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Fitting4Radmax.py
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Fitting4Radmax.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: A_BOULLE & M_SOUILAH
# Radmax project
# =============================================================================
# Fitting Module
# =============================================================================
import sys
import wx
sys.path.insert(0, './modules')
from pubsub import pub
import Parameters4Radmax as p4R
from Parameters4Radmax import P4Rm
import Settings4Radmax as S4R
from Calcul4Radmax import Calcul4Radmax
from threading import Thread, Event
from scipy.optimize import leastsq
from scipy import convolve, in1d, log10
from time import sleep
import numpy as np
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
from numpy import around, array, arange, asarray
from Def_XRD4Radmax import f_Refl, f_Refl_fit
from GSA4Radmax import gsa
from Def_Strain4Radmax import f_strain
from Def_DW4Radmax import f_DW
import logging
logger = logging.getLogger(__name__)
"""Pubsub message"""
pubsub_Read_field4Save = "ReadField4Save"
pubsub_OnFit_Graph = "OnFitGraph"
pubsub_on_refresh_GUI = "OnRefreshGUI"
pubsub_Hide_Show_GSA = "HideShowGSA"
pubsub_on_launch_thread = "OnLaunchThread"
pubsub_save_project_before_fit = "SaveProjectBeforeFit"
pubsub_adjust_nb_cycle = "AdjustNbCycle"
# -----------------------------------------------------------------------------
class Fitting4Radmax():
def on_launch_fit(self):
a = P4Rm()
b = Calcul4Radmax()
b.on_update()
pub.sendMessage(pubsub_Read_field4Save)
if a.PathDict['namefromini'] != "":
logger.log(logging.INFO, "Start Fit")
if (a.checkInitialField == 1 and a.checkGeometryField == 1 and
a.checkFittingField == 1):
P4Rm.allparameters = (a.initial_parameters +
a.fitting_parameters +
a.sample_geometry)
i = 0
for k in p4R.IP_p + p4R.F_p + p4R.SG_p:
P4Rm.AllDataDict[k] = a.allparameters[i]
i += 1
if a.AllDataDict['nb_cycle_max'] < a.AllDataDict['nb_palier']:
P4Rm.AllDataDict['nb_cycle_max'] = a.AllDataDict['nb_palier']
pub.sendMessage(pubsub_adjust_nb_cycle)
self.onLaunchtest()
else:
return
else:
pub.sendMessage(pubsub_save_project_before_fit, case=2)
def onLaunchtest(self):
test_deformation_limit = self.on_test_data_before_fit()
if test_deformation_limit is True:
self.on_launch_thread()
else:
pub.sendMessage(pubsub_Hide_Show_GSA)
def on_test_data_before_fit(self):
a = P4Rm()
P4Rm.ParamDict['sp'] = np.asarray(a.ParamDict['sp'])
P4Rm.ParamDict['dwp'] = np.asarray(a.ParamDict['dwp'])
if a.AllDataDict['model'] == 0. or a.AllDataDict['model'] == 1.:
""" do not use the last value of strain because
is out of the scope """
test_dw = (all(a.ParamDict['dwp'] > a.AllDataDict['dw_min']) and
all(a.ParamDict['dwp'][:-1] < a.AllDataDict['dw_max']))
test_strain = (all(a.ParamDict['sp'][:-1] >
a.AllDataDict['strain_min']) and
all(a.ParamDict['sp'] <
a.AllDataDict['strain_max']))
if test_dw and test_strain:
return True
else:
return False
elif a.AllDataDict['model'] == 2.:
i = 0
ls_ = [0, 4, 5, 6]
lse_ = [0, 2, 2, 4]
ld_ = [x + 6 for x in ls_]
lde_ = [x + 6 for x in lse_]
test_dw = [False] * len(a.ParamDict['dwp'])
test_strain = [False] * len(a.ParamDict['sp'])
for val_dwp, val_sp in zip(a.ParamDict['dwp'],
a.ParamDict['sp']):
if i in ls_:
v_ = ls_.index(i)
ve_ = lse_[v_]
if val_sp < a.AllDataDict[p4R.GSAp_[ve_]]:
test_strain[i] = True
elif val_sp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
test_strain[i] = True
else:
if val_sp < 0.:
test_strain[i] = True
elif val_sp > 1.:
test_strain[i] = True
j = i + 6
if j in ld_:
v_ = ld_.index(j)
ve_ = lde_[v_]
if val_dwp < a.AllDataDict[p4R.GSAp_[ve_]]:
test_dw[i] = True
elif val_dwp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
test_dw[i] = True
else:
if val_dwp < 0.:
test_dw[i] = True
elif val_dwp > 1.:
test_dw[i] = True
i += 1
if (True in test_dw) or (True in test_strain):
return False
else:
return True
def on_launch_thread(self):
a = P4Rm()
if a.fit_type == 0:
logger.log(logging.INFO, "GSA Fit has been launched")
else:
logger.log(logging.INFO, "Leastsq Fit has been launched")
P4Rm.fitlive = 1
P4Rm.ParamDictbackup['sp'] = a.ParamDict['sp']
P4Rm.ParamDictbackup['dwp'] = a.ParamDict['dwp']
P4Rm.ParamDictbackup['I_i'] = a.ParamDict['I_i']
pub.sendMessage(pubsub_OnFit_Graph)
pub.sendMessage(pubsub_on_refresh_GUI, option=0, case=0)
sleep(0.3)
pub.sendMessage(pubsub_on_launch_thread)
def on_stop_fit(self):
P4Rm.FitDict['worker_live'].stop()
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_modify_deformation_limits(self, state):
a = P4Rm()
case = state.index(True)
if a.AllDataDict['model'] == 0. or a.AllDataDict['model'] == 1.:
value = 0.1
if case == 0:
''' Modify input'''
i = 0
for val_dwp, val_sp in zip(a.ParamDict['dwp'],
a.ParamDict['sp']):
if val_dwp < a.AllDataDict['dw_min']:
val_ = a.AllDataDict['dw_min'] + value
P4Rm.ParamDict['dwp'][i] = val_
elif val_dwp > a.AllDataDict['dw_max']:
val_ = a.AllDataDict['dw_max'] - value
P4Rm.ParamDict['dwp'][i] = val_
if val_sp < a.AllDataDict['strain_min']:
val_ = a.AllDataDict['strain_min'] + value
P4Rm.ParamDict['sp'][i] = val_
elif val_sp > a.AllDataDict['strain_max']:
val_ = a.AllDataDict['strain_max'] - value
P4Rm.ParamDict['sp'][i] = val_
i += 1
self.on_launch_thread()
elif case == 1:
''' Modify limits '''
roundval = 4
t_min_dw = [False] * len(a.ParamDict['dwp'])
t_max_dw = [False] * len(a.ParamDict['dwp'])
t_min_sp = [False] * len(a.ParamDict['sp'])
t_max_sp = [False] * len(a.ParamDict['sp'])
i = 0
for val_dwp, val_sp in zip(a.ParamDict['dwp'],
a.ParamDict['sp']):
if val_dwp < a.AllDataDict['dw_min']:
t_min_dw[i] = True
elif val_dwp > a.AllDataDict['dw_max']:
t_max_dw[i] = True
if val_sp < a.AllDataDict['strain_min']:
t_min_sp[i] = True
elif val_sp > a.AllDataDict['strain_max']:
t_max_sp[i] = True
i += 1
if True in t_min_dw:
round_ = round(min(a.ParamDict['dwp']) - value, roundval)
P4Rm.AllDataDict['dw_min'] = round_
elif True in t_max_dw:
round_ = round(max(a.ParamDict['dwp']) + value, roundval)
P4Rm.AllDataDict['dw_max'] = round_
if True in t_min_sp:
round_ = round(min(a.ParamDict['sp']) - value, roundval)
P4Rm.AllDataDict['strain_min'] = round_
if True in t_max_sp:
round_ = round(max(a.ParamDict['sp']) + value, roundval)
P4Rm.AllDataDict['strain_max'] = round_
self.on_launch_thread()
elif case == 2:
return 0
elif a.AllDataDict['model'] == 2.:
value = 0.5
if case == 0:
''' Modify input'''
i = 0
ls_ = [0, 4, 5, 6]
lse_ = [0, 2, 2, 4]
ld_ = [x + 6 for x in ls_]
lde_ = [x + 6 for x in lse_]
for val_dwp, val_sp in zip(a.ParamDict['dwp'],
a.ParamDict['sp']):
if i in ls_:
v_ = ls_.index(i)
ve_ = lse_[v_]
if val_sp < a.AllDataDict[p4R.GSAp_[ve_]]:
val_ = a.AllDataDict[p4R.GSAp_[ve_]] + value
P4Rm.ParamDict['sp'][i] = val_
elif val_sp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
val_ = a.AllDataDict[p4R.GSAp_[ve_ + 1]] - value
P4Rm.ParamDict['sp'][i] = val_
else:
if val_sp < 0.:
val_ = value
P4Rm.ParamDict['sp'][i] = val_
elif val_sp > 1.:
val_ = 1. - value
P4Rm.ParamDict['sp'][i] = val_
j = i + 6
if j in ld_:
v_ = ld_.index(j)
ve_ = lde_[v_]
if val_dwp < a.AllDataDict[p4R.GSAp_[ve_]]:
val_ = a.AllDataDict[p4R.GSAp_[ve_]] + value
P4Rm.ParamDict['dwp'][i] = val_
elif val_dwp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
val_ = a.AllDataDict[p4R.GSAp_[ve_ + 1]] - value
P4Rm.ParamDict['dwp'][i] = val_
else:
if val_dwp < 0.:
val_ = value
P4Rm.ParamDict['dwp'][i] = val_
elif val_dwp > 1.:
val_ = 1. - value
P4Rm.ParamDict['dwp'][i] = val_
i += 1
self.on_launch_thread()
elif case == 1:
''' Modify limits '''
dict_min_ = ['strain_height_min', 'strain_eta_min',
'strain_eta_min', 'strain_bkg_min',
'dw_height_min', 'dw_eta_min', 'dw_eta_min',
'dw_bkg_min']
dict_max_ = ['strain_height_max', 'strain_eta_max',
'strain_eta_max', 'strain_bkg_max',
'dw_height_max', 'dw_eta_max', 'dw_eta_max',
'dw_bkg_max']
roundval = 4
i = 0
k = 0
l = 0
ls_ = [0, 4, 5, 6]
lse_ = [0, 2, 2, 4]
ld_ = [x + 6 for x in ls_]
lde_ = [x + 6 for x in lse_]
test_dw_min = [False] * len(ls_)
test_dw_max = [False] * len(ls_)
test_strain_min = [False] * len(ls_)
test_strain_max = [False] * len(ls_)
for val_dwp, val_sp in zip(a.ParamDict['dwp'],
a.ParamDict['sp']):
if i in ls_:
v_ = ls_.index(i)
ve_ = lse_[v_]
if val_sp < a.AllDataDict[p4R.GSAp_[ve_]]:
test_strain_min[k] = True
elif val_sp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
test_strain_max[k] = True
k += 1
j = i + 6
if j in ld_:
v_ = ld_.index(j)
ve_ = lde_[v_]
if val_dwp < a.AllDataDict[p4R.GSAp_[ve_]]:
test_dw_min[l] = True
elif val_dwp > a.AllDataDict[p4R.GSAp_[ve_ + 1]]:
test_dw_max[l] = True
l += 1
i += 1
if True in test_strain_min:
for a_ in test_strain_min:
if a_ is True:
v_ = test_strain_min.index(True)
val_ = a.ParamDict['sp'][ls_[v_]] - value
round_ = round(val_, roundval)
index_ = dict_min_[v_]
P4Rm.AllDataDict[index_] = round_
elif True in test_strain_max:
for a_ in test_strain_max:
if a_ is True:
v_ = test_strain_max.index(True)
val_ = a.ParamDict['sp'][ls_[v_]] + value
round_ = round(val_, roundval)
index_ = dict_max_[v_]
P4Rm.AllDataDict[index_] = round_
if True in test_dw_min:
for a_ in test_dw_min:
if a_ is True:
v_ = test_dw_min.index(True)
val_ = a.ParamDict['dwp'][ls_[v_]] - value
round_ = round(val_, roundval)
index_ = dict_min_[v_ + 4]
P4Rm.AllDataDict[index_] = round_
elif True in test_dw_max:
for a_ in test_dw_max:
if a_ is True:
v_ = test_dw_max.index(True)
val_ = a.ParamDict['dwp'][ls_[v_]] + value
round_ = round(val_, roundval)
index_ = dict_max_[v_ + 4]
P4Rm.AllDataDict[index_] = round_
self.on_launch_thread()
elif case == 2:
return 0
def on_test_lmfit(self):
a = P4Rm()
if not a.lmfit_install:
return False
else:
from lmfit import Parameters
fit_params = Parameters()
if a.AllDataDict['model'] == 2:
fit_params.add('heigt_strain', value=a.ParamDict['sp'][0],
min=a.AllDataDict['strain_height_min'],
max=a.AllDataDict['strain_height_max'],
vary=a.ParamDict['state_sp'][0])
fit_params.add('loc_strain', value=a.ParamDict['sp'][1],
min=0.,
max=1.,
vary=a.ParamDict['state_sp'][1])
fit_params.add('fwhm_1_strain', value=a.ParamDict['sp'][2],
min=0.,
max=1.,
vary=a.ParamDict['state_sp'][2])
fit_params.add('fwhm_2_strain', value=a.ParamDict['sp'][3],
min=0.,
max=1.,
vary=a.ParamDict['state_sp'][3])
fit_params.add('strain_eta_1', value=a.ParamDict['sp'][4],
min=a.AllDataDict['strain_eta_min'],
max=a.AllDataDict['strain_eta_max'],
vary=a.ParamDict['state_sp'][4])
fit_params.add('strain_eta_2', value=a.ParamDict['sp'][5],
min=a.AllDataDict['strain_eta_min'],
max=a.AllDataDict['strain_eta_max'],
vary=a.ParamDict['state_sp'][5])
fit_params.add('bkg_strain', value=a.ParamDict['sp'][6],
min=a.AllDataDict['strain_bkg_min'],
max=a.AllDataDict['strain_bkg_max'],
vary=a.ParamDict['state_sp'][6])
fit_params.add('heigt_dw', value=a.ParamDict['dwp'][0],
min=a.AllDataDict['dw_height_min'],
max=a.AllDataDict['dw_height_max'],
vary=a.ParamDict['state_sp'][0])
fit_params.add('loc_dw', value=a.ParamDict['dwp'][1],
min=0.,
max=1.,
vary=a.ParamDict['state_dwp'][1])
fit_params.add('fwhm_1_dw', value=a.ParamDict['dwp'][2],
min=0.,
max=1.,
vary=a.ParamDict['state_dwp'][2])
fit_params.add('fwhm_2_dw', value=a.ParamDict['dwp'][3],
min=0.,
max=1.,
vary=a.ParamDict['state_dwp'][3])
fit_params.add('dw_eta_1', value=a.ParamDict['dwp'][4],
min=a.AllDataDict['dw_eta_min'],
max=a.AllDataDict['dw_eta_max'],
vary=a.ParamDict['state_dwp'][4])
fit_params.add('dw_eta_2', value=a.ParamDict['dwp'][5],
min=a.AllDataDict['dw_eta_min'],
max=a.AllDataDict['dw_eta_max'],
vary=a.ParamDict['state_dwp'][5])
fit_params.add('bkg_dw', value=a.ParamDict['dwp'][6],
min=a.AllDataDict['dw_bkg_min'],
max=a.AllDataDict['dw_bkg_max'],
vary=a.ParamDict['state_dwp'][6])
else:
P4Rm.name4lmfit = []
for ii in range(len(a.ParamDict['sp'])):
name = 'sp_' + str(ii)
fit_params.add(name, value=a.ParamDict['sp'][ii],
min=a.AllDataDict['strain_min'],
max=a.AllDataDict['strain_max'],
vary=a.ParamDict['state_sp'][ii])
P4Rm.name4lmfit.append(name)
fit_params.add('nb_sp_val', value=len(a.ParamDict['sp']),
vary=False)
for jj in range(len(a.ParamDict['dwp'])):
name = 'dwp_' + str(jj)
fit_params.add(name, value=a.ParamDict['dwp'][jj],
min=a.AllDataDict['dw_min'],
max=a.AllDataDict['dw_max'],
vary=a.ParamDict['state_dwp'][jj])
P4Rm.name4lmfit.append(name)
fit_params.add('nb_dwp_val', value=len(a.ParamDict['dwp']),
vary=False)
P4Rm.FitDict['fit_params'] = fit_params
return True
def on_read_data_from_lmfit(self):
a = P4Rm()
from lmfit import fit_report
result = P4Rm.resultFit
data = []
data.append(result.success)
data.append(result.lmdif_message)
data.append(result.ier)
data.append(fit_report(result))
P4Rm.FitDict['Leastsq_report'] = data
i = 0
if a.AllDataDict['model'] == 2:
for param in result.params.values():
if i in range(1, 7):
P4Rm.ParamDict['sp'][i] = param.value
if i in range(7, 14):
P4Rm.ParamDict['dwp'][i - 7] = param.value
i += 1
else:
len_sp = int(result.params['nb_sp_val'])
len_dwp = int(result.params['nb_dwp_val'])
for ii in range(len_dwp):
name = 'dwp_' + str(ii)
P4Rm.ParamDict['dwp'][ii] = result.params[name].value
for jj in range(len_sp):
name = 'sp_' + str(jj)
P4Rm.ParamDict['sp'][jj] = result.params[name].value
# =============================================================================
# Thread part
# =============================================================================
class LiveEvent(wx.PyCommandEvent):
def __init__(self, etype, eid, value=None, data=None,
deformation=None, stopfit=None):
wx.PyCommandEvent.__init__(self, etype, eid)
self._value = value
self._data = data
self._deformation = deformation
self._stopfit = stopfit
def GetValue(self):
list4live = [self._value, self._data, self._deformation]
return list4live
def StopFit(self):
return self._stopfit
# -----------------------------------------------------------------------------
class Liveon_limit_exceeded(wx.PyCommandEvent):
def __init__(self, etype, eid, value=None):
wx.PyCommandEvent.__init__(self, etype, eid)
self._value = value
def GetValue(self):
return self._value
# -----------------------------------------------------------------------------
class Live_NbCycle(wx.PyCommandEvent):
def __init__(self, etype, eid, value=None):
wx.PyCommandEvent.__init__(self, etype, eid)
self._value = value
def GetValue(self):
return self._value
# -----------------------------------------------------------------------------
class Fit_launcher(Thread):
def __init__(self, parent, choice=None):
Thread.__init__(self)
self.parent = parent
self.choice = choice
self.need_abort = 0
self.launch = 0
self.count = 0
self.gauge_counter = 0
self.const = 0
self.pars_value = 0
self.len_sp = 0
self.len_dwp = 0
self.Data4f_Refl = []
self._stop = Event()
self.start()
self.ii = 1
def init_array(self):
a = P4Rm()
const_all = []
const_all.append(a.AllDataDict['wavelength'])
const_all.append(a.AllDataDict['damaged_depth'])
const_all.append(a.AllDataDict['number_slices'])
const_all.append(a.ConstDict['phi'])
const_all.append(a.ParamDict['t_l'])
const_all.append(a.ParamDict['b_S'])
const_all.append(a.ParamDict['thB_S'])
const_all.append(a.ParamDict['G'])
const_all.append(a.ParamDict['F0'])
const_all.append(a.ParamDict['FH'])
const_all.append(a.ParamDict['FmH'])
const_all.append(a.ParamDict['b_S_s'])
const_all.append(a.ParamDict['thB_S_s'])
const_all.append(a.ParamDict['G_s'])
const_all.append(a.ParamDict['F0_s'])
const_all.append(a.ParamDict['FH_s'])
const_all.append(a.ParamDict['FmH_s'])
const_all.append(a.AllDataDict['film_thick'])
const_all.append(a.AllDataDict['dw_thick'])
const_all.append(a.ParamDict['th'])
const_all.append(len(a.ParamDict['z']))
self.const = const_all
self.len_sp = len(a.ParamDict['sp'])
self.len_dwp = len(a.ParamDict['dwp'])
def on_limit_exceeded(self, val):
if self.need_abort == 0:
evt = Liveon_limit_exceeded(S4R.LiveLimitExceeded_COUNT, -1, val)
wx.PostEvent(self.parent, evt)
def on_count_cycles(self, val):
evt = Live_NbCycle(S4R.Live_count_NbCycle, -1, val)
wx.PostEvent(self.parent, evt)
def per_iteration(self, pars, iter, resid, *args, **kws):
a = P4Rm()
if self.need_abort == 1:
return True
if iter < 3 or iter % 10 == 0:
y_cal = self.residual_lmfit4iteration(pars)
p = []
if a.AllDataDict['model'] == 2:
for j in p4R.asym_pv_list:
p.append(pars[j].value)
else:
for j in a.name4lmfit:
p.append(pars[j].value)
P4Rm.ParamDict['_fp_min'] = p
deformation = [p]
self.f_strain_DW()
sleep(0.5)
evt = LiveEvent(S4R.Live_COUNT, -1, y_cal, None, deformation)
wx.PostEvent(self.parent, evt)
sleep(0.5)
def strain_DW(self, pars=None):
a = P4Rm()
self.Data4f_Refl = []
if pars is None:
strain = f_strain(a.ParamDict['z'],
a.ParamDict['_fp_min'][:self.len_sp:],
a.AllDataDict['damaged_depth'],
a.splinenumber[0])
DW = f_DW(a.ParamDict['z'],
a.ParamDict['_fp_min'][self.len_sp:self.len_sp +
self.len_dwp:],
a.AllDataDict['damaged_depth'], a.splinenumber[1])
else:
if a.AllDataDict['model'] == 0:
spline_DW = 5
spline_strain = 5
elif a.AllDataDict['model'] == 1:
spline_DW = 6
spline_strain = 6
elif a.AllDataDict['model'] == 2:
spline_DW = 4
spline_strain = 4
self.pars4numba(pars)
strain = f_strain(a.ParamDict['z'], self.pars_value,
a.AllDataDict['damaged_depth'], spline_strain)
DW = f_DW(a.ParamDict['z'], self.pars_value,
a.AllDataDict['damaged_depth'], spline_DW)
strain.astype(np.float64)
DW.astype(np.float64)
self.Data4f_Refl.append(strain)
self.Data4f_Refl.append(DW)
self.Data4f_Refl.append(self.const)
def residual_lmfit4iteration(self, pars):
a = P4Rm()
res = f_Refl_fit(a.AllDataDict['geometry'], self.Data4f_Refl)
y_cal = convolve(abs(res) ** 2, a.ParamDict['resol'], mode='same')
y_cal = y_cal / y_cal.max() + a.AllDataDict['background']
return y_cal
def residual_lmfit(self, pars, x, y):
a = P4Rm()
self.strain_DW(pars)
res = f_Refl_fit(a.AllDataDict['geometry'], self.Data4f_Refl)
y_cal = convolve(abs(res) ** 2, a.ParamDict['resol'], mode='same')
y_cal = y_cal / y_cal.max() + a.AllDataDict['background']
return (log10(y) - log10(y_cal))
def residual_leastsq(self, p, y, x):
a = P4Rm()
P4Rm.ParamDict['_fp_min'] = p
self.strain_DW()
res = f_Refl_fit(a.AllDataDict['geometry'], self.Data4f_Refl)
y_cal = convolve(abs(res) ** 2, a.ParamDict['resol'], mode='same')
y_cal = y_cal / y_cal.max() + a.AllDataDict['background']
self.count += 1
if self.count % 50 == 0:
self.f_strain_DW()
sleep(0.2)
deformation = [p]
evt = LiveEvent(S4R.Live_COUNT, -1, y_cal, None, deformation)
wx.PostEvent(self.parent, evt)
if self.need_abort == 1:
return (log10(y_cal) - log10(y_cal))
else:
return (log10(y) - log10(y_cal))
def residual_square(self, p, E_min, nb_minima):
a = P4Rm()
P4Rm.ParamDict['_fp_min'] = p
self.strain_DW()
res = f_Refl_fit(a.AllDataDict['geometry'], self.Data4f_Refl)
y_cal = convolve(abs(res) ** 2, a.ParamDict['resol'], mode='same')
y_cal = y_cal / y_cal.max() + a.AllDataDict['background']
y_obs = a.ParamDict['Iobs']
self.on_pass_data_to_thread(y_cal, p, E_min, nb_minima)
return ((log10(y_obs) - log10(y_cal)) ** 2).sum() / len(y_cal)
def pars4numba(self, pars):
a = P4Rm()
vals = pars.valuesdict()
const = []
if a.AllDataDict['model'] == 2:
for name in p4R.asym_pv_list:
const.append(vals[name])
else:
len_sp = int(vals['nb_sp_val'])
len_dwp = int(vals['nb_dwp_val'])
const.append(len_sp)
const.append(len_dwp)
for ii in range(len_sp):
name = 'sp_' + str(ii)
const.append(vals[name])
for ii in range(len_dwp):
name = 'dwp_' + str(ii)
const.append(vals[name])
self.pars_value = np.asarray(const, dtype=np.float64)
def on_pass_data_to_thread(self, y_cal, p, E_min, nb_minima):
self.count += 1
if self.count == 1:
self.f_strain_DW()
sleep(0.5)
evt = LiveEvent(S4R.Live_COUNT, -1, [])
wx.PostEvent(self.parent, evt)
sleep(0.2)
elif self.count % 10 == 0:
self.f_strain_DW()
sleep(0.5)
data = [E_min, nb_minima]
deformation = [p]
evt = LiveEvent(S4R.Live_COUNT, -1, y_cal, data, deformation)
wx.PostEvent(self.parent, evt)
sleep(0.2)
def run(self):
a = P4Rm()
P4Rm.par_fit = []
P4Rm.gsa_loop = 0
evt = LiveEvent(S4R.Live_COUNT, -1, [])
wx.PostEvent(self.parent, evt)
self.init_array()
if self.choice == 1 or self.choice == 2:
if a.lmfit_install:
func = self.residual_lmfit
else:
func = self.residual_leastsq
if self.choice == 1:
P4Rm.par_fit, P4Rm.success = leastsq(func, a.ParamDict['par'],
args=(a.ParamDict['Iobs'],
a.ParamDict['th']))
elif self.choice == 2:
from lmfit import minimize
maxfev_ = int(a.AllDataDict['maxfev']) * (len(a.FitDict['fit_params']) + 1)
P4Rm.resultFit = minimize(func, a.FitDict['fit_params'],
args=(a.ParamDict['th'],),
iter_cb=self.per_iteration,
scale_covar=True,
kws={'y': a.ParamDict['Iobs']},
max_nfev=(maxfev_),
ftol=a.AllDataDict['ftol'],
xtol=a.AllDataDict['xtol'])
elif self.choice == 0:
func = self.residual_square
P4Rm.par_fit = gsa(func, self.on_limit_exceeded,
self.on_count_cycles, a.AllDataDict)
if self.need_abort == 1:
evt = LiveEvent(S4R.Live_COUNT, -1, [], None, None, 1)
wx.PostEvent(self.parent, evt)
self.need_abort = 0
else:
evt = LiveEvent(S4R.Live_COUNT, -1, [], None, None, 0)
wx.PostEvent(self.parent, evt)
def stop(self):
self._stop.set()
P4Rm.gsa_loop = 1
self.need_abort = 1
def f_strain_DW(self):
a = P4Rm()
P4Rm.ParamDict['sp'] = a.ParamDict['_fp_min'][:int(a.AllDataDict['strain_basis_func'])]
P4Rm.ParamDict['dwp'] = a.ParamDict['_fp_min'][-1 * int(a.AllDataDict['dw_basis_func']):]
P4Rm.ParamDict['DW_i'] = f_DW(
a.ParamDict['z'], a.ParamDict['dwp'],
a.AllDataDict['damaged_depth'],
a.AllDataDict['model'])
P4Rm.ParamDict['strain_i'] = f_strain(
a.ParamDict['z'], a.ParamDict['sp'],
a.AllDataDict['damaged_depth'],
a.AllDataDict['model'])
t = a.AllDataDict['damaged_depth']
self.on_shifted_sp_curves(t)
self.on_shifted_dwp_curves(t)
def on_shifted_dwp_curves(self, t):
a = P4Rm()
if a.AllDataDict['model'] == 0:
temp_1 = arange(2, len(a.ParamDict['dwp']) + 1)
temp_2 = temp_1 * t / (len(a.ParamDict['dwp']))
P4Rm.ParamDict['x_dwp'] = t - temp_2
shifted_dwp = a.ParamDict['dwp'][:-1:]
temp_3 = in1d(around(a.ParamDict['depth'], decimals=3),
around(a.ParamDict['x_dwp'], decimals=3))
temp_4 = a.ParamDict['DW_i'][temp_3]
P4Rm.ParamDict['scale_dw'] = shifted_dwp / temp_4
P4Rm.ParamDict['scale_dw'][a.ParamDict['scale_dw'] == 0] = 1.
P4Rm.ParamDict['DW_shifted'] = shifted_dwp / a.ParamDict['scale_dw']
P4Rm.ParamDict['dw_out'] = a.ParamDict['dwp'][-1]
elif a.AllDataDict['model'] == 1:
temp_1 = arange(0, len(a.ParamDict['dwp']) + 1 - 3)
temp_2 = temp_1 * t / (len(a.ParamDict['dwp']) - 3)
P4Rm.ParamDict['x_dwp'] = t - temp_2
shifted_dwp = a.ParamDict['dwp'][1:-1:]
temp_3 = in1d(around(a.ParamDict['depth'], decimals=3),
around(a.ParamDict['x_dwp'], decimals=3))
temp_4 = a.ParamDict['DW_i'][temp_3]
P4Rm.ParamDict['scale_dw'] = shifted_dwp / temp_4
P4Rm.ParamDict['scale_dw'][a.ParamDict['scale_dw'] == 0] = 1.
P4Rm.ParamDict['DW_shifted'] = shifted_dwp / a.ParamDict['scale_dw']
temp_5 = array([a.ParamDict['dwp'][0], a.ParamDict['dwp'][-1]])
P4Rm.ParamDict['dw_out'] = temp_5
elif a.AllDataDict['model'] == 2:
x_dw_temp = []
x_dw_temp.append(t * (1 - a.ParamDict['dwp'][1]))
x_dw_temp.append(t * (1 - a.ParamDict['dwp'][1] +
a.ParamDict['dwp'][2] / 2))
x_dw_temp.append(t * (1 - a.ParamDict['dwp'][1] -
a.ParamDict['dwp'][3] / 2))
x_dw_temp.append(t * 0.05)
P4Rm.ParamDict['x_dwp'] = x_dw_temp
y_dw_temp = []
y_dw_temp.append(a.ParamDict['dwp'][0])
y_dw_temp.append(1. - (1 - a.ParamDict['dwp'][0]) / 2)
y_dw_temp.append(1. - (1 - a.ParamDict['dwp'][0]) / 2 -
(1 - a.ParamDict['dwp'][6]) / 2)
y_dw_temp.append(a.ParamDict['dwp'][6])
P4Rm.ParamDict['DW_shifted'] = y_dw_temp
def on_shifted_sp_curves(self, t):
a = P4Rm()
if a.AllDataDict['model'] == 0:
temp_1 = arange(2, len(a.ParamDict['sp']) + 1)
temp_2 = temp_1 * t / (len(a.ParamDict['sp']))
P4Rm.ParamDict['x_sp'] = t - temp_2
shifted_sp = a.ParamDict['sp'][:-1:]
temp_3 = in1d(around(a.ParamDict['depth'], decimals=3),
around(a.ParamDict['x_sp'], decimals=3))
temp_4 = a.ParamDict['strain_i'][temp_3]
P4Rm.ParamDict['scale_strain'] = shifted_sp / temp_4
P4Rm.ParamDict['scale_strain'][a.ParamDict['scale_strain'] == 0] = 1.
P4Rm.ParamDict['strain_shifted'] = asarray(shifted_sp) * 100. / a.ParamDict['scale_strain']
P4Rm.ParamDict['stain_out'] = a.ParamDict['sp'][-1]
elif a.AllDataDict['model'] == 1:
temp_1 = arange(0, len(a.ParamDict['sp']) + 1 - 3)
temp_2 = temp_1 * t / (len(a.ParamDict['sp']) - 3)
P4Rm.ParamDict['x_sp'] = t - temp_2
shifted_sp = a.ParamDict['sp'][1:-1:]
temp_3 = in1d(around(a.ParamDict['depth'], decimals=3),
around(a.ParamDict['x_sp'], decimals=3))
temp_4 = a.ParamDict['strain_i'][temp_3]
P4Rm.ParamDict['scale_strain'] = shifted_sp / temp_4
P4Rm.ParamDict['scale_strain'][a.ParamDict['scale_strain'] == 0] = 1.
P4Rm.ParamDict['strain_shifted'] = asarray(shifted_sp) * 100. / a.ParamDict['scale_strain']
temp_5 = array([a.ParamDict['sp'][0], a.ParamDict['sp'][-1]])
P4Rm.ParamDict['stain_out'] = temp_5
elif a.AllDataDict['model'] == 2:
x_sp_temp = []
x_sp_temp.append(t * (1 - a.ParamDict['sp'][1]))
x_sp_temp.append(t * (1 - a.ParamDict['sp'][1] +
a.ParamDict['sp'][2] / 2))
x_sp_temp.append(t * (1 - a.ParamDict['sp'][1] -
a.ParamDict['sp'][3] / 2))
x_sp_temp.append(t * 0.05)
P4Rm.ParamDict['x_sp'] = x_sp_temp
y_sp_temp = []
y_sp_temp.append(a.ParamDict['sp'][0])
y_sp_temp.append(a.ParamDict['sp'][0] / 2)
y_sp_temp.append(a.ParamDict['sp'][0] / 2 + a.ParamDict['sp'][6] / 2)
y_sp_temp.append(a.ParamDict['sp'][6])
P4Rm.ParamDict['strain_shifted'] = y_sp_temp