def calcTvalue(p, df):
t = None
if (df == 1):
t = math.cos(p*math.pi/2.)/math.sin(p*math.pi/2.)
elif (df == 2):
t = math.sqrt(2./(p*(2. - p)) - 2.)
else:
a = 1./(df - 0.5)
b = 48./(a*a)
c = ((20700.*a/b - 98.)*a - 16.)*a + 96.36
d = ((94.5/(b + c) - 3.)/b + 1.)*math.sqrt(a*math.pi*0.5)*df
x = d*p
y = pow(x, 2./df)
if (y > 0.05 + a):
x = Norm_z(0.5*(1. - p))
y = x*x
if (df < 5.):
c = c + 0.3*(df - 4.5)*(x + 0.6)
c = (((0.05*d*x - 5.)*x - 7.)*x - 2.)*x + b + c
y = (((((0.4*y + 6.3)*y + 36.)*y + 94.5)/c - y - 3.)/b + 1.)*x
y = a*y*y
if (y > 0.002):
y = math.exp(y) - 1.
else:
y = 0.5*y*y + y
t = sqrt(df*y)
else:
y = ((1./(((df + 6.)/(df*y) - 0.089*d - 0.822)*(df + 2.)*3.) + 0.5/(df + 4.))*y - 1.)*(df + 1.)/(df + 2.) + 1./y;
t = math.sqrt(df*y)
return t
def SmootBound_LSW(self, myMDP, Gamma, countXVec, beta, startDist):
lInfty=int(numpy.linalg.norm(countXVec, Inf))
Vals=[]
for k in range(lInfty):
Vals.append(self.varPhi_w(countXVec, k, Gamma)*math.exp(-k*beta))
upperBound=numpy.max(Vals)
return upperBound
def SmootBound_LSW(self, myMDP, Gamma, countXVec, beta, startDist):
lInfty = int(numpy.linalg.norm(countXVec, Inf))
Vals = []
for k in range(lInfty+1):
Vals.append(self.varPhi_w(countXVec, k, Gamma) * math.exp(-k*beta))
upperBound = numpy.max(Vals)
return upperBound
def SmoothBound_LSL(self,featurmatrix, myMDP, countXVec, rho, regCoef,beta,numTrajectories):
normPhi = numpy.linalg.norm(featurmatrix,2)
maxRho = numpy.linalg.norm(rho,Inf)
c_lambda = normPhi*maxRho/(math.sqrt(2*regCoef))
#print('===============================================')
#print(regCoef)
l2Rho = numpy.linalg.norm(rho)
phi_k = 0
Vals = []
for k in range(0, numTrajectories+1):
minVal=0
for s in range(len(myMDP.getStateSpace())):
minVal = minVal+rho[s] * min(countXVec[s]+k, numTrajectories)
phi_k = c_lambda*math.sqrt(minVal)+l2Rho
Vals.append((math.pow(phi_k,2))*math.exp(-k*beta))
upperBound=max(Vals)
return upperBound
def computeAggregateSmoothBound(self, z,beta, s,mdp,distance_upper_bound):
partitionPoint=int((len(z)+s)/2)
a= int(s/beta)
#rho=self.computeRho(partitionPoint, Dists,a)
temp_1=0
k=0
t_0=partitionPoint+(k+1)*s
tempList=[]
#print(str(t_0)+" "+str(len(z)))
while t_0 <=len(z):
rho=self.computeRho(z, t_0 , a, mdp,distance_upper_bound)
temp_2=rho*math.exp(-beta*k)
tempList.append(temp_2)
temp_1=max(temp_1, temp_2)
k+=1
t_0=partitionPoint+(k+1)*s
#print(tempList)
return 2*temp_1
def SmoothBound_LSL(self,featurmatrix, myMDP, countXVec, rho, regCoef,beta,numTrajectories):
normPhi=numpy.linalg.norm(featurmatrix)
maxRho=numpy.linalg.norm(rho,Inf)
c_lambda=normPhi*maxRho/(math.sqrt(2*regCoef))
#print('===============================================')
#print(regCoef)
l2Rho=numpy.linalg.norm(rho)
phi_k=0
Vals=[]
for k in range(0,numTrajectories):
minVal=0
for s in range(len(myMDP.getStateSpace())-1):
minVal=minVal+rho[s]*min(countXVec[s]+k,numTrajectories)
phi_k=c_lambda*math.sqrt(minVal)+l2Rho
Vals.append((math.pow(phi_k,2))*math.exp(-k*beta))
upperBound=max(Vals)
#print('Smooth upper bound= '+str(upperBound))
return upperBound
def computeAggregateSmoothBound(self, z, beta, s, mdp, distance_upper_bound):
partitionPoint=int((len(z)+s)/2)
a= int(s/beta)
#rho=self.computeRho(partitionPoint, Dists,a)
temp_1=0
k=0
t_0=partitionPoint+(k+1)*s
tempList=[]
#print(str(t_0)+" "+str(len(z)))
while t_0 <=len(z):
rho=self.computeRho(z, t_0 , a, mdp,distance_upper_bound)
temp_2=rho*math.exp(-beta*k)
tempList.append(temp_2)
temp_1=max(temp_1, temp_2)
k+=1
t_0=partitionPoint+(k+1)*s
#print(tempList)
return 2*temp_1
def f(x):
f = (math.exp(-x * x / 2)) / math.sqrt(2.0 * math.pi)
return f
def exponen(x):
return math.exp(x)
def f(inp):
return (math.exp(-inp * inp / 2)) / math.sqrt(2.0 * math.pi)
def run_fitting(i_img): # for this thesis just batch simulations, no fitting.
# passing the simulation through the fitting mechanism
# still useful for processing experimental and
# simulation patterns simultaneously
global first_run
global batch_sim
global init_radius
global init_height
global init_height_flattening_ratio
global init_lattice_length
global init_damping_length
global init_disorder_parameter
global init_beam_intensity
if batch_sim == True: # setting the simulation parameters
d_eff = 11.6 * (0.1 * (i_img - 11)) / 150
init_lattice_length = 2 * np.pi / (0.628 +
1.499 * math.exp(-d_eff / 3.31))
init_height = 1.519 + 1.367 * d_eff - 0.038 * (d_eff**2)
init_radius = init_height / 3.1
init_height_flattening_ratio = 0.66
init_disorder_parameter = 0.25
init_damping_length = 30 * nm
init_beam_intensity = 4.15e+09
real_data = load_real_data(i_img)
fit_objective = ba.FitObjective()
fit_objective.addSimulationAndData(get_simulation, real_data)
fit_objective.initPrint(1)
fit_objective.initPlot(1, PlotObserver(
)) #plotting frequency on screen (increase if OpenGL error)
params = ba.Parameters(
) #parameter limits only relevant for full fitting, otherwise ignored
min_height = 0.1
max_height = 20
min_lattice_length = 0.1
max_lattice_length = 20
min_radius = 0.1
max_radius = 20
min_damping_length = 10
max_damping_length = 1000
min_disorder_parameter = 0.1
max_disorder_parameter = 0.5
min_beam_intensity = 1e+8
max_beam_intensity = 1e+12
params.add("radius",
value=init_radius,
min=min_radius,
max=max_radius,
step=0.1 * nm,
vary=True)
params.add("height",
value=init_height,
min=min_height,
max=max_height,
step=0.1 * nm,
vary=True)
params.add("height_flattening_ratio",
value=init_height_flattening_ratio,
min=0.55,
max=0.75,
step=0.01,
vary=True)
params.add("lattice_length",
value=init_lattice_length,
min=min_lattice_length,
max=max_lattice_length,
step=0.1 * nm,
vary=True)
params.add("damping_length",
value=init_damping_length,
min=min_damping_length,
max=max_damping_length,
step=10 * nm,
vary=True)
params.add("disorder_parameter",
value=init_disorder_parameter,
min=min_disorder_parameter,
max=max_disorder_parameter,
step=0.01,
vary=True)
params.add("beam_intensity",
init_beam_intensity,
min=min_beam_intensity,
max=max_beam_intensity,
vary=False)
minimizer = ba.Minimizer()
minimizer.setMinimizer("Test") # normal simulation (no fitting)
#minimizer.setMinimizer("Minuit2", "Migrad", "MaxFunctionCalls=0;Strategy=2;") # minimizer for fitting
result = minimizer.minimize(fit_objective.evaluate,
params) # runs the simulation
fit_objective.finalize(result)
fig_name = output_folder + 'fitting_img_#32_' + repr(i_img) + '.png'
plt.savefig(fig_name, dpi=500)
plt.close(1)
print("Fitting completed.")
print("chi2:", result.minValue())
for fitPar in result.parameters():
print(fitPar.name(), fitPar.value, fitPar.error)
experimental_data = fit_objective.experimentalData()
simulation_data = fit_objective.simulationResult()
difference = fit_objective.relativeDifference()
zmin = 0.1 # range of the colormap
zmax = 100
mpl.rcParams['image.cmap'] = 'jet' # saves figures in jet colormap
plt.figure(2, figsize=(8, 6))
ba.plot_colormap(experimental_data,
title="Experimental data",
zmin=zmin,
zmax=zmax,
units=ba.AxesUnits.QSPACE,
xlabel=None,
ylabel=None,
zlabel='',
aspect=None)
fig_name = output_folder + 'exp_data_#32_' + repr(i_img) + '_jet' + '.png'
plt.savefig(fig_name, dpi=500)
plt.close(2)
plt.figure(3, figsize=(8, 6))
ba.plot_colormap(simulation_data,
title="Simulation result",
zmin=zmin,
zmax=zmax,
units=ba.AxesUnits.QSPACE,
xlabel=None,
ylabel=None,
zlabel='',
aspect=None)
fig_name = output_folder + 'sim_data_#32_' + repr(i_img) + '_jet' + '.png'
plt.savefig(fig_name, dpi=500)
plt.close(3)
mpl.rcParams[
'image.cmap'] = 'nipy_spectral' #saves figures in spectral colormap
plt.figure(4, figsize=(8, 6))
ba.plot_colormap(experimental_data,
title="Experimental data",
zmin=zmin,
zmax=zmax,
units=ba.AxesUnits.QSPACE,
xlabel=None,
ylabel=None,
zlabel='',
aspect=None)
fig_name = output_folder + 'exp_data_#32_' + repr(
i_img) + '_spectrum' + '.png'
plt.savefig(fig_name, dpi=500)
plt.close(4)
plt.figure(5, figsize=(8, 6))
ba.plot_colormap(simulation_data,
title="Simulation result",
zmin=zmin,
zmax=zmax,
units=ba.AxesUnits.QSPACE,
xlabel=None,
ylabel=None,
zlabel='',
aspect=None)
fig_name = output_folder + 'sim_data_#32_' + repr(
i_img) + '_spectrum' + '.png'
plt.savefig(fig_name, dpi=500)
plt.close(5)
"""
Euler method solving RC circuit ODE.
"""
from numpy import array, arange, zeros, empty, linalg, math
import pylab as pl
rc = 2.0
dt = 0.5
n = 1000
t = 0.0
q = 1.0
qt = []
qt0 = []
time = []
for i in range(n):
t = t + dt
q = q - q * dt / rc
q0 = math.exp(-t / rc)
qt.append(q)
qt0.append(q0)
time.append(t)
pl.plot(time, qt, 'ro', label='Euler')
pl.plot(time, qt0, 'k-', label='Analytical')
pl.xlabel('Time')
pl.ylabel('charge')
pl.xlim(0, 12)
pl.ylim(-0.2, 1.0)
pl.legend(loc='upper right')
pl.show()
def f(x):
f = (math.exp(-x*x/2))/math.sqrt(2.0*math.pi)
return f
def estimateP(n,Kn):
P = 1 - math.exp((-6 * Kn**2)/(n**3 + n**2))
return P
def plotTF(self , labelX=True , labelY=True, fontsize=12 , ylim=None, patchColor=None , labelColor=None ,
multicolor=False ,axes=None ,maxAtoms=None, recenter=None,keepValues=False,
french=False,Alpha=False,logF=False):
""" A time Frequency plot routine using Matplotlib
each atom of the approx is plotted in a time-frequency plane with a gray scale for amplitudes
Many options are available:
- labelX : whether or not to add the Time label on the X axis
- labelY : whether or not to add the Frequency label on the Y axis
- fontsize : the label fontSize
- ylim : the frequency range of the plot
- patchColor : specify a single color for all atoms
- maxAtoms : specify a maximum number of atom to take into account. Usually atoms are ordered by decreasing amplitude due to MP rules, meaning only the most salient atoms will be plotted
- recenter : a couple of values to offset the time and frequency localization of atoms
- keepValues : use atom Amplitudes for atom colorations
- french : all labels in french
- Alpha : use transparency
- logF : frequency axis in logarithmic scale
"""
# plt.figure()
if french:
labx = "Temps (s)"
laby = "Frequence (Hz)"
else:
labx = "Time (s)"
laby = "Frequency (Hz)"
Fs = self.samplingFrequency
# first loop to recover max value
maxValue = 0
maxFreq = 1.0
minFreq = 22000.0
if not keepValues:
valueArray = array([math.log10(abs(atom.getAmplitude())) for atom in self.atoms])
else:
valueArray = array([abs(atom.getAmplitude()) for atom in self.atoms])
if multicolor:
cmap = cc.LinearSegmentedColormap('jet',abs(valueArray) )
for atom in self.atoms:
if abs(atom.mdct_value) > maxValue:
maxValue = abs(atom.mdct_value)
# normalize to 0 -> 1
# if min(valueArray) < 0:
if len(valueArray) > 0 and not keepValues:
valueArray = valueArray - min(valueArray)
valueArray = valueArray/max(valueArray)
# Get target axes
if axes is None:
axes = plt.gca()
# normalize the colors
# if multicolor:
# normedValues = cc.Normalize(valueArray)
if maxAtoms is not None:
maxTom = min(maxAtoms,len(self.atoms))
else:
maxTom = len(self.atoms)
# Deal with static offsets
if recenter is not None:
yOffset= recenter[0]
xOffset= recenter[1]
else:
yOffset,xOffset = 0,0
# print yOffset,xOffset
if Alpha:
alphaCoeff=0.6
else:
alphaCoeff=1
patches = []
colors = []
for i in range(maxTom):
atom = self.atoms[i]
L = atom.length
K = L/2
freq = atom.frequencyBin
f = float(freq)*float(Fs)/float(L)
bw = ( float(Fs) / float(K) ) #/ 2
p = float(atom.timePosition + K) / float(Fs)
l = float(L - K/2) / float(Fs)
# print "f = " ,f , " Hz"
if f>maxFreq:
maxFreq = f+bw+bw
if f < minFreq:
minFreq = f-bw-10*bw
# xy = p, f-bw,
xy = p - xOffset, f - yOffset,
width, height = l, bw
# xy = p - xOffset, log10(f) - yOffset,
if logF:
xy = p - xOffset , (12*log2(f - yOffset))
height = 1.0 # BUGFIX
# print xy , f
colorvalue = math.sqrt(valueArray[i])
if multicolor:
patchtuplecolor = (math.sqrt(colorvalue),
math.exp(-((colorvalue - 0.35)**2)/(0.15)),
1-math.sqrt(colorvalue))
colors.append(colorvalue)
else:
if patchColor is None:
patchtuplecolor = (1-math.sqrt(colorvalue),1- math.sqrt(colorvalue),1- math.sqrt(colorvalue))
colors.append(colorvalue)
else:
patchtuplecolor = patchColor
colors.append(patchColor)
# patchtuplecolor = (colorvalue, colorvalue, colorvalue)
# patch = mpatches.Rectangle(xy, width, height, facecolor=patchtuplecolor, edgecolor=patchtuplecolor , zorder=colorvalue )
# xy = p + L/2 , f-bw,
patch = mpatches.Ellipse(xy, width, height, facecolor=patchtuplecolor, edgecolor=patchtuplecolor , zorder=colorvalue )
if keepValues:
patches.append(patch)
else:
axes.add_patch(patch)
if keepValues:
# first sort the patches by values
sortedIndexes = valueArray.argsort()
PatchArray = array(patches)
p = PatchCollection(PatchArray[sortedIndexes].tolist(),linewidths=0.,cmap=matplotlib.cm.copper_r,match_original=False, alpha=alphaCoeff)
# print array(colors).shape
p.set_array(valueArray[sortedIndexes])
axes.add_collection(p)
if labelColor is None:
labelColor = 'k'
# finalize graphic options
axes.set_xlim(0- xOffset , (self.length)/float(Fs)- xOffset)
if ylim is None:
axes.set_ylim(max(0 ,minFreq)- yOffset , maxFreq- yOffset)
else:
axes.set_ylim(ylim)
if labelY:
axes.set_ylabel(laby , fontsize=fontsize , color=labelColor)
# plt.ylabel.set_color(labelColor)
else:
plt.setp(axes, 'yticklabels', [])
if labelX:
axes.set_xlabel(labx, fontsize=fontsize)
else:
plt.setp(axes, 'xticklabels', [])
if keepValues:
plt.colorbar(p)
