%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Steven Huth, Sandra Sindt, 2018
%
% the program asks for a folder that contains textfiles with data
% all the distance and force data are read from each textfile
% 
% the hertz model is fit to the data using a lsqcurvefit to get a first estimation of
% the contact point, a region from shortly before the contact point until
% the end of the data array is further examined
%
% the hertz model is fitted repeatedly to the data, starting with a small part 
% around the contact point and increasing the uper fitting with each fit
%
% the young's modulus of each part of the curve is calculated and computed
% vs the fit range (which is equivalent to the indentation depth + contact point)
% a stdfilt is applied to this E-d curve in order to find the first plateau
% (where E values are constant)
%
% from this plateau region, the E value that was the result of the fit with
% lowest squared sum of residuals (chi squared) was chosen
%
% results are written into the chosen folder into a new folder 


close all
clear all


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% input parameters to be scpecified by user



% format of the textfiles to be read
num_col=10; %number of columns
format=[];
for i=1:num_col
   format=[format,'%s']; 
end
d_num=1; %  number of the column containing the position of the indenter in meter
F_num=2; %	number of the column containing Force data in newton
header=79; %number of lines in the header
del=' '; % delimiter between columns '\t' for tab

model_func=inline('p(1)*((d-p(2)).*(d>p(2))).^1.5', 'p', 'd');  % elastic model
opt=optimset('Display','off','TolFun',1E-20,'TolX',1e-20);      % fitting optionen

R=10.91E-6; %indenter radius in m
poisson=0.5; %poisson ratio
E_exp=0; % if a young's modulus is expected, it can be given as a start value for the fitting process 
startval(1)=4*sqrt(R)*E_exp/(3*(1-poisson^2));
startval(2)=0; %start value for the contact point
thresh_std=5;  % threshhold of the stdfilt (in %)
points_std=5;  % amount of points considered for the stdfilt
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

path = uigetdir('select folder with force curve data'); 
folder = dir([path '\*.txt']);
files = {folder.name};
if length(files)>1

            % creates all folders and writes user input ino 'parameters.txt'
            [~,filename,~]=fileparts(files{1});
            datestring=datestr(datetime,'yyyy-mm-dd_hh.MM');   
            results_path=[path '\hertz_results_' datestring  '\'];
            mkdir([results_path 'saturated\E_vs_d'])
            mkdir([results_path 'saturated\force_curves'])
            mkdir([results_path 'saturated\Chi'])
            mkdir([results_path 'not_saturated\E_vs_d'])
            mkdir([results_path 'not_saturated\Chi'])
            mkdir([results_path 'not_saturated\force_curves'])
            fid=fopen([results_path 'parameters.txt'],'w');
            fprintf(fid, '%s\t%g\n', 'Indenter Radius', R);
            fprintf(fid, '%s\t%f\n', 'Poisson Value', poisson);
            fprintf(fid, '%s\t%g\t%g\n', 'Start Values',startval);
            fprintf(fid, '%s\t%f\n', 'thresh_std', thresh_std);
            fprintf(fid, '%s\t%f\n', 'points_std', points_std);
            fclose(fid);
            fid2=fopen([results_path 'results.txt'],'w');
            fprintf(fid2,'%s\t%s\t%s\t%s\t%s\t%s\t%s\n', 'Youngs Modulus [kPa]', 'Chi', 'Contact Point [µm]', 'Indentation Depth [µm]', 'Saturated', 'Position', 'File');

            sat_count=[0 0];
            for k=1:length(files)
                [~,filename,~]=fileparts(files{k});
                fid=fopen([path '\' files{k}],'r');
                data=textscan(fid, format,'headerlines', header, 'delimiter',del);
                fclose(fid);
                dist=str2double(data{d_num});
                d=flipud(dist);
                d=d-d(1);

                %d now contains the indenter distance (relative to the first data point) in m
                %
                F=str2double(data{F_num}); 
                % F contains Force data in N
                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                [P_fit, ~,~]=lsqcurvefit(model_func, startval, d, F, [], [], opt);
                contact_index=find(d>=P_fit(2),1);
                start=contact_index-round((length(d)-contact_index)/2);
                if start<=0
                    start=11;
                end
                start_ind=start-10;
                d(1:start_ind)=[];
                F(1:start_ind)=[];
                % one fit is performed and d index that belongs to the resulting contact point 
                % (P_fit(2)) is found. The beginning of the data set up to shortly before the contact
                % point is dropped

                num_of_steps=30;
                steps=round(length(d)/num_of_steps);
                if steps < 1
                    steps = 1;
                end
                % num_of_steps gives the amount of fits and resulting data points in the E-d-curve.
                % higher numbers give finer results, but take more computation
                % time

                count=0;
                chi_kurz=[];
                chi=[];
                E=[];
                contact=[];
                ind_depth=[];

                for i = 1:steps:length(d)
                    count=count+1;
                    [P_fit, ~,~]=lsqcurvefit(model_func, startval, d(1:i), F(1:i), [], [], opt);
                    chi(count)=sum((F-model_func(P_fit,d)).^2)/(length(d)-2); %squared sum of residuals for the entire curve (not only up to fit range)
                    E(count)=3*1E-3*(1-poisson^2)*P_fit(1)/(4*sqrt(R)); % Young's modulus in kPa
                    contact(count)=P_fit(2); % contact point in m
                    ind_depth(count)=d(i); % indentation depth
                end


                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                local_std = stdfilt(E, ones(points_std, 1)'); 
                plateau_index = find(local_std/max(local_std) < thresh_std/100); % the 5% are a threshold, which can be adjusted
                maxfilt=find(local_std==max(local_std),1);
                plateau_index(plateau_index<=maxfilt)=[]; 
                plateau_index(find(diff(plateau_index)>1,1)+1:end)=[];

                %plateaus in the E data are found; only the first consecutive
                %array of E-data in a plateau after the maximum of the E-d
                %curve (after contact point) is taken into consideration
                if ~isempty(plateau_index)
                    sat_count(1)=sat_count(1)+1;
                    best_index=find(min(chi))+plateau_index(1)-1;
                    saturation=1;
                    sat_string='saturated\';
                else
                    sat_count(2)=sat_count(2)+1;
                    best_index=size(E,2);
                    saturation=0;
                    sat_string='not_saturated\';
                end
                E_best=E(best_index);
                chi_best=chi(best_index);
                contact_best=contact(best_index);
                ind_depth=(ind_depth-contact_best)*1E6;
                fprintf(fid2,'%f\t%g\t%g\t%g\t%i\t%i\t%s\n',  E_best, chi_best, contact_best, ind_depth(best_index), saturation, str2double(filename(end-3:end-1)), filename);
                %best index is the index where chi is minimal in the plateau
                %region. if there is no plateau detected, the last data point
                %is selected
                %the last 4 numbers of the filename are taken tio be a position index 
                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

                figure('visible','off')
                set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')'); 
                plot(ind_depth,E, 'bo')
                hold on 
                plot(ind_depth(plateau_index),E(plateau_index),'ro');
                if ~isempty(plateau_index)
                    plot(ind_depth(best_index),E_best, 'gx');
                end
                title(filename);
                ylabel('Youngs Modulus [kPa]')
                xlabel('Indentation Depth [µm]')
                saveas(gcf,[results_path sat_string 'E_vs_d\' filename '.tif']);
                savefig([results_path sat_string 'E_vs_d\' filename '.fig']);
                hold off

                i=((best_index-1)*steps)+1;
                [P_fit, ~,~]=lsqcurvefit(model_func, startval, d(1:i), F(1:i), [], [], opt);
                f=figure('visible','off');
                set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')'); 
                plot(d,F,'x', d,model_func(P_fit,d)) %force curve with hertz plot
                y=get(gca,'ylim');
                hold on
                line([d(i) d(i)],y); % fit range
                plot(P_fit(2),F(find(d>=P_fit(2),1)),'ro') % contact point
                xlabel('Distance [m]')
                ylabel('Force [N]')
                title([num2str(E_best) ',' num2str(chi_best)])
                saveas(f,[results_path  sat_string 'force_curves\' filename '.tif']);
                savefig([results_path sat_string 'force_curves\' filename '.fig']);

                % E-d-curve with marked plateau and best value as well as force curve 
                % with best fit range and contact point are plotted and saved

                
                f=figure('visible','off');
                set(gcf,'CreateFcn','set(gcf,''Visible'',''on'')'); 
                depth=d-contact_best;
                plot(depth,F,'x', depth,model_func(P_fit,d)) %force curve with hertz plot
                y=get(gca,'ylim');
                hold on
                line([depth(i) depth(i)],y); % fit range
                plot(P_fit(2)-contact_best,F(find(d>=P_fit(2),1)),'ro') % contact point
                xlabel('Indentation Depth [m]')
                ylabel('Force [N]')
                title([num2str(E_best) ',' num2str(chi_best)])
                saveas(f,[results_path sat_string filename '.tif']);
                savefig([results_path sat_string filename '.fig']);

                % E-d-curve with marked plateau and best value as well as force curve 
                % with best fit range and contact point are plotted and saved
            end
            fclose(fid2);
            fid=fopen([results_path 'number_of_saturated_curves.txt'],'w');
            fprintf(fid, '%s\t%s\n', 'saturated', 'not saturated');
            fprintf(fid, '%i\t%i\n', sat_count(1), sat_count(2));
            fclose(fid);    
    end