def residual_square(p, data):
a = P4Rm()
P4Rm.ParamDict['_fp_min'] = p
y_cal = f_Refl(a.AllDataDict['geometry'])
y_cal = y_cal/y_cal.max() + data['background']
temp = ((log10(a.ParamDict['Iobs']) - log10(y_cal))**2).sum()
return temp / len(y_cal)
def residual_square(p, data):
a = P4Rm()
P4Rm.ParamDict['_fp_min'] = p
y_cal = f_Refl(a.AllDataDict['geometry'])
y_cal = y_cal / y_cal.max() + data['background']
temp = ((log10(a.ParamDict['Iobs']) - log10(y_cal))**2).sum()
return temp / len(y_cal)
def on_fit_ending(self, case):
a = P4Rm()
P4Rm.ParamDict['I_i'] = a.ParamDict['I_fit']
y_cal = f_Refl(a.AllDataDict['geometry'])
y_cal = y_cal / y_cal.max() + a.AllDataDict['background']
temp = ((log10(a.ParamDict['Iobs']) - log10(y_cal)) ** 2).sum()
P4Rm.residual_error = temp / len(y_cal)
if a.fit_type == 0:
t_ = a.par_fit[:int(a.AllDataDict['strain_basis_func'])]
P4Rm.ParamDict['sp'] = t_
t_ = a.par_fit[-1 * int(a.AllDataDict['dw_basis_func']):]
P4Rm.ParamDict['dwp'] = t_
else:
if a.lmfit_install:
self.on_read_data_from_lmfit()
else:
t_ = a.par_fit[:int(a.AllDataDict['strain_basis_func'])]
P4Rm.ParamDict['sp'] = t_
t_ = a.par_fit[-1 * int(a.AllDataDict['dw_basis_func']):]
P4Rm.ParamDict['dwp'] = t_
def on_fit_ending(self, case):
a = P4Rm()
P4Rm.ParamDict["I_i"] = a.ParamDict["I_fit"]
y_cal = f_Refl(a.AllDataDict["geometry"])
y_cal = y_cal / y_cal.max() + a.AllDataDict["background"]
temp = ((log10(a.ParamDict["Iobs"]) - log10(y_cal)) ** 2).sum()
P4Rm.residual_error = temp / len(y_cal)
if a.fit_type == 0:
t_ = a.par_fit[: int(a.AllDataDict["strain_basis_func"])]
P4Rm.ParamDict["sp"] = t_
t_ = a.par_fit[-1 * int(a.AllDataDict["dw_basis_func"]) :]
P4Rm.ParamDict["dwp"] = t_
else:
if a.lmfit_install:
self.on_read_data_from_lmfit()
else:
t_ = a.par_fit[: int(a.AllDataDict["strain_basis_func"])]
P4Rm.ParamDict["sp"] = t_
t_ = a.par_fit[-1 * int(a.AllDataDict["dw_basis_func"]) :]
P4Rm.ParamDict["dwp"] = t_
def on_calcul_parameters(self):
a = P4Rm()
name = a.PathDict['Compound_name']
name_s = a.PathDict['substrate_name']
self.on_test_substrate()
spline_strain = a.spline_strain
spline_DW = a.spline_DW
temp = [spline_strain, spline_DW]
P4Rm.splinenumber = temp
if a.AllDataDict['model'] != 2:
nb_slice, dw_func = self.OnChangeBasisFunction(
a.AllDataDict['strain_basis_func'],
a.AllDataDict['dw_basis_func'],
spline_strain, spline_DW,
a.AllDataDict['number_slices'])
a.AllDataDict['dw_basis_func'] = dw_func
a.AllDataDict['number_slices'] = nb_slice
if name != []:
self.on_make_param_func()
P4Rm.ParamDict['par'] = np.concatenate((a.ParamDict['sp'],
a.ParamDict['dwp']),
axis=0)
x_ = a.ParamDict['th']
param = a.ParamDict['param_func_profile']
P4Rm.ParamDict['resol'] = a.ParamDict['func_profile'](x_, param)
P4Rm.ParamDict['t_l'] = (a.AllDataDict['damaged_depth'] /
a.AllDataDict['number_slices'])
P4Rm.ParamDict['z'] = (arange(a.AllDataDict['number_slices']+1) *
a.ParamDict['t_l'])
# =============================================================================
# Material Data
# =============================================================================
P4Rm.ParamDict['d'], P4Rm.ParamDict['Vol'] = f_dhkl_V(
a.AllDataDict['h'], a.AllDataDict['k'],
a.AllDataDict['l'], a.AllDataDict['a'],
a.AllDataDict['b'], a.AllDataDict['c'],
a.AllDataDict['alpha'],
a.AllDataDict['beta'],
a.AllDataDict['gamma'])
temp_1 = (a.ConstDict['re'] * a.AllDataDict['wavelength'] *
a.AllDataDict['wavelength'])
P4Rm.ParamDict['G'] = temp_1 / (np.pi * a.ParamDict['Vol'])
temp_2 = arcsin(a.AllDataDict['wavelength'] / (2*a.ParamDict['d']))
P4Rm.ParamDict['thB_S'] = temp_2
temp_3 = a.ConstDict['phi']
P4Rm.ParamDict['g0'] = sin(a.ParamDict['thB_S'] - temp_3)
P4Rm.ParamDict['gH'] = -sin(a.ParamDict['thB_S'] + temp_3)
P4Rm.ParamDict['b_S'] = a.ParamDict['g0'] / a.ParamDict['gH']
temp_4 = f_FH(a.AllDataDict['h'], a.AllDataDict['k'],
a.AllDataDict['l'], a.AllDataDict['wavelength'],
a.ParamDict['thB_S'], a.ParamDict['z'], name)
P4Rm.ParamDict['FH'] = temp_4[0]
P4Rm.ParamDict['FmH'] = temp_4[1]
P4Rm.ParamDict['F0'] = temp_4[2]
# =============================================================================
# Substrate Data
# =============================================================================
P4Rm.ParamDict['d_s'], P4Rm.ParamDict['Vol_s'] = f_dhkl_V(
a.AllDataDict['h_s'],
a.AllDataDict['k_s'],
a.AllDataDict['l_s'],
a.AllDataDict['a_s'],
a.AllDataDict['b_s'],
a.AllDataDict['c_s'],
a.AllDataDict['alpha_s'],
a.AllDataDict['beta_s'],
a.AllDataDict['gamma_s'])
temp_1 = (a.ConstDict['re'] * a.AllDataDict['wavelength'] *
a.AllDataDict['wavelength'])
P4Rm.ParamDict['G_s'] = temp_1 / (np.pi * a.ParamDict['Vol_s'])
temp_2 = arcsin(a.AllDataDict['wavelength'] /
(2*a.ParamDict['d_s']))
P4Rm.ParamDict['thB_S_s'] = temp_2
temp_3 = a.ConstDict['phi_s']
P4Rm.ParamDict['g0_s'] = sin(a.ParamDict['thB_S_s'] - temp_3)
P4Rm.ParamDict['gH_s'] = -sin(a.ParamDict['thB_S_s'] + temp_3)
P4Rm.ParamDict['b_S_s'] = a.ParamDict['g0_s'] / a.ParamDict['gH_s']
temp_4 = f_FH(a.AllDataDict['h_s'], a.AllDataDict['k_s'],
a.AllDataDict['l_s'],
a.AllDataDict['wavelength'],
a.ParamDict['thB_S_s'],
a.ParamDict['z'], name_s)
P4Rm.ParamDict['FH_s'] = temp_4[0]
P4Rm.ParamDict['FmH_s'] = temp_4[1]
P4Rm.ParamDict['F0_s'] = temp_4[2]
# =============================================================================
P4Rm.ParamDict['Ical'] = f_Refl(a.AllDataDict['geometry'])
P4Rm.ParamDict['I_i'] = (a.ParamDict['Ical'] /
a.ParamDict['Ical'].max() +
a.AllDataDict['background'])
P4Rm.ParamDict['depth'] = (a.AllDataDict['damaged_depth'] -
a.ParamDict['z'])
P4Rm.ParamDict['DW_i'] = f_DW(
a.ParamDict['z'],
a.ParamDict['dwp'],
a.AllDataDict['damaged_depth'],
spline_DW)
P4Rm.ParamDict['strain_i'] = f_strain(
a.ParamDict['z'],
a.ParamDict['sp'],
a.AllDataDict['damaged_depth'],
spline_strain)
t = a.AllDataDict['damaged_depth']
if a.AllDataDict['damaged_depth'] > 0:
self.on_shifted_sp_curves(t)
self.on_shifted_dwp_curves(t)
self.draw_curves()
else:
msg_ = "check if the structure file really exists"
logger.log(logging.WARNING, msg_)
def on_calcul_parameters(self):
a = P4Rm()
name = a.PathDict['Compound_name']
name_s = a.PathDict['substrate_name']
self.on_test_substrate()
spline_strain = a.spline_strain
spline_DW = a.spline_DW
temp = [spline_strain, spline_DW]
P4Rm.splinenumber = temp
if a.AllDataDict['model'] != 2:
nb_slice, dw_func = self.OnChangeBasisFunction(
a.AllDataDict['strain_basis_func'],
a.AllDataDict['dw_basis_func'],
spline_strain, spline_DW,
a.AllDataDict['number_slices'])
a.AllDataDict['dw_basis_func'] = dw_func
a.AllDataDict['number_slices'] = nb_slice
if name != []:
self.on_make_param_func()
P4Rm.ParamDict['par'] = np.concatenate((a.ParamDict['sp'],
a.ParamDict['dwp']),
axis=0)
x_ = a.ParamDict['th']
param = a.ParamDict['param_func_profile']
P4Rm.ParamDict['resol'] = a.ParamDict['func_profile'](x_, param)
P4Rm.ParamDict['t_l'] = (a.AllDataDict['damaged_depth'] /
a.AllDataDict['number_slices'])
P4Rm.ParamDict['z'] = (arange(a.AllDataDict['number_slices']+1) *
a.ParamDict['t_l'])
# =============================================================================
# Material Data
# =============================================================================
P4Rm.ParamDict['d'], P4Rm.ParamDict['Vol'] = f_dhkl_V(
a.AllDataDict['h'], a.AllDataDict['k'],
a.AllDataDict['l'], a.AllDataDict['a'],
a.AllDataDict['b'], a.AllDataDict['c'],
a.AllDataDict['alpha'],
a.AllDataDict['beta'],
a.AllDataDict['gamma'])
temp_1 = (a.ConstDict['re'] * a.AllDataDict['wavelength'] *
a.AllDataDict['wavelength'])
P4Rm.ParamDict['G'] = temp_1 / (np.pi * a.ParamDict['Vol'])
temp_2 = arcsin(a.AllDataDict['wavelength'] / (2*a.ParamDict['d']))
P4Rm.ParamDict['thB_S'] = temp_2
temp_3 = a.ConstDict['phi']
P4Rm.ParamDict['g0'] = sin(a.ParamDict['thB_S'] - temp_3)
P4Rm.ParamDict['gH'] = -sin(a.ParamDict['thB_S'] + temp_3)
P4Rm.ParamDict['b_S'] = a.ParamDict['g0'] / a.ParamDict['gH']
temp_4 = f_FH(a.AllDataDict['h'], a.AllDataDict['k'],
a.AllDataDict['l'], a.AllDataDict['wavelength'],
a.ParamDict['thB_S'], a.ParamDict['z'], name)
P4Rm.ParamDict['FH'] = temp_4[0]
P4Rm.ParamDict['FmH'] = temp_4[1]
P4Rm.ParamDict['F0'] = temp_4[2]
# =============================================================================
# Substrate Data
# =============================================================================
P4Rm.ParamDict['d_s'], P4Rm.ParamDict['Vol_s'] = f_dhkl_V(
a.AllDataDict['h_s'],
a.AllDataDict['k_s'],
a.AllDataDict['l_s'],
a.AllDataDict['a_s'],
a.AllDataDict['b_s'],
a.AllDataDict['c_s'],
a.AllDataDict['alpha_s'],
a.AllDataDict['beta_s'],
a.AllDataDict['gamma_s'])
temp_1 = (a.ConstDict['re'] * a.AllDataDict['wavelength'] *
a.AllDataDict['wavelength'])
P4Rm.ParamDict['G_s'] = temp_1 / (np.pi * a.ParamDict['Vol_s'])
temp_2 = arcsin(a.AllDataDict['wavelength'] /
(2*a.ParamDict['d_s']))
P4Rm.ParamDict['thB_S_s'] = temp_2
temp_3 = a.ConstDict['phi_s']
P4Rm.ParamDict['g0_s'] = sin(a.ParamDict['thB_S_s'] - temp_3)
P4Rm.ParamDict['gH_s'] = -sin(a.ParamDict['thB_S_s'] + temp_3)
P4Rm.ParamDict['b_S_s'] = a.ParamDict['g0_s'] / a.ParamDict['gH_s']
temp_4 = f_FH(a.AllDataDict['h_s'], a.AllDataDict['k_s'],
a.AllDataDict['l_s'],
a.AllDataDict['wavelength'],
a.ParamDict['thB_S_s'],
a.ParamDict['z'], name_s)
P4Rm.ParamDict['FH_s'] = temp_4[0]
P4Rm.ParamDict['FmH_s'] = temp_4[1]
P4Rm.ParamDict['F0_s'] = temp_4[2]
# =============================================================================
P4Rm.ParamDict['Ical'] = f_Refl(a.AllDataDict['geometry'])
P4Rm.ParamDict['I_i'] = (a.ParamDict['Ical'] /
a.ParamDict['Ical'].max() +
a.AllDataDict['background'])
P4Rm.ParamDict['depth'] = (a.AllDataDict['damaged_depth'] -
a.ParamDict['z'])
P4Rm.ParamDict['DW_i'] = f_DW(
a.ParamDict['z'],
a.ParamDict['dwp'],
a.AllDataDict['damaged_depth'],
spline_DW)
P4Rm.ParamDict['strain_i'] = f_strain(
a.ParamDict['z'],
a.ParamDict['sp'],
a.AllDataDict['damaged_depth'],
spline_strain)
t = a.AllDataDict['damaged_depth']
if a.AllDataDict['damaged_depth'] > 0:
self.on_shifted_sp_curves(t)
self.on_shifted_dwp_curves(t)
self.draw_curves()
else:
msg_ = "check if the structure file really exists"
logger.log(logging.WARNING, msg_)
