Source code for HavNegpy.hn_deri

# -*- coding: utf-8 -*-
"""
Created on Mon Jun 13 11:52:39 2022

@author: mkolmang
"""
import numpy as np
import os
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import mplcursors
import json



[docs]class HN_derivative: """ A class to analyze the derivaite of real part of complex permittivity with derivative HN function Fit functions include single, double, and derivative HN with electrode polarization """ def __init__(self): pass
[docs] def create_analysis_file(self): """ Creates a file to save the fit results based on the choice of fit function Provides option to use an existing file and creates a new file if not found Returns ------- None. """ res = input(str("Do you want to use an existing file to save fit results? \n eg: existing file to save HN parameters, y or n:")) global ana_file if res == 'y': ex_file = input("Enter the analysis_file_name:") try: f = open(ex_file) except FileNotFoundError as e: print(f"{e}") else: if os.path.isfile(ex_file): print("file exists") else: func_name = int(input("Choose the fit function:\n 1 -- deri_HN\n 2-- deri_HN with EP\n 3 -- double_deri_HN\n")) ex_file = input("Enter the analysis_file_name:") f = open(ex_file,'w') if func_name == 1 or func_name ==2: f.write( f'{"Temperature"}' + '\t' + f'{"beta"}'+ '\t' + f'{"gamma"}' + '\t'+ f'{"deps"}' + '\t' + f'{"log (fmax)"}'+ '\t' + f'{"EP"}' + '\t'+ f'{"s"}' +'\n') elif func_name ==3: f.write( f'{"Temperature"}' + '\t' + f'{"beta1"}'+ '\t' + f'{"gamma1"}' + '\t'+ f'{"deps1"}' + '\t' + f'{"log (fmax1)"}'+ '\t' + f'{"beta2"}'+ '\t' + f'{"gamma2"}' + '\t'+ f'{"deps2"}' + '\t' + f'{"log (fmax2)"}'+ '\t' + f'{"EP"}' + '\t'+ f'{"s"}' +'\n') print(f'{"file did not exist, created"}',ex_file) ana_file = ex_file return()
[docs] def select_range(self,x,y): """ Selects the region of interest to fit data using mplcursors allows two clicks to select the lower and upper bound of the x-axis and returns the selected x and y vaues for fitting Returns ------- x1 : array log frequency y1 : array log dielectric loss """ x = list(x) y = list(y) plt.figure(1) plt.style.use("seaborn-whitegrid") plt.scatter(x,y,marker='s',color='r',facecolors='none', s=100,linewidth=2) plt.ylabel('log ( -d$\epsilon´$/ dlog f )') plt.xlabel('log f') #plt.legend() plt.style.use("seaborn-whitegrid") mplcursors.cursor(hover=True) zoom_ok = False plt.title('zoom or pan') while not zoom_ok: zoom_ok = plt.waitforbuttonpress() plt.title('press space when ready to select points') plt.title('only two clicks are allowed, select the range') val = plt.ginput(2) val.sort() x_min,x_max = val[0][0], val[1][0] tolerance = 0.03 p1 = round(x_min,3) p2 = round(x_max,3) low_x = p1 - tolerance high_x = p2 + tolerance #print(low_x, high_x) indices = [] indices.clear() for i,j in zip(x,y): if i<= high_x and i>=low_x : k = x.index(i) indices.append(k) a,b = indices[0], indices[-1] x1 = x[a:b+1] y1 = y[a:b+1] #print(x1) #print(y1) x2 = np.array(x1) y2 = np.array(y1) #print(val) print("x_lower_limit",x_min, "x_upper_limit",x_max) return x2,y2
[docs] def deri_hn(self,x,b,g,fm,deps): """ derivaitive HN fit function to fit single peak Parameters ---------- x : float frequency. b : float symmetric fractional parameter. g : float asymmetric fractional parameter. fm : float maximum frequency of the peak. deps : float dielectric strength. Returns ------- y : array estimated log derivative of epsilon' based on the supplied parameters. """ f = 10**(x) ff = f/fm ffb = ff**(b) n = (np.pi)/2 xc = np.cos(b*n) xs = np.sin(b*n) r = 1 + 2*ffb*xc + ffb**(2) #r_w = (1/r)**(0.5*g) p2 = 1/(ffb) phi = np.arctan((xs/(p2+xc))) #e_w = deps*r_w*(np.sin(g*phi)) de_1 = b*g*deps*ffb*np.cos(b*n-(1+g)*phi) de_2 = r**((1+g)/2) deri = de_1/de_2 y = np.log10(deri)#+ep)#+condb) return y
def deri_hn_ln(self,x,b,g,fm,deps): """ derivaitive HN fit function to fit single peak Parameters ---------- x : float frequency. b : float symmetric fractional parameter. g : float asymmetric fractional parameter. fm : float maximum frequency of the peak. deps : float dielectric strength. Returns ------- y : array estimated log derivative of epsilon' based on the supplied parameters. """ f = np.exp(x) ff = f/fm ffb = ff**(b) n = (np.pi)/2 xc = np.cos(b*n) xs = np.sin(b*n) r = 1 + 2*ffb*xc + ffb**(2) #r_w = (1/r)**(0.5*g) p2 = 1/(ffb) phi = np.arctan((xs/(p2+xc))) #e_w = deps*r_w*(np.sin(g*phi)) de_1 = b*g*deps*ffb*np.cos(b*n-(1+g)*phi) de_2 = r**((1+g)/2) deri = de_1/de_2 deri = deri/np.log(10) y = np.log(deri)#+ep)#+condb) return y
[docs] def deri_hn_ep(self,x,b,g,fm,deps,A,l): """ derivaitive HN fit function to fit single peak along with electrode polarization(ep) Parameters ---------- x : float frequency. b : float symmetric fractional parameter. g : float asymmetric fractional parameter. fm : float maximum frequency of the loss peak. deps : float dielectric strength. A : float electrode polarization value. l : float power law exponent. Returns ------- y : array estimated log derivative of epsilon' based on the supplied parameters. """ f = 10**(x) #w = 2*np.pi*f ff = f/fm ffb = ff**(b) n = (np.pi)/2 xc = np.cos(b*n) xs = np.sin(b*n) r = 1 + 2*ffb*xc + ffb**(2) #r_w = (1/r)**(0.5*g) p2 = 1/(ffb) phi = np.arctan((xs/(p2+xc))) #e_w = deps*r_w*(np.sin(g*phi)) #fs= f**(s) de_1 = b*g*deps*ffb*np.cos(b*n-(1+g)*phi) de_2 = r**((1+g)/2) deri = de_1/de_2 fl = f**l ep = A/fl y = np.log10(deri+ep) return y
[docs] def deri_double_hn(self,x,b1,g1,fm1,deps1,b2,g2,fm2,deps2): """ derivaitive HN fit function to fit two peaks Parameters ---------- x : float frequency. b1 : float symmetric fractional parameter of the 1st peak. g1 : float asymmetric fractional parameter of the 1st peak. fm1 : float maximum frequency of the 1st peak. deps1 : float dielectric strength of the 1st peak. b2 : float symmetric fractional parameter of the 2nd peak. g2 : float asymmetric fractional parameter of the 2nd peak. fm2 : float maximum frequency of the 2nd peak. deps2 : float dielectric strength of the 2nd peak. Returns ------- y : array estimated log derivative of epsilon' based on the supplied parameters. """ f = 10**(x) ff1 = f/fm1 ffb1 = ff1**(b1) n = (np.pi)/2 xc1 = np.cos(b1*n) xs1 = np.sin(b1*n) r1 = 1 + 2*ffb1*xc1 + ffb1**(2) #r_w1 = (1/r1)**(0.5*g1) p2 = 1/(ffb1) phi1 = np.arctan((xs1/(p2+xc1))) de_1 = b1*g1*deps1*ffb1*np.cos(b1*n-(1+g1)*phi1) de_2 = r1**((1+g1)/2) deri1 = de_1/de_2 #e_w1 = deps1*r_w1*(np.sin(g1*phi1)) ff2 = f/fm2 ffb2 = ff2**(b2) n = (np.pi)/2 xc2 = np.cos(b2*n) xs2 = np.sin(b2*n) r2 = 1 + 2*ffb2*xc2 + ffb2**(2) #r_w2 = (1/r2)**(0.5*g2) p3 = 1/(ffb2) phi2 = np.arctan((xs2/(p3+xc2))) de_3 = b2*g2*deps2*ffb2*np.cos(b2*n-(1+g2)*phi2) de_4 = r2**((1+g2)/2) deri2 = de_3/de_4 #e_w2 = deps2*r_w2*(np.sin(g2*phi2)) y = np.log10(deri1+deri2) return y
[docs] def ep_s(self,x,A,l): """ Function to estimate the electrode polarization(EP) contribution from the total fit While fitting, the deconvoluted EP is based on this function. Parameters ---------- x : float frequency. A : float electrode polarization value. l : float power law exponent. Returns ------- y : array estimated log EP. """ f = 10**(x) fl = f**(l) ep = A/fl y = np.log10(ep) return y
[docs] def dump_parameters_deri_hn(self): """ dumps the initial fit parameters for derivative hn function as a dictionary in a json file to load it during curve fitting Returns ------- None """ b = float(input("enter the beta value:")) g = float(input("enter the gamma value:")) lf = float(input("enter the fm:")) d = float(input("enter the deps:")) ep = float(input("enter the E.P value:")) s = float(input("enter the s:")) f = 10**(lf) par = {"beta": b, "gamma": g, "freq": f,"deps":d, "ep":ep, "s":s} with open('HN_deri.json',"w") as outfile: json.dump(par,outfile) with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("dumped_parameters",loaded_par) return ()
[docs] def dump_parameters_deri_double_hn(self): """ dumps the initial fit parameters for derivative_double hn function as a dictionary in a json file to load it during curve fitting Returns ------- None """ b1 = float(input("enter the beta1 value:")) g1 = float(input("enter the gamma1 value:")) lf1 = float(input("enter the fmax1:")) d1 = float(input("enter the deps1:")) b2 = float(input("enter the beta2 value:")) g2 = float(input("enter the gamma2 value:")) lf2 = float(input("enter the fmax2:")) d2 = float(input("enter the deps2:")) ep = float(input("enter the E.P value:")) s = float(input("enter the s:")) f1 = 10**(lf1) f2 = 10**(lf2) par = {"beta1":b1,"gamma1":g1,"freq1":f1,"deps1":d1,"beta2":b2,"gamma2":g2,"freq2":f2,"deps2":d2, "ep":ep, "s":s} with open('double_HN_deri.json',"w") as outfile: json.dump(par,outfile) with open('double_HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("dumped_parameters",loaded_par) return ()
[docs] def initial_view_deri_hn(self,x,y): """ plots the derivative hn function based on the initial parameters given via the dump_parameters method Parameters ---------- x : array log frequency. y : array log derivative of epsilon'. Returns ------- None. """ try: open('HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("loaded parameters \n" ,loaded_par) hn_par_index = ['beta','gamma','freq','deps'] init_fit_par = {key:value for key,value in loaded_par.items() if key in hn_par_index} hn_sub_par = loaded_par['beta'],loaded_par['gamma'],loaded_par['freq'],loaded_par['deps'] hn_sub = self.deri_hn(x,*hn_sub_par) plt.figure() plt.scatter(x,y,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x,hn_sub,'b',label='initial guess') plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') plt.legend() return init_fit_par
[docs] def initial_view_deri_hn_ep(self,x,y): """ plots the derivative hn function with electrode polarization based on the initial parameters given via the dump_parameters method Parameters ---------- x : array log frequency. y : array log derivative of epsilon'. Returns ------- None. """ try: open('HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) init_fit_par = loaded_par print("loaded parameters \n" ,loaded_par) hn_sub_par = loaded_par['beta'],loaded_par['gamma'],loaded_par['freq'],loaded_par['deps'] ep_sub_par = loaded_par['ep'],loaded_par['s'] hn_sub = self.deri_hn(x,*hn_sub_par) ep_sub = self.ep_s(x,*ep_sub_par) plt.figure() plt.scatter(x,y,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x,hn_sub,'b',label='initial guess - peak') plt.plot(x,ep_sub,'r',label='initial guess - electrode polarization') plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') plt.legend() return init_fit_par
[docs] def initial_view_deri_double_hn(self,x,y): """ plots the derivative double hn function based on the initial parameters given via the dump_parameters method Parameters ---------- x : array log frequency. y : array log derivative of epsilon'. Returns ------- None. """ try: open('double_HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('double_HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("loaded parameters \n" ,loaded_par) double_hn_par_index = ['beta1','gamma1','freq1','deps1','beta2','gamma2','freq2','deps2'] init_fit_par = {key:value for key,value in loaded_par.items() if key in double_hn_par_index} hn_sub_par1 = loaded_par['beta1'],loaded_par['gamma1'],loaded_par['freq1'],loaded_par['deps1'] hn_sub_par2 = loaded_par['beta2'],loaded_par['gamma2'],loaded_par['freq2'],loaded_par['deps2'] hn_sub1 = self.deri_hn(x,*hn_sub_par1) hn_sub2 = self.deri_hn(x,*hn_sub_par2) plt.figure() plt.scatter(x,y,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x,hn_sub1,'b',label='initial guess - peak1') plt.plot(x,hn_sub2,'g',label='initial guess - peak2') plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') plt.legend() return init_fit_par
def sel_function(self): """ A function to select the type of fit function during curve fitting Returns ------- func_decision : int choice of the fit function. """ func_decision = int(input("Choose the fit function:\n 1 -- deri_HN\n 2-- deri_HN with EP\n 3 -- double_deri_HN\n")) return (func_decision)
[docs] def fit(self,x,y): """ Fits the derivaitve of epsilon' data with choice of fit function The fit parameters are declared as global variables to be saved via save_fit function The initial fit parameters are taken from json file and the final fit parameters are dumped in the same json file to be used for next iteration. Parameters ---------- x : array log frequency. y : array log dielectric loss. Returns ------- fit_par : dictionary dictionary containing the fit parameters. """ func_number = self.sel_function() x1 = np.array(x) y1= np.array(y) global popt1 plt.figure() global popt2 global b,g,fm,deps,ep,s,l_f,b1,g1,fm1,deps1,b2,g2,fm2,deps2,l_f1,l_f2 if func_number==1: try: open('HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) hn_p0 = [loaded_par['beta'],loaded_par['gamma'],loaded_par['freq'],loaded_par['deps']] popt1, pcov2 = curve_fit(self.deri_hn, x1, y1, hn_p0,bounds =((0,0,1e-7,0),(1,1,1e7,np.inf)),absolute_sigma=True) yfit2 = self.deri_hn(x1,*popt1) plt.scatter(x1,y1,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x1,yfit2,'m--',label='derivative HN fit', linewidth=2) plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') plt.legend() b,g,fm,deps = popt1[0:4] ep,s =0,1 #s = 0 n_s = np.sin(np.pi*b/(2+2*g))**(1/b) n_s2 = 1/(np.sin(np.pi*b*g/(2+2*g))**(1/b)) fmax = fm*n_s*n_s2 l_f = np.log10(fmax) print(*popt1) print('log fmax:',l_f) fit_par = {"beta": b, "gamma": g, "freq": fm,"deps":deps, "ep":ep, "s":s} with open('HN_deri.json',"w") as outfile: json.dump(fit_par,outfile) with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("fit parameters dumped for next iteration",loaded_par) elif func_number==2: try: open('HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) p0 = [loaded_par['beta'],loaded_par['gamma'],loaded_par['freq'],loaded_par['deps'],loaded_par['ep'],loaded_par['s']] popt2, pcov2 = curve_fit(self.deri_hn_ep, x1, y1, p0, bounds =((0,0,1e-7,0,0,0),(1,1,1e7,np.inf,np.inf,1)),absolute_sigma=True) yfit3 = self.deri_hn_ep(x1,*popt2) plt.scatter(x1,y1,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x1,yfit3,'m--',label='derivative HN with EP fit', linewidth=2) plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') hn_sub_par = popt2[0],popt2[1],popt2[2],popt2[3] ep_sub_par = popt2[4], popt2[5] hn_sub = self.deri_hn(x1,*hn_sub_par) ep_sub = self.ep_s(x1,*ep_sub_par) plt.plot(x1,hn_sub,'b',label='peak') plt.plot(x1,ep_sub,'g',label='Electrode Polarization') plt.legend() print(*popt2) b,g,fm,deps,ep,s = popt2[:] n_s = np.sin(np.pi*b/(2+2*g))**(1/b) n_s2 = 1/(np.sin(np.pi*b*g/(2+2*g))**(1/b)) fmax = fm*n_s*n_s2 l_f = np.log10(fmax) print('log fmax:',l_f) fit_par = {"beta": b, "gamma": g, "freq": fm,"deps":deps, "ep":ep, "s":s} with open('HN_deri.json',"w") as outfile: json.dump(fit_par,outfile) with open('HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("fit parameters dumped for next iteration",loaded_par) elif func_number ==3: try: open('double_HN_deri.json') except FileNotFoundError as e: print(f'{e}' + '\n', "Please dump initial fit parameters using dump.parameters method") else: with open('double_HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) p0 = [loaded_par['beta1'],loaded_par['gamma1'],loaded_par['freq1'],loaded_par['deps1'],loaded_par['beta2'],loaded_par['gamma2'],loaded_par['freq2'],loaded_par['deps2']] print(p0) popt2, pcov2 = curve_fit(self.deri_double_hn, x1, y1, p0, bounds =((0,0,1e-7,0,0,0,1e-7,0),(1,1,1e7,np.inf,1,1,1e7,np.inf)),absolute_sigma=True) yfit4 = self.deri_double_hn(x1,*popt2) plt.scatter(x1,y1,marker='s',color='r',facecolors='none',label='data',s=100,linewidth=2) plt.plot(x1,yfit4,'m--',label='derivative HN fit', linewidth=2) plt.xlabel('log ( f [Hz])') plt.ylabel('log ( -d$\epsilon´$/ dlog f )') hn_sub_par1 = popt2[0], popt2[1],popt2[2],popt2[3] hn_sub_par2 = popt2[4], popt2[5],popt2[6],popt2[7] hn_sub1 = self.deri_hn(x1,*hn_sub_par1) hn_sub2 = self.deri_hn(x1,*hn_sub_par2) plt.plot(x1,hn_sub1,'b',label='peak1') plt.plot(x1,hn_sub2,'g',label='peak2') plt.legend() b1,g1,fm1,deps1,b2,g2,fm2,deps2 = popt2[:] ep, s = 0, 1 nr_1 = np.sin(np.pi*b1/(2+2*g1))**(1/b1) nr_2 = 1/(np.sin(np.pi*b1*g1/(2+2*g1))**(1/b1)) fmax1 = fm1*nr_1*nr_2 nr_3 = np.sin(np.pi*b2/(2+2*g2))**(1/b2) nr_4 = 1/(np.sin(np.pi*b2*g2/(2+2*g2))**(1/b2)) fmax2 = fm2*nr_3*nr_4 l_f1 = np.log10(fmax1) l_f2 = np.log10(fmax2) print('log fmax1:',l_f1 ,"\n" 'log fmax2:',l_f2) fit_par = {"beta1":b1,"gamma1":g1,"freq1":fm1,"deps1":deps1,"beta2":b2,"gamma2":g2,"freq2":fm2,"deps2":deps2, "ep":ep, "s":s} with open('double_HN_deri.json',"w") as outfile: json.dump(fit_par,outfile) with open('double_HN_deri.json',"r") as openfile: loaded_par = json.load(openfile) print("fit parameters dumped for next iteration",loaded_par) return fit_par
[docs] def save_fit_deri_hn(self,T): """ saves the fit parameters of derivative hn function in a file the file must be created via create_analysis_file function Parameters ---------- T : float Temperature,or can also be an integer that corresponds to a file number during analysis. Returns ------- None. """ res_file = open(ana_file,'a') global deps deps = deps/2.303 res_file.write( f'{T}' + '\t' + f'{b:.3f}' + '\t' + f'{g:.3f}' + '\t' + f'{deps:.3f}' +'\t' + f'{l_f:.3f}' + '\t' +f'{ep:.3f}'+'\t' + f'{s:.3f}' +"\n") return()
[docs] def save_fit_deri_hn_ep(self,T): """ saves the fit parameters of derivaitve hn function with electrode polarization in a file, the file must be created via create_analysis_file function Parameters ---------- T : float Temperature,or can also be an integer that corresponds to a file number during analysis. Returns ------- None. """ res_file = open(ana_file,'a') global deps deps = deps/2.303 res_file.write( f'{T}' + '\t' + f'{b:.3f}' + '\t' + f'{g:.3f}' + '\t' + f'{deps:.3f}' +'\t' + f'{l_f:.3f}' + '\t' +f'{ep:.3f}'+'\t' + f'{s:.3f}' +"\n") return()
[docs] def save_fit_deri_double_HN(self,T): """ saves the fit parameters of derivaitve double hn function in a file, the file must be created via create_analysis_file function Parameters ---------- T : float Temperature,or can also be an integer that corresponds to a file number during analysis. Returns ------- None. """ res_file = open(ana_file,'a') global deps1,deps2 deps1 = deps1/2.303 deps2 = deps2/2.303 res_file.write( f'{T}' + '\t' + f'{b1:.3f}' + '\t' + f'{g1:.3f}' + '\t' + f'{deps1:.3f}' +'\t' + f'{l_f1:.3f}' + '\t' +f'{b2:.3f}' + '\t' + f'{g2:.3f}' + '\t' + f'{deps2:.3f}' +'\t' + f'{l_f2:.3f}'+ '\t' +f'{ep:.3f}'+'\t' + f'{s:.3f}' +"\n") return()
plt.show()