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SummatedCM.m
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%Output a summated confusion matrix
%INPUTS:
% User selects 2 x Classification*.csv files
%REQUIREMENTS
% 1. LUTS mat in current folder
% 2. kappaf function in current folder
% select rater1 TS first
%%select rater 2 MS second
%% Predefine Paths and Patient ID
% clear variables
clear
clc
%load list of selected patient number
patientnumber = readtable('patientnumber.csv');
patientnumber = table2array(patientnumber);
%Define input and output pathways
pathEY ='D:\Box Sync\Box Sync\Elton Shared\All task classifications (E.Y.) V3\';
pathMA ='D:\Box Sync\Box Sync\Elton Shared\All task classifications (M.A.) V3\';
pathTW ='D:\Box Sync\Box Sync\Elton Shared\Natural Xsens classifications (T.W.) V3 csvformat\';
pathOUT = 'D:\Box Sync\Box Sync\Elton Shared\KappaFigures\Summated CM\';
%load list of files in each rater's folder for data extraction
fileIDsEY =dir(strcat(pathEY,'*.csv'));
fileIDsEY = struct2cell(fileIDsEY)';
fileIDsEY(:,[2:6]) = [];
fileIDsMA =dir(strcat(pathMA,'*.csv'));
fileIDsMA = struct2cell(fileIDsMA)';
fileIDsMA(:,[2:6]) = [];
fileIDsTW = [dir(strcat(pathTW,'*.csv')); dir(strcat(pathTW,'*.xlsx'))];
fileIDsTW = struct2cell(fileIDsTW)';
fileIDsTW(:,[2:6]) = [];
%Predefine number of subjects for the analysis
m = 9
maxfinal = zeros(1,m);
minfinal = zeros(1,m);
% preallocate runorders for 4 category labels
RunOrderpos =zeros(999999,3,m);
RunOrderact =zeros(999999,3,m);
RunOrderfun =zeros(999999,3,m);
RunOrdertrans =zeros(999999,3,m);
%% Automatically generate and save annotation and confusion matrix in a loop
%initialise loop
c=1 %data we are looking for: 1 = xsens natural; 2 = xsens control 3 = apple
for n = 1:m %patient number, manually insert number of patient selected here.
disp(patientnumber(n))
Patient = char(patientnumber(n));
idx1 = contains(fileIDsEY, patientnumber(n,c));
rownum1 = find(idx1,1,'last');
idx2 = contains(fileIDsMA, patientnumber(n,c));
rownum2 = find(idx2,1,'last');
idx3 = contains(fileIDsTW, patientnumber(n,c));
rownum3 = find(idx3,1,'last');
%direct pathname and file directory and display raters' initials
if isempty(rownum1) == 1,
raters = 'TW&MA'
pn1 = pathTW;
else pn1 = pathEY;
raters = 'EY&MA'
end
pn2 = pathMA;
%define filename in preparation for loading in following steps
if raters == 'TW&MA'
fn1 = char(fileIDsTW(rownum3));
else fn1 = char(fileIDsEY(rownum1));
end
fn2 = char(fileIDsMA(rownum2));
%break here!!!!!!!!!!!!!!!!!!
%load rater 1's rating
F1 = pwd;
cd(pn1)
fprintf('CHOSEN FOLDER No.1: %s\n', pn1)
fprintf('\tReading: ');
rawClassData1 = readtable(fn1);
fprintf('%s [%d x %d] & ', fn1);
%load rater 2's rating
cd(pn2)
fprintf('\nCHOSEN FOLDER No.2: %s\n', pn2)
fprintf('\tReading: ');
rawClassData2 = readtable(fn2);
fprintf('%s [%d x %d] & ', fn2);
cd(F1)
clear pathEY pathMA pathTW idx1 idx2 idx3 pn1 pn2 rownum1 rownum2 rownum3 fileIDs*
% data preparation BREAK HERE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
%rater1
ClassData1 = rawClassData1(:,[7 11 12]);
ClassData1 =table2array(ClassData1);
%rater2
ClassData2 = rawClassData2(:,[7 11 12]);
ClassData2 =table2array(ClassData2);
%Convert Rater 1 annotation seconds into DeciSeconds (this is to preserve those classifications that start and end within same second)
ClassDataDS1=[ClassData1(:,[2 3])*10 ClassData1(:,1) zeros(length(ClassData1),1)];
%Convert Rater 2 annotation seconds into DeciSeconds (this is to preserve those classifications that start and end within same second)
ClassDataDS2=[ClassData2(:,[2 3])*10 ClassData2(:,1) zeros(length(ClassData2),1)];
clear rawClassData1 rawClassData2 ClassData1 ClassData2 pn1 pn2 F1
%Correct for NPT unsync
%ClassDataDS2(:,1:2) = ClassDataDS2(:,1:2)-58;
% Generate Running Order of Annotations
ClassDataDS1 =round(ClassDataDS1); %rater 1
ClassDataDS2 =round(ClassDataDS2); %rater 2
%%remove zero start index from all class files
if ClassDataDS1(1,1) ==0
ClassDataDS1(1,1)=10;
end
if ClassDataDS1(2,1) ==0
ClassDataDS1(2,1)=10;
end
if ClassDataDS2(1,1)==0
ClassDataDS2(1,1)=10;
end
if ClassDataDS2(2,1)==0
ClassDataDS2(2,1)=10;
end
% cut classification files same size
max1 =max(ClassDataDS1(:,2)); %find last annotation rater 1
max2 =max(ClassDataDS2(:,2)); %find last annotation rater 2
minfinal(1,n) = min(max1,max2); %find where to cut annotation files
maxfinal(1,n) = max(max1,max2);
% Writing into RunOrder format %BREAKHERE!!!!!!!!!!!!!!!!
%add postures to RunOrderpos
%rater 1
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3)<6
RunOrderpos(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= ClassDataDS1(i,3);
end
end
%rater 2
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3)<6
RunOrderpos(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= ClassDataDS2(i,3);
end
end
%add functional to RunOrderfun
%rater 1
funindex1 =find(ClassDataDS1(:,3)==6 | ClassDataDS1(:,3)==8 ...
| ClassDataDS1(:,3)==9 | ClassDataDS1(:,3)==27 | ClassDataDS1(:,3)==22 ...
| ClassDataDS1(:,3)==23 | ClassDataDS1(:,3)==26 | ClassDataDS1(:,3)==24);
funindex1 =[1;funindex1];
for k =1:length(funindex1)-1
t=k+1;
RunOrderfun(ClassDataDS1(funindex1(k)):ClassDataDS1(funindex1(t)),1,n)= ClassDataDS1(funindex1(t),3);
end
%rater 2
funindex2 =find(ClassDataDS2(:,3)==6 | ClassDataDS2(:,3)==8 ...
| ClassDataDS2(:,3)==9 | ClassDataDS2(:,3)==27 | ClassDataDS2(:,3)==22 ...
| ClassDataDS2(:,3)==23 | ClassDataDS2(:,3)==26 | ClassDataDS2(:,3)==24);
funindex2 =[1;funindex2];
for k =1:length(funindex2)-1
t=k+1;
RunOrderfun(ClassDataDS2(funindex2(k)):ClassDataDS2(funindex2(t)),2,n)= ClassDataDS2(funindex2(t),3);
end
%
% add activities to RunOrderact
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3)>9 && ClassDataDS1(i,3)<18
RunOrderact(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= ClassDataDS1(i,3);
end
end
%MS
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3)>9 && ClassDataDS2(i,3)<18
RunOrderact(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= ClassDataDS2(i,3);
end
end
%add transition to RunOrdertrans
%Rater1
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3) ==28
RunOrdertrans(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= ClassDataDS1(i,3);
end
end
%Rater2
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3)==28
RunOrdertrans(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= ClassDataDS2(i,3);
end
end
%BREAK HERE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
% label occluded or sensor removed periods
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3) >17 && ClassDataDS1(i,3) <21
RunOrderact(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= 18; %original:= ClassDataDS1(i,3);
end
end
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3) >17 && ClassDataDS2(i,3) <21
RunOrderact(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= 18;
end
end
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3) >17 && ClassDataDS1(i,3) <21
RunOrderpos(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= 18;
end
end
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3) >17 && ClassDataDS2(i,3) <21
RunOrderpos(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= 18;
end
end
for i=1:length(ClassDataDS1)
if ClassDataDS1(i,3) >17 && ClassDataDS1(i,3) <21
RunOrderfun(ClassDataDS1(i,1): ClassDataDS1(i,2),1,n)= 18;
end
end
for i=1:length(ClassDataDS2)
if ClassDataDS2(i,3) >17 && ClassDataDS2(i,3) <21
RunOrderfun(ClassDataDS2(i,1): ClassDataDS2(i,2),2,n)= 18;
end
end
% Remove non-task / non-rated zero rows
% where no-task period is remain unlabeled by both raters, increasing
% agreement on the "non-labelled" categories and increase kappa
% %activities
% for i = length(RunOrderact):-1:1
% if RunOrderact(i,1) == 0 && RunOrderact(i,2) == 0,
% RunOrderact(i,:) = [];
% end
% %posture
% if RunOrderpos(i,1) == 0 && RunOrderpos(i,2) == 0,
% RunOrderpos(i,:) = [];
% end
% %functional
% if RunOrderfun(i,1) == 0 && RunOrderfun(i,2) == 0,
% RunOrderfun(i,:) = [];
% end
% end
%
%Locate disagreement between two raters for plotting figures
% RunOrderpos = RunOrderpos(all(RunOrderpos(:,1:2),2),:);
RunOrderpos(:,3,n)=RunOrderpos(:,1,n)~=RunOrderpos(:,2,n);
% RunOrderfun = RunOrderfun(all(RunOrderfun(:,1:2),2),:);
RunOrderfun(:,3,n)=RunOrderfun(:,1,n)~=RunOrderfun(:,2,n);
% RunOrderact = RunOrderact(all(RunOrderact(:,1:2),2),:);
RunOrderact(:,3,n)=RunOrderact(:,1,n)~=RunOrderact(:,2,n);
% RunOrdertrans = RunOrdertrans(all(RunOrdertrans(:,1:2),2),:);
RunOrdertrans(:,3,n)=RunOrdertrans(:,1,n)~=RunOrdertrans(:,2,n);
%clear current workspace
clear ClassDataDS* fn* funindex* i max1 max2 raters Patient
%Re-initialise with path details
pathEY ='D:\Box Sync\Box Sync\Elton Shared\All task classifications (E.Y.) V3\';
pathMA ='D:\Box Sync\Box Sync\Elton Shared\All task classifications (M.A.) V3\';
pathTW ='D:\Box Sync\Box Sync\Elton Shared\Natural Xsens classifications (T.W.) V3 csvformat\';
%load list of files in each rater's folder for data extraction
fileIDsEY =dir(strcat(pathEY,'*.csv'));
fileIDsEY = struct2cell(fileIDsEY)';
fileIDsEY(:,[2:6]) = [];
fileIDsMA =dir(strcat(pathMA,'*.csv'));
fileIDsMA = struct2cell(fileIDsMA)';
fileIDsMA(:,[2:6]) = [];
fileIDsTW = [dir(strcat(pathTW,'*.csv')); dir(strcat(pathTW,'*.xlsx'))];
fileIDsTW = struct2cell(fileIDsTW)';
fileIDsTW(:,[2:6]) = [];
end
%%
%Stagger all posture score into one matrix for a summated CM to show
%distribution and incidence of the categories
ALLRunOrderpos = cat(1,RunOrderpos(1:minfinal(1,1),:,1),RunOrderpos(1:minfinal(1,2),:,2),...
RunOrderpos(1:minfinal(1,3),:,3),RunOrderpos(1:minfinal(1,4),:,4),...
RunOrderpos(1:minfinal(1,5),:,5),RunOrderpos(1:minfinal(1,6),:,6),...
RunOrderpos(1:minfinal(1,7),:,7),RunOrderpos(1:minfinal(1,8),:,8),...
RunOrderpos(1:minfinal(1,9),:,9));%,RunOrderpos(1:minfinal(1,10),:,10),...
% RunOrderpos(1:minfinal(1,11),:,11),RunOrderpos(1:minfinal(1,12),:,12),...
% RunOrderpos(1:minfinal(1,13),:,13),RunOrderpos(1:minfinal(1,14),:,14),...
% RunOrderpos(1:minfinal(1,15),:,15),RunOrderpos(1:minfinal(1,16),:,16),...
% RunOrderpos(1:minfinal(1,17),:,17),RunOrderpos(1:minfinal(1,18),:,18),...
% RunOrderpos(1:minfinal(1,19),:,19),RunOrderpos(1:minfinal(1,20),:,20),...
% RunOrderpos(1:minfinal(1,21),:,21),RunOrderpos(1:minfinal(1,22),:,22),...
% RunOrderpos(1:minfinal(1,23),:,23),RunOrderpos(1:minfinal(1,24),:,24),...
% RunOrderpos(1:minfinal(1,25),:,25),RunOrderpos(1:minfinal(1,26),:,26),...
% RunOrderpos(1:minfinal(1,27),:,27),RunOrderpos(1:minfinal(1,28),:,28),...
% RunOrderpos(1:minfinal(1,29),:,29),RunOrderpos(1:minfinal(1,30),:,30),...
% RunOrderpos(1:minfinal(1,31),:,31),RunOrderpos(1:minfinal(1,32),:,32),...
% RunOrderpos(1:minfinal(1,33),:,33),RunOrderpos(1:minfinal(1,34),:,34),...
% RunOrderpos(1:minfinal(1,35),:,35),RunOrderpos(1:minfinal(1,36),:,36),...
% RunOrderpos(1:minfinal(1,37),:,37),RunOrderpos(1:minfinal(1,38),:,38),...
% RunOrderpos(1:minfinal(1,39),:,39),RunOrderpos(1:minfinal(1,40),:,40),...
% RunOrderpos(1:minfinal(1,41),:,41),RunOrderpos(1:minfinal(1,42),:,42),...
% RunOrderpos(1:minfinal(1,43),:,43),RunOrderpos(1:minfinal(1,44),:,44),...
% RunOrderpos(1:minfinal(1,45),:,45),RunOrderpos(1:minfinal(1,46),:,46),...
% RunOrderpos(1:minfinal(1,47),:,47),RunOrderpos(1:minfinal(1,48),:,48),...
% RunOrderpos(1:minfinal(1,49),:,49));
% %
ALLRunOrderfun = cat(1,RunOrderfun(1:minfinal(1,1),:,1),RunOrderfun(1:minfinal(1,2),:,2),...
RunOrderfun(1:minfinal(1,3),:,3),RunOrderfun(1:minfinal(1,4),:,4),...
RunOrderfun(1:minfinal(1,5),:,5),RunOrderfun(1:minfinal(1,6),:,6),...
RunOrderfun(1:minfinal(1,7),:,7),RunOrderfun(1:minfinal(1,8),:,8),...
RunOrderfun(1:minfinal(1,9),:,9));%,RunOrderfun(1:minfinal(1,10),:,10),...
% RunOrderfun(1:minfinal(1,11),:,11),RunOrderfun(1:minfinal(1,12),:,12),...
% RunOrderfun(1:minfinal(1,13),:,13),RunOrderfun(1:minfinal(1,14),:,14),...
% RunOrderfun(1:minfinal(1,15),:,15),RunOrderfun(1:minfinal(1,16),:,16),...
% RunOrderfun(1:minfinal(1,17),:,17),RunOrderfun(1:minfinal(1,18),:,18),...
% RunOrderfun(1:minfinal(1,19),:,19),RunOrderfun(1:minfinal(1,20),:,20),...
% RunOrderfun(1:minfinal(1,21),:,21),RunOrderfun(1:minfinal(1,22),:,22),...
% RunOrderfun(1:minfinal(1,23),:,23),RunOrderfun(1:minfinal(1,24),:,24),...
% RunOrderfun(1:minfinal(1,25),:,25),RunOrderfun(1:minfinal(1,26),:,26),...
% RunOrderfun(1:minfinal(1,27),:,27),RunOrderfun(1:minfinal(1,28),:,28),...
% RunOrderfun(1:minfinal(1,29),:,29),RunOrderfun(1:minfinal(1,30),:,30),...
% RunOrderfun(1:minfinal(1,31),:,31),RunOrderfun(1:minfinal(1,32),:,32),...
% RunOrderfun(1:minfinal(1,33),:,33),RunOrderfun(1:minfinal(1,34),:,34),...
% RunOrderfun(1:minfinal(1,35),:,35),RunOrderfun(1:minfinal(1,36),:,36),...
% RunOrderfun(1:minfinal(1,37),:,37),RunOrderfun(1:minfinal(1,38),:,38),...
% RunOrderfun(1:minfinal(1,39),:,39),RunOrderfun(1:minfinal(1,40),:,40),...
% RunOrderfun(1:minfinal(1,41),:,41),RunOrderfun(1:minfinal(1,42),:,42),...
% RunOrderfun(1:minfinal(1,43),:,43),RunOrderfun(1:minfinal(1,44),:,44),...
% RunOrderfun(1:minfinal(1,45),:,45),RunOrderfun(1:minfinal(1,46),:,46),...
% RunOrderfun(1:minfinal(1,47),:,47),RunOrderfun(1:minfinal(1,48),:,48),...
% RunOrderfun(1:minfinal(1,49),:,49));
% %
ALLRunOrderact = cat(1,RunOrderact(1:minfinal(1,1),:,1),RunOrderact(1:minfinal(1,2),:,2),...
RunOrderact(1:minfinal(1,3),:,3),RunOrderact(1:minfinal(1,4),:,4),...
RunOrderact(1:minfinal(1,5),:,5),RunOrderact(1:minfinal(1,6),:,6),...
RunOrderact(1:minfinal(1,7),:,7),RunOrderact(1:minfinal(1,8),:,8),...
RunOrderact(1:minfinal(1,9),:,9));%,RunOrderact(1:minfinal(1,10),:,10),...
% RunOrderact(1:minfinal(1,11),:,11),RunOrderact(1:minfinal(1,12),:,12),...
% RunOrderact(1:minfinal(1,13),:,13),RunOrderact(1:minfinal(1,14),:,14),...
% RunOrderact(1:minfinal(1,15),:,15),RunOrderact(1:minfinal(1,16),:,16),...
% RunOrderact(1:minfinal(1,17),:,17),RunOrderact(1:minfinal(1,18),:,18),...
% RunOrderact(1:minfinal(1,19),:,19),RunOrderact(1:minfinal(1,20),:,20),...
% RunOrderact(1:minfinal(1,21),:,21),RunOrderact(1:minfinal(1,22),:,22),...
% RunOrderact(1:minfinal(1,23),:,23),RunOrderact(1:minfinal(1,24),:,24),...
% RunOrderact(1:minfinal(1,25),:,25),RunOrderact(1:minfinal(1,26),:,26),...
% RunOrderact(1:minfinal(1,27),:,27),RunOrderact(1:minfinal(1,28),:,28),...
% RunOrderact(1:minfinal(1,29),:,29),RunOrderact(1:minfinal(1,30),:,30),...
% RunOrderact(1:minfinal(1,31),:,31),RunOrderact(1:minfinal(1,32),:,32),...
% RunOrderact(1:minfinal(1,33),:,33),RunOrderact(1:minfinal(1,34),:,34),...
% RunOrderact(1:minfinal(1,35),:,35),RunOrderact(1:minfinal(1,36),:,36),...
% RunOrderact(1:minfinal(1,37),:,37),RunOrderact(1:minfinal(1,38),:,38),...
% RunOrderact(1:minfinal(1,39),:,39),RunOrderact(1:minfinal(1,40),:,40),...
% RunOrderact(1:minfinal(1,41),:,41),RunOrderact(1:minfinal(1,42),:,42),...
% RunOrderact(1:minfinal(1,43),:,43),RunOrderact(1:minfinal(1,44),:,44),...
% RunOrderact(1:minfinal(1,45),:,45),RunOrderact(1:minfinal(1,46),:,46),...
% RunOrderact(1:minfinal(1,47),:,47),RunOrderact(1:minfinal(1,48),:,48),...
% RunOrderact(1:minfinal(1,49),:,49));
%%
% Remove occluded rows
% %wait bar
% H = waitbar(0, 'Please wait...');
% d = 0;
% u = length(ALLRunOrderact);
%
% %activity
%
% for i = length(ALLRunOrderact):-1:1
% if ALLRunOrderact(i,1) == 18 || ALLRunOrderact(i,2) ==18;
% ALLRunOrderact(i,:) = [];
% end
% %posture
% if ALLRunOrderpos(i,1) == 18 || ALLRunOrderpos(i,2) ==18;
% ALLRunOrderpos(i,:) = [];
% end
% %functional
% if ALLRunOrderfun(i,1) == 18 || ALLRunOrderfun(i,2) ==18;
% ALLRunOrderfun(i,:) = [];
% end
%
% if ~ishghandle(H)
% error('User closed waitbar.');
% end
% d = d + 1;
% waitbar(d / u, H, sprintf('%d of %d', d, u));
%
%
% end
ALLRunOrderact(ALLRunOrderact(:,1)==18,:) = [];
ALLRunOrderact(ALLRunOrderact(:,2)==18,:) = [];
ALLRunOrderpos(ALLRunOrderpos(:,1)==18,:) = [];
ALLRunOrderpos(ALLRunOrderpos(:,2)==18,:) = [];
ALLRunOrderfun(ALLRunOrderfun(:,1)==18,:) = [];
ALLRunOrderfun(ALLRunOrderfun(:,2)==18,:) = [];
%%
%generate confusion matrix for posture, functional, and activities
figure(10)
ALLRunOrderpos(ALLRunOrderpos ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderpos(:,1),ALLRunOrderpos(:,2));
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Postures';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
figure(11)
ALLRunOrderpos(ALLRunOrderpos ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderpos(:,1),ALLRunOrderpos(:,2));
cm.Normalization = 'total-normalized';
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Postures';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
%
figure (12)
ALLRunOrderfun(ALLRunOrderfun ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderfun(:,1),ALLRunOrderfun(:,2));
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Functional';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
figure (13)
ALLRunOrderfun(ALLRunOrderfun ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderfun(:,1),ALLRunOrderfun(:,2));
cm.Normalization = 'total-normalized';
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Functional';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
% Observe and test
figure(14)
ALLRunOrderact(ALLRunOrderact ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderact(:,1),ALLRunOrderact(:,2));
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Activities';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
figure(15)
ALLRunOrderact(ALLRunOrderact ==0)=99; %label non-rated packages as 99 for cm
cm =confusionchart(ALLRunOrderact(:,1),ALLRunOrderact(:,2));
cm.Normalization = 'total-normalized';
cm.XLabel = 'Rater 1';
cm.YLabel = 'Rater 2';
cm.Title = 'Apple Summated CM Activities';
cm.RowSummary = 'row-normalized';
cm.ColumnSummary = 'column-normalized';
%% save figures
cd(pathOUT)
filename = 'Corrected-Apple_summatedCM_pos(exclude occluded,oof,removal).jpeg';
saveas(figure(10),filename)
filename = 'Corrected-Apple_summatedCM_pos_normalized(exclude occluded,oof,removal).jpeg';
saveas(figure(11),filename)
filename = 'Corrected-Apple_summatedCM_fun(exclude occluded,oof,removal).jpeg';
saveas(figure(12),filename)
filename = 'Corrected-Apple_summatedCM_fun_normalized(exclude occluded,oof,removal).jpeg';
saveas(figure(13),filename)
filename = 'Corrected-Apple_summatedCM_act(exclude occluded,oof,removal).jpeg';
saveas(figure(14),filename)
filename = 'Corrected-Apple_summatedCM_act_normalized(exclude occluded,oof,removal).jpeg';
saveas(figure(15),filename)