% This program analyzes the primary cell Global response and takes off the influence of the secondary responses.
%The this program requires the expfit function, which I downloaded from the
%Matlab Central: http://www.mathworks.com/matlabcentral/fileexchange/21959-exponential-fit-without-start-guess
%and made s1=0 for caseval=1.
% Single poke with penetration experiments.

clc;
clear;

files=dir('*.xls');
fileIndex = find(~[files.isdir]);

for j=1:length(fileIndex)% the number of files in that folder
    [status,sheets] = xlsfinfo(files(j).name);
    numel (sheets);
    
    for p=1:1:(numel(sheets)/2);%the number of sheets from which you want to read the data/2, each represents an expeirment
        [num,txt,raw] = xlsread(files.name,(2*p)-1,'A1');%loads the information on the entire sheet
        Data.Name{j}{p}= txt;%Reads the name of the file, which is located in the first entry of the sheet (2*i)-1
        Data.RAW{j}{p}= xlsread(files.name,p*2); %reads the data
        
        a=[Data.Name{j}{p}];
        
        NoFrames =numel(Data.RAW{j}{p}(:,1));%the number of frames
        NoCells =numel(Data.RAW{j}{p}(1,:));%the number of ellipses
        Data.NoCells{j}{p}=numel(Data.RAW{j}{p}(1,:));
        frame=(1:1:NoFrames);
        
        Data.TimePerFrame=.335;  % +-10ms on average as calculated from the force curves this can be changed accordingly with every sequence
        
        colours='bgmckrbgmckr';
        for k=1:NoCells
            Data.Cell{j}{p}{k} =Data.RAW{j}{p}(:,k);%the number of ellipses
            % right now Data.Cell{j}{i}{k} contains the kth column intensity
            % profile of the ith sheet in the jth file
        end
        
        Data.LocalInt{j}{p}=Data.Cell{j}{p}{1};
        Data.PrimaryInt{j}{p}=Data.Cell{j}{p}{2};
        Data.Vector{j}{p}=Data.Cell{j}{p}{3};
        
        for l=4:1:NoCells
            Data.Vector{j}{p}=[Data.Vector{j}{p}, Data.Cell{j}{p}{l}];
        end
        
        %getting the linear combination coefficients for the Primary cell
        Data.CoeffVec{j}{p} = Data.Vector{j}{p}\Data.PrimaryInt{j}{p};
        
        %%% the linear combination will be given by the dot product of the matrix
        %%% CELL and the Vector.
        Data.LinearComb{j}{p} = Data.Vector{j}{p} * Data.CoeffVec{j}{p};
        Data.Cell{j}{p}{NoCells+1} =Data.LinearComb{j}{p};
        
        figure()
        plot(Data.PrimaryInt{j}{p},'r','LineWidth',2);
        title('Select the point where the light was turned off')
        hold on;
        [x1,y1]=ginput(1);%cuts the data in case the bright field light was on
        
        
        figure();
        for k=2:NoCells+1
            Data.s{j}{p}{k}=expfit(frame(x1:end),Data.Cell{j}{p}{k}(x1:end) ,1); %here we are doing the fit with the exponential to account for the bleaching
            Data.y{j}{p}{k}=Data.s{j}{p}{k}(2)*exp(-frame/Data.s{j}{p}{k}(3));
            
            S1=size(Data.Cell{j}{p}{k}(x1:end));
            plot((Data.Cell{j}{p}{k}(x1:end)-Data.Cell{j}{p}{k}(end-S1(1)+1)),[colours(k)],'LineWidth',2);
            hold on;
            S2=size(Data.y{j}{p}{k}(x1:end));
            plot((Data.y{j}{p}{k}(x1:end)-Data.Cell{j}{p}{k}(end-S1(1)+1))',[colours(k)],'LineWidth',2);
            title([files.name ' Cell_' num2str(p)]);
            xlabel('frame'); ylabel('Avg Intensity');
            legend('Primary','Exp','Cell3','Exp','Cell4','Exp','Cell5','Exp','Cell6','Exp','Cell7','Exp','Cell8','Exp','Cell9','Exp','Cell10','Exp')
            
        end
        plot((Data.Cell{j}{p}{k}(x1:end)-Data.Cell{j}{p}{k}(end-S1(1)+1)),'r.','LineWidth',1);
        plot((Data.y{j}{p}{k}(x1:end)-Data.Cell{j}{p}{k}(end-S1(1)+1))','r.','LineWidth',2);
        %the graph plotted in red dots is the linear combination graph,
        %which has to be compared to the Pirmary response
        
        figure()
        plot(Data.Cell{j}{p}{1}(x1:end));
        hold on;
        plot((Data.Cell{j}{p}{NoCells+1}(x1:end)),'r.','LineWidth',1);
        title('Compare Primary and LC, Select the point where the response starts');
        
        %If the responses are different, then we can continue with the analysis as follows:
        %Calculating the Linear combination of the extremes
        [Inix,Iniy1]=ginput(1);
        Inix1=Inix+x1;
        Data.PrimaryIntBefore{j}{p}=Data.Cell{j}{p}{2}(x1:Inix1);
        Data.PrimaryIntAfter{j}{p}=Data.Cell{j}{p}{2}(end-25:end);
        Data.PrimaryIntExt{j}{p}=[Data.PrimaryIntBefore{j}{p};Data.PrimaryIntAfter{j}{p}];
        
        Data.VectorExt{j}{p}=[Data.Cell{j}{p}{3}(x1:Inix1);Data.Cell{j}{p}{3}(end-25:end)];
        
        for l=4:1:NoCells
            Data.CellExt{j}{p}{l}=[Data.Cell{j}{p}{l}(x1:Inix1);Data.Cell{j}{p}{l}(end-25:end)];
            Data.VectorExt{j}{p}=[Data.VectorExt{j}{p}, Data.CellExt{j}{p}{l}];
        end
        
        %         %getting the linear combination coefficients for the Primary
        %         cellextremes
        
        Data.CoeffVecExt{j}{p} = Data.VectorExt{j}{p}\Data.PrimaryIntExt{j}{p};
        
        %%% the linear combination will be given by the dot product of the matrix
        %%% CELL and the Vector.
        Data.LinearCombExt{j}{p} = Data.Vector{j}{p} * Data.CoeffVecExt{j}{p};
        Data.Cell{j}{p}{NoCells+2} =Data.LinearCombExt{j}{p}(x1:end);
        
        Data.s{j}{p}{NoCells+2}=expfit(frame(x1:end),Data.Cell{j}{p}{NoCells+2},1); %here we are doing the fit with the exponential to account for the bleaching
        Data.y{j}{p}{NoCells+2}=Data.s{j}{p}{NoCells+2}(2)*exp(-frame(x1:end)/Data.s{j}{p}{NoCells+2}(3));
        
        %unbleaching each cell with the LC extremes exponential
        Data.UnbLCCell{j}{p}{2}= Data.Cell{j}{p}{2}(x1:end)./(Data.y{j}{p}{NoCells+2})';% Primary cell corrected for bleaching using LCextremes exponential
        Data.UnbLCCell{j}{p}{NoCells+2}= Data.Cell{j}{p}{NoCells+2}./(Data.y{j}{p}{NoCells+2})';%LC extremes corrected for bleaching using LCextremes exponential
        
        figure();
        plot(Data.UnbLCCell{j}{p}{2},'b','LineWidth',2);
        hold on;
        plot(Data.UnbLCCell{j}{p}{NoCells+2},'g','LineWidth',2);
        title([files.name ' Cell_' num2str(p) ' Primary vs LC Unbleached']);
        xlabel('frame'); ylabel('Avg intensity');
        legend('Primary', 'LC')
        
        
        %Ask for secondareies
        
        GLOBAL= input('Is there GLOBAL RESPONSE? press 1 if there is, enter otherwise:');
        
        if GLOBAL==1 %if there is LOCAL RESPONSE!!
            
            Secondary= input('IF THE SECONDARIES ARE INTERFERING WITH THE LINEAR COMBINATION, ENTER THE NUMBER OF THE SECONDARY RESPONSES IN []:');
            
            
            %DEFINING THE PRIMARY, THE SECONDARY RESPONSES AND THE SOURROUNDING
            %CELL PROFILES
            Data.PrimaryCell{j}{p}=Data.Cell{j}{p}{2}(x1:end);
            
            Secondary1=[];
            Secondary1=[2 Secondary];
            % Here we select the elements that are NOT the secondary responses NOR the primary!
            %We define:
            NoCellsVector= (2:1:NoCells);
            
            %Now
            r = zeros(1,length(NoCellsVector)-length(Secondary1)-2);
            r_c = 1;
            a=NoCellsVector;
            b=Secondary1;
            for i = 1:max(a)
                k = (sum(a==i) - sum(b==i));
                if k > 0
                    for j = 1:k
                        r(r_c) = i;
                        r_c = r_c + 1;
                    end
                end
            end
            
            
            NonSecondaryCells=r;%These are indexes of the cells that contribute to the LC, non secondaries
            
            
            % Now we have to take each of the elements and build up the vector
            % for the Linear Combination
            for k=1: numel(NonSecondaryCells)
                %{NonSecondaryCells(k)} THIS IS MY NEW INDEX, IT INDICATES THE CELL WHICH HAS TO BE TAKEN INTO ACCOUNT TO FORM THE LINEAR COMBINATION!
                Data.LinearCombinationCell{j}{p}{k}=Data.Cell{j}{p}{NonSecondaryCells(k)}(x1:end);
            end
            
            % Building the Vector Matrix to find the linear combination
            Data.NonSecondaryVector{j}{p}=Data.LinearCombinationCell{j}{p}{1};
            for l=2:1:numel(NonSecondaryCells)
                Data.NonSecondaryVector{j}{p}=[Data.NonSecondaryVector{j}{p}, Data.LinearCombinationCell{j}{p}{l}]; % this matrix contains only the cells around the plate which are not responding
            end
            
            if Secondary>=1
                %We have:
                %Data.PrimaryCell{j}{p} ; which size is (x1:end)
                %Data.NonSecondaryVector{j}{p}%which is the matrix of the
                %vectors that will contribute to the LC ; which size is (x1:end)
                
                %we now build the extremes vector:
                %Data.Cell{j}{p}{Secondary1(l)}(x1:end)
                l=1;
                Data.SecondaryIntBefore{j}{p}=Data.Cell{j}{p}{Secondary1(l)}(x1:Inix1);
                Data.SecondaryIntAfter{j}{p}=Data.Cell{j}{p}{Secondary1(l)}(end-25:end);
                Data.SecondaryIntExt{j}{p}=[Data.SecondaryIntBefore{j}{p};Data.SecondaryIntAfter{j}{p}];
                
                Data.NonSecondaryVectorExt{j}{p}=[Data.Cell{j}{p}{NonSecondaryCells(1)}(x1:Inix1);Data.Cell{j}{p}{NonSecondaryCells(1)}(end-25:end)];
                
                for l=2:1:numel(NonSecondaryCells)
                    Data.NonSecondaryCellExt{j}{p}{l}=[Data.Cell{j}{p}{NonSecondaryCells(l)}(x1:Inix1);Data.Cell{j}{p}{NonSecondaryCells(l)}(end-25:end)];
                    Data.NonSecondaryVectorExt{j}{p}=[Data.NonSecondaryVectorExt{j}{p}, Data.NonSecondaryCellExt{j}{p}{l}];
                end
                
                %getting the linear combination coefficients for the Primary cell extremes
                
                Data.NonSecondaryCoeffVecExt{j}{p} = Data.NonSecondaryVectorExt{j}{p}\Data.SecondaryIntExt{j}{p};
                
                %%% the linear combination will be given by the dot product of the matrix
                %%% CELL and the Vector.
                Data.NonSecondaryLinearCombExt{j}{p} = Data.NonSecondaryVector{j}{p} * Data.NonSecondaryCoeffVecExt{j}{p};
                Data.Cell{j}{p}{NoCells+2}=[];
                Data.Cell{j}{p}{NoCells+2} =Data.NonSecondaryLinearCombExt{j}{p};
                
                Data.s{j}{p}{NoCells+2}=expfit(frame(x1:end),Data.Cell{j}{p}{NoCells+2},1); %here we are doing the fit with the exponential to account for the bleaching
                Data.y{j}{p}{NoCells+2}=Data.s{j}{p}{NoCells+2}(2)*exp(-frame(x1:end)/Data.s{j}{p}{NoCells+2}(3));
                
                Data.LinearCombinationS{j}{p}{1}=Data.s{j}{p}{NoCells+2};
                Data.LinearCombinationY{j}{p}{1}=Data.y{j}{p}{NoCells+2};
                %          %unbleaching each cell with the LC extremes exponential
                Data.UnbPrimaryCell{j}{p}= Data.Cell{j}{p}{2}(x1:end)./Data.LinearCombinationY{j}{p}{1}';% Primary cell corrected for bleaching using LCextremes exponential
                Data.UnbLCCell{j}{p}{NoCells+2}= Data.Cell{j}{p}{NoCells+2}./(Data.LinearCombinationY{j}{p}{1})';%LC extremes corrected for bleaching using LCextremes exponential
                
                
                
            else  %this is what it will do when there are no secondaries! So the result doesn't change, JUST REDEFINE!
                
                for k=3:NoCells
                    Data.LinearCombinationCell{j}{p}{k-2}=Data.Cell{j}{p}{k}(x1:end);%the cells not responding that contribute to the LC
                end
                Data.LinearCombinationS{j}{p}{1}=Data.s{j}{p}{NoCells+2};% THIS IS THE EXPONENTIAL COEFFS OF THE extremes LINEAR COMBINATION
                Data.LinearCombinationY{j}{p}{1}=Data.y{j}{p}{NoCells+2}; %THIS IS THE EXPONENTIAL FIT OF THE extremes LINEAR COMBINATION
                %                 %unbleaching each cell with the LC extremes exponential
                %                  %unbleaching each cell with the LC extremes exponential
                Data.UnbPrimaryCell{j}{p}= Data.Cell{j}{p}{2}(x1:end)./Data.LinearCombinationY{j}{p}{1}';% Primary cell corrected for bleaching using LCextremes exponential
                Data.UnbLCCell{j}{p}{NoCells+2}= Data.Cell{j}{p}{NoCells+2}./(Data.LinearCombinationY{j}{p}{1})';%LC extremes corrected for bleaching using LCextremes exponential
                %
            end
            
            
        end
        figure()
        plot(Data.UnbPrimaryCell{j}{p})
        hold on;
        plot(Data.UnbLCCell{j}{p}{NoCells+2},'g');
        title('Bleaching corrected Primary response and LC, COMPARE!')
        
        %  NOW WE HAVE TO ANALYZE THE RESPONSES!
        GLOBAL2= input('Is there still GLOBAL RESPONSE? press 1 if there is, enter otherwise:');
        if GLOBAL2==1 %if there is LOCAL RESPONSE!!
            
            
            %MEASURING THE NOISE LEVEL OF THE SIGNAL!
            %Data.UnbPrimaryCell{j}{p}{q}
            figure()
            plot(Data.UnbPrimaryCell{j}{p})
            hold on;
            title('Select the points that limit the interval in which you want to start the NOISE CALCULATION');
            xlabel('frame'); ylabel('Avg Fluorescence Intensity');
            [xNoise,yNoise] = ginput(2);
            frame=frame(1:numel(Data.UnbPrimaryCell{j}{p}));
            [r s] = polyfit(frame(xNoise(1):xNoise(2))', Data.UnbPrimaryCell{j}{p}(xNoise(1):xNoise(2)), 1); %Takes the curve between xNoise1 and xNoise2, and fits a 1st grade polynomial
            [y_fit Data.delta{j}{p}] = polyval(r, frame(xNoise(1):xNoise(2))', s); %calculates the stdev around the fit
            
            plot(frame(xNoise(1):xNoise(2))', y_fit + 2 * Data.delta{j}{p}, ':', frame(xNoise(1):xNoise(2))', y_fit - 2 * Data.delta{j}{p}, ':') %plots the curve and the noise around it
            Data.Noise{j}{p}=2*mean(Data.delta{j}{p}); % 2 delta corresponding roughly to the 95% confidence interval. The mean is the average of the delta value.
            
            Noise={'Noise Intensity'; Data.Noise{j}{p}};%%% save the NOISE LEVEL!!!
            %xlswrite(files.name, Noise, (i*2)-1, 'B3');
            %xlswrite(files.name,Data.Noise{j}{i},(i*2)-1,'B4');
            
            
            %             f=figure;
            %             h = uicontrol('Position',[20 20 200 40],'String','Continue',...
            %                 'Callback','uiresume(gcbf)');
            plot(Data.UnbPrimaryCell{j}{p}, [colours(2)], 'LineWidth',1);
            hold on;
            Data.UnbPrimaryCellS{j}{p}=smooth(Data.UnbPrimaryCell{j}{p});
            plot(Data.UnbPrimaryCellS{j}{p}, [colours(2)], 'LineWidth',2);
            title('SELECT THE START AND END OF EACH OF THE GLOBAL RESPONSE; the start:determines the basal and A')
            xlabel('frame')
            ylabel('Avg Fluorescence Intensity')
            %             uiwait(gcf);
            
            Data.NoPeaks{j}{p}= 1;%input('How many peaks do you want to analyze?');
            P=Data.NoPeaks{j}{p}*2;
            NoPeaks= Data.NoPeaks{j}{p};
            [x,y] = ginput(P);
            Data.x{j}{p}=[x];
            Data.y{j}{p}=[y];
            point=[x,y];
            %close (f);
            
            
            %             for m=1:2:P-1
            %here we determine the interval of THE peak; the initial value
            %will determine the basal level
            m=1;%only one response!
            myIndices1=find(frame>=x(m));%for each of the secondaries
            myIndices2=find(frame<=x(m+1));%for each of the secondaries
            frame2=frame(myIndices1(1):myIndices2(end));%frame effective piece
            
            Data.PeakFrames{j}{p}=frame2%from the fple j, the cell i, the peak m
            Data.PeakInt{j}{p}=Data.UnbPrimaryCellS{j}{p}(myIndices1(1):myIndices2(end)); %intensity effective piece, the response will start at zero SAVE!
            
            figure()
            plot(Data.PeakInt{j}{p},'k')
            hold;
            %close (gcf);
            
            [maxintens,index1] =max(Data.PeakInt{j}{p});
            Data.PeakAmpl{j}{p}=max(Data.PeakInt{j}{p})-Data.PeakInt{j}{p}(1);%amplitude, measured from the the point of the response at y(1) [NoPeaks]
            
            Data.PeakHalfMax{j}{p}=Data.PeakAmpl{j}{p}/2; %save the Peak Half Max, now that we know it exists.
            plot(frame(index1),Data.PeakInt{j}{p},'r.')%plots the peak intensity
            
            %now we have to measure the duration!!!, WE'LL SEE HOW IT
            %WORKS FOR THE RESPONSES WHICH STAY UP!
            
            %Before: A
            intensA=Data.PeakInt{j}{p}(1:index1)-Data.PeakInt{j}{p}(1);%the portion before the maximum
            %     [halfmaxA,index2]=max(intensA)/2;
            index2=find(intensA<=Data.PeakHalfMax{j}{p});%antes del halfmax
            frameA{j}{p}=frame(index2);
            Data.HalfMaxFrameA{j}{p}=frameA{j}{p}(end); %save!
            plot(Data.HalfMaxFrameA{j}{p},Data.PeakInt{j}{p},'b.')
            
            %After: D
            intensD=Data.PeakInt{j}{p}(index1:end)-Data.PeakInt{j}{p}(1);%the portion after the maximum, translated the same amount as intensA
            index3=find(intensD>=Data.PeakHalfMax{j}{p});%antes del halfmax
            
            frameD{j}{p}=frame(index1+index3);
            Data.HalfMaxFrameD{j}{p}=frameD{j}{p}(end);%save!
            plot(Data.HalfMaxFrameD{j}{p},Data.PeakInt{j}{p},'b.')
            
            
            %%% SAVE THE NEXT THREE IN THE PROPER CASE!!!!
            Data.FrameDuration{j}{p}=Data.HalfMaxFrameD{j}{p}-Data.HalfMaxFrameA{j}{p};%duration of avg amplitude
            Data.TimeDuration{j}{p}= (Data.FrameDuration{j}{p}).*Data.TimePerFrame;%duration of avg amplitude
            Data.Amount{j}{p}=Data.PeakAmpl{j}{p}*Data.TimeDuration{j}{p};
            
            fileN=[files.name(1:end-4) '_Cell_' num2str(p)]
            SaveAllFigures(fileN,'fig');
            
            
            Alphabet={'A','B','C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P','Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', 'AA','AB', 'AC', 'AD', 'AE', 'AF', 'AG', 'AH', 'AI', 'AJ', 'AK', 'AL', 'AM', 'AN', 'AO', 'AP', 'AQ', 'AR', 'AS', 'AT', 'AU', 'AV', 'AW', 'AX', 'AY', 'AZ'};
            
            %save the linear combination vector and the coefficients the coefficients
            NoResp=numel(Secondary1);%the number of responses!
            myName=[];
            myName{1}=['LCCoeffs'];
            myName{1+NoResp}=['LC_Vector'];
            myName{1+(2*NoResp)}=['LC_Exp'];
            %myName{4}=['Unb_Local'];
            headers = [myName];
            
            letter1=[Alphabet(NoCells+(3))];
            CoeffPosition1A=[letter1 '1'];
            CoeffPosition1=strcat(CoeffPosition1A(1), CoeffPosition1A(2));
            varargin=CoeffPosition1;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, headers,p*2,myString);
            
            CoeffPosition2A=[letter1 '2'];
            CoeffPosition2=strcat(CoeffPosition2A(1), CoeffPosition2A(2));
            varargin=CoeffPosition2;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, Data.CoeffVec{j}{p},p*2,myString);
            
            Data.PrimaryLinearComb{j}{p}=Data.Cell{j}{p}{NoCells+2};
            letter2=[Alphabet(NoCells+(3+(NoResp)))];
            LinearCombPositionA=[letter2 '2'];
            LinearCombPosition=strcat(LinearCombPositionA(1), LinearCombPositionA(2));
            varargin=LinearCombPosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, Data.PrimaryLinearComb{j}{p},p*2,myString);
            
            letter3=[Alphabet(NoCells+(3+(NoResp*2)))];
            UnbExpPositionA=[letter3 '2'];
            UnbExpPosition=strcat(UnbExpPositionA(1), UnbExpPositionA(2));
            varargin=UnbExpPosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, Data.LinearCombinationS{j}{p}{1},p*2,myString);
            
            myName1{1}=['Noise in Primary and Secondaries'];
            headers1 = [myName1];
            L1=[Alphabet(2*NoCells +2)];
            
            NoisePosition1A=[L1 '3'];
            NoisePosition1=strcat(NoisePosition1A(1), NoisePosition1A(2));
            varargin=NoisePosition1;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, headers1,p*2-1,myString);
            
            NoisePosition2A=[L1 '4'];
            NoisePosition2=strcat(NoisePosition2A(1), NoisePosition2A(2));
            varargin=NoisePosition2;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, Data.Noise{j}{p},p*2-1,myString);
            
            %      SAVING THE ORIGINAL EXPONENTIAL FIT FOR ALL THE CELLS
            
            NameExp{1}=['a*exp(-t/b)'];
            NameExp{2}=['a'];
            NameExp{3}=['b'];
            
            letter1=[Alphabet(NoCells+(3+(NoResp*3)+2))];
            
            %THE HEADER
            CoeffPosition1A=[letter1 '1'];
            CoeffPosition1=strcat(CoeffPosition1A(1), CoeffPosition1A(2));
            varargin=CoeffPosition1;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, NameExp',p*2,myString);
            
            
            for k=2:NoCells+1
                myCell{k}=['Cell' num2str(k)];
                ExpFitCell_1{k} =[Data.s{j}{p}{k}(2)];
                ExpFitCell_2{k} =[Data.s{j}{p}{k}(3)];
                
            end
            
            headerCELL= [myCell]';
            
            letter1=[Alphabet(NoCells+(3+(NoResp*3)+2))];
            
            %THE HEADER
            CoeffPosition1A=[letter1 '1'];
            CoeffPosition1=strcat(CoeffPosition1A(1), CoeffPosition1A(2));
            varargin=CoeffPosition1;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, headerCELL',p*2,myString);
            
            
            % A COEFFICIENT FROM THE EXPONENTIAL FIT
            CoeffPosition2A=[letter1 '2'];
            CoeffPosition2=strcat(CoeffPosition2A(1), CoeffPosition2A(2));
            varargin=CoeffPosition2;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, ExpFitCell_1,p*2,myString);
            
            %b MEAN TIME OF THE EXPONENTIAL FIT
            CoeffPosition3A=[letter1 '3'];
            CoeffPosition3=strcat(CoeffPosition3A(1), CoeffPosition3A(2));
            varargin=CoeffPosition3;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, ExpFitCell_2,p*2,myString);
            
            
            
            
            %SAVING THE ANALYSIS OF THE AMOUNT OF Ca
            
            finalExpLetter=Alphabet(((NoCells+1)*2+2));
            
            NoPeaks=numel (Secondary)+1;
            myPeak=[];
            for l= 1:NoPeaks
                myPeak{2*l-1}=['Response_' num2str(l) 't_i'];
                myPeak{2*l}=['Response_' num2str(l) 't_f'];
            end
            headerPeak = [myPeak]';
            
            
            PeakPositionHA=[Alphabet((NoCells+1)*2+4) '7'];
            PeakPositionH=strcat(PeakPositionHA(1), PeakPositionHA(2));
            varargin=PeakPositionH;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, headerPeak,p*2-1,myString);
            
            
            myPeakH{1}=['Frame'];
            myPeakH{2}=['Time'];
            myPeakH{3}=['Intensity i/f'];
            myPeakH{4}=['Frame duration'];
            myPeakH{5}=['Time duration'];
            myPeakH{6}=['Amplitude'];
            myPeakH{7}=['Amount'];
            myPeakH{8}=['Cell_Response'];
            
            PeakHeader= [myPeakH];
            PeakHPosA=[Alphabet((NoCells+1)*2+5) '6'];
            PeakHPos=strcat(PeakHPosA(1), PeakHPosA(2));
            varargin=PeakHPos;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, PeakHeader ,(p*2)-1,myString);
            
            
            
            xPeakPosition= [Data.x{j}{p}];
            yPeakPosition=[Data.y{j}{p}];
            
            PeakFrameDuration =[Data.FrameDuration{j}{p}];
            PeakTimeDuration= [ Data.TimeDuration{j}{p}];
            PeakAmpl=[Data.PeakAmpl{j}{p}];
            PeakAmount= [Data.Amount{j}{p}];
            
            
            %             Frame Begining and end of the peak
            PeakTimePositionA=[Alphabet((NoCells+1)*2+5) '7'];
            PeakTimePosition=strcat(PeakTimePositionA(1), PeakTimePositionA(2));
            varargin=PeakTimePosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, xPeakPosition,p*2-1,myString);%Data.x{j}{p}
            
            
            %             Temporal Begining and end of the peak
            PeakTimePositionA=[Alphabet((NoCells+1)*2+6) '7'];
            PeakTimePosition=strcat(PeakTimePositionA(1), PeakTimePositionA(2));
            varargin=PeakTimePosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, xPeakPosition*0.345,p*2-1,myString);%Data.x{j}{p}
            
            
            
            
            %             Intensity at the x chosen point
            PeakTimePositionA=[Alphabet((NoCells+1)*2+7) '7'];
            PeakTimePosition=strcat(PeakTimePositionA(1), PeakTimePositionA(2));
            varargin=PeakTimePosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, yPeakPosition,p*2-1,myString);%Data.y{j}{p}
            
            
            %             Response Frame Duration
            FrameDurationPositionA=[Alphabet((NoCells+1)*2+8) '7'];
            FrameDurationPosition=strcat(FrameDurationPositionA(1), FrameDurationPositionA(2));
            varargin=FrameDurationPosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, PeakFrameDuration' ,p*2-1,myString);
            
            %             Response Time Duration
            TimeDurationPositionA=[Alphabet((NoCells+1)*2+9) '7'];
            TimeDurationPosition=strcat(TimeDurationPositionA(1), TimeDurationPositionA(2));
            varargin=TimeDurationPosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, PeakTimeDuration' ,p*2-1,myString);
            
            %             Amplitude
            AmplitudePositionA=[Alphabet((NoCells+1)*2+10) '7'];
            AmplitudePosition=strcat(AmplitudePositionA(1), AmplitudePositionA(2));
            varargin=AmplitudePosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, PeakAmpl' ,p*2-1,myString);
            
            %             Amount
            AmountPositionA=[Alphabet((NoCells+1)*2+11) '7'];
            AmountPosition=strcat(AmountPositionA(1), AmountPositionA(2));
            varargin=AmountPosition;
            myString = '';
            for i=1:length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            xlswrite(files.name, PeakAmount' ,p*2-1,myString);
            
            
            %             Secondary1
            ResponsePositionA=[Alphabet((NoCells+1)*2+12) '7'];
            ResponsePosition=strcat(ResponsePositionA(1), ResponsePositionA(2));
            varargin=ResponsePosition;
            myString = '';
            for i=1:1%length(varargin)
                if isnumeric(varargin{i})
                    myString = [myString num2str(varargin{i}) ','];
                else
                    myString = [myString varargin{i} ','];
                end
            end
            S=Secondary1(1)';%S=Secondary1';
            xlswrite(files.name, S ,p*2-1,myString);
        else    
        end
    end
    close all;
end






%now we need to choose where the force curve is done in the movie, which curve to choose and which frames shall we take for the force curves