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 calc_abs_correction(Q, abs_length, thickness, angle):
"""Function to calculate the absorption correction.
This function can be used to calculate the absorption correction for the diamond
or for any other object between the sample and the detector.
The characteristics for some diamonds can be found here:
http://www.almax-easylab.com/DiamondSelectionPage.aspx
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
abs_length : float
absorption length (cm), @33keV 1.208cm
thickness : float
object thickness (cm)
angle : float
object rotation angle respect the XRay beam (deg)
Returns
-------
corr_factor : numpy array
correction factor
"""
# for now...
# wavelenght : float
# XRay beam wavelenght (nm), @ESRF ID27 0.03738nm
# wavelenght = 0.03738 # nm
# two_theta = Qto2theta(Q) # rad
two_theta = UtilityAnalysis.Qto2theta(Q)
mu_l = 1 / abs_length
angle = np.radians(angle)
path_lenght = thickness / np.cos(two_theta - angle)
corr_factor = np.exp(-mu_l * path_lenght)
# I_Qeff = I_Q / corr_factor
return corr_factor
def check_phi_matrix(Q, ws1, ws2, r1, r2, d, phiMatrixCalcFlag, phiMatrixPath):
"""Function to make or read from file the phi matrix.
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
ws1 : float
distance between the slits of first set (cm)
ws2 : float
distance between the slits of second set (cm)
r1 : float
first radius
r2 : float
second radius
d : float
dimension of slit
phiMatrixCalcFlag : string
flag for the phi matrix calculation
phiMatrixPath : string
phi matrix path
Returns
-------
phi_matrix : 2D numpy array
dispersion angle matrix for sample+DAC (rad)
"""
two_theta = UtilityAnalysis.Qto2theta(Q)
if phiMatrixCalcFlag.lower() == "y":
phi_matrix = calc_phi_matrix(two_theta, ws1, ws2, r1, r2, d)
np.save(phiMatrixPath, phi_matrix)
else:
phi_matrix = np.load(phiMatrixPath)
thickness_sampling = np.linspace(0, 0.17, num=1000)
return (thickness_sampling, phi_matrix)
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