetectorResolutionFunction(
- ba.ResolutionFunction2DGaussian(sigma_factor*d_alpha, sigma_factor*d_phi))
+ ba.ResolutionFunction2DGaussian(sigma_factor * d_alpha,
+ sigma_factor * d_phi))
return simulation
diff --git a/Examples/Python/sim21_Reflectometry/BasicPolarizedReflectometry.py b/Examples/Python/sim21_Reflectometry/BasicPolarizedReflectometry.py
index 32b55eff4e354744972b67e5bdc414356c85cf93..e8685ce27c7c01fa519bff0f7910f0e9b60946c9 100644
--- a/Examples/Python/sim21_Reflectometry/BasicPolarizedReflectometry.py
+++ b/Examples/Python/sim21_Reflectometry/BasicPolarizedReflectometry.py
@@ -8,6 +8,7 @@ from bornagain import deg, angstrom
import matplotlib.pyplot as plt
+
def get_sample():
"""
Defines sample and returns it
@@ -15,8 +16,7 @@ def get_sample():
# creating materials
m_ambient = ba.MaterialBySLD("Ambient", 0.0, 0.0)
- m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8,
- ba.kvector_t(0.0, 1e8, 0.0))
+ m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8, ba.kvector_t(0.0, 1e8, 0.0))
m_substrate = ba.MaterialBySLD("Substrate", 7e-5, 2e-6)
# creating layers
@@ -38,8 +38,7 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 5.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 5.0 * deg)
simulation.setScan(scan)
return simulation
@@ -62,27 +61,23 @@ def run_simulation(polarization=ba.kvector_t(0, 1, 0),
def plot(data, labels):
-
+
plt.figure()
for d, l in zip(data, labels):
- plt.semilogy( d.axis(),
- d.array(),
- label=l, linewidth=1)
-
- plt.legend( loc='upper right' )
+ plt.semilogy(d.axis(), d.array(), label=l, linewidth=1)
+
+ plt.legend(loc='upper right')
plt.gca().yaxis.set_ticks_position('both')
plt.gca().xaxis.set_ticks_position('both')
-
+
plt.xlabel(r"$\alpha_i$ [deg]")
plt.ylabel("Reflectivity")
-
+
plt.tight_layout()
plt.show()
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/Python/sim21_Reflectometry/BasicSpecularSimulation.py b/Examples/Python/sim21_Reflectometry/BasicSpecularSimulation.py
index 17cf311218884224341f91a8f05b7b133a2dbf8d..ae9055c64212a6ed77d9ce70095a12afadc11f08 100644
--- a/Examples/Python/sim21_Reflectometry/BasicSpecularSimulation.py
+++ b/Examples/Python/sim21_Reflectometry/BasicSpecularSimulation.py
@@ -39,8 +39,7 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 2.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 2.0 * deg)
simulation.setScan(scan)
return simulation
diff --git a/Examples/Python/sim21_Reflectometry/BeamAngularDivergence.py b/Examples/Python/sim21_Reflectometry/BeamAngularDivergence.py
index 54392356753dd94851e76c40ff808b9bf3946192..05de2b19dc425bff7dff3da1964e343d7f09384e 100644
--- a/Examples/Python/sim21_Reflectometry/BeamAngularDivergence.py
+++ b/Examples/Python/sim21_Reflectometry/BeamAngularDivergence.py
@@ -56,9 +56,11 @@ def create_real_data():
Loading data from genx_angular_divergence.dat
"""
filepath = path.join(path.dirname(path.realpath(__file__)),
- "genx_angular_divergence.dat.gz")
+ "genx_angular_divergence.dat.gz")
ax_values, real_data = np.loadtxt(filepath,
- usecols=(0, 1), skiprows=3, unpack=True)
+ usecols=(0, 1),
+ skiprows=3,
+ unpack=True)
# translating axis values from double incident angle # to incident angle
ax_values *= 0.5
@@ -107,9 +109,7 @@ def plot(results):
genx_axis, genx_values = create_real_data()
plt.semilogy(genx_axis, genx_values, 'ko', markevery=300)
- plt.legend(['BornAgain',
- 'GenX'],
- loc='upper right')
+ plt.legend(['BornAgain', 'GenX'], loc='upper right')
plt.show()
diff --git a/Examples/Python/sim21_Reflectometry/FootprintCorrection.py b/Examples/Python/sim21_Reflectometry/FootprintCorrection.py
index 1be10c62811243ac04efa656b7c1120e8ff4be46..73a9e4be335b62153c71444d611d325672d26bff 100644
--- a/Examples/Python/sim21_Reflectometry/FootprintCorrection.py
+++ b/Examples/Python/sim21_Reflectometry/FootprintCorrection.py
@@ -41,8 +41,7 @@ def get_simulation(footprint):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(
- 1.54 * angstrom, 500 , 0.0 * deg, 0.6 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, 500, 0.0 * deg, 0.6 * deg)
scan.setFootprintFactor(footprint)
simulation.setScan(scan)
return simulation
@@ -69,13 +68,11 @@ def plot(sim_result_1, sim_result_2):
x1, y1 = get_plot_data(sim_result_1)
x2, y2 = get_plot_data(sim_result_2)
plt.semilogy(x1, y1, x2, y2)
-
+
plt.xlabel(r'$\alpha_i \; (deg)$', fontsize=16)
plt.ylabel(r'Intensity', fontsize=16)
- plt.legend(['With footprint',
- 'Without footprint'],
- loc='upper right')
+ plt.legend(['With footprint', 'Without footprint'], loc='upper right')
plt.show()
@@ -83,9 +80,6 @@ def plot(sim_result_1, sim_result_2):
if __name__ == '__main__':
beam_sample_ratio = 0.01 # beam-to-sample size ratio
result_with_fp = run_simulation(
- get_simulation(
- footprint=ba.FootprintSquare(beam_sample_ratio)
- )
- )
+ get_simulation(footprint=ba.FootprintSquare(beam_sample_ratio)))
result_without_fp = run_simulation(get_simulation(footprint=None))
plot(result_with_fp, result_without_fp)
diff --git a/Examples/Python/sim21_Reflectometry/PolarizedNoAnalyzer.py b/Examples/Python/sim21_Reflectometry/PolarizedNoAnalyzer.py
index b001eb19fb0a5373048c591986ad76e5785f8b77..78a4e88e7dc133bf82841ad3f45c425a5515c19f 100644
--- a/Examples/Python/sim21_Reflectometry/PolarizedNoAnalyzer.py
+++ b/Examples/Python/sim21_Reflectometry/PolarizedNoAnalyzer.py
@@ -9,7 +9,6 @@ import bornagain as ba
from bornagain import deg, angstrom
-
def get_sample():
"""
Defines sample and returns it
@@ -17,15 +16,12 @@ def get_sample():
# creating materials
magnetizationMagnitude = 1e8
- angle = 30 * deg
- magnetizationVector = ba.kvector_t(
- magnetizationMagnitude * numpy.sin(angle),
- magnetizationMagnitude * numpy.cos(angle),
- 0)
+ angle = 30 * deg
+ magnetizationVector = ba.kvector_t(magnetizationMagnitude * numpy.sin(angle),
+ magnetizationMagnitude * numpy.cos(angle), 0)
m_ambient = ba.MaterialBySLD("Ambient", 0.0, 0.0)
- m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8,
- magnetizationVector)
+ m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8, magnetizationVector)
m_substrate = ba.MaterialBySLD("Substrate", 7e-5, 2e-6)
# creating layers
@@ -47,14 +43,12 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 5.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 5.0 * deg)
simulation.setScan(scan)
return simulation
-def run_simulation(polarization=ba.kvector_t(0.0, 1.0, 0.0),
- analyzer=None):
+def run_simulation(polarization=ba.kvector_t(0.0, 1.0, 0.0), analyzer=None):
"""
Runs simulation and returns its result.
"""
@@ -64,7 +58,7 @@ def run_simulation(polarization=ba.kvector_t(0.0, 1.0, 0.0),
# adding polarization and analyzer operator
simulation.setBeamPolarization(polarization)
if analyzer:
- simulation.setAnalyzerProperties(analyzer, 1.0, 0.5)
+ simulation.setAnalyzerProperties(analyzer, 1.0, 0.5)
simulation.setSample(sample)
simulation.runSimulation()
@@ -73,48 +67,36 @@ def run_simulation(polarization=ba.kvector_t(0.0, 1.0, 0.0),
def plot(axis, data, labels):
-
+
plt.figure()
for d, l in zip(data, labels):
- plt.semilogy( axis,
- d,
- label=l, linewidth=1)
-
- plt.legend( loc='upper right' )
+ plt.semilogy(axis, d, label=l, linewidth=1)
+
+ plt.legend(loc='upper right')
plt.gca().yaxis.set_ticks_position('both')
plt.gca().xaxis.set_ticks_position('both')
-
+
plt.xlabel(r"$\alpha_i$ [deg]")
plt.ylabel("Reflectivity")
-
+
plt.tight_layout()
if __name__ == '__main__':
- 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))
-
- q, results_pm = run_simulation(ba.kvector_t(0, 1, 0),
- ba.kvector_t(0, -1, 0))
- q, results_mp = run_simulation(ba.kvector_t(0, -1, 0),
- ba.kvector_t(0, 1, 0))
-
- r_plus = results_pp + results_pm
+ 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))
+
+ q, results_pm = run_simulation(ba.kvector_t(0, 1, 0), ba.kvector_t(0, -1, 0))
+ q, results_mp = run_simulation(ba.kvector_t(0, -1, 0), ba.kvector_t(0, 1, 0))
+
+ r_plus = results_pp + results_pm
r_minus = results_mm + results_mp
- plot(q,
- [r_plus, r_minus],
- ["$+$", "$-$"])
-
+ plot(q, [r_plus, r_minus], ["$+$", "$-$"])
+
# same result, but need half the computational time
- q, results_p = run_simulation(ba.kvector_t(0, 1, 0))
+ q, results_p = run_simulation(ba.kvector_t(0, 1, 0))
q, results_m = run_simulation(ba.kvector_t(0, -1, 0))
-
- plot(q,
- [results_p, results_m],
- ["$+$", "$-$"])
+
+ plot(q, [results_p, results_m], ["$+$", "$-$"])
plt.show()
-
-
diff --git a/Examples/Python/sim21_Reflectometry/PolarizedNonperfectAnalyzerPolarizer.py b/Examples/Python/sim21_Reflectometry/PolarizedNonperfectAnalyzerPolarizer.py
index e42e4f1d78cae590768d95f8cbf598aea3e36dad..f159c526c24ad649cd95213c5c76513bba83c0c7 100644
--- a/Examples/Python/sim21_Reflectometry/PolarizedNonperfectAnalyzerPolarizer.py
+++ b/Examples/Python/sim21_Reflectometry/PolarizedNonperfectAnalyzerPolarizer.py
@@ -5,21 +5,19 @@ following Devishvili et al., Rev. Sci. Instrum. 84, 025112 (2013)
"""
import numpy
import matplotlib.pyplot as plt
-
+
import bornagain as ba
from bornagain import deg, angstrom
-
-sldFe = (8.0241e-06, 6.0448e-10)
-sldPd = (4.0099e-6, 1.3019e-09)
+sldFe = (8.0241e-06, 6.0448e-10)
+sldPd = (4.0099e-6, 1.3019e-09)
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)
+angle = 0
+magnetizationVector = ba.kvector_t(magnetizationMagnitude * numpy.sin(angle * deg),
+ magnetizationMagnitude * numpy.cos(angle * deg),
+ 0)
def get_sample(*, magnetization=magnetizationVector):
@@ -28,111 +26,113 @@ def get_sample(*, magnetization=magnetizationVector):
"""
# create materials
- mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
- mat_Pd = ba.MaterialBySLD("Pd", *sldPd)
- mat_Fe = ba.MaterialBySLD("Fe", *sldFe,
- magnetizationVector)
+ mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
+ mat_Pd = ba.MaterialBySLD("Pd", *sldPd)
+ mat_Fe = ba.MaterialBySLD("Fe", *sldFe, magnetizationVector)
mat_substrate = ba.MaterialBySLD("MgO", *sldMgO)
# create layers
- layer_vacuum = ba.Layer( mat_vacuum )
- layer_Pd = ba.Layer( mat_Pd, 120 * angstrom )
- layer_Fe = ba.Layer( mat_Fe, 1000 * angstrom )
- layer_substrate = ba.Layer( mat_substrate )
+ layer_vacuum = ba.Layer(mat_vacuum)
+ layer_Pd = ba.Layer(mat_Pd, 120 * angstrom)
+ layer_Fe = ba.Layer(mat_Fe, 1000 * angstrom)
+ layer_substrate = ba.Layer(mat_substrate)
roughness = ba.LayerRoughness()
- roughness.setSigma( 20 * angstrom)
-
+ roughness.setSigma(20 * angstrom)
+
# create sample
multi_layer = ba.MultiLayer()
-
+
multi_layer.addLayer(layer_vacuum)
multi_layer.addLayerWithTopRoughness(layer_Pd, roughness)
multi_layer.addLayerWithTopRoughness(layer_Fe, roughness)
multi_layer.addLayerWithTopRoughness(layer_substrate, roughness)
-
+
return multi_layer
-def get_simulation( scan_size=1500 ):
+def get_simulation(scan_size=1500):
"""
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
qzs = numpy.linspace(0.1, 1.5, scan_size)
-
+
n_sig = 4.0
n_samples = 25
distr = ba.RangedDistributionGaussian(n_samples, n_sig)
scan = ba.QSpecScan(qzs)
scan.setAbsoluteQResolution(distr, 0.008)
-
+
simulation.setScan(scan)
return simulation
-def run_simulation(*, polarization=ba.kvector_t(0, 1, 0),
- polarizer_efficiency=1,
- analyzer=ba.kvector_t(0, 1, 0),
- analyzer_efficiency=1):
+def run_simulation(*,
+ polarization=ba.kvector_t(0, 1, 0),
+ polarizer_efficiency=1,
+ analyzer=ba.kvector_t(0, 1, 0),
+ analyzer_efficiency=1):
"""
Runs simulation and returns its result.
"""
sample = get_sample()
-
+
simulation = get_simulation()
simulation.setBeamPolarization(polarization * polarizer_efficiency)
simulation.setAnalyzerProperties(analyzer, analyzer_efficiency, 0.5)
-
- simulation.setBackground( ba.ConstantBackground( 1e-7 ) )
-
+
+ simulation.setBackground(ba.ConstantBackground(1e-7))
+
simulation.setSample(sample)
simulation.runSimulation()
return simulation.result()
def plot(data, labels):
-
+
plt.figure()
for d, l in zip(data, labels):
- plt.semilogy(numpy.array( d.axis(ba.Axes.QSPACE) ),
- d.array(ba.Axes.QSPACE), label=l, linewidth=1)
-
- plt.legend( loc='upper right' )
+ plt.semilogy(numpy.array(d.axis(ba.Axes.QSPACE)),
+ d.array(ba.Axes.QSPACE),
+ label=l,
+ linewidth=1)
+
+ plt.legend(loc='upper right')
plt.gca().yaxis.set_ticks_position('both')
plt.gca().xaxis.set_ticks_position('both')
-
+
plt.xlabel("$Q$ [nm${}^{-1}$]")
plt.ylabel("Reflectivity")
-
+
plt.tight_layout()
plt.show()
if __name__ == '__main__':
-
+
polarizer_efficiency = 0.986
- analyzer_efficiency = 0.970
-
- results_pp = run_simulation(polarization = ba.kvector_t(0, 1, 0),
- analyzer = ba.kvector_t(0, 1, 0),
- polarizer_efficiency = polarizer_efficiency,
- analyzer_efficiency = analyzer_efficiency )
- results_mm = run_simulation(polarization = ba.kvector_t(0, -1, 0),
- analyzer = ba.kvector_t(0, -1, 0),
- polarizer_efficiency = polarizer_efficiency,
- analyzer_efficiency = analyzer_efficiency )
-
- results_pm = run_simulation(polarization = ba.kvector_t(0, 1, 0),
- analyzer = ba.kvector_t(0, -1, 0),
- polarizer_efficiency = polarizer_efficiency,
- analyzer_efficiency = analyzer_efficiency )
- results_mp = run_simulation(polarization = ba.kvector_t(0, -1, 0),
- analyzer = ba.kvector_t(0, 1, 0),
- polarizer_efficiency = polarizer_efficiency,
- analyzer_efficiency = analyzer_efficiency )
-
- plot([results_pp, results_mm, results_pm, results_mp],
+ analyzer_efficiency = 0.970
+
+ results_pp = run_simulation(polarization=ba.kvector_t(0, 1, 0),
+ analyzer=ba.kvector_t(0, 1, 0),
+ polarizer_efficiency=polarizer_efficiency,
+ analyzer_efficiency=analyzer_efficiency)
+ results_mm = run_simulation(polarization=ba.kvector_t(0, -1, 0),
+ analyzer=ba.kvector_t(0, -1, 0),
+ polarizer_efficiency=polarizer_efficiency,
+ analyzer_efficiency=analyzer_efficiency)
+
+ results_pm = run_simulation(polarization=ba.kvector_t(0, 1, 0),
+ analyzer=ba.kvector_t(0, -1, 0),
+ polarizer_efficiency=polarizer_efficiency,
+ analyzer_efficiency=analyzer_efficiency)
+ results_mp = run_simulation(polarization=ba.kvector_t(0, -1, 0),
+ analyzer=ba.kvector_t(0, 1, 0),
+ polarizer_efficiency=polarizer_efficiency,
+ analyzer_efficiency=analyzer_efficiency)
+
+ plot([results_pp, results_mm, results_pm, results_mp],
["$++$", "$--$", "$+-$", "$-+$"])
diff --git a/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetry.py b/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetry.py
index 6a6e15442313e458d2435ed8b85f56f3d433ceb4..247cde5ccc4f8c91c0490154663296b3b026edb4 100644
--- a/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetry.py
+++ b/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetry.py
@@ -28,57 +28,52 @@ qmin = 0.05997
qmax = 1.96
# number of points on which the computed result is plotted
-scan_size=1500
+scan_size = 1500
# The SLD of the substrate is kept constant
-sldMao = (5.377e-06, 0)
+sldMao = (5.377e-06, 0)
# constant to convert between magnetization and magnetic SLD
RhoMconst = 2.910429812376859e-12
-
-
-
-
####################################################################
# Create Sample and Simulation #
####################################################################
-
-
+
+
def get_sample(params):
"""
construct the sample with the given parameters
"""
magnetizationMagnitude = params["rhoM_Mafo"] * 1e-6 / RhoMconst
- angle = 0
- magnetizationVector = ba.kvector_t(
- magnetizationMagnitude * numpy.sin(angle * deg),
- magnetizationMagnitude * numpy.cos(angle * deg),
- 0)
-
- mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
- mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4",
- params["rho_Mafo"] * 1e-6, 0, magnetizationVector)
+ angle = 0
+ magnetizationVector = ba.kvector_t(
+ magnetizationMagnitude * numpy.sin(angle * deg),
+ magnetizationMagnitude * numpy.cos(angle * deg), 0)
+
+ mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
+ 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)
layer = ba.Layer(mat_layer, params["t_Mafo"] * angstrom)
substrate_layer = ba.Layer(mat_substrate)
-
+
r_Mafo = ba.LayerRoughness()
r_Mafo.setSigma(params["r_Mafo"] * angstrom)
-
+
r_substrate = ba.LayerRoughness()
r_substrate.setSigma(params["r_Mao"] * angstrom)
-
+
multi_layer = ba.MultiLayer()
multi_layer.addLayer(ambient_layer)
multi_layer.addLayerWithTopRoughness(layer, r_Mafo)
multi_layer.addLayerWithTopRoughness(substrate_layer, r_substrate)
-
+
return multi_layer
-
-
+
+
def get_simulation(q_axis, parameters, polarization, analyzer):
"""
Returns a simulation object.
@@ -88,21 +83,21 @@ def get_simulation(q_axis, parameters, polarization, analyzer):
simulation = ba.SpecularSimulation()
q_axis = q_axis + parameters["q_offset"]
scan = ba.QSpecScan(q_axis)
-
+
dq = parameters["q_res"] * q_axis
n_sig = 4.0
n_samples = 25
-
+
distr = ba.RangedDistributionGaussian(n_samples, n_sig)
scan.setAbsoluteQResolution(distr, parameters["q_res"])
-
+
simulation.setBeamPolarization(polarization)
simulation.setAnalyzerProperties(analyzer, 1.0, 0.5)
-
+
simulation.setScan(scan)
return simulation
-
-
+
+
def run_simulation(q_axis, fitParams, *, polarization, analyzer):
"""
Run a simulation on the given q-axis, where the sample is
@@ -110,10 +105,9 @@ def run_simulation(q_axis, fitParams, *, polarization, analyzer):
Vectors for polarization and analyzer need to be provided
"""
parameters = dict(fitParams, **fixedParams)
-
+
sample = get_sample(parameters)
- simulation = get_simulation(q_axis, parameters,
- polarization, analyzer)
+ simulation = get_simulation(q_axis, parameters, polarization, analyzer)
simulation.setSample(sample)
simulation.runSimulation()
@@ -125,38 +119,42 @@ def qr(result):
Returns two arrays that hold the q-values as well as the
reflectivity from a given simulation result
"""
- q = numpy.array( result.result().axis(ba.Axes.QSPACE) )
- r = numpy.array( result.result().array(ba.Axes.QSPACE) )
-
- return q, r
-
+ q = numpy.array(result.result().axis(ba.Axes.QSPACE))
+ r = numpy.array(result.result().array(ba.Axes.QSPACE))
+ return q, r
####################################################################
# Plot Handling #
####################################################################
+
def plot(qs, rs, exps, labels, filename):
"""
Plot the simulated result together with the experimental data
"""
fig = plt.figure()
ax = fig.add_subplot(111)
-
+
for q, r, exp, l in zip(qs, rs, exps, labels):
-
- ax.errorbar( exp[0], exp[1], xerr=exp[3], yerr=exp[2],
- fmt='.', markersize=0.75, linewidth=0.5)
-
- ax.plot(q, r, label=l)
-
+
+ ax.errorbar(exp[0],
+ exp[1],
+ xerr=exp[3],
+ yerr=exp[2],
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5)
+
+ ax.plot(q, r, label=l)
+
ax.set_yscale('log')
plt.legend()
-
+
plt.xlabel("Q [nm${}^{-1}$]")
plt.ylabel("R")
-
+
plt.tight_layout()
plt.savefig(filename)
@@ -166,32 +164,33 @@ def plotSpinAsymmetry(data_pp, data_mm, q, r_pp, r_mm, filename):
Plot the simulated spin asymmetry as well its
experimental counterpart with errorbars
"""
-
+
# compute the errorbars of the spin asymmetry
delta = numpy.sqrt(4 * (data_pp[1]**2 * data_mm[2]**2 + \
- data_mm[1]**2 * data_pp[2]**2 ) /
+ data_mm[1]**2 * data_pp[2]**2 ) /
( data_pp[1] + data_mm[1] )**4 )
-
+
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]),
- xerr = data_pp[3], yerr = delta,
- fmt='.', markersize=0.75, linewidth=0.5 )
-
- ax.plot(q, (r_pp - r_mm)/(r_pp + r_mm))
-
+
+ ax.errorbar(data_pp[0], (data_pp[1] - data_mm[1]) / (data_pp[1] + data_mm[1]),
+ xerr=data_pp[3],
+ yerr=delta,
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5)
+
+ ax.plot(q, (r_pp - r_mm) / (r_pp + r_mm))
+
plt.gca().set_ylim((-0.3, 0.5))
-
+
plt.xlabel("Q [nm${}^{-1}$]")
plt.ylabel("Spin asymmetry")
-
+
plt.tight_layout()
plt.savefig(filename)
-
####################################################################
# Data Handling #
####################################################################
@@ -203,119 +202,109 @@ def normalizeData(data):
normalizes it such that the maximum of the reflectivity is
unity and rescales the q-axis to inverse nm
"""
-
- r0 = numpy.where( data[0] - numpy.roll(data[0], 1) == 0)
+
+ r0 = numpy.where(data[0] - numpy.roll(data[0], 1) == 0)
data = numpy.delete(data, r0, 1)
-
+
data[0] = data[0] / angstrom
data[3] = data[3] / angstrom
-
- norm = numpy.max( data[1] )
- data[1] = data[1] / norm
- data[2] = data[2] / norm
-
- so = numpy.argsort( data[0] )
- data = data[:,so]
-
+
+ norm = numpy.max(data[1])
+ data[1] = data[1] / norm
+ data[2] = data[2] / norm
+
+ so = numpy.argsort(data[0])
+ data = data[:, so]
+
return data
+
def filterData(data, qmin, qmax):
- minIndex = numpy.argmin( numpy.abs( data[0] - qmin ) )
- maxIndex = numpy.argmin( numpy.abs( data[0] - qmax ) )
-
- return data[:,minIndex:maxIndex+1]
+ minIndex = numpy.argmin(numpy.abs(data[0] - qmin))
+ maxIndex = numpy.argmin(numpy.abs(data[0] - qmax))
+
+ return data[:, minIndex:maxIndex + 1]
+
def get_Experimental_data(qmin, qmax):
if hasattr(get_Experimental_data, "raw_data"):
data_pp = get_Experimental_data.raw_data_pp
data_mm = get_Experimental_data.raw_data_mm
-
+
else:
input_Data = downloadAndExtractData()
data_pp = normalizeData(input_Data[0])
data_mm = normalizeData(input_Data[1])
-
+
get_Experimental_data.data_pp = data_pp
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():
url = "https://www.nist.gov/document/spinelfilmzip"
-
+
if not isfile("spinelfilm.zip"):
- downloadfile = urlopen(url)
- with open("spinelfilm.zip", 'wb') as outfile:
- outfile.write(downloadfile.read())
-
+ downloadfile = urlopen(url)
+ with open("spinelfilm.zip", 'wb') as outfile:
+ outfile.write(downloadfile.read())
+
zipfile = ZipFile("spinelfilm.zip")
rawdata = zipfile.open("MAFO_Saturated.refl").\
read().decode("utf-8")
-
- table_pp = match(
- r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
- rawdata, DOTALL).group(1)
- table_mm = match(
- 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)
-
- return (data_pp, data_mm)
+ table_pp = match(r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
+ table_mm = match(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)
+
+ return (data_pp, data_mm)
####################################################################
# Main Function #
####################################################################
-
if __name__ == '__main__':
fixedParams = {
- # parameters from our own fit run
- 'q_res': (0.01027065792503683, ),
- 'q_offset': (8.977754679340925e-05, ),
-
- 'rho_Mafo': (6.373962950920891, ),
- 'rhoM_Mafo': (0.2383070807371731, ),
- 't_Mafo': (137.73795730237237, ),
-
- 'r_Mao': (7.004715629445297, ),
- 'r_Mafo': (3.8860835236521702, ),
- }
-
- fixedParams = { d:v[0] for d, v in fixedParams.items() }
-
- def run_Simulation_pp( qzs, params ):
- return run_simulation(qzs, params,
- polarization = ba.kvector_t(0, 1, 0),
- analyzer = ba.kvector_t(0, 1, 0))
-
- def run_Simulation_mm( qzs, params ):
- return run_simulation(qzs, params,
- polarization = ba.kvector_t(0, -1, 0),
- analyzer = ba.kvector_t(0, -1, 0))
+ # parameters from our own fit run
+ 'q_res': (0.01027065792503683, ),
+ 'q_offset': (8.977754679340925e-05, ),
+ 'rho_Mafo': (6.373962950920891, ),
+ 'rhoM_Mafo': (0.2383070807371731, ),
+ 't_Mafo': (137.73795730237237, ),
+ 'r_Mao': (7.004715629445297, ),
+ 'r_Mafo': (3.8860835236521702, ),
+ }
+
+ fixedParams = {d: v[0] for d, v in fixedParams.items()}
+
+ def run_Simulation_pp(qzs, params):
+ return run_simulation(qzs,
+ params,
+ polarization=ba.kvector_t(0, 1, 0),
+ analyzer=ba.kvector_t(0, 1, 0))
+
+ def run_Simulation_mm(qzs, params):
+ return run_simulation(qzs,
+ params,
+ polarization=ba.kvector_t(0, -1, 0),
+ analyzer=ba.kvector_t(0, -1, 0))
qzs = numpy.linspace(qmin, qmax, scan_size)
- q_pp, r_pp = qr( run_Simulation_pp( qzs, fixedParams ) )
- q_mm, r_mm = qr( run_Simulation_mm( qzs, fixedParams ) )
-
+ q_pp, r_pp = qr(run_Simulation_pp(qzs, fixedParams))
+ q_mm, r_mm = qr(run_Simulation_mm(qzs, fixedParams))
+
data_pp, data_mm = get_Experimental_data(qmin, qmax)
-
- plot([q_pp, q_mm], [r_pp, r_mm],
- [data_pp, data_mm], ["$++$", "$--$"],
- f'MAFO_Saturated.pdf' )
-
- plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
+
+ plot([q_pp, q_mm], [r_pp, r_mm], [data_pp, data_mm], ["$++$", "$--$"],
+ f'MAFO_Saturated.pdf')
+
+ plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
"MAFO_Saturated_spin_asymmetry.pdf")
-
-
-
diff --git a/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetryFit.py b/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetryFit.py
index 3e193e00606552d88ffb3580cf3a031964e6d6a1..ab5b87d582b1c80d4a3c3c1fbbabb84f1638976a 100644
--- a/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetryFit.py
+++ b/Examples/Python/sim21_Reflectometry/PolarizedSpinAsymmetryFit.py
@@ -28,18 +28,14 @@ qmin = 0.05997
qmax = 1.96
# number of points on which the computed result is plotted
-scan_size=1500
+scan_size = 1500
# The SLD of the substrate is kept constant
-sldMao = (5.377e-06, 0)
+sldMao = (5.377e-06, 0)
# constant to convert between magnetization and magnetic SLD
RhoMconst = 2.910429812376859e-12
-
-
-
-
####################################################################
# Create Sample and Simulation #
####################################################################
@@ -50,15 +46,14 @@ def get_sample(params):
construct the sample with the given parameters
"""
magnetizationMagnitude = params["rhoM_Mafo"] * 1e-6 / RhoMconst
- angle = 0
- magnetizationVector = ba.kvector_t(
- magnetizationMagnitude * numpy.sin(angle * deg),
- magnetizationMagnitude * numpy.cos(angle * deg),
- 0)
-
- mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
- mat_layer = ba.MaterialBySLD("(Mg,Al,Fe)3O4",
- params["rho_Mafo"] * 1e-6, 0, magnetizationVector)
+ angle = 0
+ magnetizationVector = ba.kvector_t(
+ magnetizationMagnitude * numpy.sin(angle * deg),
+ magnetizationMagnitude * numpy.cos(angle * deg), 0)
+
+ mat_vacuum = ba.MaterialBySLD("Vacuum", 0.0, 0.0)
+ 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)
@@ -67,15 +62,15 @@ def get_sample(params):
r_Mafo = ba.LayerRoughness()
r_Mafo.setSigma(params["r_Mafo"] * angstrom)
-
+
r_substrate = ba.LayerRoughness()
r_substrate.setSigma(params["r_Mao"] * angstrom)
-
+
multi_layer = ba.MultiLayer()
multi_layer.addLayer(ambient_layer)
multi_layer.addLayerWithTopRoughness(layer, r_Mafo)
multi_layer.addLayerWithTopRoughness(substrate_layer, r_substrate)
-
+
return multi_layer
@@ -88,7 +83,7 @@ def get_simulation(q_axis, parameters, polarization, analyzer):
simulation = ba.SpecularSimulation()
q_axis = q_axis + parameters["q_offset"]
scan = ba.QSpecScan(q_axis)
-
+
dq = parameters["q_res"] * q_axis
n_sig = 4.0
n_samples = 25
@@ -98,7 +93,7 @@ def get_simulation(q_axis, parameters, polarization, analyzer):
simulation.setBeamPolarization(polarization)
simulation.setAnalyzerProperties(analyzer, 1.0, 0.5)
-
+
simulation.setScan(scan)
return simulation
@@ -110,10 +105,9 @@ def run_simulation(q_axis, fitParams, *, polarization, analyzer):
Vectors for polarization and analyzer need to be provided
"""
parameters = dict(fitParams, **fixedParams)
-
+
sample = get_sample(parameters)
- simulation = get_simulation(q_axis, parameters,
- polarization, analyzer)
+ simulation = get_simulation(q_axis, parameters, polarization, analyzer)
simulation.setSample(sample)
simulation.runSimulation()
@@ -125,9 +119,9 @@ def qr(result):
Returns two arrays that hold the q-values as well as the
reflectivity from a given simulation result
"""
- q = numpy.array( result.result().axis(ba.Axes.QSPACE) )
- r = numpy.array( result.result().array(ba.Axes.QSPACE) )
-
+ q = numpy.array(result.result().axis(ba.Axes.QSPACE))
+ r = numpy.array(result.result().array(ba.Axes.QSPACE))
+
return q, r
@@ -136,27 +130,31 @@ def qr(result):
####################################################################
-
def plot(qs, rs, exps, labels, filename):
"""
Plot the simulated result together with the experimental data
"""
fig = plt.figure()
ax = fig.add_subplot(111)
-
+
for q, r, exp, l in zip(qs, rs, exps, labels):
-
- ax.errorbar( exp[0], exp[1], xerr=exp[3], yerr=exp[2],
- fmt='.', markersize=0.75, linewidth=0.5)
-
- ax.plot(q, r, label=l)
-
+
+ ax.errorbar(exp[0],
+ exp[1],
+ xerr=exp[3],
+ yerr=exp[2],
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5)
+
+ ax.plot(q, r, label=l)
+
ax.set_yscale('log')
plt.legend()
-
+
plt.xlabel("Q [nm${}^{-1}$]")
plt.ylabel("R")
-
+
plt.tight_layout()
plt.savefig(filename)
@@ -166,27 +164,29 @@ def plotSpinAsymmetry(data_pp, data_mm, q, r_pp, r_mm, filename):
Plot the simulated spin asymmetry as well its
experimental counterpart with errorbars
"""
-
+
# compute the errorbars of the spin asymmetry
delta = numpy.sqrt(4 * (data_pp[1]**2 * data_mm[2]**2 + \
- data_mm[1]**2 * data_pp[2]**2 ) /
+ data_mm[1]**2 * data_pp[2]**2 ) /
( data_pp[1] + data_mm[1] )**4 )
-
+
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]),
- xerr = data_pp[3], yerr = delta,
- fmt='.', markersize=0.75, linewidth=0.5 )
-
- ax.plot(q, (r_pp - r_mm)/(r_pp + r_mm))
-
+
+ ax.errorbar(data_pp[0], (data_pp[1] - data_mm[1]) / (data_pp[1] + data_mm[1]),
+ xerr=data_pp[3],
+ yerr=delta,
+ fmt='.',
+ markersize=0.75,
+ linewidth=0.5)
+
+ ax.plot(q, (r_pp - r_mm) / (r_pp + r_mm))
+
plt.gca().set_ylim((-0.3, 0.5))
-
+
plt.xlabel("Q [nm${}^{-1}$]")
plt.ylabel("Spin asymmetry")
-
+
plt.tight_layout()
plt.savefig(filename)
@@ -202,74 +202,68 @@ def normalizeData(data):
normalizes it such that the maximum of the reflectivity is
unity and rescales the q-axis to inverse nm
"""
-
- r0 = numpy.where( data[0] - numpy.roll(data[0], 1) == 0)
+
+ r0 = numpy.where(data[0] - numpy.roll(data[0], 1) == 0)
data = numpy.delete(data, r0, 1)
-
+
data[0] = data[0] / angstrom
data[3] = data[3] / angstrom
-
- norm = numpy.max( data[1] )
- data[1] = data[1] / norm
- data[2] = data[2] / norm
-
- so = numpy.argsort( data[0] )
- data = data[:,so]
-
+
+ norm = numpy.max(data[1])
+ data[1] = data[1] / norm
+ data[2] = data[2] / norm
+
+ so = numpy.argsort(data[0])
+ data = data[:, so]
+
return data
+
def filterData(data, qmin, qmax):
- minIndex = numpy.argmin( numpy.abs( data[0] - qmin ) )
- maxIndex = numpy.argmin( numpy.abs( data[0] - qmax ) )
-
- return data[:,minIndex:maxIndex+1]
+ minIndex = numpy.argmin(numpy.abs(data[0] - qmin))
+ maxIndex = numpy.argmin(numpy.abs(data[0] - qmax))
+
+ return data[:, minIndex:maxIndex + 1]
+
def get_Experimental_data(qmin, qmax):
if hasattr(get_Experimental_data, "raw_data"):
data_pp = get_Experimental_data.raw_data_pp
data_mm = get_Experimental_data.raw_data_mm
-
+
else:
input_Data = downloadAndExtractData()
data_pp = normalizeData(input_Data[0])
data_mm = normalizeData(input_Data[1])
-
+
get_Experimental_data.data_pp = data_pp
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():
url = "https://www.nist.gov/document/spinelfilmzip"
-
+
if not isfile("spinelfilm.zip"):
- downloadfile = urlopen(url)
- with open("spinelfilm.zip", 'wb') as outfile:
- outfile.write(downloadfile.read())
-
+ downloadfile = urlopen(url)
+ with open("spinelfilm.zip", 'wb') as outfile:
+ outfile.write(downloadfile.read())
+
zipfile = ZipFile("spinelfilm.zip")
-
+
rawdata = zipfile.open("MAFO_Saturated.refl").read().decode("utf-8")
-
- table_pp = match(
- r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
- rawdata, DOTALL).group(1)
- table_mm = match(
- 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)
-
- return (data_pp, data_mm)
+ table_pp = match(r'.*# "polarization": "\+\+"\n#.*?\n# "units".*?\n(.*?)#.*',
+ rawdata, DOTALL).group(1)
+ table_mm = match(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)
+ return (data_pp, data_mm)
####################################################################
@@ -278,118 +272,104 @@ def downloadAndExtractData():
def run_fit_ba(q_axis, rdata, simulationFactory, startParams):
-
+
fit_objective = ba.FitObjective()
fit_objective.setObjectiveMetric("reldiff")
-
- fit_objective.addSimulationAndData(
- lambda params: simulationFactory[0](q_axis[0], params),
- rdata[0], 1.0)
- fit_objective.addSimulationAndData(
- lambda params: simulationFactory[1](q_axis[1], params),
- rdata[1], 1.0)
-
+
+ fit_objective.addSimulationAndData(
+ lambda params: simulationFactory[0](q_axis[0], params), rdata[0], 1.0)
+ fit_objective.addSimulationAndData(
+ lambda params: simulationFactory[1](q_axis[1], params), rdata[1], 1.0)
+
fit_objective.initPrint(10)
-
+
params = ba.Parameters()
for name, p in startParams.items():
params.add(name, p[0], min=p[1], max=p[2])
-
+
minimizer = ba.Minimizer()
-
+
result = minimizer.minimize(fit_objective.evaluate, params)
fit_objective.finalize(result)
-
- return { r.name():r.value for r in result.parameters() }
-
-
+ return {r.name(): r.value for r in result.parameters()}
####################################################################
# Main Function #
####################################################################
-
if __name__ == '__main__':
if len(argv) > 1 and argv[1] == "fit":
fixedParams = {
- # parameters can be moved here to keep them fixed
- }
+ # parameters can be moved here to keep them fixed
+ }
startParams = {
- # own starting values
- "q_res":(0.0, 0, 0.1),
- "q_offset":(0, -0.002, 0.002),
-
- "rho_Mafo":(6.3649, 2, 7),
- "rhoM_Mafo":(0, 0, 2),
- "t_Mafo":(150, 60, 180),
-
- "r_Mao":( 1, 0, 12),
- "r_Mafo":(1, 0, 12),
- }
+ # own starting values
+ "q_res": (0.0, 0, 0.1),
+ "q_offset": (0, -0.002, 0.002),
+ "rho_Mafo": (6.3649, 2, 7),
+ "rhoM_Mafo": (0, 0, 2),
+ "t_Mafo": (150, 60, 180),
+ "r_Mao": (1, 0, 12),
+ "r_Mafo": (1, 0, 12),
+ }
fit = True
-
+
else:
startParams = {}
fixedParams = {
- # parameters from our own fit run
- 'q_res': (0.01027065792503683, ),
- 'q_offset': (8.977754679340925e-05, ),
-
- 'rho_Mafo': (6.373962950920891, ),
- 'rhoM_Mafo': (0.2383070807371731, ),
- 't_Mafo': (137.73795730237237, ),
-
- 'r_Mao': (7.004715629445297, ),
- 'r_Mafo': (3.8860835236521702, ),
- }
+ # parameters from our own fit run
+ 'q_res': (0.01027065792503683, ),
+ 'q_offset': (8.977754679340925e-05, ),
+ 'rho_Mafo': (6.373962950920891, ),
+ 'rhoM_Mafo': (0.2383070807371731, ),
+ 't_Mafo': (137.73795730237237, ),
+ 'r_Mao': (7.004715629445297, ),
+ 'r_Mafo': (3.8860835236521702, ),
+ }
fit = False
-
- fixedParams = { d:v[0] for d, v in fixedParams.items() }
- paramsInitial = {d:v[0] for d, v in startParams.items()}
-
- def run_Simulation_pp( qzs, params ):
- return run_simulation(qzs, params,
- polarization = ba.kvector_t(0, 1, 0),
- analyzer = ba.kvector_t(0, 1, 0))
+ fixedParams = {d: v[0] for d, v in fixedParams.items()}
+ paramsInitial = {d: v[0] for d, v in startParams.items()}
+
+ def run_Simulation_pp(qzs, params):
+ return run_simulation(qzs,
+ params,
+ polarization=ba.kvector_t(0, 1, 0),
+ analyzer=ba.kvector_t(0, 1, 0))
- def run_Simulation_mm( qzs, params ):
- return run_simulation(qzs, params,
- polarization = ba.kvector_t(0, -1, 0),
- analyzer = ba.kvector_t(0, -1, 0))
+ def run_Simulation_mm(qzs, params):
+ return run_simulation(qzs,
+ params,
+ polarization=ba.kvector_t(0, -1, 0),
+ analyzer=ba.kvector_t(0, -1, 0))
qzs = numpy.linspace(qmin, qmax, scan_size)
- q_pp, r_pp = qr( run_Simulation_pp( qzs, paramsInitial ) )
- q_mm, r_mm = qr( run_Simulation_mm( qzs, paramsInitial ) )
-
+ q_pp, r_pp = qr(run_Simulation_pp(qzs, paramsInitial))
+ q_mm, r_mm = qr(run_Simulation_mm(qzs, paramsInitial))
+
data_pp, data_mm = get_Experimental_data(qmin, qmax)
-
- plot([q_pp, q_mm], [r_pp, r_mm],
- [data_pp, data_mm], ["$++$", "$--$"],
- f'MAFO_Saturated_initial.pdf' )
-
- plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
+
+ plot([q_pp, q_mm], [r_pp, r_mm], [data_pp, data_mm], ["$++$", "$--$"],
+ f'MAFO_Saturated_initial.pdf')
+
+ plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
"MAFO_Saturated_spin_asymmetry_initial.pdf")
-
+
if fit:
- fitResult = run_fit_ba([data_pp[0], data_mm[0]],
- [data_pp[1], data_mm[1]],
- [run_Simulation_pp, run_Simulation_mm], startParams)
+ fitResult = run_fit_ba([data_pp[0], data_mm[0]], [data_pp[1], data_mm[1]],
+ [run_Simulation_pp, run_Simulation_mm], startParams)
print("Fit Result:")
print(fitResult)
-
- 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' )
-
- plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
+
+ 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')
+
+ plotSpinAsymmetry(data_pp, data_mm, qzs, r_pp, r_mm,
"MAFO_Saturated_spin_asymmetry_fit.pdf")
-
-
diff --git a/Examples/Python/sim21_Reflectometry/PolarizedSpinFlip.py b/Examples/Python/sim21_Reflectometry/PolarizedSpinFlip.py
index 86799d8a01209c410ad2b131447be72b76f1f27d..f0d732b4480b3f0c7ba93caa809778640842ae1b 100644
--- a/Examples/Python/sim21_Reflectometry/PolarizedSpinFlip.py
+++ b/Examples/Python/sim21_Reflectometry/PolarizedSpinFlip.py
@@ -9,23 +9,21 @@ from bornagain import deg, angstrom
import matplotlib.pyplot as plt
+
def get_sample():
"""
Defines sample and returns it
"""
-
+
# parametrize the magnetization
magnetizationMagnitude = 1e8
- angle = 30 * deg
- magnetizationVector = ba.kvector_t(
- magnetizationMagnitude * numpy.sin(angle),
- magnetizationMagnitude * numpy.cos(angle),
- 0)
+ angle = 30 * deg
+ magnetizationVector = ba.kvector_t(magnetizationMagnitude * numpy.sin(angle),
+ magnetizationMagnitude * numpy.cos(angle), 0)
# creating materials
m_ambient = ba.MaterialBySLD("Ambient", 0.0, 0.0)
- m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8,
- magnetizationVector)
+ m_layer_mat = ba.MaterialBySLD("Layer", 1e-4, 1e-8, magnetizationVector)
m_substrate = ba.MaterialBySLD("Substrate", 7e-5, 2e-6)
# creating layers
@@ -47,8 +45,7 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 5.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 5.0 * deg)
simulation.setScan(scan)
return simulation
@@ -71,34 +68,28 @@ def run_simulation(polarization=ba.kvector_t(0, 1, 0),
def plot(data, labels):
-
+
plt.figure()
for d, l in zip(data, labels):
- plt.semilogy( d.axis(),
- d.array(),
- label=l, linewidth=1)
-
- plt.legend( loc='upper right' )
+ plt.semilogy(d.axis(), d.array(), label=l, linewidth=1)
+
+ plt.legend(loc='upper right')
plt.gca().yaxis.set_ticks_position('both')
plt.gca().xaxis.set_ticks_position('both')
-
+
plt.xlabel(r"$\alpha_i$ [deg]")
plt.ylabel("Reflectivity")
-
+
plt.tight_layout()
plt.show()
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))
- 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_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],
+ plot([results_pp, results_mm, results_pm, results_mp],
["$++$", "$--$", "$+-$", "$-+$"])
diff --git a/Examples/Python/sim21_Reflectometry/RoughnessModel.py b/Examples/Python/sim21_Reflectometry/RoughnessModel.py
index fc05f5a3129cda72ba502fe68fca87638392e611..59f3d14324b037e3acefd34c3b176c8bb2b2be02 100644
--- a/Examples/Python/sim21_Reflectometry/RoughnessModel.py
+++ b/Examples/Python/sim21_Reflectometry/RoughnessModel.py
@@ -8,6 +8,7 @@ from matplotlib import pyplot as plt
import bornagain as ba
from bornagain import deg, angstrom, nm
+
def get_sample(roughness_model):
"""
Defines sample and returns it
@@ -36,7 +37,7 @@ def get_sample(roughness_model):
multi_layer.addLayerWithTopRoughness(ti_layer, roughness)
multi_layer.addLayerWithTopRoughness(ni_layer, roughness)
multi_layer.addLayerWithTopRoughness(substrate_layer, roughness)
-
+
multi_layer.setRoughnessModel(roughness_model)
return multi_layer
@@ -47,8 +48,7 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 2.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 2.0 * deg)
simulation.setScan(scan)
return simulation
@@ -65,20 +65,21 @@ def run_simulation(roughness_model=ba.RoughnessModel.TANH):
def plot(result_tanh, result_nevot_croce):
-
- plt.semilogy(result_nevot_croce.axis(), result_nevot_croce.array(),
+
+ plt.semilogy(result_nevot_croce.axis(),
+ result_nevot_croce.array(),
label="Névot-Croce")
plt.semilogy(result_tanh.axis(), result_tanh.array(), label="Tanh")
-
+
plt.xlabel(r'$\alpha_i \; (deg)$', fontsize=12)
plt.ylabel(r'Intensity', fontsize=12)
-
+
plt.legend()
plt.show()
if __name__ == '__main__':
result_tanh = run_simulation(roughness_model=ba.RoughnessModel.TANH)
- result_nevot_croce = run_simulation(
+ result_nevot_croce = run_simulation(
roughness_model=ba.RoughnessModel.NEVOT_CROCE)
plot(result_tanh, result_nevot_croce)
diff --git a/Examples/Python/sim21_Reflectometry/SpecularSimulationWithRoughness.py b/Examples/Python/sim21_Reflectometry/SpecularSimulationWithRoughness.py
index 461545a99b24003715b181112b5b8d8af9f800a8..b3e8863138bd6cf095cc42ae947c1586a321151f 100644
--- a/Examples/Python/sim21_Reflectometry/SpecularSimulationWithRoughness.py
+++ b/Examples/Python/sim21_Reflectometry/SpecularSimulationWithRoughness.py
@@ -44,8 +44,7 @@ def get_simulation(scan_size=500):
Defines and returns a specular simulation.
"""
simulation = ba.SpecularSimulation()
- scan = ba.AngularSpecScan(1.54 * angstrom, scan_size,
- 0.0 * deg, 2.0 * deg)
+ scan = ba.AngularSpecScan(1.54 * angstrom, scan_size, 0.0 * deg, 2.0 * deg)
simulation.setScan(scan)
return simulation
diff --git a/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py b/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
index c401213ac521c676c2660c1de80d17726a549c72..640b83dceca0b0e7828ab42f6ae4b3d123668506 100644
--- a/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
+++ b/Examples/Python/sim22_OffSpecular/BoxesWithSpecularPeak.py
@@ -15,14 +15,15 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 3e-5, 2e-8)
# cylindrical particle
- box_ff = ba.FormFactorBox(5*nm, 5*nm, 10*nm)
+ box_ff = ba.FormFactorBox(5 * nm, 5 * nm, 10 * nm)
box = ba.Particle(m_particle, box_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(box)
# interference function
- interference = ba.InterferenceFunction2DLattice(ba.SquareLattice2D(8*nm, 0*deg))
- pdf = ba.FTDecayFunction2DCauchy(100*nm, 100*nm, 0)
+ interference = ba.InterferenceFunction2DLattice(
+ ba.SquareLattice2D(8 * nm, 0 * deg))
+ pdf = ba.FTDecayFunction2DCauchy(100 * nm, 100 * nm, 0)
interference.setDecayFunction(pdf)
particle_layout.setInterferenceFunction(interference)
@@ -41,9 +42,9 @@ 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)
+ 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)
simulation.getOptions().setUseAvgMaterials(True)
simulation.getOptions().setIncludeSpecular(True)
return simulation
diff --git a/Examples/Python/sim23_SAS/PolarizedSANS.py b/Examples/Python/sim23_SAS/PolarizedSANS.py
index ce4f30ebc72f482284c6dd61f2c16f00f47ec93f..6620a09bd01d2799584827ce4220c9654d10065d 100644
--- a/Examples/Python/sim23_SAS/PolarizedSANS.py
+++ b/Examples/Python/sim23_SAS/PolarizedSANS.py
@@ -16,8 +16,7 @@ def get_sample():
"""
# Defining Materials
mat_solvent = ba.HomogeneousMaterial("Solvent", 5e-6, 0.0)
- mat_core = ba.HomogeneousMaterial("Core", 6e-6, 2e-8,
- magnetization_core)
+ mat_core = ba.HomogeneousMaterial("Core", 6e-6, 2e-8, magnetization_core)
mat_shell = ba.HomogeneousMaterial("Shell", 1e-7, 2e-8)
# Defining Layer
@@ -25,8 +24,8 @@ def get_sample():
# Defining particle layout with a core-shell particle
layout = ba.ParticleLayout()
- core_sphere_ff = ba.FormFactorFullSphere(10*nm)
- shell_sphere_ff = ba.FormFactorFullSphere(12*nm)
+ core_sphere_ff = ba.FormFactorFullSphere(10 * nm)
+ shell_sphere_ff = ba.FormFactorFullSphere(12 * nm)
core = ba.Particle(mat_core, core_sphere_ff)
shell = ba.Particle(mat_shell, shell_sphere_ff)
position = kvector_t(0.0, 0.0, 2.0)
@@ -49,10 +48,11 @@ def get_simulation():
simulation = ba.GISASSimulation()
# Defining detector
- simulation.setDetectorParameters(200, -3.0*deg, 3.0*deg, 200, -3.0*deg, 3.0*deg)
+ simulation.setDetectorParameters(200, -3.0 * deg, 3.0 * deg, 200, -3.0 * deg,
+ 3.0 * deg)
# Defining beam parameters
- simulation.setBeamParameters(0.5*nm, 0.0*deg, 0.0*deg)
+ simulation.setBeamParameters(0.5 * nm, 0.0 * deg, 0.0 * deg)
simulation.setBeamIntensity(1e12)
# Defining beam polarization and polarization analysis for spin-flip channel
@@ -74,7 +74,9 @@ def run_simulation():
return simulation.result()
-if __name__ == '__main__':
+if __name__ == '__main__':
result = run_simulation()
- ba.plot_simulation_result(result, cmap='jet', units=ba.Axes.QSPACE,
+ ba.plot_simulation_result(result,
+ cmap='jet',
+ units=ba.Axes.QSPACE,
aspect='auto')
diff --git a/Examples/Python/sim29_DepthProbe/DepthProbe.py b/Examples/Python/sim29_DepthProbe/DepthProbe.py
index 577293610a824546b5f3b6fa69937cfbf90cf3f6..7126872e21364e67fd442e3f3dec21e88c342b93 100644
--- a/Examples/Python/sim29_DepthProbe/DepthProbe.py
+++ b/Examples/Python/sim29_DepthProbe/DepthProbe.py
@@ -35,7 +35,7 @@ t_TiO2 = 30.0 * angstrom
# beam data
ai_min = 0.0 * deg # minimum incident angle
ai_max = 1.0 * deg # maximum incident angle
-n_ai_bins = 5000 # number of bins in incident angle axis
+n_ai_bins = 5000 # number of bins in incident angle axis
beam_sample_ratio = 0.01 # beam-to-sample size ratio
wl = 10 * angstrom # wavelength in angstroms
diff --git a/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py b/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
index 3f923e86ee0a35726522912458fbe5e36e9d9291..dfa3d4d93b4e8e122aff2787b665f72dbd57d7ae 100644
--- a/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
+++ b/Examples/Python/sim31_Parameterization/AccessingSimulationResults.py
@@ -20,7 +20,7 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
particle_layout = ba.ParticleLayout()
particle_layout.addParticle(cylinder, 1.0)
@@ -40,9 +40,9 @@ def get_simulation():
Returns a GISAXS simulation with beam and detector defined.
"""
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(201, -2.0*deg, 2.0*deg,
- 201, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
+ simulation.setDetectorParameters(201, -2.0 * deg, 2.0 * deg, 201, 0.0 * deg,
+ 2.0 * deg)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * deg, 0.0 * deg)
simulation.setBeamIntensity(1e+05)
return simulation
@@ -55,17 +55,21 @@ def get_noisy_image(hist):
noise_factor = 2.0
for i in range(0, result.getTotalNumberOfBins()):
amplitude = result.binContent(i)
- sigma = noise_factor*math.sqrt(amplitude)
+ sigma = noise_factor * math.sqrt(amplitude)
noisy_amplitude = random.gauss(amplitude, sigma)
result.setBinContent(i, noisy_amplitude)
return result
def plot_histogram(hist, zmin=None, zmax=None):
- ba.plot_histogram(hist, xlabel=r'$\varphi_f ^{\circ}$',
+ ba.plot_histogram(hist,
+ xlabel=r'$\varphi_f ^{\circ}$',
ylabel=r'$\alpha_f ^{\circ}$',
- zlabel="", zmin=zmin, zmax=zmax,
- cmap='jet', aspect='auto')
+ zlabel="",
+ zmin=zmin,
+ zmax=zmax,
+ cmap='jet',
+ aspect='auto')
def get_relative_difference(hist):
@@ -85,15 +89,11 @@ def plot_slices(hist):
# projection along Y, slice at fixed x-value
proj1 = noisy.projectionY(0.0)
- plt.semilogy(proj1.binCenters(),
- proj1.binValues(),
- label=r'$\phi=0.0^{\circ}$')
+ plt.semilogy(proj1.binCenters(), proj1.binValues(), label=r'$\phi=0.0^{\circ}$')
# projection along Y, slice at fixed x-value
proj2 = noisy.projectionY(0.5) # slice at fixed value
- plt.semilogy(proj2.binCenters(),
- proj2.binValues(),
- label=r'$\phi=0.5^{\circ}$')
+ plt.semilogy(proj2.binCenters(), proj2.binValues(), label=r'$\phi=0.5^{\circ}$')
# projection along Y for all X values between [xlow, xup], averaged
proj3 = noisy.projectionY(0.41, 0.59)
@@ -102,7 +102,7 @@ def plot_slices(hist):
label=r'$<\phi>=0.5^{\circ}$')
plt.xlim(proj1.getXmin(), proj1.getXmax())
- plt.ylim(proj2.getMinimum(), proj1.getMaximum()*10.0)
+ plt.ylim(proj2.getMinimum(), proj1.getMaximum() * 10.0)
plt.xlabel(r'$\alpha_f ^{\circ}$', fontsize=16)
plt.legend(loc='upper right')
plt.tight_layout()
diff --git a/Examples/Python/sim31_Parameterization/SimulationParameters.py b/Examples/Python/sim31_Parameterization/SimulationParameters.py
index ad5586ffc84dcf63131da45934648dd00c38c30a..58ce805d58cf59ff2330e1ba217379637893b6aa 100644
--- a/Examples/Python/sim31_Parameterization/SimulationParameters.py
+++ b/Examples/Python/sim31_Parameterization/SimulationParameters.py
@@ -21,9 +21,9 @@ def get_sample():
m_particle = ba.HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nm, 5*nm)
+ cylinder_ff = ba.FormFactorCylinder(5 * nm, 5 * nm)
cylinder = ba.Particle(m_particle, cylinder_ff)
- prism_ff = ba.FormFactorPrism3(5*nm, 5*nm)
+ prism_ff = ba.FormFactorPrism3(5 * nm, 5 * nm)
prism = ba.Particle(m_particle, prism_ff)
layout = ba.ParticleLayout()
@@ -47,9 +47,9 @@ def get_simulation():
Create and return 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.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)
return simulation
@@ -77,21 +77,22 @@ def run_simulation():
# simulation #2
# one sample parameter (cylinder height) is changed using exact parameter name
- simulation.setParameterValue("/GISASSimulation/MultiLayer/Layer0/ParticleLayout"
- "/Particle0/Cylinder/Height", 10.0*nm)
+ simulation.setParameterValue(
+ "/GISASSimulation/MultiLayer/Layer0/ParticleLayout"
+ "/Particle0/Cylinder/Height", 10.0 * nm)
simulation.runSimulation()
results[1] = simulation.result()
# simulation #3
# all parameters matching criteria will be changed (cylinder height in this case)
- simulation.setParameterValue("*/Cylinder/Height", 100.0*nm)
+ simulation.setParameterValue("*/Cylinder/Height", 100.0 * nm)
simulation.runSimulation()
results[2] = simulation.result()
# simulation #4
# all parameters which are matching criteria will be changed
- simulation.setParameterValue("*/Cylinder/Height", 10.0*nm)
- simulation.setParameterValue("*/Prism3/*", 10.0*nm)
+ simulation.setParameterValue("*/Cylinder/Height", 10.0 * nm)
+ simulation.setParameterValue("*/Prism3/*", 10.0 * nm)
simulation.runSimulation()
results[3] = simulation.result()
@@ -107,7 +108,7 @@ def plot(results):
plt.figure(figsize=(12.80, 10.24))
for nplot, hist in results.items():
- plt.subplot(2, 2, nplot+1)
+ plt.subplot(2, 2, nplot + 1)
ba.plot_colormap(hist, zlabel="", cmap='jet', aspect='auto')
plt.tight_layout()
plt.show()
diff --git a/Examples/Python/utils/plot_intensity_data.py b/Examples/Python/utils/plot_intensity_data.py
index 077bdbc2c014527463b4760296f77a0089eeadc2..8f8e8ee8e7a14cfe6593f017b179c80cd7b18145 100755
--- a/Examples/Python/utils/plot_intensity_data.py
+++ b/Examples/Python/utils/plot_intensity_data.py
@@ -10,7 +10,7 @@ import numpy as np
import bornagain as ba
from matplotlib import pyplot as plt
from matplotlib import rc, colors
-rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
+rc('font', **{'family': 'sans-serif', 'sans-serif': ['Helvetica']})
rc('text', usetex=True)
@@ -27,10 +27,12 @@ def plot_intensity_data(file_name, intensity_max=None):
def plot_intensity_data_2d(histogram, intensity_max):
- plot_raw_data_2d(histogram.array(),
- [histogram.getXmin() / ba.deg, histogram.getXmax() / ba.deg,
- histogram.getYmin() / ba.deg, histogram.getYmax() / ba.deg],
- intensity_max)
+ plot_raw_data_2d(histogram.array(), [
+ histogram.getXmin() / ba.deg,
+ histogram.getXmax() / ba.deg,
+ histogram.getYmin() / ba.deg,
+ histogram.getYmax() / ba.deg
+ ], intensity_max)
def plot_raw_data_2d(values, extent_array, intensity_max):
@@ -62,10 +64,10 @@ def plot_raw_data_1d(axis, values, log_y=True):
if __name__ == '__main__':
- if len(sys.argv)<2 or len(sys.argv)>3:
+ if len(sys.argv) < 2 or len(sys.argv) > 3:
exit("Usage: plot_intensity_data.py intensity_file.int.gz [intensity_max]")
- if len(sys.argv)==2:
+ if len(sys.argv) == 2:
plot_intensity_data(sys.argv[1])
else:
plot_intensity_data(sys.argv[1], float(sys.argv[2]))
diff --git a/Examples/Python/utils/plot_intensity_data_diff.py b/Examples/Python/utils/plot_intensity_data_diff.py
index d79dd4ce5c13b5c329df0cd6e21f18f305585175..ceed9162b4aba4a25dbf71fecef97f16ace5247c 100755
--- a/Examples/Python/utils/plot_intensity_data_diff.py
+++ b/Examples/Python/utils/plot_intensity_data_diff.py
@@ -19,12 +19,12 @@ def plot_intensity_data_diff(filename1, filename2):
exit("Both data sets are equal, there is nothing to plot.")
rank = intensity_ref.rank()
if rank == 2:
- pid.plot_raw_data_2d(data,
- [intensity_ref.getXmin() / ba.deg,
- intensity_ref.getXmax() / ba.deg,
- intensity_ref.getYmin() / ba.deg,
- intensity_ref.getYmax() / ba.deg],
- data.max())
+ pid.plot_raw_data_2d(data, [
+ intensity_ref.getXmin() / ba.deg,
+ intensity_ref.getXmax() / ba.deg,
+ intensity_ref.getYmin() / ba.deg,
+ intensity_ref.getYmax() / ba.deg
+ ], data.max())
elif rank == 1:
axis_values = np.asarray(intensity_ref.xAxis().binCenters()) / ba.deg
pid.plot_raw_data_1d(axis_values, data, log_y=False)
@@ -33,7 +33,7 @@ def plot_intensity_data_diff(filename1, filename2):
if __name__ == '__main__':
- if len(sys.argv)!=3:
+ if len(sys.argv) != 3:
exit("Usage: plot_intensity_data_diff.py reference.int.gz other.int.gz")
plot_intensity_data_diff(sys.argv[1], sys.argv[2])
diff --git a/Examples/Python/utils/show2d.py b/Examples/Python/utils/show2d.py
index 73a3d4ec22bcb2ba7dd54af37ec4b1384981565d..1b5bfea82f91403ca231b76ffe71403d3ff4c43f 100755
--- a/Examples/Python/utils/show2d.py
+++ b/Examples/Python/utils/show2d.py
@@ -8,26 +8,27 @@ from matplotlib.colors import LogNorm
import argparse
import os
-
# Define a nice colormap
-cdict = {'red': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
- 'green': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
- 'blue': ((0.0, 0.0, 0.0), (0.5, 1.0, 1.0), (1.0, 1.0, 1.0))}
+cdict = {
+ 'red': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
+ 'green': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (1.0, 1.0, 1.0)),
+ 'blue': ((0.0, 0.0, 0.0), (0.5, 1.0, 1.0), (1.0, 1.0, 1.0))
+}
blue_cmap = matplotlib.colors.LinearSegmentedColormap('blue_map', cdict, 256)
-def PlotNumpyArray(a, zmin = 1, zmax = None):
+def PlotNumpyArray(a, zmin=1, zmax=None):
# Make a plot of the data
#print( "plotting..." )
- amax=a.flatten().max()
- amean=np.sum(a)/a.size
- aminplot=amean**2/amax
- a=np.maximum(a, zmin)
- dataarray=np.flipud(np.transpose(a))
+ amax = a.flatten().max()
+ amean = np.sum(a) / a.size
+ aminplot = amean**2 / amax
+ a = np.maximum(a, zmin)
+ dataarray = np.flipud(np.transpose(a))
plt.xlabel(r'$\phi_f$', fontsize=20)
plt.ylabel(r'$\alpha_f$', fontsize=20)
# Use one of the predefined colormaps or the above defined 'blue_cmap':
- im=plt.imshow(dataarray, norm=LogNorm(), vmax=zmax, cmap=cm.jet)
+ im = plt.imshow(dataarray, norm=LogNorm(), vmax=zmax, cmap=cm.jet)
plt.gca().axes.get_xaxis().set_ticks([])
plt.gca().axes.get_yaxis().set_ticks([])
plt.colorbar(im)
@@ -46,14 +47,22 @@ def PlotNumpyArray(a, zmin = 1, zmax = None):
if __name__ == '__main__':
# Define the arguments to the script
parser = argparse.ArgumentParser(description='Plot 2D data table on log scale.')
- parser.add_argument('-m', '--minz', dest='zmin', metavar='MINZ',
- help='minimum z-value to display [default: 1]',
- default='1')
- parser.add_argument('-M', '--maxz', dest='zmax', metavar='MAXZ',
+ parser.add_argument('-m',
+ '--minz',
+ dest='zmin',
+ metavar='MINZ',
+ help='minimum z-value to display [default: 1]',
+ default='1')
+ parser.add_argument(
+ '-M',
+ '--maxz',
+ dest='zmax',
+ metavar='MAXZ',
help='maximum z-value to display [default: maximum value of data set]',
default=None)
- parser.add_argument('filename', metavar='filename',
- help='filename of the data file')
+ parser.add_argument('filename',
+ metavar='filename',
+ help='filename of the data file')
# Parse the script's arguments
args = parser.parse_args()
@@ -65,8 +74,8 @@ if __name__ == '__main__':
filename = args.filename
# Load the file's data
- print( "loading..." )
- a=np.loadtxt(filename)
+ print("loading...")
+ a = np.loadtxt(filename)
file_no_prefix = os.path.splitext(os.path.basename(filename))[0]
print('Filename: ', file_no_prefix)
print('Data shape: ', a.shape)
diff --git a/Examples/Python/utils/show2d_root.py b/Examples/Python/utils/show2d_root.py
index 10252373a0e67eac77021cf7f118136a6e6208af..777f65f9c441c2a547c8bb48c097e7f42d885627 100755
--- a/Examples/Python/utils/show2d_root.py
+++ b/Examples/Python/utils/show2d_root.py
@@ -10,14 +10,14 @@ import ROOT
from pylab import *
-def PlotNumpyArrayWithROOT(a, zmin = 1, zmax = None):
+def PlotNumpyArrayWithROOT(a, zmin=1, zmax=None):
nx = a.shape[0]
ny = a.shape[1]
- hist = ROOT.TH2D("hist","hist",nx,0,nx, ny, 0, ny)
- for (x,y), value in numpy.ndenumerate(a):
- hist.Fill(x,y,value)
+ hist = ROOT.TH2D("hist", "hist", nx, 0, nx, ny, 0, ny)
+ for (x, y), value in numpy.ndenumerate(a):
+ hist.Fill(x, y, value)
- c1 = ROOT.TCanvas("c1","numpy array", 1024,768)
+ c1 = ROOT.TCanvas("c1", "numpy array", 1024, 768)
c1.SetLogz()
hist.SetMinimum(zmin)
hist.Draw("CONT4Z")
@@ -25,8 +25,8 @@ def PlotNumpyArrayWithROOT(a, zmin = 1, zmax = None):
ROOT.gApplication.Run()
#Interrupt = False
#while not Interrupt:
- #Interrupt = ROOT.gSystem.ProcessEvents()
- #ROOT.gSystem.Sleep(10)
+ #Interrupt = ROOT.gSystem.ProcessEvents()
+ #ROOT.gSystem.Sleep(10)
#-------------------------------------------------------------
@@ -35,14 +35,22 @@ def PlotNumpyArrayWithROOT(a, zmin = 1, zmax = None):
if __name__ == '__main__':
# Define the arguments to the script
parser = argparse.ArgumentParser(description='Plot 2D data table on log scale.')
- parser.add_argument('-m', '--minz', dest='zmin', metavar='MINZ',
- help='minimum z-value to display [default: 1]',
- default='1')
- parser.add_argument('-M', '--maxz', dest='zmax', metavar='MAXZ',
+ parser.add_argument('-m',
+ '--minz',
+ dest='zmin',
+ metavar='MINZ',
+ help='minimum z-value to display [default: 1]',
+ default='1')
+ parser.add_argument(
+ '-M',
+ '--maxz',
+ dest='zmax',
+ metavar='MAXZ',
help='maximum z-value to display [default: maximum value of data set]',
default=None)
- parser.add_argument('filename', metavar='filename',
- help='filename of the data file')
+ parser.add_argument('filename',
+ metavar='filename',
+ help='filename of the data file')
# Parse the script's arguments
args = parser.parse_args()
@@ -54,8 +62,8 @@ if __name__ == '__main__':
filename = args.filename
# Load the file's data
- print( "loading..." )
- a=np.loadtxt(filename)
+ print("loading...")
+ a = np.loadtxt(filename)
file_no_prefix = os.path.splitext(os.path.basename(filename))[0]
print('Filename: ', file_no_prefix)
print('Data shape: ', a.shape)
@@ -63,5 +71,3 @@ if __name__ == '__main__':
print('Maximum value of data: ', a.flatten().max())
PlotNumpyArrayWithROOT(a, zmin, zmax)
-
-
diff --git a/Tests/Functional/Python/PyCore/histogram2d.py b/Tests/Functional/Python/PyCore/histogram2d.py
index 6249360b0ae94037d455d908a10d1e6865a0facc..b1756c525e970b86b9c508a2033dcd591e507060 100644
--- a/Tests/Functional/Python/PyCore/histogram2d.py
+++ b/Tests/Functional/Python/PyCore/histogram2d.py
@@ -3,16 +3,15 @@ import numpy, os, sys, unittest
sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
-class Histogram2DTest(unittest.TestCase):
+class Histogram2DTest(unittest.TestCase):
def test_constructFromNumpyInt(self):
"""
Testing construction of 2D histogram from numpy array.
Automatic conversion under Python3 is not working, that's why it is float64 and not int64
"""
- arr = numpy.array([[ 1, 2, 3, 4, 5],
- [ 6, 7, 8, 9, 10],
- [11, 12, 13, 14, 15]], numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5], [6, 7, 8, 9, 10], [11, 12, 13, 14, 15]],
+ numpy.float64)
hist = ba.Histogram2D(arr)
self.assertEqual(hist.getNbinsX(), 5)
@@ -36,9 +35,9 @@ class Histogram2DTest(unittest.TestCase):
"""
Testing construction of 2D histogram from numpy array
"""
- arr = numpy.array([[ 1.0, 2.0, 3.0, 4.0, 5.0],
- [ 6.0, 7.0, 8.0, 9.0, 10.0],
- [11.0, 12.0, 13.0, 14.0, 15.0]], dtype=numpy.float64)
+ arr = numpy.array([[1.0, 2.0, 3.0, 4.0, 5.0], [6.0, 7.0, 8.0, 9.0, 10.0],
+ [11.0, 12.0, 13.0, 14.0, 15.0]],
+ dtype=numpy.float64)
hist = ba.Histogram2D(arr)
self.assertEqual(hist.getNbinsX(), 5)
@@ -62,9 +61,8 @@ class Histogram2DTest(unittest.TestCase):
"""
Adding to the histogram content from numpy array
"""
- arr = numpy.array([[ 1, 2, 3, 4, 5],
- [ 6, 7, 8, 9, 10],
- [11, 12, 13, 14, 15]], dtype=numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5], [6, 7, 8, 9, 10], [11, 12, 13, 14, 15]],
+ dtype=numpy.float64)
print(type(arr))
hist = ba.Histogram2D(arr)
# adding same content once again
@@ -72,22 +70,22 @@ class Histogram2DTest(unittest.TestCase):
arr_from_hist = hist.getArray()
for (x, y), element in numpy.ndenumerate(arr):
- self.assertEqual(element*2.0, arr_from_hist[x][y])
+ self.assertEqual(element * 2.0, arr_from_hist[x][y])
def test_constructAndAddFromNumpyDouble(self):
"""
Adding to the histogram content from numpy array
"""
- arr = numpy.array([[ 1.0, 2.0, 3.0, 4.0, 5.0],
- [ 6.0, 7.0, 8.0, 9.0, 10.0],
- [11.0, 12.0, 13.0, 14.0, 15.0]], dtype=numpy.float64)
+ arr = numpy.array([[1.0, 2.0, 3.0, 4.0, 5.0], [6.0, 7.0, 8.0, 9.0, 10.0],
+ [11.0, 12.0, 13.0, 14.0, 15.0]],
+ dtype=numpy.float64)
hist = ba.Histogram2D(arr)
# adding same content once again
hist.addContent(arr)
arr_from_hist = hist.getArray()
for (x, y), element in numpy.ndenumerate(arr):
- self.assertEqual(element*2.0, arr_from_hist[x][y])
+ self.assertEqual(element * 2.0, arr_from_hist[x][y])
def create_histogram(self, arr):
"""
@@ -99,9 +97,8 @@ class Histogram2DTest(unittest.TestCase):
"""
Testing newly create object
"""
- arr = numpy.array([[ 1, 2, 3, 4, 5],
- [ 6, 7, 8, 9, 10],
- [11, 12, 13, 14, 15]], dtype=numpy.float64)
+ arr = numpy.array([[1, 2, 3, 4, 5], [6, 7, 8, 9, 10], [11, 12, 13, 14, 15]],
+ dtype=numpy.float64)
hist = self.create_histogram(arr)
arr_from_hist = hist.getArray()
@@ -112,9 +109,9 @@ class Histogram2DTest(unittest.TestCase):
"""
Testing newly create object
"""
- arr = numpy.array([[ 1.0, 2.0, 3.0, 4.0, 5.0],
- [ 6.0, 7.0, 8.0, 9.0, 10.0],
- [11.0, 12.0, 13.0, 14.0, 15.0]], dtype=numpy.float64)
+ arr = numpy.array([[1.0, 2.0, 3.0, 4.0, 5.0], [6.0, 7.0, 8.0, 9.0, 10.0],
+ [11.0, 12.0, 13.0, 14.0, 15.0]],
+ dtype=numpy.float64)
hist = self.create_histogram(arr)
arr_from_hist = hist.getArray()
diff --git a/Tests/Functional/Python/PyCore/intensitydata.py b/Tests/Functional/Python/PyCore/intensitydata.py
index 9aef58b5ea8aae44c908a0e977fe4630c7a634d9..2b52c4e84830a758aec53537335e20210bf0ae94 100644
--- a/Tests/Functional/Python/PyCore/intensitydata.py
+++ b/Tests/Functional/Python/PyCore/intensitydata.py
@@ -51,7 +51,7 @@ class IntensityDataTest(unittest.TestCase):
data.setAllTo(1.0)
self.assertEqual(200.0, data.totalSum())
for i in range(0, data.getAllocatedSize()):
- data[i] = data[i]*-1.0
+ data[i] = data[i] * -1.0
self.assertEqual(-200.0, data.totalSum())
def test_access_simulation_intensity(self):
diff --git a/Tests/Functional/Python/PyCore/intensitydata_io.py b/Tests/Functional/Python/PyCore/intensitydata_io.py
index f764771c8484075f7d83d0eebb197507748dff93..13e804c6d66c4d154387d546298ab66272c9949d 100644
--- a/Tests/Functional/Python/PyCore/intensitydata_io.py
+++ b/Tests/Functional/Python/PyCore/intensitydata_io.py
@@ -6,6 +6,7 @@ sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
from bornagain import degree, deg2rad, rad2deg
+
def fill_data(data):
"""
Fills intensity data with some numbers
@@ -13,6 +14,7 @@ def fill_data(data):
for i in range(0, data.getAllocatedSize()):
data[i] = i
+
def is_the_same_data(data1, data2):
"""
Checks if two data are identical
@@ -29,16 +31,17 @@ def is_the_same_data(data1, data2):
return False
return True
+
def get_boundaries_flat_in_sin(nbins, start, end):
"""
Returns flat_in_sin binning of angle axis
"""
result = []
- start_sin = math.sin( deg2rad(start))
- end_sin = math.sin( deg2rad(end))
- step = (end_sin - start_sin)/nbins
- for i in range(0, nbins+1):
- result.append( rad2deg(math.asin(start_sin + step*i)))
+ start_sin = math.sin(deg2rad(start))
+ end_sin = math.sin(deg2rad(end))
+ step = (end_sin - start_sin) / nbins
+ for i in range(0, nbins + 1):
+ result.append(rad2deg(math.asin(start_sin + step * i)))
return result
@@ -75,7 +78,9 @@ 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, -5.0, 5.0)))
+ data.addAxis(
+ ba.VariableBinAxis("axis0", 10,
+ get_boundaries_flat_in_sin(10, -5.0, 5.0)))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -83,8 +88,11 @@ 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, -5.0, 5.0)))
- data.addAxis(ba.VariableBinAxis("axis1", 3, get_boundaries_flat_in_sin(3, 0.0, 2.0)))
+ data.addAxis(
+ ba.VariableBinAxis("axis0", 10,
+ get_boundaries_flat_in_sin(10, -5.0, 5.0)))
+ data.addAxis(
+ ba.VariableBinAxis("axis1", 3, get_boundaries_flat_in_sin(3, 0.0, 2.0)))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -93,7 +101,8 @@ class OutputDataIOTest(unittest.TestCase):
def test_06_VariableAndFixedMix(self):
data = ba.IntensityData()
data.addAxis(ba.FixedBinAxis("axis0", 10, -5.0, 5.0))
- data.addAxis(ba.VariableBinAxis("axis1", 3, get_boundaries_flat_in_sin(3, 0.0, 2.0)))
+ data.addAxis(
+ ba.VariableBinAxis("axis1", 3, get_boundaries_flat_in_sin(3, 0.0, 2.0)))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -101,8 +110,9 @@ class OutputDataIOTest(unittest.TestCase):
def test_07_ConstKBinAxis_2D(self):
data = ba.IntensityData()
- data.addAxis(ba.ConstKBinAxis("axis0", 9, -1.00000001*degree, 1.0*degree))
- data.addAxis(ba.ConstKBinAxis("axis1", 3, -4.0*degree, 5.0*degree))
+ data.addAxis(ba.ConstKBinAxis("axis0", 9, -1.00000001 * degree,
+ 1.0 * degree))
+ data.addAxis(ba.ConstKBinAxis("axis1", 3, -4.0 * degree, 5.0 * degree))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -110,8 +120,9 @@ class OutputDataIOTest(unittest.TestCase):
def test_08_CustomBinAxis_2D(self):
data = ba.IntensityData()
- data.addAxis(ba.CustomBinAxis("axis0", 9, -1.00000001*degree, 1.0*degree))
- data.addAxis(ba.CustomBinAxis("axis1", 3, -4.0*degree, 5.0*degree))
+ data.addAxis(ba.CustomBinAxis("axis0", 9, -1.00000001 * degree,
+ 1.0 * degree))
+ data.addAxis(ba.CustomBinAxis("axis1", 3, -4.0 * degree, 5.0 * degree))
fill_data(data)
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.int")
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.int")
@@ -146,25 +157,20 @@ class OutputDataIOTest(unittest.TestCase):
self.assertTrue(is_the_same_data(data, newdata))
def test_SaveNumpyArray_ReadOutputData(self):
- arr = numpy.array([
- [0.0, 1.0, 2.0, 3.0],
- [4.0, 5.0, 6.0, 7.0],
- [8.0, 9.0, 10.0, 11.0]
- ])
+ arr = numpy.array([[0.0, 1.0, 2.0, 3.0], [4.0, 5.0, 6.0, 7.0],
+ [8.0, 9.0, 10.0, 11.0]])
numpy.savetxt('tmp.txt', arr)
newdata = ba.IntensityDataIOFactory.readOutputData("tmp.txt")
- self.assertTrue(numpy.array_equal(newdata.getArray(),arr))
+ self.assertTrue(numpy.array_equal(newdata.getArray(), arr))
def test_SaveNumpyArray_ReadRawDataVector(self):
- arr = numpy.array([
- [0.0, 1.0, 2.0, 3.0],
- [4.0, 5.0, 6.0, 7.0],
- [8.0, 9.0, 10.0, 11.0]
- ])
+ arr = numpy.array([[0.0, 1.0, 2.0, 3.0], [4.0, 5.0, 6.0, 7.0],
+ [8.0, 9.0, 10.0, 11.0]])
numpy.savetxt('tmp.txt', arr)
- newdata = numpy.array(ba.IntensityDataIOFactory.readOutputData("tmp.txt").getRawDataVector())
- expected = numpy.array([8.,4.,0.,9.,5.,1.,10.,6.,2.,11.,7.,3.])
- self.assertTrue(numpy.array_equal(newdata,expected))
+ newdata = numpy.array(
+ ba.IntensityDataIOFactory.readOutputData("tmp.txt").getRawDataVector())
+ expected = numpy.array([8., 4., 0., 9., 5., 1., 10., 6., 2., 11., 7., 3.])
+ self.assertTrue(numpy.array_equal(newdata, expected))
def test_SaveOutputData_ReadNumpyArray(self):
data = ba.IntensityData()
@@ -175,7 +181,7 @@ class OutputDataIOTest(unittest.TestCase):
ba.IntensityDataIOFactory.writeOutputData(data, "tmp.txt")
arr = numpy.loadtxt("tmp.txt")
- self.assertTrue(numpy.array_equal(data.getArray(),arr))
+ self.assertTrue(numpy.array_equal(data.getArray(), arr))
if __name__ == '__main__':
diff --git a/Tests/Functional/Python/PyCore/mesocrystal1.py b/Tests/Functional/Python/PyCore/mesocrystal1.py
index 484bee4064e93f63782db68c8419e808dd27e894..a2ee892f8a56680656fe37628926f6b925267def 100644
--- a/Tests/Functional/Python/PyCore/mesocrystal1.py
+++ b/Tests/Functional/Python/PyCore/mesocrystal1.py
@@ -7,6 +7,7 @@ import ctypes, math, numpy, os, sys, time
import utils
from bornagain import *
+
# ----------------------------------------------------------------------------
# Sample builder to build mixture of cylinders and prisms on top of substrate
# ----------------------------------------------------------------------------
@@ -15,41 +16,60 @@ class MySampleBuilder(ISampleBuilder):
ISampleBuilder.__init__(self)
self.sample = None
# parameters describing the sample
- self.lattice_length_a = ctypes.c_double(6.2091e+00*nm)
- self.lattice_length_c = ctypes.c_double(6.5677e+00*nm)
- self.nanoparticle_radius = ctypes.c_double(4.6976e+00*nm)
- self.sigma_nanoparticle_radius = ctypes.c_double(3.6720e-01*nm)
- self.meso_height = ctypes.c_double(1.1221e+02*nm)
- self.meso_radius = ctypes.c_double(9.4567e+02*nm)
- self.sigma_lattice_length_a = ctypes.c_double(1.1601e+00*nm)
+ self.lattice_length_a = ctypes.c_double(6.2091e+00 * nm)
+ self.lattice_length_c = ctypes.c_double(6.5677e+00 * nm)
+ self.nanoparticle_radius = ctypes.c_double(4.6976e+00 * nm)
+ self.sigma_nanoparticle_radius = ctypes.c_double(3.6720e-01 * nm)
+ self.meso_height = ctypes.c_double(1.1221e+02 * nm)
+ self.meso_radius = ctypes.c_double(9.4567e+02 * nm)
+ self.sigma_lattice_length_a = ctypes.c_double(1.1601e+00 * nm)
self.surface_filling_ratio = ctypes.c_double(1.7286e-01)
- self.roughness = ctypes.c_double(2.8746e+01*nm)
+ self.roughness = ctypes.c_double(2.8746e+01 * nm)
# register parameters
- self.registerParameter("lattice_length_a", ctypes.addressof(self.lattice_length_a)).setUnit("nm").setNonnegative()
- self.registerParameter("lattice_length_c", ctypes.addressof(self.lattice_length_c)).setUnit("nm").setNonnegative()
- self.registerParameter("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()
- self.registerParameter("sigma_lattice_length_a", ctypes.addressof(self.sigma_lattice_length_a)).setUnit("nm").setNonnegative()
- self.registerParameter("surface_filling_ratio", ctypes.addressof(self.surface_filling_ratio) ).setNonnegative()
- self.registerParameter("roughness", ctypes.addressof(self.roughness)).setUnit("nm").setNonnegative()
+ self.registerParameter(
+ "lattice_length_a",
+ ctypes.addressof(self.lattice_length_a)).setUnit("nm").setNonnegative()
+ self.registerParameter(
+ "lattice_length_c",
+ ctypes.addressof(self.lattice_length_c)).setUnit("nm").setNonnegative()
+ self.registerParameter(
+ "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()
+ self.registerParameter(
+ "sigma_lattice_length_a", ctypes.addressof(
+ self.sigma_lattice_length_a)).setUnit("nm").setNonnegative()
+ self.registerParameter("surface_filling_ratio",
+ ctypes.addressof(
+ self.surface_filling_ratio)).setNonnegative()
+ self.registerParameter("roughness", ctypes.addressof(
+ self.roughness)).setUnit("nm").setNonnegative()
# -------------------------------------------------------------------------
# constructs the sample for current values of parameters
# -------------------------------------------------------------------------
def buildSample(self):
- surface_density = self.surface_filling_ratio.value/numpy.pi/self.meso_radius.value/self.meso_radius.value
- 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))
- n_particle_adapted = complex(numpy.sqrt(n_avg*n_avg + n_particle*n_particle - 1.0))
+ surface_density = self.surface_filling_ratio.value / numpy.pi / self.meso_radius.value / self.meso_radius.value
+ 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))
+ n_particle_adapted = complex(
+ numpy.sqrt(n_avg * n_avg + n_particle * n_particle - 1.0))
ff = FormFactorCylinder(self.meso_radius.value, self.meso_height.value)
# Create multilayer
p_multi_layer = MultiLayer()
n_air = complex(1.0, 0.0)
- n_substrate = complex(1.0-7.57e-6, 1.73e-7)
+ 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)
@@ -62,25 +82,28 @@ class MySampleBuilder(ISampleBuilder):
n_max_phi_rotation_steps = 2
n_alpha_rotation_steps = 1
- alpha_step = 5.0*deg/n_alpha_rotation_steps
- alpha_start = - (n_alpha_rotation_steps/2.0)*alpha_step
+ alpha_step = 5.0 * deg / n_alpha_rotation_steps
+ alpha_start = -(n_alpha_rotation_steps / 2.0) * alpha_step
- phi_step = 2*numpy.pi/3.0/n_max_phi_rotation_steps
+ phi_step = 2 * numpy.pi / 3.0 / n_max_phi_rotation_steps
phi_start = 0.0
for i in range(0, n_max_phi_rotation_steps):
for j in range(0, n_alpha_rotation_steps):
- total_transform = RotationZ(phi_start + i*phi_step)
- meso = self.createMesoCrystal(self.lattice_length_a.value, self.lattice_length_c.value, n_particle_adapted, ff)
+ total_transform = RotationZ(phi_start + i * phi_step)
+ meso = self.createMesoCrystal(self.lattice_length_a.value,
+ self.lattice_length_c.value,
+ n_particle_adapted, ff)
meso.setPosition(0.0, 0.0, -self.meso_height.value)
- particle_layout.addParticle(meso, 1.0, kvector_t(0,0,0), total_transform)
+ particle_layout.addParticle(meso, 1.0, kvector_t(0, 0, 0),
+ total_transform)
particle_layout.setTotalParticleSurfaceDensity(surface_density)
particle_layout.setInterferenceFunction(p_interference_function)
avg_layer.addLayout(particle_layout)
- roughness = LayerRoughness(self.roughness.value, 0.3, 500.0*nm)
+ roughness = LayerRoughness(self.roughness.value, 0.3, 500.0 * nm)
p_multi_layer.addLayer(vacuum_layer)
p_multi_layer.addLayer(avg_layer)
@@ -91,24 +114,26 @@ class MySampleBuilder(ISampleBuilder):
# -------------------------------------------------------------------------
# building meso crystal
# -------------------------------------------------------------------------
- def createMesoCrystal(self,stacking_radius_a, stacking_radius_c, n_particle, p_meso_form_factor):
+ def createMesoCrystal(self, stacking_radius_a, stacking_radius_c, n_particle,
+ p_meso_form_factor):
- mParticle = HomogeneousMaterial("Particle", n_particle )
+ mParticle = HomogeneousMaterial("Particle", n_particle)
p_lat = self.createLattice(stacking_radius_a, stacking_radius_c)
bas_a = p_lat.getBasisVectorA()
bas_b = p_lat.getBasisVectorB()
bas_c = p_lat.getBasisVectorC()
- ff = FormFactorSphereGaussianRadius(self.nanoparticle_radius.value, self.sigma_nanoparticle_radius.value)
- particle = Particle(mParticle, ff )
+ ff = FormFactorSphereGaussianRadius(self.nanoparticle_radius.value,
+ self.sigma_nanoparticle_radius.value)
+ particle = Particle(mParticle, ff)
position_0 = kvector_t(0.0, 0.0, 0.0)
- position_1 = 1.0/3.0*(2.0*bas_a + bas_b + bas_c)
- position_2 = 1.0/3.0*(bas_a + 2.0*bas_b + 2.0*bas_c)
- positions = [ position_0, position_1, position_2 ]
+ position_1 = 1.0 / 3.0 * (2.0 * bas_a + bas_b + bas_c)
+ position_2 = 1.0 / 3.0 * (bas_a + 2.0 * bas_b + 2.0 * bas_c)
+ positions = [position_0, position_1, position_2]
basis = ParticleComposition()
basis.addParticles(particle, positions)
- position_variance = self.sigma_lattice_length_a.value*self.sigma_lattice_length_a.value/3.0
+ position_variance = self.sigma_lattice_length_a.value * self.sigma_lattice_length_a.value / 3.0
npc = Crystal(basis, p_lat, position_variance)
meso = MesoCrystal(npc, p_meso_form_factor)
return meso
@@ -117,7 +142,8 @@ class MySampleBuilder(ISampleBuilder):
# create lattice
# -------------------------------------------------------------------------
def createLattice(self, stacking_radius_a, stacking_radius_c):
- result = HexagonalLattice(stacking_radius_a*2.0, stacking_radius_c*2.0*2.3)
+ result = HexagonalLattice(stacking_radius_a * 2.0,
+ stacking_radius_c * 2.0 * 2.3)
result.setSelectionRule(SimpleSelectionRule(-1, 1, 1, 3))
return result
@@ -129,7 +155,7 @@ def runTest():
# setting simulation
sample_builder = MySampleBuilder()
simulation = createSimulation()
- simulation.setSampleBuilder( sample_builder )
+ simulation.setSampleBuilder(sample_builder)
reference = utils.get_reference_data("mesocrystal01_reference.int.gz")
@@ -147,9 +173,10 @@ def runTest():
# create simulation
def createSimulation():
simulation = GISASSimulation()
- simulation.setBeamParameters(1.77*angstrom, 0.4*deg, 0.0*deg)
+ simulation.setBeamParameters(1.77 * angstrom, 0.4 * deg, 0.0 * deg)
simulation.setBeamIntensity(5.0090e+12)
- simulation.setDetectorParameters(50, 0.2*deg, 2.5*deg, 50, 0.0*deg, 2.5*deg)
+ simulation.setDetectorParameters(50, 0.2 * deg, 2.5 * deg, 50, 0.0 * deg,
+ 2.5 * deg)
return simulation
diff --git a/Tests/Functional/Python/PyCore/parameterpool.py b/Tests/Functional/Python/PyCore/parameterpool.py
index 6f03869afe9d9983f15b39befe87b9396a85905f..3afeae72925d82db8d1c3693417a3009e619bb20 100644
--- a/Tests/Functional/Python/PyCore/parameterpool.py
+++ b/Tests/Functional/Python/PyCore/parameterpool.py
@@ -6,12 +6,11 @@ from bornagain import nm
class ParameterPoolTest(unittest.TestCase):
-
def test_parameterPoolAccess(self):
"""
Checks values in particle's parameter pool
"""
- ff = ba.FormFactorCylinder(5*nm, 6*nm)
+ ff = ba.FormFactorCylinder(5 * nm, 6 * nm)
particle = ba.Particle(ba.HomogeneousMaterial("Vacuum", 0.0, 0.0), ff)
particle.setAbundance(1.0)
particle.setPosition(2.0, 3.0, 4.0)
@@ -21,9 +20,15 @@ class ParameterPoolTest(unittest.TestCase):
pool = particle.parameterPool()
self.assertEqual(pool.size(), 4)
- self.assertEqual(pool.parameterNames(), ('Abundance', 'PositionX', 'PositionY', 'PositionZ'))
-
- expected = {'Abundance': 1.0, 'PositionX': 2.0, 'PositionY': 3.0, 'PositionZ': 4.0}
+ self.assertEqual(pool.parameterNames(),
+ ('Abundance', 'PositionX', 'PositionY', 'PositionZ'))
+
+ expected = {
+ 'Abundance': 1.0,
+ 'PositionX': 2.0,
+ 'PositionY': 3.0,
+ 'PositionZ': 4.0
+ }
for par in pool:
print(par.value(), par.getName(), par.limits().toString())
self.assertEqual(par.value(), expected[par.getName()])
@@ -32,7 +37,7 @@ class ParameterPoolTest(unittest.TestCase):
"""
Modification of particle parameters via parameter pool
"""
- ff = ba.FormFactorCylinder(5*nm, 6*nm)
+ ff = ba.FormFactorCylinder(5 * nm, 6 * nm)
particle = ba.Particle(ba.HomogeneousMaterial("Vacuum", 0.0, 0.0), ff)
particle.setAbundance(1.0)
particle.setPosition(2.0, 3.0, 4.0)
@@ -42,7 +47,12 @@ class ParameterPoolTest(unittest.TestCase):
pool[1].setValue(20.0) # PositionX
pool.parameter('PositionY').setValue(30.0)
- expected = {'Abundance': 10.0, 'PositionX': 20.0, 'PositionY': 30.0, 'PositionZ': 4.0}
+ expected = {
+ 'Abundance': 10.0,
+ 'PositionX': 20.0,
+ 'PositionY': 30.0,
+ 'PositionZ': 4.0
+ }
for par in pool:
self.assertEqual(par.value(), expected[par.getName()])
@@ -52,16 +62,21 @@ class ParameterPoolTest(unittest.TestCase):
Checks values in particle's parameter tree. Parameter tree is a pool with parameters of
particle and its children (in given case, form factor of cylinder)
"""
- ff = ba.FormFactorCylinder(5*nm, 6*nm)
+ ff = ba.FormFactorCylinder(5 * nm, 6 * nm)
particle = ba.Particle(ba.HomogeneousMaterial("Vacuum", 0.0, 0.0), ff)
particle.setAbundance(1.0)
particle.setPosition(2.0, 3.0, 4.0)
pool = particle.createParameterTree()
- expected = {'/Particle/Abundance': 1.0, '/Particle/PositionX': 2.0,
- '/Particle/PositionY': 3.0, '/Particle/PositionZ': 4.0,
- '/Particle/Cylinder/Radius': 5.0, '/Particle/Cylinder/Height': 6.0}
+ expected = {
+ '/Particle/Abundance': 1.0,
+ '/Particle/PositionX': 2.0,
+ '/Particle/PositionY': 3.0,
+ '/Particle/PositionZ': 4.0,
+ '/Particle/Cylinder/Radius': 5.0,
+ '/Particle/Cylinder/Height': 6.0
+ }
for par in pool:
self.assertEqual(par.value(), expected[par.getName()])
@@ -70,7 +85,7 @@ class ParameterPoolTest(unittest.TestCase):
"""
Modifies values of particle's parameter tree.
"""
- ff = ba.FormFactorCylinder(5*nm, 6*nm)
+ ff = ba.FormFactorCylinder(5 * nm, 6 * nm)
particle = ba.Particle(ba.HomogeneousMaterial("Vacuum", 0.0, 0.0), ff)
particle.setAbundance(1.0)
particle.setPosition(2.0, 3.0, 4.0)
@@ -84,9 +99,14 @@ class ParameterPoolTest(unittest.TestCase):
pool.parameter('/Particle/PositionY').setValue(30.0)
pool.setMatchedParametersValue('*Cylinder*', 50.0)
- expected = {'/Particle/Abundance': 10.0, '/Particle/PositionX': 20.0,
- '/Particle/PositionY': 30.0, '/Particle/PositionZ': 4.0,
- '/Particle/Cylinder/Radius': 50.0, '/Particle/Cylinder/Height': 50.0}
+ expected = {
+ '/Particle/Abundance': 10.0,
+ '/Particle/PositionX': 20.0,
+ '/Particle/PositionY': 30.0,
+ '/Particle/PositionZ': 4.0,
+ '/Particle/Cylinder/Radius': 50.0,
+ '/Particle/Cylinder/Height': 50.0
+ }
for par in pool:
self.assertEqual(par.value(), expected[par.getName()])
@@ -95,7 +115,7 @@ class ParameterPoolTest(unittest.TestCase):
"""
Modification of particle's parameters without intermediate access to parameter pool
"""
- ff = ba.FormFactorCylinder(5*nm, 6*nm)
+ ff = ba.FormFactorCylinder(5 * nm, 6 * nm)
particle = ba.Particle(ba.HomogeneousMaterial("Vacuum", 0.0, 0.0), ff)
particle.setAbundance(1.0)
particle.setPosition(2.0, 3.0, 4.0)
diff --git a/Tests/Functional/Python/PyCore/polmagcylinders1.py b/Tests/Functional/Python/PyCore/polmagcylinders1.py
index e848cf6d29754314e4d5728d1f0723eefc564a66..2e315e3aebd1143dec0c4a6234927aa25d311c8c 100644
--- a/Tests/Functional/Python/PyCore/polmagcylinders1.py
+++ b/Tests/Functional/Python/PyCore/polmagcylinders1.py
@@ -16,9 +16,9 @@ def runSimulation():
magnetic_field = ba.kvector_t(0, 0, 0)
- magParticle = ba.HomogeneousMaterial("magParticle", 6e-4, 2e-8, magnetic_field )
+ magParticle = ba.HomogeneousMaterial("magParticle", 6e-4, 2e-8, magnetic_field)
# collection of particles
- cylinder_ff = ba.FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder_ff = ba.FormFactorCylinder(5 * nanometer, 5 * nanometer)
cylinder = ba.Particle(magParticle, cylinder_ff)
particle_layout = ba.ParticleLayout()
@@ -36,8 +36,9 @@ def runSimulation():
# build and run experiment
simulation = ba.GISASSimulation()
- simulation.setDetectorParameters(100, 0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setDetectorParameters(100, 0 * degree, 2.0 * degree, 100,
+ 0.0 * degree, 2.0 * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setSample(multi_layer)
simulation.setBeamIntensity(1e2)
simulation.runSimulation()
@@ -65,5 +66,5 @@ def run_test():
if __name__ == '__main__':
name, description, diff, status = run_test()
print(name, description, diff, status)
- if("FAILED" in status):
+ if ("FAILED" in status):
exit(1)
diff --git a/Tests/Functional/Python/PyCore/polmagcylinders2.py b/Tests/Functional/Python/PyCore/polmagcylinders2.py
index 6864e65b63e4a0c93b760f322639e907c7bc6af9..097fa5b618c441510ed4e43bbe6f2a81124c8f8d 100644
--- a/Tests/Functional/Python/PyCore/polmagcylinders2.py
+++ b/Tests/Functional/Python/PyCore/polmagcylinders2.py
@@ -10,6 +10,7 @@ from bornagain import *
REFERENCE_DIR = "@TEST_REFERENCE_DIR@/Python"
+
# ----------------------------------
# describe sample and run simulation
# ----------------------------------
@@ -21,9 +22,9 @@ def getSimulationIntensity(rho_beam, efficiency):
magnetization = kvector_t(0, 1e6, 0)
- magParticle = HomogeneousMaterial("magParticle", 5e-6, 0.0, magnetization )
+ magParticle = HomogeneousMaterial("magParticle", 5e-6, 0.0, magnetization)
# collection of particles
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder_ff = FormFactorCylinder(5 * nanometer, 5 * nanometer)
cylinder = Particle(magParticle, cylinder_ff)
particle_layout = ParticleLayout()
@@ -41,10 +42,11 @@ def getSimulationIntensity(rho_beam, efficiency):
# build and run experiment
simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -1*degree, 1.0*degree, 100, 0.0*degree, 2.0*degree)
+ simulation.setDetectorParameters(100, -1 * degree, 1.0 * degree, 100,
+ 0.0 * degree, 2.0 * degree)
zplus = kvector_t(0.0, 0.0, 1.0)
simulation.setAnalyzerProperties(zplus, efficiency, 0.5)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
simulation.setBeamPolarization(rho_beam)
simulation.setSample(multi_layer)
simulation.setBeamIntensity(1e9)
@@ -58,12 +60,13 @@ def get_reference_data(filename):
"""
read and return reference data from file
"""
- path = os.path.join(REFERENCE_DIR,filename)
+ path = os.path.join(REFERENCE_DIR, filename)
print("- read reference from", path, flush=True)
ret = IntensityDataIOFactory.readIntensityData(path)
print("- - reference read", flush=True)
return ret
+
# --------------------------------------------------------------
# run test and analyse test results
# --------------------------------------------------------------
@@ -77,14 +80,18 @@ def run_test():
# IntensityDataIOFactory.writeIntensityData(getSimulationIntensity(zmin, 1.0), 'polmagcylinders2_reference_10.int')
# IntensityDataIOFactory.writeIntensityData(getSimulationIntensity(zmin, -1.0), 'polmagcylinders2_reference_11.int')
diff = 0.0
- diff += get_difference(getSimulationIntensity(zplus, 1.0).array(),
- get_reference_data('polmagcylinders2_reference_00.int.gz').getArray())
- diff += get_difference(getSimulationIntensity(zplus, -1.0).array(),
- get_reference_data('polmagcylinders2_reference_01.int.gz').getArray())
- diff += get_difference(getSimulationIntensity(zmin, 1.0).array(),
- get_reference_data('polmagcylinders2_reference_10.int.gz').getArray())
- diff += get_difference(getSimulationIntensity(zmin, -1.0).array(),
- get_reference_data('polmagcylinders2_reference_11.int.gz').getArray())
+ diff += get_difference(
+ getSimulationIntensity(zplus, 1.0).array(),
+ get_reference_data('polmagcylinders2_reference_00.int.gz').getArray())
+ diff += get_difference(
+ getSimulationIntensity(zplus, -1.0).array(),
+ get_reference_data('polmagcylinders2_reference_01.int.gz').getArray())
+ diff += get_difference(
+ getSimulationIntensity(zmin, 1.0).array(),
+ get_reference_data('polmagcylinders2_reference_10.int.gz').getArray())
+ diff += get_difference(
+ getSimulationIntensity(zmin, -1.0).array(),
+ get_reference_data('polmagcylinders2_reference_11.int.gz').getArray())
diff /= 4.0
status = "OK"
@@ -96,5 +103,5 @@ def run_test():
if __name__ == '__main__':
name, description, diff, status = run_test()
print(name, description, diff, status)
- if("FAILED" in status):
+ if ("FAILED" in status):
exit(1)
diff --git a/Tests/Functional/Python/PyCore/samplebuilder.py b/Tests/Functional/Python/PyCore/samplebuilder.py
index 83c9d8d8dc43058bb5af1ad2c05a49dcdc42d80f..0333dc8abe316ea747ad74b272579e4ef84930d8 100644
--- a/Tests/Functional/Python/PyCore/samplebuilder.py
+++ b/Tests/Functional/Python/PyCore/samplebuilder.py
@@ -4,7 +4,6 @@ import inspect
sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
-
initial_width = 42
initial_length = 42
@@ -48,16 +47,17 @@ class BuilderPrototype(ba.ISampleBuilder):
def register_prototype(self, par_name, var_key):
var_key = var_key.split("self.", 1).pop()
if not var_key in self.__dict__:
- raise Exception("Can't find variable self."+var_key+" in given class")
+ raise Exception("Can't find variable self." + var_key +
+ " in given class")
# defining the name for new ctype variable and creating dynamic attribute
- wrapper_key = "wrapper_"+var_key
+ wrapper_key = "wrapper_" + 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):
-
def test_registerParameters(self):
"""
Checking parameter registration and setting the value.
diff --git a/Tests/Functional/Python/PyCore/shape2d.py b/Tests/Functional/Python/PyCore/shape2d.py
index 3501f6bf849796ef26df8ddb667060da8027e576..e7afb21b2abf8fda799452f4e0735822d21ae9e6 100644
--- a/Tests/Functional/Python/PyCore/shape2d.py
+++ b/Tests/Functional/Python/PyCore/shape2d.py
@@ -3,8 +3,8 @@ import numpy, os, sys, unittest
sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
import bornagain as ba
-class Shape2DTest(unittest.TestCase):
+class Shape2DTest(unittest.TestCase):
def test_constructPolygonFromList(self):
"""
Testing construction of polygon from two Numpy arrays
diff --git a/Tests/Functional/Python/PyCore/sliced_composition.py b/Tests/Functional/Python/PyCore/sliced_composition.py
index a4e9b46bd8509b02709dfeb9057d0b475c70a00d..9664566c0c3a627f00acd707b9e0fb9612c1a139 100644
--- a/Tests/Functional/Python/PyCore/sliced_composition.py
+++ b/Tests/Functional/Python/PyCore/sliced_composition.py
@@ -18,7 +18,6 @@ bottom_cup_height = 4.0
class SlicedSpheresTest(unittest.TestCase):
-
def get_sample(self, particle_to_air=None, particle_to_substrate=None):
"""
Helper function returning a multilayer (air, substrate) using particles provided
@@ -54,8 +53,14 @@ class SlicedSpheresTest(unittest.TestCase):
Origin of new object is at the bottom of resulting sphere.
"""
- topCup = ba.Particle(top_material, 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))
+ topCup = ba.Particle(
+ top_material,
+ 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))
# origin of resulting sphere will be at the bottom
result = ba.ParticleComposition()
@@ -71,9 +76,14 @@ class SlicedSpheresTest(unittest.TestCase):
Rotation is used to get bottom part
"""
- topCup = ba.Particle(top_material, ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius*2 - bottom_cup_height, 0))
- bottomCup = ba.Particle(bottom_material, ba.FormFactorTruncatedSphere(sphere_radius, bottom_cup_height, 0))
- bottomCup.setRotation(ba.RotationX(180*deg))
+ topCup = ba.Particle(
+ top_material,
+ ba.FormFactorTruncatedSphere(sphere_radius,
+ sphere_radius * 2 - bottom_cup_height, 0))
+ bottomCup = ba.Particle(
+ bottom_material,
+ ba.FormFactorTruncatedSphere(sphere_radius, bottom_cup_height, 0))
+ bottomCup.setRotation(ba.RotationX(180 * deg))
# origin of resulting sphere will be at the bottom
result = ba.ParticleComposition()
@@ -119,7 +129,6 @@ class SlicedSpheresTest(unittest.TestCase):
print(diff)
self.assertLess(diff, 1e-10)
-
def testInvisibleComposition(self):
"""
Compares two simulation intended to provide identical results.
@@ -150,7 +159,7 @@ class SlicedSpheresTest(unittest.TestCase):
Both particles are inserted in vacuum layer with shift to go below interface
"""
- shift = 3*nm
+ shift = 3 * nm
# spherical particle
sphere = ba.Particle(mParticle, ba.FormFactorFullSphere(sphere_radius))
@@ -176,7 +185,10 @@ 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))
+ truncatedSphere = ba.Particle(
+ mParticle,
+ 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/Python/PyCore/sliced_spheres.py b/Tests/Functional/Python/PyCore/sliced_spheres.py
index 1195f1df170735d0ded43919fc0ce1a8cbafbb3b..4e2b89aba3aa5167d9e1f37fa9286f555355e1d4 100644
--- a/Tests/Functional/Python/PyCore/sliced_spheres.py
+++ b/Tests/Functional/Python/PyCore/sliced_spheres.py
@@ -13,8 +13,8 @@ from bornagain import deg, kvector_t
mSubstrate = ba.HomogeneousMaterial("Substrate", 3.212e-6, 3.244e-8)
mAmbience = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
-class SlicedSpheresTest(unittest.TestCase):
+class SlicedSpheresTest(unittest.TestCase):
def get_sample(self, particle_to_air=None, particle_to_substrate=None):
"""
Helper function returning a multilayer (air, substrate) using particles provided
@@ -57,7 +57,10 @@ class SlicedSpheresTest(unittest.TestCase):
sphere_shift = 4.0 # shift beneath interface in absolute units
# truncated sphere on top of substrate with height 16nm
- truncatedSphere = ba.Particle(mSubstrate, ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius*2 - sphere_shift, 0))
+ truncatedSphere = ba.Particle(
+ mSubstrate,
+ ba.FormFactorTruncatedSphere(sphere_radius,
+ sphere_radius * 2 - sphere_shift, 0))
reference = self.get_result(truncatedSphere)
# sphere crossing interface to look like truncated sphere above
@@ -79,7 +82,10 @@ class SlicedSpheresTest(unittest.TestCase):
sphere_shift = 4.0 # shift beneath interface in absolute units
# Sphere truncated from top. Intended to go below interface.
- truncatedSphere = ba.Particle(mAmbience, ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius*2, sphere_radius*2 - sphere_shift))
+ truncatedSphere = ba.Particle(
+ mAmbience,
+ ba.FormFactorTruncatedSphere(sphere_radius, sphere_radius * 2,
+ sphere_radius * 2 - sphere_shift))
truncatedSphere.setPosition(0, 0, -sphere_shift)
reference = self.get_result(truncatedSphere)
diff --git a/Tests/Functional/Python/PyCore/transform_BoxComposition.py b/Tests/Functional/Python/PyCore/transform_BoxComposition.py
index bc2f1c7e65e9b664812a42d6da331d99954c8230..1e92af9215b87576ae286971027d66448834cb8d 100644
--- a/Tests/Functional/Python/PyCore/transform_BoxComposition.py
+++ b/Tests/Functional/Python/PyCore/transform_BoxComposition.py
@@ -19,11 +19,11 @@ com_width = 20.0
com_height = 10.0
particle_material = HomogeneousMaterial("Ag", 1.245e-5, 5.419e-7)
-class TransformBoxCompositionTest(unittest.TestCase):
+class TransformBoxCompositionTest(unittest.TestCase):
def get_sample(self, particle):
mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0)
- mMiddle= HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
+ mMiddle = HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
mSubstrate = HomogeneousMaterial("Substrate", 3.212e-6, 3.244e-8)
layout = ParticleLayout()
@@ -56,18 +56,20 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 20.0
height = 10.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(kvector_t(0, 0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxComposition.int")
# composition
- box = Particle(particle_material, FormFactorBox(com_length/2.0, com_width, com_height))
+ box = Particle(particle_material,
+ FormFactorBox(com_length / 2.0, com_width, com_height))
composition = ParticleComposition()
# composition = ParticleComposition(box, positions)
composition.addParticle(box, kvector_t(0.0, 0.0, 0.0))
- composition.addParticle(box, kvector_t(com_length/2.0, 0.0, 0.0))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - com_height/2.0))
+ composition.addParticle(box, kvector_t(com_length / 2.0, 0.0, 0.0))
+ composition.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - com_height / 2.0))
data = self.get_result(composition)
@@ -85,18 +87,19 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 10.0
height = 20.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(kvector_t(0, 0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateX.int")
# composition
- box = Particle(particle_material, FormFactorBox(com_length/2.0, com_width, com_height))
+ box = Particle(particle_material,
+ FormFactorBox(com_length / 2.0, com_width, com_height))
composition = ParticleComposition()
composition.addParticle(box, kvector_t(0.0, 0.0, 0.0))
- composition.addParticle(box, kvector_t(com_length/2.0, 0.0, 0.0))
- composition.setRotation(RotationX(90*deg))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.))
+ composition.addParticle(box, kvector_t(com_length / 2.0, 0.0, 0.0))
+ composition.setRotation(RotationX(90 * deg))
+ composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness / 2.))
data = self.get_result(composition)
@@ -114,18 +117,20 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 20.0
height = 50.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0, 0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(kvector_t(0, 0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateY.int")
# composition
- box = Particle(particle_material, FormFactorBox(com_length/2.0, com_width, com_height))
+ box = Particle(particle_material,
+ FormFactorBox(com_length / 2.0, com_width, com_height))
composition = ParticleComposition()
composition.addParticle(box, kvector_t(0.0, 0.0, 0.0))
- composition.addParticle(box, kvector_t(com_length/2.0, 0.0, 0.0))
- composition.setRotation(RotationY(90*deg))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2. + com_length/4.))
+ composition.addParticle(box, kvector_t(com_length / 2.0, 0.0, 0.0))
+ composition.setRotation(RotationY(90 * deg))
+ composition.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2. + com_length / 4.))
data = self.get_result(composition)
@@ -143,18 +148,21 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 50.0
height = 10.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateZ.int")
# composition
- box = Particle(particle_material, FormFactorBox(com_length/2.0, com_width, com_height))
+ box = Particle(particle_material,
+ FormFactorBox(com_length / 2.0, com_width, com_height))
composition = ParticleComposition()
composition.addParticle(box, kvector_t(0.0, 0.0, 0.0))
- composition.addParticle(box, kvector_t(com_length/2.0, 0.0, 0.0))
- composition.setRotation(RotationZ(90*deg))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - com_height/2.0))
+ composition.addParticle(box, kvector_t(com_length / 2.0, 0.0, 0.0))
+ composition.setRotation(RotationZ(90 * deg))
+ composition.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - com_height / 2.0))
data = self.get_result(composition)
@@ -172,19 +180,21 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 50.0
height = 20.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxCompositionRotateZandY.int")
# composition
- box = Particle(particle_material, FormFactorBox(com_length/2.0, com_width, com_height))
+ box = Particle(particle_material,
+ FormFactorBox(com_length / 2.0, com_width, com_height))
composition = ParticleComposition()
composition.addParticle(box, kvector_t(0.0, 0.0, 0.0))
- composition.addParticle(box, kvector_t(com_length/2.0, 0.0, 0.0))
- composition.setRotation(RotationZ(90*deg))
- composition.rotate(RotationY(90*deg))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.))
+ composition.addParticle(box, kvector_t(com_length / 2.0, 0.0, 0.0))
+ composition.setRotation(RotationZ(90 * deg))
+ composition.rotate(RotationY(90 * deg))
+ composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness / 2.))
data = self.get_result(composition)
@@ -202,7 +212,8 @@ class TransformBoxCompositionTest(unittest.TestCase):
width = 20.0
height = 50.0
particle = Particle(particle_material, FormFactorBox(length, width, height))
- particle.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - height/2.0))
+ particle.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - height / 2.0))
reference_data = self.get_result(particle)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_BoxStackComposition.int")
@@ -213,21 +224,23 @@ 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.setRotation(RotationZ(90*deg))
+ 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.setRotation(RotationY(90*deg))
- box2.setPosition(kvector_t(-box2_height/2.0, 0.0, box2_length/2.0))
+ box2 = Particle(particle_material,
+ FormFactorBox(box2_length, box2_width, box2_height))
+ box2.setRotation(RotationY(90 * deg))
+ box2.setPosition(kvector_t(-box2_height / 2.0, 0.0, box2_length / 2.0))
composition.addParticle(box1, kvector_t(0.0, 0.0, 0.0))
composition.addParticle(box2, kvector_t(0.0, 0.0, box1_height))
- composition.setRotation(RotationY(90*deg))
- composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.))
+ composition.setRotation(RotationY(90 * deg))
+ composition.setPosition(kvector_t(0.0, 0.0, -layer_thickness / 2.))
data = self.get_result(composition)
diff --git a/Tests/Functional/Python/PyCore/transform_CoreShellBox.py b/Tests/Functional/Python/PyCore/transform_CoreShellBox.py
index 008bd3aba92da3e11bc5d33c20188e1438150ca0..e505f2d065e790d0f7e708f66d9a16f13d1b0369 100644
--- a/Tests/Functional/Python/PyCore/transform_CoreShellBox.py
+++ b/Tests/Functional/Python/PyCore/transform_CoreShellBox.py
@@ -14,11 +14,11 @@ from bornagain import *
layer_thickness = 100.0
-class TransformCoreShellBoxTest(unittest.TestCase):
+class TransformCoreShellBoxTest(unittest.TestCase):
def get_sample(self, particle):
mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0)
- mMiddle= HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
+ mMiddle = HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
mSubstrate = HomogeneousMaterial("Substrate", 3.212e-6, 3.244e-8)
layout = ParticleLayout()
@@ -51,18 +51,23 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 50.0
shell_width = 20.0
shell_height = 10.0
- particle = Particle(mCore, FormFactorBox(shell_length, shell_width, shell_height))
- particle.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0))
+ particle = Particle(mCore,
+ FormFactorBox(shell_length, shell_width, shell_height))
+ particle.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - shell_height / 2.0))
reference_data = self.get_result(particle)
- 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_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))
- coreshell = ParticleCoreShell(shell, core, kvector_t(0.0, 0.0, (shell_height-core_height)/2.0))
- coreshell.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0))
+ coreshell = ParticleCoreShell(
+ shell, core, kvector_t(0.0, 0.0, (shell_height - core_height) / 2.0))
+ coreshell.setPosition(
+ kvector_t(0.0, 0.0, -layer_thickness / 2.0 - shell_height / 2.0))
data = self.get_result(coreshell)
@@ -83,14 +88,21 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 20.0
shell_width = 50.0
shell_height = 10.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
-
- 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, 0.0, (shell_height-core_height)/2.0))
- coreshell_ref.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0)) # center of coreshell in center of the layer
+ core_length = shell_length / 2.0
+ core_width = shell_width / 2.0
+ core_height = shell_height / 2.0
+
+ 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, 0.0, (shell_height - core_height) / 2.0))
+ coreshell_ref.setPosition(
+ kvector_t(
+ 0.0, 0.0, -layer_thickness / 2.0 -
+ shell_height / 2.0)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
@@ -98,15 +110,20 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 50.0
shell_width = 20.0
shell_height = 10.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
+ core_length = shell_length / 2.0
+ 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))
- coreshell = ParticleCoreShell(shell, core, kvector_t(0.0, 0.0, (shell_height-core_height)/2.0))
- coreshell.setRotation(RotationZ(90.0*degree))
- coreshell.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0)) # center of coreshell in center of the layer
+ shell = Particle(mShell,
+ FormFactorBox(shell_length, shell_width, shell_height))
+ coreshell = ParticleCoreShell(
+ shell, core, kvector_t(0.0, 0.0, (shell_height - core_height) / 2.0))
+ coreshell.setRotation(RotationZ(90.0 * degree))
+ coreshell.setPosition(
+ kvector_t(
+ 0.0, 0.0, -layer_thickness / 2.0 -
+ shell_height / 2.0)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
@@ -127,14 +144,21 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 10.0
shell_width = 20.0
shell_height = 50.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
-
- 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, 0.0, (shell_height-core_height)/2.0))
- coreshell_ref.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0)) # center of coreshell in center of the layer
+ core_length = shell_length / 2.0
+ core_width = shell_width / 2.0
+ core_height = shell_height / 2.0
+
+ 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, 0.0, (shell_height - core_height) / 2.0))
+ coreshell_ref.setPosition(
+ kvector_t(
+ 0.0, 0.0, -layer_thickness / 2.0 -
+ shell_height / 2.0)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
@@ -142,15 +166,19 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 50.0
shell_width = 20.0
shell_height = 10.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
+ core_length = shell_length / 2.0
+ 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))
- coreshell = ParticleCoreShell(shell, core, kvector_t(0.0, 0.0, (shell_height-core_height)/2.0))
- coreshell.setRotation(RotationY(90.*degree))
- coreshell.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0)) # center of coreshell in center of the layer
+ shell = Particle(mShell,
+ FormFactorBox(shell_length, shell_width, shell_height))
+ coreshell = ParticleCoreShell(
+ shell, core, kvector_t(0.0, 0.0, (shell_height - core_height) / 2.0))
+ coreshell.setRotation(RotationY(90. * degree))
+ coreshell.setPosition(kvector_t(
+ 0.0, 0.0,
+ -layer_thickness / 2.0)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
@@ -171,14 +199,21 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 10.0
shell_width = 50.0
shell_height = 20.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
-
- 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, 0.0, (shell_height-core_height)/2.0))
- coreshell_ref.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0 - shell_height/2.0)) # center of coreshell in center of the layer
+ core_length = shell_length / 2.0
+ core_width = shell_width / 2.0
+ core_height = shell_height / 2.0
+
+ 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, 0.0, (shell_height - core_height) / 2.0))
+ coreshell_ref.setPosition(
+ kvector_t(
+ 0.0, 0.0, -layer_thickness / 2.0 -
+ shell_height / 2.0)) # center of coreshell in center of the layer
reference_data = self.get_result(coreshell_ref)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_CoreShellBoxRotateZandY.int")
@@ -187,17 +222,21 @@ class TransformCoreShellBoxTest(unittest.TestCase):
shell_length = 50.0
shell_width = 20.0
shell_height = 10.0
- core_length = shell_length/2.0
- core_width = shell_width/2.0
- core_height = shell_height/2.0
+ core_length = shell_length / 2.0
+ 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))
- coreshell = ParticleCoreShell(shell, core, kvector_t(0.0, 0.0, (shell_height-core_height)/2.0))
- coreshell.setRotation(RotationZ(90.0*degree))
- coreshell.rotate(RotationY(90.0*degree))
+ shell = Particle(mShell,
+ FormFactorBox(shell_length, shell_width, shell_height))
+ coreshell = ParticleCoreShell(
+ shell, core, kvector_t(0.0, 0.0, (shell_height - core_height) / 2.0))
+ coreshell.setRotation(RotationZ(90.0 * degree))
+ coreshell.rotate(RotationY(90.0 * degree))
# rotation changes reference point, which now coincide with center of the volume
- coreshell.setPosition(kvector_t(0.0, 0.0, -layer_thickness/2.0)) # center of coreshell in center of the layer
+ coreshell.setPosition(kvector_t(
+ 0.0, 0.0,
+ -layer_thickness / 2.0)) # center of coreshell in center of the layer
data = self.get_result(coreshell)
diff --git a/Tests/Functional/Python/PyCore/transform_box.py b/Tests/Functional/Python/PyCore/transform_box.py
index 6090c6a7564919d927a3842a5bd46979601152cb..0813cd702f9c47245a6791dbcffbaf498d3749fe 100644
--- a/Tests/Functional/Python/PyCore/transform_box.py
+++ b/Tests/Functional/Python/PyCore/transform_box.py
@@ -13,11 +13,11 @@ from bornagain import deg, kvector_t
layer_thickness = 100
-class BoxTransformationsTest(unittest.TestCase):
+class BoxTransformationsTest(unittest.TestCase):
def get_sample(self, particle):
mAmbience = ba.HomogeneousMaterial("Vacuum", 0.0, 0.0)
- mMiddle= ba.HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
+ mMiddle = ba.HomogeneousMaterial("Teflon", 2.900e-6, 6.019e-9)
mSubstrate = ba.HomogeneousMaterial("Substrate", 3.212e-6, 3.244e-8)
layout = ba.ParticleLayout()
@@ -53,7 +53,7 @@ class BoxTransformationsTest(unittest.TestCase):
height = 20
box = ba.Particle(mParticle, ba.FormFactorBox(length, width, height))
- box.setPosition(kvector_t(0, 0, -layer_thickness/2 - height/2))
+ box.setPosition(kvector_t(0, 0, -layer_thickness / 2 - height / 2))
reference_data = self.get_result(box)
#IntensityDataIOFactory.writeIntensityData(reference_data, "ref_TransformBox.int")
@@ -62,9 +62,9 @@ class BoxTransformationsTest(unittest.TestCase):
width = 20
height = 10
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))
+ box.setRotation(ba.RotationZ(90 * deg))
+ box.rotate(ba.RotationY(90 * deg))
+ box.setPosition(kvector_t(0, 0, -layer_thickness / 2))
data = self.get_result(box)
diff --git a/Tests/Functional/Python/PyCore/transform_cube.py b/Tests/Functional/Python/PyCore/transform_cube.py
index cd586e043ac3bae411163e75e193ace46503ae4c..eb59168c419e5f645e02df11de1084bb7bb0033c 100644
--- a/Tests/Functional/Python/PyCore/transform_cube.py
+++ b/Tests/Functional/Python/PyCore/transform_cube.py
@@ -13,10 +13,16 @@ class RotationsCubeTest(unittest.TestCase):
"""
Test of rotations and translations of simple cube in three layers system
"""
- def get_sample(self, formfactor, rot = None, pos = None, layout_rot = None, layout_pos = None, add_to="Vacuum"):
+ def get_sample(self,
+ formfactor,
+ rot=None,
+ pos=None,
+ layout_rot=None,
+ layout_pos=None,
+ add_to="Vacuum"):
mAmbience = HomogeneousMaterial("Vacuum", 0.0, 0.0)
mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
- mMiddle= HomogeneousMaterial("MidleLayer", 5e-5, 2e-8)
+ mMiddle = HomogeneousMaterial("MidleLayer", 5e-5, 2e-8)
mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
particle = Particle(mParticle, formfactor)
@@ -75,12 +81,14 @@ class RotationsCubeTest(unittest.TestCase):
data_to_test = [
# ff rot pos layout_rot layout_pos
- (box, None, None, None, None), # reference
- (box, RotationZ(90.*degree), None, None, None), # rotating particle
- (box, RotationZ(-90.*degree), None, None, None),
- (box, RotationZ(180.*degree), None, None, None),
- (box, None, None, RotationZ(90.*degree), None), # rotating through layout
- (box, RotationZ(45.*degree), None, RotationZ(45.*degree), None), # cumulative rotation
+ (box, None, None, None, None), # reference
+ (box, RotationZ(90. * degree), None, None, None), # rotating particle
+ (box, RotationZ(-90. * degree), None, None, None),
+ (box, RotationZ(180. * degree), None, None, None),
+ (box, None, None, RotationZ(90. * degree),
+ None), # rotating through layout
+ (box, RotationZ(45. * degree), None, RotationZ(45. * degree),
+ None), # cumulative rotation
]
reference_data = self.get_result(data_to_test[0])
@@ -88,8 +96,9 @@ class RotationsCubeTest(unittest.TestCase):
isSuccess = True
for i in range(1, len(data_to_test)):
diff = self.get_difference(reference_data, data_to_test[i])
- print("{0} #{1} diff {2:.2e}".format(self.testRotationZ.__name__, i, diff))
- if(diff > 1e-10) : isSuccess=False
+ print("{0} #{1} diff {2:.2e}".format(self.testRotationZ.__name__, i,
+ diff))
+ if (diff > 1e-10): isSuccess = False
self.assertTrue(isSuccess)
@@ -102,11 +111,16 @@ class RotationsCubeTest(unittest.TestCase):
data_to_test = [
# ff rot pos layout_rot layout_pos
- (box, None, None, None, None), # reference
- (box, RotationY(90.*degree), kvector_t(0,0,5.0), None, None), # rotating and translating
- (box, None, None, RotationY(90.*degree), kvector_t(0,0,5.0)), # rotating and translating
- (box, RotationY(90.*degree), None, None, kvector_t(0,0,5.0)), # rotating and translating
- (box, RotationY(45.*degree), kvector_t(0,0,0.0), RotationY(45.*degree), kvector_t(0,0,5.0)), # rotating and translating
+ (box, None, None, None, None), # reference
+ (box, RotationY(90. * degree), kvector_t(0, 0, 5.0), None,
+ None), # rotating and translating
+ (box, None, None, RotationY(90. * degree),
+ kvector_t(0, 0, 5.0)), # rotating and translating
+ (box, RotationY(90. * degree), None, None,
+ kvector_t(0, 0, 5.0)), # rotating and translating
+ (box, RotationY(45. * degree), kvector_t(0, 0, 0.0),
+ RotationY(45. * degree), kvector_t(0, 0,
+ 5.0)), # rotating and translating
]
reference_data = self.get_result(data_to_test[0])
@@ -114,8 +128,9 @@ class RotationsCubeTest(unittest.TestCase):
isSuccess = True
for i in range(1, len(data_to_test)):
diff = self.get_difference(reference_data, data_to_test[i])
- print("{0} #{1} diff {2:.2e}".format(self.testRotationY.__name__, i, diff))
- if(diff > 1e-10) : isSuccess=False
+ print("{0} #{1} diff {2:.2e}".format(self.testRotationY.__name__, i,
+ diff))
+ if (diff > 1e-10): isSuccess = False
self.assertTrue(isSuccess)
@@ -128,11 +143,16 @@ class RotationsCubeTest(unittest.TestCase):
data_to_test = [
# ff rot pos layout_rot layout_pos
- (box, None, None, None, None), # reference
- (box, RotationX(90.*degree), kvector_t(0,0,5.0), None, None), # rotating and translating
- (box, None, None, RotationX(90.*degree), kvector_t(0,0,5.0)), # rotating and translating
- (box, RotationX(90.*degree), None, None, kvector_t(0,0,5.0)), # rotating and translating
- (box, RotationX(45.*degree), kvector_t(0,0,0.0), RotationX(45.*degree), kvector_t(0,0,5.0)), # rotating and translating
+ (box, None, None, None, None), # reference
+ (box, RotationX(90. * degree), kvector_t(0, 0, 5.0), None,
+ None), # rotating and translating
+ (box, None, None, RotationX(90. * degree),
+ kvector_t(0, 0, 5.0)), # rotating and translating
+ (box, RotationX(90. * degree), None, None,
+ kvector_t(0, 0, 5.0)), # rotating and translating
+ (box, RotationX(45. * degree), kvector_t(0, 0, 0.0),
+ RotationX(45. * degree), kvector_t(0, 0,
+ 5.0)), # rotating and translating
]
reference_data = self.get_result(data_to_test[0])
@@ -140,8 +160,9 @@ class RotationsCubeTest(unittest.TestCase):
isSuccess = True
for i in range(1, len(data_to_test)):
diff = self.get_difference(reference_data, data_to_test[i])
- print("{0} #{1} diff {2:.2e}".format(self.testRotationX.__name__, i, diff))
- if(diff > 1e-10) : isSuccess=False
+ print("{0} #{1} diff {2:.2e}".format(self.testRotationX.__name__, i,
+ diff))
+ if (diff > 1e-10): isSuccess = False
self.assertTrue(isSuccess)
@@ -152,17 +173,20 @@ class RotationsCubeTest(unittest.TestCase):
data_to_test = [
# ff rot pos layout_rot layout_pos
- (box, None, kvector_t(0,0,-25.0), None, None), # reference
- (box, RotationX(90.*degree), kvector_t(0,0,-20.0), None, None), # rotating and translating
+ (box, None, kvector_t(0, 0, -25.0), None, None), # reference
+ (box, RotationX(90. * degree), kvector_t(0, 0, -20.0), None,
+ None), # rotating and translating
]
reference_data = self.get_result(data_to_test[0], "add_to_middle")
isSuccess = True
for i in range(1, len(data_to_test)):
- diff = self.get_difference(reference_data, data_to_test[i], "add_to_middle")
- print("{0} #{1} diff {2:.2e}".format(self.testRotationX.__name__, i, diff))
- if(diff > 1e-10) : isSuccess=False
+ diff = self.get_difference(reference_data, data_to_test[i],
+ "add_to_middle")
+ print("{0} #{1} diff {2:.2e}".format(self.testRotationX.__name__, i,
+ diff))
+ if (diff > 1e-10): isSuccess = False
self.assertTrue(isSuccess)
diff --git a/Tests/Functional/Python/PyCore/utils.py b/Tests/Functional/Python/PyCore/utils.py
index e92450f978e91b5f3d251d1aef6b40fc2dc3855b..2d7551b69f0d735216b5c01b9195248455d34345 100644
--- a/Tests/Functional/Python/PyCore/utils.py
+++ b/Tests/Functional/Python/PyCore/utils.py
@@ -10,6 +10,7 @@ from bornagain import deg, angstrom
REFERENCE_DIR = "@PYCORE_REFERENCE_DIR@"
+
def get_difference(data, reference):
"""
calculate numeric difference between result and reference data
@@ -24,36 +25,43 @@ def get_difference(data, reference):
if v1 <= epsilon and v2 <= epsilon:
diff += 0.0
elif v2 <= epsilon:
- diff += abs(v1/epsilon)
+ diff += abs(v1 / epsilon)
else:
- diff += abs(v1/v2)
- diff = diff/data.size
+ diff += abs(v1 / v2)
+ diff = diff / data.size
if numpy.isnan(diff):
raise ba.Exception("get_difference", "isnan")
return diff
+
def get_reference_data(filename):
"""
read and return reference data from file
"""
- return ba.IntensityDataIOFactory.readIntensityData(os.path.join(REFERENCE_DIR, filename))
+ return ba.IntensityDataIOFactory.readIntensityData(
+ os.path.join(REFERENCE_DIR, filename))
+
-def get_simulation_MiniGISAS(sample = None):
+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)
+ 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):
+
+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)
+ 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_intensity_data(intensity):
import matplotlib, pylab
data = intensity.getArray() + 1
@@ -62,7 +70,8 @@ def plot_intensity_data(intensity):
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(),
+ 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)
diff --git a/Tests/Functional/Python/PyExamples/check_functionality.py b/Tests/Functional/Python/PyExamples/check_functionality.py
index 067316c751b0d558973cf8feef3b9a0d16c61a2d..ac3cae2123ef489f708844fc07d77fda1e711e4d 100644
--- a/Tests/Functional/Python/PyExamples/check_functionality.py
+++ b/Tests/Functional/Python/PyExamples/check_functionality.py
@@ -17,6 +17,7 @@ sys.path.append("@CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
output_dir = "@output_dir@"
+
def get_figure(filename):
"""
Returns pyplot figure of appropriate size
@@ -27,7 +28,7 @@ def get_figure(filename):
xsize, ysize = 640, 480
dpi = 72.
- return plt.figure(figsize=(xsize/dpi, ysize/dpi))
+ return plt.figure(figsize=(xsize / dpi, ysize / dpi))
def exec_full(filepath):
@@ -50,17 +51,18 @@ 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")
+ raise Exception("Example script '" + filename + "' not found")
- print("Input script: "+filename)
+ print("Input script: " + filename)
fig = get_figure(filename)
exec_full(filename)
- plot_file_name = os.path.join(output_dir,
- os.path.splitext(os.path.basename(filename))[0] + ".png")
- print("Output image: "+plot_file_name)
+ 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)
@@ -74,6 +76,8 @@ def run_example(filename):
if __name__ == '__main__':
if len(sys.argv) != 2:
- exit("Auxiliary script check_functionality called with wrong number of arguments")
+ exit(
+ "Auxiliary script check_functionality called with wrong number of arguments"
+ )
run_example(sys.argv[1])
diff --git a/Tests/Functional/Python/PyFit/fitobjective_api.py b/Tests/Functional/Python/PyFit/fitobjective_api.py
index 3de3426e85309b6b493c7aa5fa7f151e3f741395..d65fee8e078e7e16da4b1f6bcf48a30f570f181c 100644
--- a/Tests/Functional/Python/PyFit/fitobjective_api.py
+++ b/Tests/Functional/Python/PyFit/fitobjective_api.py
@@ -18,7 +18,7 @@ class SimulationBuilder:
self.m_ncol = 4
def size(self):
- return self.m_nrow*self.m_ncol
+ return self.m_nrow * self.m_ncol
def build_simulation(self, pars):
self.m_ncalls += 1
@@ -31,7 +31,8 @@ class SimulationBuilder:
simulation = ba.GISASSimulation()
simulation.setSample(ml)
- simulation.setDetectorParameters(self.m_ncol, 0.0, 1.0, self.m_nrow, 0.0, 1.0)
+ simulation.setDetectorParameters(self.m_ncol, 0.0, 1.0, self.m_nrow, 0.0,
+ 1.0)
return simulation
def create_data(self):
@@ -49,7 +50,6 @@ class FitObserver:
class FitObjectiveAPITest(unittest.TestCase):
-
def test_SimulationBuilderCallback(self):
"""
Testing simulation construction using Python callback
@@ -76,7 +76,7 @@ class FitObjectiveAPITest(unittest.TestCase):
# checking arrays of experimental and simulated data
expected_sim = []
- expected_data=[]
+ expected_data = []
for i in range(0, builder.size()):
expected_sim.append(0.0)
expected_data.append(1.0)
diff --git a/Tests/Functional/Python/PyFit/minimizer_api.py b/Tests/Functional/Python/PyFit/minimizer_api.py
index b04126ba6cefbcabe07b8cbcf48ddf7bccaa7bc9..8eabce41be48ae779115c228a7f641801afda22e 100644
--- a/Tests/Functional/Python/PyFit/minimizer_api.py
+++ b/Tests/Functional/Python/PyFit/minimizer_api.py
@@ -21,7 +21,6 @@ class TestMinimizerHelper:
class MinimizerAPITest(unittest.TestCase):
-
def test_ParameterAttribute(self):
"""
Testing p.value attribute
@@ -69,7 +68,6 @@ class MinimizerAPITest(unittest.TestCase):
self.assertTrue(params["par4"].limits().isFixed())
-
def test_SimpleMinimizer(self):
minimizer = ba.Minimizer()
minimizer.setMinimizer("Test")
diff --git a/Tests/Functional/Python/PyFit/standalone_fits.py b/Tests/Functional/Python/PyFit/standalone_fits.py
index e74e97725322338db965596ddd6e10c7a5dacf88..531285aebbd238faaa63e2f8c91785deb48182b6 100644
--- a/Tests/Functional/Python/PyFit/standalone_fits.py
+++ b/Tests/Functional/Python/PyFit/standalone_fits.py
@@ -32,7 +32,7 @@ def decaying_sin(params, x):
phaseshift = params['phase'].value
freq = params['frequency'].value
decay = params['decay'].value
- return amp * np.sin(x*freq + phaseshift) * np.exp(-x*x*decay)
+ return amp * np.sin(x * freq + phaseshift) * np.exp(-x * x * decay)
class DecayingSin:
@@ -53,7 +53,6 @@ class DecayingSin:
class StandaloneFitTest(unittest.TestCase):
-
def test_RosenbrockFit(self):
"""
Testing fit of rosenbrock function
@@ -73,9 +72,8 @@ class StandaloneFitTest(unittest.TestCase):
model.m_expected_params, 3)
# check found minimum
- np.testing.assert_almost_equal(result.minValue(),
- model.m_expected_minimum, 3)
-
+ np.testing.assert_almost_equal(result.minValue(), model.m_expected_minimum,
+ 3)
def test_DecayingSinFit(self):
params = ba.Parameters()
@@ -88,12 +86,12 @@ class StandaloneFitTest(unittest.TestCase):
minimizer = ba.Minimizer()
result = minimizer.minimize(model.objective_function, params)
-
print(result.toString())
# check found parameter values
np.testing.assert_almost_equal(result.parameters().values(),
model.m_params.values(), 3)
+
if __name__ == '__main__':
unittest.main()
diff --git a/Tests/Performance/Python/test_performance.py b/Tests/Performance/Python/test_performance.py
index 165765cfcc9d0103d22bf515ef9d3284fdfcb19e..b4eb0b9c40a8ddac414c6a4961301e1119d80a67 100755
--- a/Tests/Performance/Python/test_performance.py
+++ b/Tests/Performance/Python/test_performance.py
@@ -1,5 +1,5 @@
#!/usr/bin/python
- # -*- coding: utf-8 -*-
+# -*- coding: utf-8 -*-
## ************************************************************************** ##
##
@@ -41,11 +41,11 @@ except:
record_cpu_time = False
get_cpu_time = lambda: None
-
# globals used in custom form factor
phi_min, phi_max = -1.0, 1.0
alpha_min, alpha_max = 0.0, 2.0
+
# user-defined custom form factor
class CustomFormFactor(IBornFF):
"""
@@ -71,7 +71,8 @@ class CustomFormFactor(IBornFF):
return cloned_ff
def evaluate_for_q(self, q):
- return self.V*1.0/math.cosh(q.mag()*self.L)
+ return self.V * 1.0 / math.cosh(q.mag() * self.L)
+
# class for performance test, constructed using sample factories
class FactoryTest:
@@ -88,8 +89,10 @@ class FactoryTest:
if simulation_name != None and sample_builder != None:
self.m_sample_factory = SampleBuilderFactory()
self.m_simulation_factory = SimulationFactory()
- self.m_simulation = self.m_simulation_factory.createItem(self.m_simulation_name)
- self.m_sample = self.m_sample_factory.createSampleByName(self.m_sample_builder_name)
+ self.m_simulation = self.m_simulation_factory.createItem(
+ self.m_simulation_name)
+ self.m_sample = self.m_sample_factory.createSampleByName(
+ self.m_sample_builder_name)
else:
self.m_sample_factory = None
self.m_simulation_factory = None
@@ -127,12 +130,12 @@ class FactoryTest:
if record_cpu_time:
self.m_cpu_time = end_cpu_time - start_cpu_time
- logfile.write("OK: %-6.3f (wall sec), %-6.3f (cpu sec) \n" % (self.m_wall_time, self.m_cpu_time))
+ logfile.write("OK: %-6.3f (wall sec), %-6.3f (cpu sec) \n" %
+ (self.m_wall_time, self.m_cpu_time))
else:
logfile.write("OK: %-6.3f (wall sec)\n" % (self.m_wall_time))
-
# special performance test case: custom form factor
class CustomTest(FactoryTest):
def __init__(self, name, nrepetitions):
@@ -160,7 +163,7 @@ class CustomTest(FactoryTest):
m_particle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
# collection of particles
- ff = CustomFormFactor(343.0*nanometer, 7.0*nanometer)
+ ff = CustomFormFactor(343.0 * nanometer, 7.0 * nanometer)
particle = Particle(m_particle, ff)
particle_layout = ParticleLayout()
particle_layout.addParticle(particle, 1.0)
@@ -182,8 +185,9 @@ class CustomTest(FactoryTest):
"""
simulation = GISASSimulation()
simulation.getOptions().setNumberOfThreads(-1)
- simulation.setDetectorParameters(100, phi_min*degree, phi_max*degree, 100, alpha_min*degree, alpha_max*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setDetectorParameters(100, phi_min * degree, phi_max * degree,
+ 100, alpha_min * degree, alpha_max * degree)
+ simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree)
return simulation
@@ -197,40 +201,44 @@ 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("CoreShell", "MaxiGISAS", "CoreShellParticleBuilder", 10)
- 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("Mesocrystal", "MaxiGISAS", "MesoCrystalBuilder", 2)
- self.add("PolMagCyl", "MaxiGISAS00", "MagneticCylindersBuilder", 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", 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)
# custom form factor is a special case since it's not in the registry
self.m_tests.append(CustomTest("Custom FF", 10))
- logfile.write("\nPreparing to run %d performance tests.\n\n" % len(self.m_tests))
+ logfile.write("\nPreparing to run %d performance tests.\n\n" %
+ len(self.m_tests))
def add(self, name, simulation_name, sample_builder, nrepetitions):
- self.m_tests.append(FactoryTest(name, simulation_name, sample_builder, nrepetitions))
+ self.m_tests.append(
+ FactoryTest(name, simulation_name, sample_builder, nrepetitions))
# execute all performance tests
def execute(self):
self.init_sysinfo()
- for test in self.m_tests: test.run()
+ for test in self.m_tests:
+ test.run()
self.write_results()
-
# write out system information and test results to file
def write_results(self):
- if ( self.m_filename != None ):
+ if (self.m_filename != None):
try:
write_file = open(self.m_filename, "a")
except:
- sys.stderr.write("Could not open filed '%' for writing. Writing to stdout instead.\n" % self.m_filename)
+ sys.stderr.write(
+ "Could not open filed '%' for writing. Writing to stdout instead.\n"
+ % self.m_filename)
write_file = sys.stdout
self.m_filename = None
@@ -265,17 +273,19 @@ class PerformanceTests:
write_file.write("\n")
write_file.flush()
- if ( self.m_filename != None ):
+ if (self.m_filename != None):
write_file.close()
# determine platform, architecture, python version, etc.
def init_sysinfo(self):
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_datime = datetime.datetime.strftime(datetime.datetime.now(),
+ '%Y-%m-%d %H:%M:%S')
self.m_hostname = node
self.m_sysinfo = "%s %s" % (system, machine)
self.m_pyversion = "%d.%d" % (sys.version_info[:2])
+
# used for writing the summary with proper formatting
def pretty_write(dictionary, file):
header = "|"
@@ -291,9 +301,10 @@ def pretty_write(dictionary, file):
file.write(header + "\n")
file.write(footer + "\n")
+
if __name__ == '__main__':
- if ( len(sys.argv) > 2 ):
+ if (len(sys.argv) > 2):
print("Usage: test_performance.py [output file]")
exit(0)
diff --git a/Wrap/Python/bornagain_python_install.py b/Wrap/Python/bornagain_python_install.py
index ed50aea5d77b09684fdb3f4fc76a77b8264eb6b1..f0f39b41233074c3321d2252e771998d82ec0e43 100644
--- a/Wrap/Python/bornagain_python_install.py
+++ b/Wrap/Python/bornagain_python_install.py
@@ -31,36 +31,41 @@ import site
import subprocess
from distutils.sysconfig import get_python_lib
-
BORNAGAIN_VERSION = "0.0"
+
def is_python3():
if (sys.version_info > (3, 0)):
return True
else:
return False
+
def python_version_string():
return str(sys.version_info[0]) + "." + str(sys.version_info[1])
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
def change_rpath(oldpath, newpath, filename):
print("change_rpath ", oldpath, newpath, filename)
- p = subprocess.Popen(['install_name_tool', '-change', oldpath, newpath, filename], stdout=subprocess.PIPE)
+ p = subprocess.Popen(
+ ['install_name_tool', '-change', oldpath, newpath, filename],
+ stdout=subprocess.PIPE)
p.communicate()
return
def delete_rpath(todelete, filename):
print("delete_rpath ", todelete, filename)
- p = subprocess.Popen(['install_name_tool', '-delete_rpath', todelete, filename], stdout=subprocess.PIPE)
+ p = subprocess.Popen(['install_name_tool', '-delete_rpath', todelete, filename],
+ stdout=subprocess.PIPE)
p.communicate()
return
@@ -84,8 +89,9 @@ 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')
- result = sys.prefix+"/lib/libpython"+suffix+".dylib"
+ suffix = sysconfig.get_config_var('LDVERSION') or sysconfig.get_config_var(
+ 'VERSION')
+ result = sys.prefix + "/lib/libpython" + suffix + ".dylib"
return result
@@ -109,9 +115,9 @@ def get_application_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)
+ exit("Can't find BornAgain libraries in " + app_dir)
BORNAGAIN_VERSION = lib_dir[0].split("BornAgain-")[1]
return app_dir
@@ -185,7 +191,8 @@ 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, "bornagain")
+ 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(libexec_dir, package_dir))
shutil.copytree(libexec_dir, package_dir)
@@ -197,11 +204,13 @@ def copy_libraries(app_dir, destination_dir):
Copy libraries from BornAgain.app into corresponding BornAgain Python package directory
"""
print("--> Copying libraries from '{0}'".format(app_dir))
- app_bornagainlib_dir = os.path.join(app_dir, "Contents", "lib", "BornAgain-"+BORNAGAIN_VERSION)
+ app_bornagainlib_dir = os.path.join(app_dir, "Contents", "lib",
+ "BornAgain-" + BORNAGAIN_VERSION)
app_frameworks_dir = os.path.join(app_dir, "Contents", "Frameworks")
# copying BornAgain libraries
- shutil.copytree(app_bornagainlib_dir, os.path.join(destination_dir, "BornAgain-"+BORNAGAIN_VERSION))
+ shutil.copytree(app_bornagainlib_dir,
+ os.path.join(destination_dir, "BornAgain-" + BORNAGAIN_VERSION))
# cleaning unnecessary files
libfiles = glob.glob(os.path.join(destination_dir, '*/libBornAgainGUI*'))
@@ -222,11 +231,12 @@ def patch_libraries(dir_name):
"""
Patches libraries depending on Python to point on the same shared libpython2.7.dylib which current interpreter is using
"""
- print("--> Patching libraries to rely on '{0}'".format(get_python_shared_library()))
+ print("--> Patching libraries to rely on '{0}'".format(
+ get_python_shared_library()))
libfiles = glob.glob(os.path.join(dir_name, '*/_libBornAgain*'))
for f in libfiles:
for lib in ["Base", "Fit", "Param", "Sample", "Device", "Core"]:
- if "libBornAgain"+lib in f:
+ if "libBornAgain" + lib in f:
delete_rpath("@loader_path/../../Frameworks", f)
add_rpath("@loader_path/../Frameworks", f)
if "libBornAgainCore" in f:
@@ -234,8 +244,9 @@ def patch_libraries(dir_name):
libfiles += glob.glob(os.path.join(dir_name, '*/libboost_python*'))
for f in libfiles:
- change_rpath("@rpath/Python.framework/Versions/"+python_version_string()+"/Python", get_python_shared_library(), f)
-
+ change_rpath(
+ "@rpath/Python.framework/Versions/" + python_version_string() +
+ "/Python", get_python_shared_library(), f)
pass
@@ -245,9 +256,9 @@ def create_bundle(app_dir):
Creates ready to install BornAgain Python bundle package
"""
bundle_dir = create_bundle_tem_dir()
- print('-'*80)
+ print('-' * 80)
print("Generating Python bundle in temporary '{0}'".format(bundle_dir))
- print('-'*80)
+ print('-' * 80)
print("--> Generating bundle setup files")
@@ -260,8 +271,12 @@ def create_bundle(app_dir):
patch_libraries(library_dir)
- print("\nBornAgain Python bundle is successfully created in temporary directory '{0}'".format(bundle_dir))
- print("Run 'python setup.py install' from there to install it into your Python's site-packages")
+ print(
+ "\nBornAgain Python bundle is successfully created in temporary directory '{0}'"
+ .format(bundle_dir))
+ print(
+ "Run 'python setup.py install' from there to install it into your Python's site-packages"
+ )
return bundle_dir
@@ -269,14 +284,15 @@ def install_bundle(dir_name):
"""
Installs BornAgain Python bundle previously generated in the directory dir_name
"""
- print('-'*80)
+ print('-' * 80)
print("Installing bundle in Python site-packages '{0}'".format(get_python_lib()))
- print('-'*80)
+ print('-' * 80)
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!")
@@ -286,9 +302,11 @@ if __name__ == '__main__':
app_dir = get_application_dir()
- print('-'*80)
- print("Installation of BornAgain-{0} libraries into site-packages of your Python".format(BORNAGAIN_VERSION))
- print('-'*80)
+ print('-' * 80)
+ print(
+ "Installation of BornAgain-{0} libraries into site-packages of your Python".
+ format(BORNAGAIN_VERSION))
+ print('-' * 80)
print("From :", app_dir)
print("To :", get_python_lib())
print(" ")
diff --git a/Wrap/Python/plot_utils.py b/Wrap/Python/plot_utils.py
index f21d57b1c379beb7b030a2e39de49a766704944d..654dd8170686e6fd39e6b5b6e10b31986130df57 100644
--- a/Wrap/Python/plot_utils.py
+++ b/Wrap/Python/plot_utils.py
@@ -22,7 +22,6 @@ try: # workaround for build servers
except Exception as e:
print("In plot_utils.py: {:s}".format(str(e)))
-
label_fontsize = 16
@@ -34,8 +33,9 @@ def get_axes_limits(result, units):
:return: axes ranges as a flat list
"""
axis_infos = result.axisInfo(units)
- limits = [ [axis_infos[i].m_min, axis_infos[i].m_max] for i in range(len(axis_infos)) ]
- flat_limits = [ v for sublist in limits for v in sublist ]
+ limits = [[axis_infos[i].m_min, axis_infos[i].m_max]
+ for i in range(len(axis_infos))]
+ flat_limits = [v for sublist in limits for v in sublist]
return flat_limits
@@ -47,23 +47,22 @@ def translate_axis_label(label):
:return: LaTeX representation
"""
label_dict = {
- 'X [nbins]' : r'$X \; $(bins)',
- 'phi_f [rad]' : r'$\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 \; $(mm)',
- 'Qz [1/nm]' : r'$Q_z \; $(nm$^{-1}$)',
- 'Position [nm]' : r'$Position \; $(nm)'
- }
+ 'X [nbins]': r'$X \; $(bins)',
+ 'phi_f [rad]': r'$\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 \; $(mm)',
+ 'Qz [1/nm]': r'$Q_z \; $(nm$^{-1}$)',
+ 'Position [nm]': r'$Position \; $(nm)'
+ }
if label in label_dict.keys():
return label_dict[label]
else:
@@ -78,13 +77,22 @@ def get_axes_labels(result, units):
:return: axes ranges as a flat list
"""
axis_infos = result.axisInfo(units)
- labels = [ translate_axis_label(axis_infos[i].m_name) for i in range(len(axis_infos)) ]
+ labels = [
+ translate_axis_label(axis_infos[i].m_name) for i in range(len(axis_infos))
+ ]
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,
+ zmin=None,
+ zmax=None,
+ xlabel=None,
+ ylabel=None,
+ zlabel=None,
+ title=None,
+ axes_limits=None,
+ **kwargs):
"""
Plots numpy array as a colormap in log scale.
"""
@@ -92,7 +100,7 @@ def plot_array(array, zmin=None, zmax=None, xlabel=None, ylabel=None, zlabel=Non
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
+ zmin = 1e-6 * zmax if zmin is None else zmin
if zmin == zmax == 0.0:
norm = colors.Normalize(0, 1)
@@ -115,8 +123,14 @@ def plot_array(array, zmin=None, zmax=None, xlabel=None, ylabel=None, zlabel=Non
plt.title(title)
-def plot_histogram(hist, zmin=None, zmax=None, xlabel=None, ylabel=None, zlabel=None,
- title=None, **kwargs):
+def plot_histogram(hist,
+ zmin=None,
+ zmax=None,
+ xlabel=None,
+ ylabel=None,
+ zlabel=None,
+ title=None,
+ **kwargs):
"""
Plots intensity data as color map
:param intensity: Histogram2D object obtained from GISASSimulation
@@ -130,16 +144,28 @@ def plot_histogram(hist, zmin=None, zmax=None, xlabel=None, ylabel=None, zlabel=
if not ylabel:
ylabel = translate_axis_label(hist.yAxis().getName())
- axes_limits = [hist.getXmin(), hist.getXmax(),
- hist.getYmin(), 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):
+ axes_limits = [hist.getXmin(), hist.getXmax(), hist.getYmin(), 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):
"""
Plots intensity data as color map
:param result: SimulationResult from GISAS/OffSpecSimulation
@@ -152,12 +178,25 @@ def plot_colormap(result, zmin=None, zmax=None, units=ba.Axes.DEFAULT,
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):
+ 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):
"""
Plots intensity data for specular simulation result
:param result: SimulationResult from SpecularSimulation
@@ -188,8 +227,15 @@ def plot_specular_simulation_result(result, ymin=None, ymax=None, units=ba.Axes.
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,
+ intensity_min=None,
+ intensity_max=None,
+ units=ba.Axes.DEFAULT,
+ xlabel=None,
+ ylabel=None,
+ postpone_show=False,
+ title=None,
+ **kwargs):
"""
Draws simulation result and (optionally) shows the plot.
:param result_: SimulationResult object obtained from GISAS/OffSpec/SpecularSimulation
@@ -199,18 +245,30 @@ def plot_simulation_result(result, intensity_min=None, intensity_max=None, units
:param postpone_show: postpone showing the plot for later tuning (False by default)
"""
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, intensity_min, intensity_max, units,
+ **kwargs)
else:
- plot_colormap(result, intensity_min, intensity_max, units, xlabel, ylabel,
- title=title, **kwargs)
+ plot_colormap(result,
+ intensity_min,
+ intensity_max,
+ units,
+ xlabel,
+ ylabel,
+ title=title,
+ **kwargs)
plt.tight_layout()
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):
+ 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()
@@ -230,8 +288,13 @@ class Plotter:
class PlotterGISAS(Plotter):
- def __init__(self, zmin=None, zmax=None, xlabel=None, ylabel=None,
- units=ba.Axes.DEFAULT, aspect=None):
+ 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
@@ -251,21 +314,39 @@ class PlotterGISAS(Plotter):
# 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)
+ 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)
+ 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)
+ 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')
@@ -273,13 +354,14 @@ class PlotterGISAS(Plotter):
iteration_info = fit_objective.iterationInfo()
- plt.text(0.01, 0.85, "Iterations " + '{:d}'.
- format(iteration_info.iterationCount()))
+ 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]))
+ plt.text(0.01, 0.55 - index * 0.1,
+ '{:30.30s}: {:6.3f}'.format(key, params[key]))
index = index + 1
Plotter.plot(self)
@@ -290,7 +372,6 @@ 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)
@@ -334,24 +415,34 @@ class PlotterSpecular(Plotter):
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
+ 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}$'.format(self.as_si(rel_dif, n_digits))]]
+ [
+ "$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}$'.format(self.as_si(value, n_digits))])
+ table_data.append([
+ '{:s}'.format(self.trunc_str(key, trunc_length)),
+ '${: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])
+ 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
@@ -365,16 +456,20 @@ class PlotterSpecular(Plotter):
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(), real_values, 'k--')
+ 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.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]
diff --git a/Wrap/swig/doxy2swig.py b/Wrap/swig/doxy2swig.py
index 0491aff06fbc38bbb0fb8a63fa74dce156ae34a6..1ef67ec7b474dbfdaaf882f97eb158a3b6cfd772 100755
--- a/Wrap/swig/doxy2swig.py
+++ b/Wrap/swig/doxy2swig.py
@@ -34,6 +34,7 @@ def my_open_read(source):
else:
return open(source)
+
def my_open_write(dest, mode='w'):
if hasattr(dest, "write"):
return dest
@@ -47,7 +48,6 @@ class Doxy2SWIG:
is stored in self.pieces.
"""
-
def __init__(self, src):
"""Initialize the instance given a source object (file or
filename).
@@ -67,10 +67,9 @@ class Doxy2SWIG:
self.multi = 0
self.ignores = ('inheritancegraph', 'param', 'listofallmembers',
'innerclass', 'name', 'declname', 'incdepgraph',
- 'invincdepgraph', 'programlisting', 'type',
- 'references', 'referencedby', 'location',
- 'collaborationgraph', 'reimplements',
- 'reimplementedby', 'derivedcompoundref',
+ 'invincdepgraph', 'programlisting', 'type', 'references',
+ 'referencedby', 'location', 'collaborationgraph',
+ 'reimplements', 'reimplementedby', 'derivedcompoundref',
'basecompoundref')
#self.generics = []
@@ -87,7 +86,7 @@ class Doxy2SWIG:
nodes.
"""
- pm = getattr(self, "parse_%s"%node.__class__.__name__)
+ pm = getattr(self, "parse_%s" % node.__class__.__name__)
pm(node)
def parse_Document(self, node):
@@ -181,7 +180,7 @@ class Doxy2SWIG:
def do_compoundname(self, node):
self.add_text('\n\n')
data = node.firstChild.data
- self.add_text('%%feature("docstring") %s "\n'%data)
+ self.add_text('%%feature("docstring") %s "\n' % data)
def do_compounddef(self, node):
kind = node.attributes['kind'].value
@@ -189,14 +188,14 @@ 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):
if n in first:
self.parse(first[n])
- self.add_text(['";','\n'])
+ self.add_text(['";', '\n'])
for n in node.childNodes:
if n not in first.values():
self.parse(n)
@@ -219,7 +218,7 @@ class Doxy2SWIG:
def do_parametername(self, node):
self.add_text('\n')
- self.add_text("%s: "%node.firstChild.data)
+ self.add_text("%s: " % node.firstChild.data)
def do_parameterdefinition(self, node):
self.generic_parse(node, pad=1)
@@ -241,7 +240,7 @@ class Doxy2SWIG:
if prot == 'public':
first = self.get_specific_nodes(node, ('definition', 'name'))
name = first['name'].firstChild.data
- if name[:8] == 'operator': # Don't handle operators yet.
+ if name[:8] == 'operator': # Don't handle operators yet.
return
defn = first['definition'].firstChild.data
@@ -255,14 +254,14 @@ class Doxy2SWIG:
ns_node = anc.getElementsByTagName('compoundname')
if ns_node:
ns = ns_node[0].firstChild.data
- self.add_text(' %s::%s "\n%s'%(ns, name, defn))
+ self.add_text(' %s::%s "\n%s' % (ns, name, defn))
else:
- self.add_text(' %s "\n%s'%(name, defn))
+ self.add_text(' %s "\n%s' % (name, defn))
elif cdef_kind in ('class', 'struct'):
# Get the full function name.
anc_node = anc.getElementsByTagName('compoundname')
cname = anc_node[0].firstChild.data
- self.add_text(' %s::%s "\n%s'%(cname, name, defn))
+ self.add_text(' %s::%s "\n%s' % (cname, name, defn))
for n in node.childNodes:
if n not in first.values():
@@ -271,7 +270,7 @@ class Doxy2SWIG:
def do_definition(self, node):
data = node.firstChild.data
- self.add_text('%s "\n%s'%(data, data))
+ self.add_text('%s "\n%s' % (data, data))
def do_sectiondef(self, node):
kind = node.attributes['kind'].value
@@ -308,7 +307,7 @@ class Doxy2SWIG:
refid = c.attributes['refid'].value
fname = refid + '.xml'
if not os.path.exists(fname):
- fname = os.path.join(self.my_dir, fname)
+ fname = os.path.join(self.my_dir, fname)
# print("parsing file: %s"%fname)
p = Doxy2SWIG(fname)
p.generate()
@@ -340,7 +339,7 @@ class Doxy2SWIG:
elif count > 2:
ret.append('\n\n')
elif count:
- ret.append('\n'*count)
+ ret.append('\n' * count)
count = 0
ret.append(i)
@@ -349,7 +348,7 @@ class Doxy2SWIG:
for i in _data.split('\n\n'):
if i == 'Parameters:':
ret.extend(['Parameters:\n-----------', '\n\n'])
- elif i.find('// File:') > -1: # leave comments alone.
+ elif i.find('// File:') > -1: # leave comments alone.
ret.extend([i, '\n'])
else:
#_tmp = textwrap.fill(i.strip())
diff --git a/Wrap/swig/tweaks.py b/Wrap/swig/tweaks.py
index 2d8bf7b80c4b001e23e9a3e7e9fd098588e4238b..35994c153c4626706ba9004bc19fb87ebb3a533c 100644
--- a/Wrap/swig/tweaks.py
+++ b/Wrap/swig/tweaks.py
@@ -5,15 +5,17 @@ import sys
import os
import string
+
# compatibility with windows filename conventions
def windowsify(filename):
- if ( sys.platform == "win32" ):
+ if (sys.platform == "win32"):
new_filename = filename.replace("/", "\\")
else:
new_filename = filename
return os.path.abspath(new_filename)
+
if len(sys.argv) != 3:
print("Usage: tweaks.py inputfile outputfile")
exit(1)
@@ -29,13 +31,17 @@ fd.close()
text_out = []
for line in text_in:
- line = line.replace("_libBornAgainBase.ICloneable_transferToCPP(self)", "self.__disown__()")
- line = line.replace("_libBornAgainCore.Histogram1D_binCenters(self)", "self.binCentersNumpy()")
- line = line.replace("_libBornAgainCore.Histogram1D_binErrors(self)", "self.binErrorsNumpy()")
- line = line.replace("_libBornAgainCore.Histogram1D_binValues(self)", "self.binValuesNumpy()")
+ line = line.replace("_libBornAgainBase.ICloneable_transferToCPP(self)",
+ "self.__disown__()")
+ line = line.replace("_libBornAgainCore.Histogram1D_binCenters(self)",
+ "self.binCentersNumpy()")
+ line = line.replace("_libBornAgainCore.Histogram1D_binErrors(self)",
+ "self.binErrorsNumpy()")
+ line = line.replace("_libBornAgainCore.Histogram1D_binValues(self)",
+ "self.binValuesNumpy()")
text_out.append(line)
# done the search/replace
fd = open(out_name, "w")
-fd.write( "\n".join( text_out ) )
+fd.write("\n".join(text_out))
fd.close()
diff --git a/cmake/pack/fix_apple_bundle.py b/cmake/pack/fix_apple_bundle.py
index f40cc3e32f118d9f77396a3064f069e22e94591c..415e7119cbdaffc75b7c6ce64cd5d91c41d1b4e9 100644
--- a/cmake/pack/fix_apple_bundle.py
+++ b/cmake/pack/fix_apple_bundle.py
@@ -18,6 +18,7 @@ BUNDLE_DIR = ""
# Locations
# -----------------------------------------------------------------------------
+
def is_python3():
if (sys.version_info > (3, 0)):
return True
@@ -52,7 +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():
@@ -64,7 +66,8 @@ def qtplugins_path():
def bundle_libraries():
- return glob.glob(os.path.join(bundle_dir(), "Contents", "lib", "BornAgain-*", "*"))
+ return glob.glob(
+ os.path.join(bundle_dir(), "Contents", "lib", "BornAgain-*", "*"))
def bundle_plugins():
@@ -82,7 +85,7 @@ def get_list_of_files(dirname):
result = []
for root, directories, filenames in os.walk(dirname):
for filename in filenames:
- result.append(os.path.join(root,filename))
+ result.append(os.path.join(root, filename))
return result
@@ -131,7 +134,8 @@ def setId(filename, newId):
"""
Sets new id for binary file
"""
- p = subprocess.Popen(['install_name_tool', '-id', newId, filename], stdout=subprocess.PIPE)
+ p = subprocess.Popen(['install_name_tool', '-id', newId, filename],
+ stdout=subprocess.PIPE)
p.communicate()
return
@@ -141,7 +145,8 @@ 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
@@ -213,7 +218,7 @@ def get_dependency_libId(dependency):
return "@rpath/" + bundle_python_library()
if is_qt_framework_dependency(dependency):
- return "@rpath/" + libname +".framework/Versions/5/"+libname
+ return "@rpath/" + libname + ".framework/Versions/5/" + libname
# all other libraries
return "@rpath/" + libname
@@ -235,7 +240,7 @@ def get_dependency_orig_location(dependency):
elif is_qt_framework_dependency(dependency):
libname = os.path.basename(dependency)
- libpath = os.path.join(libname+".framework", "Versions", "5")
+ libpath = os.path.join(libname + ".framework", "Versions", "5")
result = os.path.join(qtlibs_path(), libpath, libname)
return result
@@ -251,7 +256,7 @@ def get_dependency_dest_location(dependency):
return os.path.join(bundle_frameworks_path(), bundle_python_library())
if is_qt_framework_dependency(dependency):
- libpath = os.path.join(libname+".framework", "Versions", "5")
+ libpath = os.path.join(libname + ".framework", "Versions", "5")
return os.path.join(bundle_frameworks_path(), libpath, libname)
return os.path.join(bundle_frameworks_path(), libname)
@@ -266,7 +271,7 @@ def get_special_dependency_id(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 "@rpath/" + libname + ".framework/Versions/5/" + libname
return None
@@ -283,8 +288,9 @@ 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')
- result = sys.prefix+"/lib/libpython"+suffix+".dylib"
+ 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
@@ -313,11 +319,14 @@ def copy_python_framework():
def copy_qt_libraries():
print("--> Copying Qt libraries")
- libs = ['QtCore', 'QtDBus', 'QtDesigner', 'QtGui', 'QtPrintSupport', 'QtWidgets', 'QtXml', 'QtSvg', 'QtNetwork', 'QtOpenGL']
+ libs = [
+ 'QtCore', 'QtDBus', 'QtDesigner', 'QtGui', 'QtPrintSupport', 'QtWidgets',
+ 'QtXml', 'QtSvg', 'QtNetwork', 'QtOpenGL'
+ ]
print(" ", end="")
for libname in libs:
print(libname, end="")
- libpath = os.path.join(libname+".framework", "Versions", "5")
+ libpath = os.path.join(libname + ".framework", "Versions", "5")
srcfile = os.path.join(qtlibs_path(), libpath, libname)
if os.path.exists(srcfile):
dstdir = os.path.join(bundle_frameworks_path(), libpath)
@@ -326,8 +335,11 @@ def copy_qt_libraries():
def copy_qt_plugins():
print("--> Copying Qt plugins")
- plugins = ['platforms/libqcocoa.dylib', 'iconengines/libqsvgicon.dylib',
- 'imageformats/libqjpeg.dylib', 'imageformats/libqsvg.dylib', 'styles/libqmacstyle.dylib']
+ plugins = [
+ 'platforms/libqcocoa.dylib', 'iconengines/libqsvgicon.dylib',
+ 'imageformats/libqjpeg.dylib', 'imageformats/libqsvg.dylib',
+ 'styles/libqmacstyle.dylib'
+ ]
print(" ", end="")
for name in plugins:
print(name, end="")
@@ -344,7 +356,7 @@ def process_dependency(dependency):
"""
libId = get_dependency_libId(dependency)
- origLocation = get_dependency_orig_location(dependency)
+ origLocation = get_dependency_orig_location(dependency)
destLocation = get_dependency_dest_location(dependency)
print(" ------")
@@ -394,7 +406,7 @@ def validate_dependencies():
"""
binaries = bornagain_binaries()
libraries = get_list_of_files(bundle_frameworks_path())
- file_list = binaries+libraries
+ file_list = binaries + libraries
files_with_missed_dependencies = []
for file_name in file_list:
for dependency in otool(file_name):
@@ -413,9 +425,9 @@ def validate_dependencies():
def fix_apple_bundle():
- print('-'*80)
+ print('-' * 80)
print("Fixing OS X bundle at '{0}'".format(bundle_dir()))
- print('-'*80)
+ print('-' * 80)
# # copy_python_framework()
# FIXME provide automatic recognition of Qt dependency type (@rpath or hard coded)
# copy_qt_libraries() # this line should be uncommented for macport based builds