normaliseCurve.m

%% normaliseCurve
'load variables'
Variables % load Variables file
if  exist('CrossCorr.mat', 'file') == 2
     % File exists.
     load('CrossCorr.mat')
else
    CrossMaker
     % File does not exist.
end


%% set tables
ToT_FF_T_BIG2(:,3,:) = 0; %can be removed in final setting
ToT_FF_T_BIG2(:,4,:) = 0; % can be removed in final setting
ToT_FF_size = (4 * 256 * 256); % should be calculated at a sooner point

%% creates a M = 1024 by 1 matrix

o = 1;
while o < toToT+1
    M(o,1) = o;
    o = o + 1;
end
x = M;

clear o 

%% Calculates the normalised function

% goes to x:3:x
% moving mean goes to x:4:x
% summed x:3:x goes to x:5:x

o = 1;

while o < ToT_FF_size
    
    A = ToT_FF_T_BIG2(:,1,o); % makes a single string
    if fromToT == 1
        calc = 0;
    else
        calc = sum(A(1:fromToT)); % calculates the ammount of count from ToT 1 till set start ToT
        A(1:fromToT,1) = 0; % Sets the first ToT values to 0 to a certain value
    end
    totalPixelCount = ToT_FF_T_BIG2(1,2,o) - calc;% - sum(ToT_FF_T_BIG2(1:fromToT,1,o)); %- sum(ToT_FF_T_BIG2(1:fromToT,1,o));
    ToT_FF_T_BIG2(20,2,o) = totalPixelCount; % Puts the cutoff event count in the table
    A = A(:,1)./totalPixelCount; % normalises the events
    ToT_FF_T_BIG2(:,3,o) = A; % puts normalised events at position 3
    xsize = 1024;
    p = 1;
    
    % This loop calculates the cummulative normalised occurance
    while p < xsize + 1
        if p == 1
            ToT_FF_T_BIG2(p,5,o) = ToT_FF_T_BIG2(p,3,o);
        else
            P = p - 1;
            ToT_FF_T_BIG2(p,5,o) = ToT_FF_T_BIG2(p,3,o)+ToT_FF_T_BIG2(P,5,o);
        end
        p = p + 1;
    end
    o = o + 1;
end

clear o p xsize A totalPixelcount calc P

%% call Averagetest
% Calculates the Average ToT response as well as the the curve fits for the
% summation of this line % Creates Table for Curve fit information as well
% as a table with the Averages, cumulative averages
tic
if UsePoly == 2
    AverageTest2_imp % Uses the Polynome to second power fitting (could be buggy)
elseif UsePoly == 3
    if RunCrossCorrect == 1
        cout = "Running new Crosscorrect Average"
        AverageTest_poly3_Cross % Uses the Polynome to third power fitting (latest method) 
    elseif RunCrossCorrect == 0
        cout = "Running old"
        AverageTest_poly3
    end
else
    error('no curefitting "poly" was set')
end

AverageTest_Finished = toc

clearvars AverageTest_Finished
%% Per pixel difference map
% uses histogram fitting

ToT_FF_T_BIG3 = zeros(1024,3,ToT_FF_size); % Creates extra and final table
ToT_FF_T_BIG3(:,1,:) = ToT_FF_T_BIG2(:,3,:); %copies the normalised event occurance in position 1
ToT_FF_T_BIG3(:,2,:) = ToT_FF_T_BIG2(:,2,:); % copies the extra information like total occurance counts in

F = zeros(1024,4);
o = 1;

k = 0


if new == 1
    PrepareCor
    if RunCrossCorrect == 1
        cout = "Running new Crosscorrection"
       
        Tryout4_Cross % Runs Tryout 4 Cross corrected
    elseif RunCrossCorrect == 0
        cout = "Running old correction"
        Tryout4 % runs Tryout 4 (newest version)
    end
    
    
    %clear AverageTable
    
else %outdated
    
    while o < ToT_FF_size + 1
        if ToT_FF_T_BIG2(1,2,o) > 30000
            D = ToT_FF_T_BIG2(:,5,o);
            Tryout3
            
        else
            o;
        end
        o = o + 1;
    end
    
end
 
%close(h)
toc
%%
clearvars a b c d Curve Averagecurve_succesfull Avtot Dinky esttime expectedToT F h i ik ikke is ji KATY KT loady M memoryToT N NTNUMERO o s st starters steps titleHandle totalPixelCount Try y
clearvars NUMERO NT minimumCounts AverageTable AverageTest_Finished outlierRemovalStrength
%% Fix Matrix

k= 1;
kstart = 0;
kend = 0;
d = 0

ToT_final_M = zeros(4,256,256,1024);
while k < 5
    
    kstart = kend
    kend = k*256*256
    DINKY = permute(reshape(ToT_FF_T_BIG3(:,3,kstart+1:kend),1024,256,256),[2,3,1]);
    ToT_final_M(k,:,:,:) =  DINKY(:,:,:);
    k = k +1;
    d = 1;
end

ToT_final_M = round(ToT_final_M);

%%
clear totalPixelCount o n B ans ToTpin ix corr_fact_ToT fromToT toToT expectedToT ans Avtot Avvan calc counter Curve d D F Gx intercept kend kstart  starters step steps tester
clearvars AverageTest_Finished k