def plotMiddle(self):
"""Function to plot the graph on the Middle Canvas"""
self.ui.factorPlot.canvas.ax.cla()
self.ui.factorPlot.canvas.ax.grid(True)
self.elementList = Utility.molToElemList(self.molecule)
self.elementParameters = Utility.read_parameters(
self.elementList, "./elementParameters.txt")
if self.ui.formFactorCheck.isChecked():
# print("test fe check")
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q = UtilityAnalysis.check_data_length(
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q, self.ui.minQ.value(),
self.ui.maxQ.value())
self.fe_Q, self.Ztot = MainFunctions.calc_eeff(
self.elementList, self.Q, self.elementParameters)
self.ui.factorPlot.canvas.ax.plot(self.Q,
self.fe_Q,
label=r"$f_e(Q)$")
self.ui.factorPlot.canvas.ax.legend()
self.ui.factorPlot.canvas.draw()
# else:
# # print("test unchecked")
# self.ui.factorPlot.canvas.ax.lines.pop(0)
# self.ui.factorPlot.canvas.draw()
if self.ui.SQCheck.isChecked():
S_Q = self.SQ()
self.ui.factorPlot.canvas.ax.plot(self.Q, S_Q, label=r"$S(Q)$")
self.ui.factorPlot.canvas.ax.legend()
self.ui.factorPlot.canvas.draw()
if self.ui.incohCheck.isChecked():
self.Iincoh_Q = MainFunctions.calc_Iincoh(self.elementList, self.Q,
self.elementParameters)
self.ui.factorPlot.canvas.ax.plot(self.Q,
self.Iincoh_Q,
label=r"$I_{incoh}(Q)$")
self.ui.factorPlot.canvas.ax.legend()
self.ui.factorPlot.canvas.draw()
if self.ui.QiQCheck.isChecked():
self.Sinf = MainFunctions.calc_Sinf(self.elementList, self.fe_Q,
self.Q, self.Ztot,
self.elementParameters)
self.i_Q = MainFunctions.calc_iQ(S_Q, self.Sinf)
# self.r = MainFunctions.calc_r(self.Q)
Qi_Q = self.Q * self.i_Q
self.ui.factorPlot.canvas.ax.plot(self.Q, Qi_Q, label=r"$Qi(Q)$")
self.ui.factorPlot.canvas.ax.legend()
self.ui.factorPlot.canvas.draw()
def test3_checkOrArgGroups(self):
"""
Given no argument while expecting 2 'orArg' arguments in a single group,
Should return 'False' and an error message
"""
myUtility = Utility.Utility()
myDebug = Debug.Debug()
myCommandLine = CommandLine.CommandLine(description='Blah blah blah.',
objDebug=myDebug,
objUtility=myUtility)
myCommandLine._argDict['arg1'] = {
'value': None,
'orArgGroup': 'group1'
}
myCommandLine._argDict['arg2'] = {
'value': None,
'orArgGroup': 'group1'
}
orArgsAreOk, message = myCommandLine.checkOrArgGroups()
self.assertFalse(orArgsAreOk)
self.assertNotEqual(message, '')
def test3_checkArgsMatchRules(self):
"""
Given 2 invalid arguments 'integer1' and 'integer2',
Should return 'False'
"""
integer1Value = 12.34
integer2Value = 'a'
integerRule = '(\d+)'
myUtility = Utility.Utility()
myDebug = Debug.Debug()
myCommandLine = CommandLine.CommandLine(description='Blah blah blah.',
objDebug=myDebug,
objUtility=myUtility)
myCommandLine._argDict['integer1'] = {
'value': integer1Value,
'rule': integerRule,
}
myCommandLine._argDict['integer2'] = {
'value': integer2Value,
'rule': integerRule,
}
self.assertEqual(myCommandLine.checkArgsMatchRules(), False)
def test1_isNumber(self):
"""
Given the number 42
should return True
"""
myUtility = Utility.Utility()
self.assertEqual(myUtility.isNumber(42), True)
def test4_isNumber(self):
"""
Given the number '' (empty string)
should return False
"""
myUtility = Utility.Utility()
self.assertEqual(myUtility.isNumber(''), False)
def import_data(self):
"""Function to load and plot the data file"""
# commented just for testing
# if self.ui.dataFileName.toPlainText() == "":
# path, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Load Data File",
# r"../data/cea_files/Ar", "Data File(*chi *xy)")
# else:
# path = self.dirpath + "/" + self.ui.dataFileName.toPlainText()
# # if self.ui.dataPathName.toPlainText() == "":
# # self.dirpath = str(QtWidgets.QFileDialog.getExistingDirectory(self, "Open directory",
# # r"..\data\cea_files\Ar", QtWidgets.QFileDialog.ShowDirsOnly))
# # else:
# # self.dirpath = self.ui.dataPathName.toPlainText()
# # path = self.dirpath + "/" + self.ui.dataFileName.toPlainText()
path = r"../data/cea_files/Ar/HT2_034T++_rem.chi"
pathDir, fileName = os.path.split(path)
self.ui.dataPathName.setPlainText(pathDir)
self.ui.dataFileName.setPlainText(fileName)
self.Q, self.I_Q = Utility.read_file(path)
self.orgQ = self.Q
self.orgI_Q = self.I_Q
self.ui.rawDataPlot.canvas.ax.plot(self.Q, self.I_Q, "b", label="Data")
self.ui.rawDataPlot.canvas.ax.legend()
self.ui.rawDataPlot.canvas.draw()
def test5_isNumber(self):
"""
Given the string '1.2.3'
should return False
"""
myUtility = Utility.Utility()
self.assertEqual(myUtility.isNumber('1.2.3'), False)
def import_bkg(self):
"""Function to load and plot the bkg file"""
# commented just for testing
# if self.ui.bkgFileName.toPlainText() == "":
# path, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Load Bkg File",
# r"../data/cea_files/Ar", "Data File(*chi *xy)")
# else:
# path = self.dirpath + "/" + self.ui.bkgFileName.toPlainText()
path = r"../data/cea_files/Ar/HT2_036T++_rem.chi"
pathDir, fileName = os.path.split(path)
self.ui.dataPathName.setPlainText(pathDir)
self.ui.bkgFileName.setPlainText(fileName)
self.Qbkg, self.Ibkg_Q = Utility.read_file(path)
self.orgQbkg = self.Qbkg
self.orgIbkg_Q = self.Ibkg_Q
path = ""
self.ui.rawDataPlot.canvas.ax.plot(self.Qbkg,
self.Ibkg_Q,
"g--",
label="Bkg")
self.ui.rawDataPlot.canvas.ax.legend()
self.ui.rawDataPlot.canvas.draw()
def test2_isNumber(self):
"""
Given the number -273.15
should return True
"""
myUtility = Utility.Utility()
self.assertEqual(myUtility.isNumber(-273.15), True)
def geometry_correction(Q, I_Q, Qbkg, Ibkg_Q, variables, phi_matrix_flag):
"""Function to calcultate all intensity geometrical corrections.
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
I_Q : numpy array
measured scattering intensity
Qbkg : numpy array
background momentum transfer (nm^-1)
Ibkg_Q : numpy array
background scattering intensity
variables : module
input variables setted by the user
phi_matrix_flag : string
flag for the phi matrix calculation:
"y": calculate phi matrix and save on file
"n": read the phi matrix from file
Returns
-------
I_Q : numpy array
corrected measured sample intensity
Ibkg_Q : numpy array
corrected background intensity
"""
two_theta = UtilityAnalysis.Qto2theta(Q)
abs_corr_factor = calcAbsCorrection(variables.abs_length, \
two_theta, variables.dac_thickness, 0)
num_point = 1000
phi_matrix_path = "./phi_matrix_" + variables.molecule
if phi_matrix_flag.lower() == "y":
ws1, ws2, r1, r2, d = Utility.read_MCC_file(variables.MCC_path,
variables.MCC_type)
thickness_sampling, phi_matrix = calc_phi_matrix(variables.phi_matrix_thickness, \
two_theta, ws1, ws2, r1, r2, d, num_point)
np.save(phi_matrix_path, phi_matrix)
else:
thickness_sampling = np.linspace(0,
variables.phi_matrix_thickness,
num=num_point)
phi_matrix = np.load(phi_matrix_path + ".npy")
T_MCC_sample3, T_MCC_DAC3, T_MCC_ALL3 = calc_T_MCC(0.003, thickness_sampling, \
phi_matrix, "y")
T_MCC_sample4, T_MCC_DAC4, T_MCC_ALL4 = calc_T_MCC(0.004, thickness_sampling, \
phi_matrix, "y")
T_MCC_corr_factor_bkg = calc_T_DAC_MCC_bkg_corr(T_MCC_DAC4, T_MCC_DAC3)
I_Q = I_Q / (abs_corr_factor * T_MCC_sample4)
Ibkg_Q = Ibkg_Q * T_MCC_corr_factor_bkg / (abs_corr_factor * T_MCC_sample4)
return (I_Q, Ibkg_Q)
def test3_isNumber(self):
"""
Given the number "this is not a number, AAARGL!"
should return False
"""
myUtility = Utility.Utility()
self.assertEqual(myUtility.isNumber('this is not a number, AAARGL!'),
False)
def test1_computePercentage(self):
"""
Given a number and a total (both are >0)
should return a percentage (float) : 0 <= number <= 100
"""
myUtility = Utility.Utility()
number = 12
total = 42
percentage = myUtility.computePercentage(number, total)
self.assertTrue((percentage >= 0) and (percentage <= 100))
def test2_computePercentage(self):
"""
Given any number and total == 0
should return 0
"""
myUtility = Utility.Utility()
number = 12
total = 0
expected = 0
self.assertEqual(myUtility.computePercentage(number, total), expected)
def test3_computeExitStatus(self):
"""
Given a CPU load > crit threshold
should return the 'CRITICAL' Nagios plugin exit status
"""
self._objUtility = Utility.Utility()
self._objDebug = Debug.Debug()
myPlugin = CheckLocalCpu.CheckLocalCpu(
name='CHECK LOCAL CPU',
objDebug=self._objDebug,
)
myPlugin.cpuUsagePercent = critical + 1
exitStatus = myPlugin.computeExitStatus(warningThreshold=warning,
criticalThreshold=critical)
self.assertEqual(exitStatus, 'CRITICAL')
def calc_IFFT_Fr(r, F_r):
"""Function to calculate the FFT following the IGOR procedure.
I do not agree with this procedure, but I follow it to compare my results
with Igor Pro's ones.
Parameters
----------
r : numpy array
atomic distance (nm)
F_r : numpy array
F(r)
Returns
-------
Q : numpy array
momentum transfer (nm^-1)
Qi_Q : numpy array
Qi(Q)
"""
NumPoints = 2**math.ceil(math.log(len(F_r)-1)/math.log(2))
F_r = Utility.resize_zero(F_r, NumPoints)
Q = np.linspace(0.0, 109, 550)
DelQ = 2*np.pi/(np.mean(np.diff(r))*NumPoints)
meanDeltar = np.mean(np.diff(r))
Q1 = fftpack.fftfreq(r.size, meanDeltar)
Qi_Q = fftpack.fft(F_r)
Qi_Q = Qi_Q[np.where(Q1>=0.0)]
Qi_Q = -np.imag(Qi_Q)*meanDeltar
Q1 = np.arange(0.0, 0.0+DelQ*len(Qi_Q), DelQ)
idxArray = np.zeros(550, dtype=np.int)
for i in range(len(Q)):
idxArray[i], _ = UtilityAnalysis.find_nearest(Q1, Q[i])
Qi_Q = Qi_Q[idxArray]
return (Q, Qi_Q)
def calc_FFT_QiQ(Q, Qi_Q, QmaxIntegrate):
"""Function to calculate the FFT following the Igor Pro procedure.
I do not agree with this procedure, but I follow it to compare my results
with Igor Pro's ones.
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
Qi_Q : numpy array
Q*i(Q)
QmaxIntegrate : float
maximum Q value for the integrations
Returns
-------
r : numpy array
atomic distance (nm)
F_r : numpy array
F(r)
"""
pMax, elem = UtilityAnalysis.find_nearest(Q, QmaxIntegrate)
NumPoints = 2*2*2**math.ceil(math.log(5*(pMax+1))/math.log(2))
DelR = 2*np.pi/(np.mean(np.diff(Q))*NumPoints)
Qi_Q = Utility.resize_zero(Qi_Q[Q<=QmaxIntegrate], NumPoints)
Qi_Q[pMax+1:] = 0.0
Q = np.arange(np.amin(Q), np.amin(Q)+np.mean(np.diff(Q))*NumPoints, np.mean(np.diff(Q)))
r = MainFunctions.calc_r(Q)
F_r = fftpack.fft(Qi_Q)
F_r = F_r[np.where(r>=0.0)]
F_r = -np.imag(F_r)*np.mean(np.diff(Q))*2/np.pi
r = np.arange(0.0, 0.0+DelR*len(F_r), DelR)
return (r, F_r)
def calc_iintra(Q, fe_Q, Ztot, QmaxIntegrate, maxQ, elementList, element, x, y,
z, elementParameters):
"""Function to calculate the intramolecular contribution of i(Q) (eq. 41).
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
fe_Q : numpy array
effective electric form factor
Ztot : int
total Z number
QmaxIntegrate : float
maximum Q value for the intagrations
maxQ : float
maximum Q value
elementList : dictionary("element": multiplicity)
chemical elements of the sample with their multiplicity
element : string
chemical element
multiplicity : int
chemical element multiplicity
element : string array
array with the elements in the xyz_file
x, y, z : float array
atomic coordinate in the xyz_file (nm)
elementParameters : dictionary("element": parameters)
chemical elements of the sample with their parameters
element : string
chemical element
parameters : list
list of the parameters
(Z, a1, b1, a2, b2, a3, b3, a4, b4, c, M, K, L)
Returns
-------
iintra_Q : numpy array
intramolecular contribution of i(Q)
"""
iintra_Q = np.zeros(Q.size)
sinpq = np.zeros(Q.size)
for ielem in range(len(element)):
for jelem in range(len(element)):
if ielem != jelem:
Kpi = MainFunctions.calc_Kp(fe_Q, element[ielem], Q,
elementParameters)
Kpj = MainFunctions.calc_Kp(fe_Q, element[jelem], Q,
elementParameters)
KK = Kpi * Kpj
d = Utility.calc_distMol(x[ielem], y[ielem], z[ielem],
x[jelem], y[jelem], z[jelem])
if d != 0.0:
iintra_Q += KK * np.sin(d * Q) / (d * Q)
iintra_Q[Q == 0.0] = KK
iintra_Q[(Q > QmaxIntegrate) & (Q <= maxQ)] = 0.0
iintra_Q /= Ztot**2
# iintra_Q /= 3
return iintra_Q
# pip install psutil
# Installing "psutil" this way requires the (Debian) packages :
# python-pip
# python-dev
#
# KNOWN BUGS AND LIMITATIONS :
# 1.
#
########################################## ##########################################################
from modules import CommandLine
from modules import CheckLocalCpu
from modules import Debug
from modules import Utility
myUtility = Utility.Utility()
myDebug = Debug.Debug()
myCommandLine = CommandLine.CommandLine(
description='Check the local CPU usage.',
objDebug=myDebug,
objUtility=myUtility)
myPlugin = CheckLocalCpu.CheckLocalCpu(
name='CHECK LOCAL CPU',
objDebug=myDebug,
)
myCommandLine.declareArgument({
'shortOption': 'w',
'longOption': 'warning',
def calc_iintraFZ(Q, QmaxIntegrate, maxQ, elementList, element, x, y, z,
elementParameters, aff_mean_squared):
"""Function to calculate the intramolecular contribution of i(Q) (eq. 41).
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
fe_Q : numpy array
effective electric form factor
Ztot : int
total Z number
QmaxIntegrate : float
maximum Q value for the intagrations
maxQ : float
maximum Q value
elementList : dictionary("element": multiplicity)
chemical elements of the sample with their multiplicity
element : string
chemical element
multiplicity : int
chemical element multiplicity
element : string array
array with the elements in the xyz_file
x, y, z : float array
atomic coordinate in the xyz_file (nm)
elementParameters : dictionary("element": parameters)
chemical elements of the sample with their parameters
element : string
chemical element
parameters : list
list of the parameters
(Z, a1, b1, a2, b2, a3, b3, a4, b4, c, M, K, L)
Returns
-------
iintra_Q : numpy array
intramolecular contribution of i(Q)
"""
iintra_Q = np.zeros(Q.size)
sinpq = np.zeros(Q.size)
for ielem in range(len(element)):
for jelem in range(len(element)):
if ielem != jelem:
# print(ielem, jelem)
# print(type(element[ielem]))
# print(element[ielem], elementList[element[ielem]], element[jelem], elementList[element[jelem]])
f_Qi = MainFunctions.calc_aff(element[ielem], Q,
elementParameters)
f_Qj = MainFunctions.calc_aff(element[jelem], Q,
elementParameters)
f_i = np.mean(elementList[element[ielem]] * f_Qi / 3)
f_j = np.mean(elementList[element[jelem]] * f_Qj / 3)
# f_i = np.mean(f_Qi)
# f_j = np.mean(f_Qj)
ff = f_i * f_j
d = Utility.calc_distMol(x[ielem], y[ielem], z[ielem],
x[jelem], y[jelem], z[jelem])
if d != 0.0:
iintra_Q += ff * np.sin(d * Q) / (d * Q)
iintra_Q[Q == 0.0] = ff
iintra_Q[(Q > QmaxIntegrate) & (Q <= maxQ)] = 0.0
iintra_Q /= np.mean(aff_mean_squared)
# iintra_Q /= 3
return iintra_Q
def SQ(self):
"""Function to calculate and plot the structure factor S(Q)"""
self.elementList = Utility.molToElemList(self.molecule)
# self.elementList = Utility.molToElemList("Ar")
self.elementParameters = Utility.read_parameters(
self.elementList, "./elementParameters.txt")
# print(elementList)
# print(elementParameters)
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q = UtilityAnalysis.check_data_length(
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q, self.ui.minQ.value(),
self.ui.maxQ.value())
two_theta = UtilityAnalysis.Qto2theta(self.Q)
absCorrFactor = Geometry.calcAbsCorrection(
self.ui.absLength.value(), two_theta, self.ui.dacThickness.value(),
self.ui.dacAngle.value())
self.I_Q = self.I_Q / absCorrFactor
self.Ibkg_Q = self.Ibkg_Q / absCorrFactor
self.fe_Q, self.Ztot = MainFunctions.calc_eeff(self.elementList,
self.Q,
self.elementParameters)
self.Iincoh_Q = MainFunctions.calc_Iincoh(self.elementList, self.Q,
self.elementParameters)
self.J_Q = MainFunctions.calc_JQ(self.Iincoh_Q, self.Ztot, self.fe_Q)
self.Sinf = MainFunctions.calc_Sinf(self.elementList, self.fe_Q,
self.Q, self.Ztot,
self.elementParameters)
self.dampingFunct = UtilityAnalysis.calc_dampingFunction(
self.Q,
self.ui.dampingFactor.value(), self.ui.QmaxIntegrate.value(),
self.ui.dampingFunction.currentText())
Isample_Q = MainFunctions.calc_IsampleQ(
self.I_Q, self.ui.scaleFactorValue.value(), self.Ibkg_Q)
alpha = MainFunctions.calc_alpha(
self.J_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Sinf,
self.Q[self.Q <= self.ui.QmaxIntegrate.value()],
Isample_Q[self.Q <= self.ui.QmaxIntegrate.value()],
self.fe_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Ztot,
self.ui.densityValue.value())
Icoh_Q = MainFunctions.calc_Icoh(alpha, Isample_Q, self.Iincoh_Q)
S_Q = MainFunctions.calc_SQ(Icoh_Q, self.Ztot, self.fe_Q, self.Sinf,
self.Q, self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
Ssmooth_Q = UtilityAnalysis.calc_SQsmoothing(
self.Q, S_Q, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.minQ.value(), self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
self.SsmoothDamp_Q = UtilityAnalysis.calc_SQdamp(
Ssmooth_Q, self.Sinf, self.dampingFunct)
# self.ui.factorPlot.canvas.ax.plot(self.Q, self.SsmoothDamp_Q, "b", label=r"$S(Q)$")
# self.ui.factorPlot.canvas.ax.legend()
# self.ui.factorPlot.canvas.draw()
return self.SsmoothDamp_Q
# from modules import Geometry
from modules import IgorFunctions
# from modules import KaplowMethod
from modules import MainFunctions
# from modules import Minimization
from modules import Optimization
from modules import Utility
from modules import UtilityAnalysis
# from PyQt5.QtWidgets import QApplication, QVBoxLayout, QWidget
if __name__ == "__main__":
# ---------------------------Files reading---------------------------------
variables = Utility.read_inputFile("./inputFile.txt")
elementList = Utility.molToelemList(variables.molecule)
elementParameters = Utility.read_parameters(elementList,
variables.element_params_path)
path = Utility.path_xyz_file(variables.molecule)
numAtoms, element, x, y, z = Utility.read_xyz_file(path)
Q, I_Q = Utility.read_file(variables.data_file)
Qbkg, Ibkg_Q = Utility.read_file(variables.bkg_file)
# -------------------Preliminary calculation-------------------------------
fe_Q, Ztot = MainFunctions.calc_eeff(elementList, Q, elementParameters)
Iincoh_Q = MainFunctions.calc_Iincoh(elementList, Q, elementParameters)
def Optimization(self):
"""Function to optimize and plot F(r)"""
#-------------------Intra-molecular components-----------------------------
# numAtoms, element, x, y, z = Utility.read_xyz_file(self.XYZFilePath)
numAtoms, element, x, y, z = Utility.read_xyz_file(
"/Users/ciccio/work/ID27/LASDiA/xyzFiles/Ar.xyz")
iintra_Q = Optimization.calc_iintra(self.Q, self.fe_Q, self.Ztot,
self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value(),
self.elementList, element, x, y, z,
self.elementParameters)
iintradamp_Q = UtilityAnalysis.calc_iintradamp(iintra_Q,
self.dampingFunct)
Qiintradamp_Q = self.Q * iintradamp_Q
rintra, Fintra_r = MainFunctions.calc_Fr(
self.Q[self.Q <= self.ui.QmaxIntegrate.value()],
Qiintradamp_Q[self.Q <= self.ui.QmaxIntegrate.value()])
scaleFactor = self.ui.scaleFactorValue.value()
density0 = self.ui.densityValue.value()
# ----------------------First scale minimization---------------------------
scaleStep = 0.05
# sth = 0.008
# s0th = 0.006
sth = 0.0
s0th = 0.0
phi_matrix = 0.0
thickness_sampling = 0.0
scaleFactor = Minimization.OptimizeScale(
self.Q, self.I_Q, self.Ibkg_Q, self.J_Q, self.Iincoh_Q, self.fe_Q,
self.ui.maxQ.value(), self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(), self.Ztot, density0,
scaleFactor, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.rmin.value(), self.dampingFunct, Fintra_r,
self.ui.iterations.value(), scaleStep, sth, s0th,
thickness_sampling, phi_matrix, "n")
# ----------------------First density minimization-------------------------
densityStep = density0 / 50
densityStepEnd = density0 / 250
density = Minimization.OptimizeDensity(
self.Q, self.I_Q, self.Ibkg_Q, self.J_Q, self.Iincoh_Q, self.fe_Q,
self.ui.maxQ.value(), self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(), self.Ztot, density0,
scaleFactor, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.rmin.value(), self.dampingFunct, Fintra_r,
self.ui.iterations.value(), densityStep, densityStepEnd, sth, s0th,
thickness_sampling, phi_matrix, "n")
# print("density0, density", density0, density)
numLoopIteration = 0
while 1:
if np.abs(density - density0) > density / 25:
# print("First")
scaleStep = 0.006
densityStep = density / 10
WSamplestep = 0.0008
WRefstep = 0.0008
elif np.abs(density - density0) > density / 75:
# print("Second")
scaleStep = 0.0006
densityStep = density / 100
WSamplestep = 0.0002
WRefstep = 0.0002
else:
# print("Third")
scaleStep = 0.00006
densityStep = density / 1000
WSamplestep = 0.0001
WRefstep = 0.0001
scaleFactor = Minimization.OptimizeScale(
self.Q, self.I_Q, self.Ibkg_Q, self.J_Q, self.Iincoh_Q,
self.fe_Q, self.ui.maxQ.value(), self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(), self.Ztot, density,
scaleFactor, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.rmin.value(), self.dampingFunct, Fintra_r,
self.ui.iterations.value(), scaleStep, sth, s0th,
thickness_sampling, phi_matrix, "n")
density0 = density
density = Minimization.OptimizeDensity(
self.Q, self.I_Q, self.Ibkg_Q, self.J_Q, self.Iincoh_Q,
self.fe_Q, self.ui.maxQ.value(), self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(), self.Ztot, density0,
scaleFactor, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.rmin.value(), self.dampingFunct, Fintra_r,
self.ui.iterations.value(), densityStep, density / 250, sth,
s0th, thickness_sampling, phi_matrix, "n")
numLoopIteration += 1
# print("numLoopIteration", numLoopIteration, scaleFactor, density)
if (np.abs(density - density0) > np.abs(
density / 2500)) and (numLoopIteration <= 30):
continue
else:
break
# print("final scale", scaleFactor, "final density", density)
self.ui.scaleFactorValue.setValue(scaleFactor)
self.ui.densityValue.setValue(density)
Isample_Q = MainFunctions.calc_IsampleQ(self.I_Q, scaleFactor,
self.Ibkg_Q)
alpha = MainFunctions.calc_alpha(
self.J_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Sinf,
self.Q[self.Q <= self.ui.QmaxIntegrate.value()],
Isample_Q[self.Q <= self.ui.QmaxIntegrate.value()],
self.fe_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Ztot,
density)
Icoh_Q = MainFunctions.calc_Icoh(alpha, Isample_Q, self.Iincoh_Q)
S_Q = MainFunctions.calc_SQ(Icoh_Q, self.Ztot, self.fe_Q, self.Sinf,
self.Q, self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
Ssmooth_Q = UtilityAnalysis.calc_SQsmoothing(
self.Q, S_Q, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.minQ.value(), self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
SsmoothDamp_Q = UtilityAnalysis.calc_SQdamp(Ssmooth_Q, self.Sinf,
self.dampingFunct)
i_Q = MainFunctions.calc_iQ(SsmoothDamp_Q, self.Sinf)
Qi_Q = self.Q * i_Q
r, F_r = MainFunctions.calc_Fr(
self.Q[self.Q <= self.ui.QmaxIntegrate.value()],
Qi_Q[self.Q <= self.ui.QmaxIntegrate.value()])
Fopt_r, deltaFopt_r = Optimization.calc_optimize_Fr(
self.ui.iterations.value(), F_r, Fintra_r, density,
i_Q[self.Q <= self.ui.QmaxIntegrate.value()],
self.Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Sinf,
self.J_Q[self.Q <= self.ui.QmaxIntegrate.value()], r,
self.ui.rmin.value(), "n")
Scorr_Q = MainFunctions.calc_SQCorr(Fopt_r, r, self.Q, self.Sinf)
self.ui.distfuncPlot.canvas.ax.plot(r,
Fopt_r,
"g",
label=r"$F_{opt}(r)$")
self.ui.distfuncPlot.canvas.ax.legend()
self.ui.distfuncPlot.canvas.draw()
self.ui.factorPlot.canvas.ax.plot(self.Q,
Scorr_Q,
"g",
label=r"$S_{opt}(Q)$")
self.ui.factorPlot.canvas.ax.legend()
self.ui.factorPlot.canvas.draw()
default_dir = environ["HOME"]
app = QApplication(argv)
filename, _ = QFileDialog.getOpenFileName(caption="Load Input File",
directory=default_dir,
filter="*txt")
app.exit()
return filename
if __name__ == "__main__":
#---------------------------Files reading----------------------------------
# inputFile_path = open_file("./")
inputVariables = Utility.read_inputFile("./inputFile.txt")
elementList = Utility.molToElemList(inputVariables["molecule"])
elementParameters = Utility.read_parameters(
elementList, inputVariables["elementParamsPath"])
elementPosition = Utility.read_xyz_file(inputVariables["xyzPath"])
Q, I_Q = Utility.read_file(inputVariables["dataFile"])
Qbkg, Ibkg_Q = Utility.read_file(inputVariables["bkgFile"])
# plt.plot(Q, I_Q)
# plt.plot(Qbkg, Ibkg_Q)
# plt.show
#--------------------Preliminary calculation-------------------------------