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fix ps.ContourIntersection() error #18

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fix ps.ContourIntersection() error #18

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970b25b
fix inverse
fxw97 May 25, 2021
d67ce5c
Fix erros in Visualization of the Contour Intersection Inversion Method
fxw97 May 25, 2021
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96 changes: 52 additions & 44 deletions PyMieScatt/Inverse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def coerceDType(d):
return d

def Inversion(Qsca,Qabs,wavelength,diameter,nMin=1,nMax=3,kMin=0.001,kMax=1,scatteringPrecision=0.010,absorptionPrecision=0.010,spaceSize=120,interp=2):

nRange = np.linspace(nMin,nMax,spaceSize)
kRange = np.logspace(np.log10(kMin),np.log10(kMax),spaceSize)
scaSpace = np.zeros((spaceSize,spaceSize))
Expand All @@ -32,13 +32,13 @@ def Inversion(Qsca,Qabs,wavelength,diameter,nMin=1,nMax=3,kMin=0.001,kMax=1,scat
kRange = zoom(kRange,interp)
scaSpace = zoom(scaSpace,interp)
absSpace = zoom(absSpace,interp)

scaSolutions = np.where(np.logical_and(Qsca*(1-scatteringPrecision)<scaSpace, scaSpace<Qsca*(1+scatteringPrecision)))
absSolutions = np.where(np.logical_and(Qabs*(1-absorptionPrecision)<absSpace, absSpace<Qabs*(1+absorptionPrecision)))

validScattering = nRange[scaSolutions[0]]+1j*kRange[scaSolutions[1]]
validAbsorption = nRange[absSolutions[0]]+1j*kRange[absSolutions[1]]

solution = np.intersect1d(validScattering,validAbsorption)
# errors = [error()]

Expand Down Expand Up @@ -79,13 +79,13 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
if k == 0.0:
kMin = -0.1
axisOption = 1

error = lambda measured,calculated: np.abs((calculated-measured)/measured)
if Qback is not None:
if gridPoints*interpolationFactor<400:
gridPoints = 2*gridPoints
labels = []

incErrors = False
if type(Qsca) in [list, tuple, np.ndarray]:
incErrors = True
Expand All @@ -95,7 +95,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
else:
scaError = None
labels.append("Qsca = {b:1.3f}".format(b=Qsca))

if type(Qabs) in [list, tuple, np.ndarray]:
incErrors = True
absError = Qabs[1]
Expand All @@ -104,7 +104,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
else:
absError = None
labels.append("Qabs = {b:1.3f}".format(b=Qabs))

if type(Qback) in [list, tuple, np.ndarray]:
backError = Qback[1]
Qback = Qback[0]
Expand All @@ -114,7 +114,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
labels.append("Qback - {b:1.3f}".format(b=Qback))
else:
backError = None

nRange = np.linspace(nMin,nMax,gridPoints)
if k == 0.0:
kRange = np.linspace(kMin,kMax,gridPoints)
Expand All @@ -135,25 +135,25 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
QscaList = zoom(np.transpose(np.array(QscaList)),interpolationFactor)
QabsList = zoom(np.transpose(np.array(QabsList)),interpolationFactor)
QbackList = zoom(np.transpose(np.array(QbackList)),interpolationFactor)

_n = zoom(nRange,interpolationFactor)
_k = zoom(kRange,interpolationFactor)

if fig is None and ax is None:
fig, ax = plt.subplots()
elif fig is None:
fig = ax.get_figure()
elif ax is None:
ax = fig.gca()

scaLevels = np.array([Qsca])
absLevels = np.array([Qabs])

if Qback is not None:
backLevels = np.array([Qback])
if backError is not None:
backErrorLevels = np.array([Qback+x for x in [-backError,backError]])

if n is None:
scaChart = ax.contour(_n,_k,QscaList,scaLevels,origin='lower',linestyles='dashdot',linewidths=1.5,colors=('red'))
if scaError is not None:
Expand All @@ -166,7 +166,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
scaChart = ax.vlines(n[0],kMin,kMax,linestyle='dashdot',linewidth=1.5,color='r')
else:
scaChart = ax.vlines(n,kMin,kMax,linestyle='dashdot',linewidth=1.5,color='r')

if k is None:
absChart = ax.contour(_n,_k,QabsList,absLevels,origin='lower',linewidths=1.5,colors=('blue'))
if absError is not None:
Expand All @@ -179,23 +179,23 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
absChart = ax.hlines(k[0],nMin,nMax,linestyle='solid',linewidth=1.5,color='b')
else:
absChart = ax.hlines(k,nMin,nMax,linestyle='solid',linewidth=1.5,color='b')

if Qback is not None:
backChart = ax.contour(_n,_k,QbackList,backLevels,origin='lower',linestyles='dotted',linewidths=1.5,colors=('green'))
if backError is not None:
backErrorLevels = np.array([Qback+x for x in [-backError, backError]])
ax.contourf(_n,_k,QbackList,backErrorLevels,origin='lower',colors=('green'),alpha=0.15)
ax.contour(_n,_k,QbackList,backErrorLevels,origin='lower',linewidths=0.5,colors=('green'),alpha=0.5)

m1 = find_intersections(scaChart,absChart)

if n is not None and type(n) in [list, tuple, np.ndarray]:
scaChart = ax.vlines(scaErrorLevels,kMin,kMax,linestyle='dashdot',linewidth=0.5,color='r',alpha=0.5)
ax.axvspan(scaErrorLevels[0],scaErrorLevels[1],alpha=0.15,color='r')
if k is not None and type(k) in [list, tuple, np.ndarray]:
absChart = ax.hlines(absErrorLevels,nMin,nMax,linestyle='solid',linewidth=0.5,color='b',alpha=0.5)
ax.axhspan(absErrorLevels[0],absErrorLevels[1],alpha=0.15,color='b')

if Qback is not None:
m2 = find_intersections(scaChart,backChart)
r1 = [np.round(x+y*1j,2) for x,y in zip(m1[0],m1[1])]
Expand All @@ -204,7 +204,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
nSolution,kSolution = [xx.real for xx in m_sol],[xx.imag for xx in m_sol]
else:
nSolution,kSolution = m1[0],m1[1]

if type(nSolution)==np.float64:
solutionSet = [nSolution + (0+1j)*kSolution]
else:
Expand All @@ -221,7 +221,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
solutionSet = np.array(solutionSet)
forwardCalculations = np.array(forwardCalculations)
solutionErrors = np.array(solutionErrors)

if n is None and k is None:
proper = solutionErrors <= maxError
solution = []
Expand All @@ -230,30 +230,30 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
solution.append(True)
else:
solution.append(False)

solutionSet = solutionSet[solution]
forwardCalculations = forwardCalculations[solution]
solutionErrors = solutionErrors[solution]
nSolutionsToPlot,kSolutionsToPlot = [x.real for x in solutionSet],[x.imag for x in solutionSet]
else:
nSolutionsToPlot,kSolutionsToPlot = m1[0],m1[1]

ax.scatter(nSolutionsToPlot,kSolutionsToPlot,marker='o',s=128,linewidth=1.5,edgecolor='k',facecolor='none',zorder=3)
ax.scatter(nSolutionsToPlot,kSolutionsToPlot,marker='o',s=128,linewidth=0,edgecolor='none',facecolor='c',zorder=1,alpha=0.25)

for x,y,s in zip(nSolutionsToPlot,kSolutionsToPlot,solutionErrors):
if n is not None:
ax.axhline(y,linewidth=0.5,alpha=0.5,zorder=0)
if k is not None:
ax.axvline(x,linewidth=0.5,alpha=0.5,zorder=0)

ax.set_xlabel('n',fontsize=16)
ax.set_ylabel('k',fontsize=16)

ax.set_xlim((np.min(nRange),np.max(nRange)))
ax.set_ylim((np.min(kRange),np.max(kRange)))
ax.tick_params(which='both',direction='in')

if axisOption == 0:
if max(kSolutionsToPlot) <= 0.5 or kMax <= 1:
ax.set_yscale('log')
Expand All @@ -271,7 +271,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
ax.set_yscale('log')
else:
pass

_c = ax.get_children()
if Qback is None:
if incErrors:
Expand All @@ -290,7 +290,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
'CrosshairsH':_c[4:-10:2],'CrosshairsV':_c[5:-10:2], # solution crosshairs
'LeftSpine':_c[-10],'RightSpine':_c[-9],'BottomSpine':_c[-8],'TopSpine':_c[-7], # spines
'XAxis':_c[-6],'YAxis':_c[-5]} # the axes

else:
if incErrors:
# with Qback and error bounds
Expand All @@ -308,7 +308,7 @@ def ContourIntersection(Qsca,Qabs,wavelength,diameter,Qback=None,n=None,k=None,n
'CrosshairsH':_c[5:-10:2],'CrosshairsV':_c[6:-10:2], # solution crosshairs
'LeftSpine':_c[-10],'RightSpine':_c[-9],'BottomSpine':_c[-8],'TopSpine':_c[-7], # spines
'XAxis':_c[-6],'YAxis':_c[-5]} # the axes

return solutionSet,forwardCalculations,solutionErrors, fig, ax, graphElements

def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax=3,kMin=0.00001,kMax=1,SMPS=True,Bback=None,gridPoints=60,interpolationFactor=2,maxError=0.005,fig=None,ax=None,axisOption=0):
Expand All @@ -320,13 +320,13 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
if k == 0.0:
kMin = -0.1
axisOption = 1

error = lambda measured,calculated: np.abs((calculated-measured)/measured)
if Bback is not None:
if gridPoints*interpolationFactor<120:
gridPoints = 2*gridPoints
labels = []

incErrors = False
if type(Bsca) in [list, tuple, np.ndarray]:
incErrors = True
Expand All @@ -336,7 +336,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
else:
scaError = None
labels.append("Bsca = {b:1.1f}".format(b=Bsca))

if type(Babs) in [list, tuple, np.ndarray]:
incErrors = True
absError = Babs[1]
Expand All @@ -345,7 +345,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
else:
absError = None
labels.append("Babs = {b:1.1f}".format(b=Babs))

if type(Bback) in [list, tuple, np.ndarray]:
backError = Bback[1]
Bback = Bback[0]
Expand All @@ -358,7 +358,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax

dp = coerceDType(dp)
ndp = coerceDType(ndp)

nRange = np.linspace(nMin,nMax,gridPoints)
if k == 0.0:
kRange = np.linspace(kMin,kMax,gridPoints)
Expand Down Expand Up @@ -410,7 +410,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
scaChart = ax.vlines(n[0],kMin,kMax,linestyle='dashdot',linewidth=1.5,color='r')
else:
scaChart = ax.vlines(n,kMin,kMax,linestyle='dashdot',linewidth=1.5,color='r')

if k is None:
absChart = ax.contour(_n,_k,BabsList,absLevels,origin='lower',linewidths=1.5,colors=('blue'))
if absError is not None:
Expand All @@ -423,7 +423,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
absChart = ax.hlines(k[0],nMin,nMax,linestyle='solid',linewidth=1.5,color='b')
else:
absChart = ax.hlines(k,nMin,nMax,linestyle='solid',linewidth=1.5,color='b')

if Bback is not None:
backChart = ax.contour(_n,_k,BbackList,backLevels,origin='lower',linestyles='dotted',linewidths=1.5,colors=('green'))
if backError is not None:
Expand All @@ -432,14 +432,14 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
ax.contour(_n,_k,BbackList,backErrorLevels,origin='lower',linewidths=0.5,colors=('green'),alpha=0.5)

m1 = find_intersections(scaChart,absChart)

if n is not None and type(n) in [list, tuple, np.ndarray]:
scaChart = ax.vlines(scaErrorLevels,kMin,kMax,linestyle='dashdot',linewidth=0.5,color='r',alpha=0.5)
ax.axvspan(scaErrorLevels[0],scaErrorLevels[1],alpha=0.15,color='r')
if k is not None and type(k) in [list, tuple, np.ndarray]:
absChart = ax.hlines(absErrorLevels,nMin,nMax,linestyle='solid',linewidth=0.5,color='b',alpha=0.5)
ax.axhspan(absErrorLevels[0],absErrorLevels[1],alpha=0.15,color='b')

if Bback is not None:
m2 = find_intersections(scaChart,backChart)
r1 = [np.round(x+y*1j,2) for x,y in zip(m1[0],m1[1])]
Expand Down Expand Up @@ -474,23 +474,23 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
solution.append(True)
else:
solution.append(False)

solutionSet = solutionSet[solution]
forwardCalculations = forwardCalculations[solution]
solutionErrors = solutionErrors[solution]
nSolutionsToPlot,kSolutionsToPlot = [x.real for x in solutionSet],[x.imag for x in solutionSet]
else:
nSolutionsToPlot,kSolutionsToPlot = m1[0],m1[1]

ax.scatter(nSolutionsToPlot,kSolutionsToPlot,marker='o',s=128,linewidth=1.5,edgecolor='k',facecolor='none',zorder=3)
ax.scatter(nSolutionsToPlot,kSolutionsToPlot,marker='o',s=128,linewidth=0,edgecolor='none',facecolor='c',zorder=1,alpha=0.25)

for x,y,s in zip(nSolutionsToPlot,kSolutionsToPlot,solutionErrors):
if n is not None:
ax.axhline(y,linewidth=0.5,alpha=0.5,zorder=0)
if k is not None:
ax.axvline(x,linewidth=0.5,alpha=0.5,zorder=0)

for x,y,s in zip(nSolutionsToPlot,kSolutionsToPlot,solutionErrors):
ax.axhline(y,linewidth=0.5,alpha=0.5,zorder=0)
ax.axvline(x,linewidth=0.5,alpha=0.5,zorder=0)
Expand Down Expand Up @@ -540,7 +540,7 @@ def ContourIntersection_SD(Bsca,Babs,wavelength,dp,ndp,n=None,k=None,nMin=1,nMax
'CrosshairsH':_c[4:-10:2],'CrosshairsV':_c[5:-10:2], # solution crosshairs
'LeftSpine':_c[-10],'RightSpine':_c[-9],'BottomSpine':_c[-8],'TopSpine':_c[-7], # spines
'XAxis':_c[-6],'YAxis':_c[-5]} # the axes

else:
if incErrors:
# with Bback and error bounds
Expand Down Expand Up @@ -585,10 +585,18 @@ def find_intersections(A,B):
if type(sol)==geometry.point.Point:
X.append(sol.x)
Y.append(sol.y)
else:
elif type(sol)==geometry.MultiPoint:
for s in sol:
X.append(s.x)
Y.append(s.y)
elif type(sol)==geometry.LineString:
for s in sol.coords:
X.append(s.x)
Y.append(s.y)
else:
for s in sol.collections:
X.append(s.x)
Y.append(s.y)

return X,Y

Expand Down
12 changes: 6 additions & 6 deletions docs/examples.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -514,21 +514,21 @@ This example illustrates the algorithm used by the contour intersection method.
qbackerrs = [Qm[2]-Qm[2]*err,Qm[2]+Qm[2]*err]

ax1.plot_surface(nSurf,kSurf,QscaSurf,rstride=1,cstride=1,cmap=c1,alpha=0.5)
ax1.contour(nSurf,kSurf,QscaSurf,Qm[0],linewidths=2,colors='r',linestyles='dashdot')
ax1.contour(nSurf,kSurf,QscaSurf,[Qm[0]],linewidths=2,colors='r',linestyles='dashdot')
ax1.contour(nSurf,kSurf,QscaSurf,qscaerrs,linewidths=0.5,colors='r',linestyles='dashdot',alpha=0.75)
ax1.contour(nSurf,kSurf,QscaSurf,Qm[0],linewidths=2,colors='r',linestyles='dashdot',offset=0)
ax1.contour(nSurf,kSurf,QscaSurf,[Qm[0]],linewidths=2,colors='r',linestyles='dashdot',offset=0)
ax1.contourf(nSurf,kSurf,QscaSurf,qscaerrs,colors='r',offset=0,alpha=0.25)

ax2.plot_surface(nSurf,kSurf,QabsSurf,rstride=1,cstride=1,cmap=c2,alpha=0.5)
ax2.contour(nSurf,kSurf,QabsSurf,Qm[1],linewidths=2,colors='b',linestyles='solid')
ax2.contour(nSurf,kSurf,QabsSurf,[Q]m[1]],linewidths=2,colors='b',linestyles='solid')
ax2.contour(nSurf,kSurf,QabsSurf,qabserrs,linewidths=0.5,colors='b',linestyles='solid',alpha=0.75)
ax2.contour(nSurf,kSurf,QabsSurf,Qm[1],linewidths=2,colors='b',linestyles='solid',offset=0)
ax2.contour(nSurf,kSurf,QabsSurf,[Qm[1]],linewidths=2,colors='b',linestyles='solid',offset=0)
ax2.contourf(nSurf,kSurf,QabsSurf,qabserrs,colors='b',offset=0,alpha=0.25)

ax3.plot_surface(nSurf,kSurf,QbackSurf,rstride=1,cstride=1,cmap=c3,alpha=0.5)
ax3.contour(nSurf,kSurf,QbackSurf,Qm[2],linewidths=2,colors='g',linestyles='dotted')
ax3.contour(nSurf,kSurf,QbackSurf,[Qm[2]],linewidths=2,colors='g',linestyles='dotted')
ax3.contour(nSurf,kSurf,QbackSurf,qbackerrs,linewidths=0.5,colors='g',linestyles='dotted',alpha=0.75)
ax3.contour(nSurf,kSurf,QbackSurf,Qm[2],linewidths=2,colors='g',linestyles='dotted',offset=0)
ax3.contour(nSurf,kSurf,QbackSurf,[Qm[2]],linewidths=2,colors='g',linestyles='dotted',offset=0)
ax3.contourf(nSurf,kSurf,QbackSurf,qbackerrs,colors='g',offset=0,alpha=0.25)

boxLabels = ["Qsca","Qabs","Qback"]
Expand Down