function [nbr_types,confusion_matrix_aut_Vis1,confusion_matrix_aut_Vis2,confusion_matrix_Vis1_Vis2,confusion_matrix_Vis2_Vis1,confusion_matrix_aut_Vis1uVis2,confusion_matrix_aut_Vis1nVis2]=assessmentMethod(filename_edf,filename_Automatic_detection,filename_Visual_scoring1,filename_Visual_scoring2,filename_Hypnogram,duration_event)
% Function assessmentMethod.m compare the automatic and visual annotations of one type of micro-event.
% It uses as inputs:
% filename_edf : filename of the polysomnographic recording (in the European Data Format) from which the annoted channel is extracted. 
% filename_Automatic_detection : filename of a textual file containing, in the first line, the name of the detection and then, 2 columns with the beginnings (first column) and durations (second column) of the automatically detected micro-events (in second)
% filename_Visual_scoring1  : filename of a textual file containing, in the first line, the name of the detection and then, 2 columns with the beginnings (first column) and durations (second column) of the visually scored micro-events by expert 1(in second)
% filename_Visual_scoring2 : filename of a textual file containing, in the first line, the name of the detection and then, 2 columns with the beginnings (first column) and durations (second column) of the visually scored micro-events by expert 2(in second)
% If this second annotation is not available, use filename_Visual_scoring2='';
% filename_Hypnogram: filename of a textual file containing from the second line the hypnogram information, with one value per 5 sec.
%   5=wake
%   4=REM stage
%   3=sleep stage S1
%   2=sleep stage S2
%   1=sleep stage S3
%   0=sleep stage S4
%   -1=sleep stage movement
%   -2 or -3 =unknow sleep stage %
% If this Hypnogram is not available, use filename_Hypnogram='';
% duration_event: is the average duration (in second) of the microevent detected (for the approximation of the True Negative number #TN) in confusion matrixes
%
% Function assessmentMethod.m returns the structure "nbr_types" with the following fields:
% nbr_types.nbrtot_scored_by_system = total number of events scored by the automatic system, in each stages (wake,REM,S1,S2,S3,S4), and in total (=> vector with 7 values)
% nbr_types.nbrtot_scored_by_visual1 = total number of events scored by the expert 1, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbrtot_scored_by_visual2 = total number of events scored by the expert 2, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_sys__type2 = number of coverings scored by only system (of type T2), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_vis1__type3A = number of coverings scored by only scorer #1 (of type T 3A), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_vis2__type3B = number of coverings scored by only scorer #2 (of type T3B), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_systEvis1__type1A = number of coverings scored by only system & scorer #1(of type T1A), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_systEvis2__type1B = number of coverings scored by only system & scorer #2 (of type T1B), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_only_by_vis1Evis2__type3C = number of coverings scored by only scorer #1 & scorer #2 (of type T3C), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C = number of coverings scored by system & scorer #1 & #2 (of type T1C), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.type3D = number of coverings of type T3D, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.type5A = number of coverings of type T5A, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.type5B = number of coverings of type T5B, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.type5C = number of coverings of type T5C, in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_aut_multiple = number of automatic quotation implied in a multiple covering (3D, 5A,5B or 5C), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_vis1_multiple = number of quotation of scorer 1 implied in a multiple covering (3D, 5A,5B or 5C), in each stages (wake,REM,S1,S2,S3,S4), and in total 
% nbr_types.nbr_vis2_multiple = number of quotation of scorer 2 implied in a multiple covering (3D, 5A,5B or 5C), in each stages (wake,REM,S1,S2,S3,S4), and in total 
%
% It also returns the different possible confusion matrixes:
% confusion_matrix_aut_Vis1 = confusion matrix of the automatic detection compared to the expert 1 scoring
% confusion_matrix_aut_Vis2 = confusion matrix of the automatic detection compared to the expert 2 scoring
% confusion_matrix_Vis1_Vis2 = confusion matrix of the expert 1 scoring compared to the expert 2 scoring
% confusion_matrix_Vis2_Vis1 = confusion matrix of the expert 2 scoring compared to the expert 1 scoring
% confusion_matrix_aut_Vis1uVis2= confusion matrix of the automatic detection compared to the union of the expert 1 scoring and the expert 2 scoring
% confusion_matrix_aut_Vis1nVis2= confusion matrix of the automatic detection compared to the intersection of the expert 1 scoring and the expert 2 scoring (i.e. when a micro event is considered as real when both scorers marked it as such)
%
% NB: in these confusion matrixes, the number of true negative is aproximate by : (total duration of the excerpt/average duration of the microevent) - (number of true positives + number of false positives + number of false negatives)
%
% Examples:
% filename_edf='C:\DEVUYST\DataBaseSpindles\excerpt1.edf';
% filename_Automatic_detection='C:\DEVUYST\DataBaseSpindles\Automatic_detection_excerpt1.txt';
% filename_Visual_scoring1='C:\DEVUYST\DataBaseSpindles\Visual_scoring1_excerpt1.txt';
% filename_Visual_scoring2='C:\DEVUYST\DataBaseSpindles\Visual_scoring2_excerpt1.txt';
% filename_Hypnogram='C:\DEVUYST\DataBaseSpindles\Hypnogram_excerpt1.txt';
% duration_event=1;
% [nbr_types,confusion_matrix_aut_Vis1,confusion_matrix_aut_Vis2,confusion_matrix_Vis1_Vis2,confusion_matrix_Vis2_Vis1,confusion_matrix_aut_Vis1uVis2,confusion_matrix_aut_Vis1nVis2]=assessmentMethod(filename_edf,filename_Automatic_detection,filename_Visual_scoring1,filename_Visual_scoring2,filename_Hypnogram,duration_event)
% 
% or
% filename_edf='C:\DEVUYST\DataBasePLMs\excerpt1.edf';
% filename_Automatic_detection='C:\DEVUYST\DataBasePLMs\Automatic_detection_excerpt1.txt';
% filename_Visual_scoring1='C:\DEVUYST\DataBasePLMs\Visual_scoring1_excerpt1.txt';
% filename_Visual_scoring2='';
% filename_Hypnogram='';
% duration_event=3;
% [nbr_types,confusion_matrix_aut_Vis1,confusion_matrix_aut_Vis2,confusion_matrix_Vis1_Vis2,confusion_matrix_Vis2_Vis1,confusion_matrix_aut_Vis1uVis2,confusion_matrix_aut_Vis1nVis2]=assessmentMethod(filename_edf,filename_Automatic_detection,filename_Visual_scoring1,filename_Visual_scoring2,filename_Hypnogram,duration_event)


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%   DETERMINATION DE LA FREQUENCE D'ECHANTILLONAGE ET DE LA DUREE DE L'ENREGISTREMENT  %   %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%determination du nom de signal concerné
%---------------------------------------
newpid=fopen(filename_Automatic_detection, 'rb+');%ouvre un fichier texte du nom de filename en lecture et écriture binaire
C_text = textscan(newpid, '%s',1);
nom_annotation=C_text{1,1};
[temp,signal_concerne]=strtok(nom_annotation{1},'/');
signal_concerne=signal_concerne(2:end-1);
fclose(newpid); 

%detrmination de fech
%---------------------
pid=fopen(filename_edf,'rb');
fseek(pid,236,-1);%on se met à la position par rapport au début du fichier
nb_records=str2num(sprintf('%c',fread(pid,8,'char')));
duration_record=str2num(sprintf('%c',fread(pid,8,'char')));
nb_tot_signals=str2num(sprintf('%c',fread(pid,4,'char')));
signals=[];
for i=1:nb_tot_signals
    fseek(pid,256+(i-1)*16,-1);
    signals(i).label=strtok(sprintf('%c',fread(pid,16,'char')),' ');
    fseek(pid,256+nb_tot_signals*(16+80)+(i-1)*8,-1);
    signals(i).phys_dim=strtok(sprintf('%c',fread(pid,8,'char')),' ');
    fseek(pid,256+nb_tot_signals*(16+80+8)+(i-1)*8,-1);
    signals(i).phys_min=str2num(sprintf('%c',fread(pid,8,'char')));
    fseek(pid,256+nb_tot_signals*(16+80+8+8)+(i-1)*8,-1);
    signals(i).phys_max=str2num(sprintf('%c',fread(pid,8,'char')));
    fseek(pid,256+nb_tot_signals*(16+80+8+8+8)+(i-1)*8,-1);
    signals(i).digit_min=str2num(sprintf('%c',fread(pid,8,'char')));
    fseek(pid,256+nb_tot_signals*(16+80+8+8+8+8)+(i-1)*8,-1);
    signals(i).digit_max=str2num(sprintf('%c',fread(pid,8,'char')));
    fseek(pid,256+nb_tot_signals*(16+80+8+8+8+8+8+80)+(i-1)*8,-1);
    signals(i).nb_samples=str2num(sprintf('%c',fread(pid,8,'char')));
    signals(i).fech=signals(i).nb_samples/duration_record;    
end
fseek(pid,256+nb_tot_signals*(16+80+8*5+80),-1);
for i=1:nb_tot_signals
    nr_tot_signals(i)=str2num(sprintf('%c',fread(pid,8,'char')));
end
handles.header.info_tot_signals=signals;
fclose(pid);

%[handles]=readEdf ({},filename_edf,[],1,0);%chargement de son entête (duration bloc etc)
fech=0;
for i=1:length(handles.header.info_tot_signals)
    if strcmp(handles.header.info_tot_signals(i).label,signal_concerne)
        fech=handles.header.info_tot_signals(i).fech;
    end
end
if fech==0
    if ismember(handles.header.info_tot_signals(1).fech ,[50, 100,200])
        fech=handles.header.info_tot_signals(1).fech;
    else
        error('blem avec fech')
    end
end

%detrmination de la duree de l'enregistrement
%---------------------------------------------
duree_enregistrement=duration_record*nb_records;


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHARGEMENT COTATION ATOMATIQUE %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
newpid=fopen(filename_Automatic_detection, 'rb+');%ouvre un fichier texte du nom de filename en lecture et écriture binaire
C_text = textscan(newpid, '%s',1);
nom_annotation=C_text{1};
C_data = textscan(newpid, '%f %f');
cotation_automatique.debut=C_data{1}*fech;
cotation_automatique.duree=C_data{2}*fech;
fclose(newpid);     

[val_sort,pos_sort]=sort(cotation_automatique.debut);
cotation_automatique.debut=cotation_automatique.debut(pos_sort);
cotation_automatique.duree=cotation_automatique.duree(pos_sort);
if size(cotation_automatique.debut,2)==1
    cotation_automatique.debut=cotation_automatique.debut';
    cotation_automatique.duree=cotation_automatique.duree';
end
temp=find(cotation_automatique.debut+cotation_automatique.duree>=[cotation_automatique.debut(2:end), cotation_automatique.debut(end)+cotation_automatique.duree(end)+1]);
milieu=floor(cotation_automatique.debut(temp+1)+((cotation_automatique.debut(temp)+cotation_automatique.duree(temp)-1)-cotation_automatique.debut(temp+1))/2);
cotation_automatique.duree(temp)=milieu-cotation_automatique.debut(temp);
cotation_automatique.duree(temp+1)=(cotation_automatique.debut(temp+1)+cotation_automatique.duree(temp+1)-1)-milieu;
cotation_automatique.debut(temp+1)=milieu+1;

    
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHARGEMENT COTATION SURLIGNEE 1 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
newpid=fopen(filename_Visual_scoring1, 'rb+');%ouvre un fichier texte du nom de filename en lecture et écriture binaire
C_text = textscan(newpid, '%s',1);
nom_annotation=C_text{1};
C_data = textscan(newpid, '%f %f');
cotation_reference.debut=C_data{1}*fech;
cotation_reference.duree=C_data{2}*fech;
fclose(newpid);     

[val_sort,pos_sort]=sort(cotation_reference.debut);
cotation_reference.debut=cotation_reference.debut(pos_sort);
cotation_reference.duree=cotation_reference.duree(pos_sort);
if size(cotation_reference.debut,2)==1
    cotation_reference.debut=cotation_reference.debut';
    cotation_reference.duree=cotation_reference.duree';
end
temp=find(cotation_reference.debut+cotation_reference.duree>=[cotation_reference.debut(2:end), cotation_reference.debut(end)+cotation_reference.duree(end)+1]);
milieu=floor(cotation_reference.debut(temp+1)+((cotation_reference.debut(temp)+cotation_reference.duree(temp)-1)-cotation_reference.debut(temp+1))/2);
cotation_reference.duree(temp)=milieu-cotation_reference.debut(temp);
cotation_reference.duree(temp+1)=(cotation_reference.debut(temp+1)+cotation_reference.duree(temp+1)-1)-milieu;
cotation_reference.debut(temp+1)=milieu+1;



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHARGEMENT COTATION SURLIGNEE 2 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~strcmp(filename_Visual_scoring2,'') 
    newpid=fopen(filename_Visual_scoring2, 'rb+');%ouvre un fichier texte du nom de filename en lecture et écriture binaire
    C_text = textscan(newpid, '%s',1);
    nom_annotation=C_text{1};
    C_data = textscan(newpid, '%f %f');
    cotation_reference.debut2=C_data{1}*fech;
    cotation_reference.duree2=C_data{2}*fech;
    fclose(newpid);     

    [val_sort,pos_sort]=sort(cotation_reference.debut2);
    cotation_reference.debut2=cotation_reference.debut2(pos_sort);
    cotation_reference.duree2=cotation_reference.duree2(pos_sort);
    if size(cotation_reference.debut2,2)==1
        cotation_reference.debut2=cotation_reference.debut2';
        cotation_reference.duree2=cotation_reference.duree2';
    end
    temp=find(cotation_reference.debut2+cotation_reference.duree2>=[cotation_reference.debut2(2:end), cotation_reference.debut2(end)+cotation_reference.duree2(end)+1]);
    milieu=floor(cotation_reference.debut2(temp+1)+((cotation_reference.debut2(temp)+cotation_reference.duree2(temp)-1)-cotation_reference.debut2(temp+1))/2);
    cotation_reference.duree2(temp)=milieu-cotation_reference.debut2(temp);
    cotation_reference.duree2(temp+1)=(cotation_reference.debut2(temp+1)+cotation_reference.duree2(temp+1)-1)-milieu;
    cotation_reference.debut2(temp+1)=milieu+1;
else
    cotation_reference.debut2=[];
    cotation_reference.duree2=[];
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% creation d'une cotation d'union  et d'une cotation d'intersection %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~strcmp(filename_Visual_scoring2,'')    
    num_inter=0;
    cotation_reference.debut_union=cotation_reference.debut;
    cotation_reference.duree_union=cotation_reference.duree;
    for i=1:length(cotation_reference.debut2)
        temp=find ( cotation_reference.debut_union<=(cotation_reference.debut2(i)+cotation_reference.duree2(i)-1)  & (cotation_reference.debut_union+cotation_reference.duree_union-1)>=cotation_reference.debut2(i)) ;
        if ~isempty(temp)
            num_inter=num_inter+1;
            deb=min([cotation_reference.debut_union(temp),cotation_reference.debut2(i)]);
            dur=max([cotation_reference.debut_union(temp)+cotation_reference.duree_union(temp)-1,cotation_reference.debut2(i)+cotation_reference.duree2(i)-1])-deb+1;
            cotation_reference.debut_union(temp(1))=deb;
            cotation_reference.duree_union(temp(1))=dur;
            cotation_reference.debut_inter(num_inter)=deb;
            cotation_reference.duree_inter(num_inter)=dur;
            if length(temp)>1
                cotation_reference.debut_union(temp(2:end))=[];
                cotation_reference.duree_union(temp(2:end))=[];
            end
        else%
            cotation_reference.debut_union=[cotation_reference.debut_union , cotation_reference.debut2(i)];
            cotation_reference.duree_union=[cotation_reference.duree_union , cotation_reference.duree2(i)];
        end                
    end
    [val_sort,pos_sort]=sort(cotation_reference.debut_inter);
    temp=find(val_sort==[val_sort(2:end) 0] & cotation_reference.duree_inter(pos_sort)==[cotation_reference.duree_inter(pos_sort(2:end)) 0]);
    cotation_reference.debut_inter(pos_sort(temp))=[];%qui est égal à cotation_reference.debut_inter(pos_sort(temp+1))
    cotation_reference.duree_inter(pos_sort(temp))=[];
    [val_sort,pos_sort]=sort(cotation_reference.debut_union);
    temp=find(val_sort==[val_sort(2:end) 0] & cotation_reference.duree_union(pos_sort)==[cotation_reference.duree_union(pos_sort(2:end)) 0]);
    cotation_reference.debut_union(pos_sort(temp))=[];%qui est égal à cotation_reference.debut_union(pos_sort(temp+1))
    cotation_reference.duree_union(pos_sort(temp))=[];
else
    cotation_reference.debut_union=cotation_reference.debut;
    cotation_reference.duree_union=cotation_reference.duree;
    cotation_reference.debut_inter=[];
    cotation_reference.duree_inter=[];
end



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  CALCUL DES DIFFERENTS TYPE D'EVENEMENTS  %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~isempty(cotation_automatique.debut)
    if isempty(cotation_reference.debut2)
        caca=zeros(1,ceil(max([cotation_reference.debut(end)+cotation_reference.duree(end),cotation_automatique.debut(end)+cotation_automatique.duree(end)])));
    else
        caca=zeros(1,ceil(max([cotation_reference.debut2(end)+cotation_reference.duree2(end),cotation_reference.debut(end)+cotation_reference.duree(end),cotation_automatique.debut(end)+cotation_automatique.duree(end)])));
    end
else
    if isempty(cotation_reference.debut2)
        caca=zeros(1,ceil(max([cotation_reference.debut(end)+cotation_reference.duree(end)])));
    else
        caca=zeros(1,ceil(max([cotation_reference.debut2(end)+cotation_reference.duree2(end),cotation_reference.debut(end)+cotation_reference.duree(end)])));
    end
end
for i=1:length(cotation_automatique.debut)
    caca(round(cotation_automatique.debut(i):(cotation_automatique.debut(i)+cotation_automatique.duree(i)-1)))=caca(round(cotation_automatique.debut(i):(cotation_automatique.debut(i)+cotation_automatique.duree(i)-1)))+3;
end
for i=1:length(cotation_reference.debut)
    caca(round(cotation_reference.debut(i):(cotation_reference.debut(i)+cotation_reference.duree(i)-1)))=caca(round(cotation_reference.debut(i):(cotation_reference.debut(i)+cotation_reference.duree(i)-1)))+5;
end
for i=1:length(cotation_reference.debut2)
    caca(round(cotation_reference.debut2(i):(cotation_reference.debut2(i)+cotation_reference.duree2(i)-1)))=caca(round(cotation_reference.debut2(i):(cotation_reference.debut2(i)+cotation_reference.duree2(i)-1)))+7;
end
caca=[0 caca 0];
pos_deb_type=find(caca(1:end-1)==0 & caca(2:end)~=0);
pos_fin_type=find(caca(2:end)==0 & caca(1:end-1)~=0)+1;

type1A=zeros(1,7);
type1B=zeros(1,7);
type1C=zeros(1,7);
type2=zeros(1,7);
type3A=zeros(1,7);
type3B=zeros(1,7);
type3C=zeros(1,7);
type3D=zeros(1,7);
type5A=zeros(1,7);
type5B=zeros(1,7);
type5C=zeros(1,7);

nombre_auto=zeros(1,7);
nombre_visu1=zeros(1,7);
nombre_visu2=zeros(1,7);

nbr_aut_multiple=zeros(1,7);
nbr_vis1_multiple=zeros(1,7);
nbr_vis2_multiple=zeros(1,7);

if ~strcmp(filename_Hypnogram,'')
    newpid=fopen(filename_Hypnogram, 'rb+');%ouvre un fichier texte du nom de filename en lecture et écriture binaire
    C_text = textscan(newpid, '%s',1);
    nom_annotation=C_text{1};
    C_data = textscan(newpid, '%f');
    num_stade=C_data{1};
    fclose(newpid);     
    data_hypn=reshape((num_stade*ones(1,5*fech))',1,size(num_stade,1)*5*fech);
    
    if (length(data_hypn)~=duree_enregistrement*fech)
        error('la duree de l''hypnogramme ne correspond pas à la duree de l''enregistrement')
    end
    for i=1:length(cotation_automatique.debut)
        numstade=abs(data_hypn(round(cotation_automatique.debut(i)+cotation_automatique.duree(i)/2))-5)+1;
        nombre_auto(numstade)=nombre_auto(numstade)+1;
    end
    for i=1:length(cotation_reference.debut)
        numstade=abs(data_hypn(round(cotation_reference.debut(i)+cotation_reference.duree(i)/2))-5)+1;
        nombre_visu1(numstade)=nombre_visu1(numstade)+1;
    end
    for i=1:length(cotation_reference.debut2)
        numstade=abs(data_hypn(round(cotation_reference.debut2(i)+cotation_reference.duree2(i)/2))-5)+1;
        nombre_visu2(numstade)=nombre_visu2(numstade)+1;
    end
end
nombre_auto(7)=length(cotation_automatique.debut);
nombre_visu1(7)=length(cotation_reference.debut);
nombre_visu2(7)=length(cotation_reference.debut2);


for i=1:length(pos_deb_type)
    if ~strcmp(filename_Hypnogram,'')
        numstade=abs(data_hypn(round((pos_deb_type(i)+pos_fin_type(i))/2))-5)+1;
    else
        numstade=7;
    end
    type=caca(pos_deb_type(i):pos_fin_type(i));
    if ~any(type==8 | type==10 | type==12 | type==15)%y'a aucune sommme =>c'est type 2 ou 3A ou 3B
        if any(type==5)%c'est type 3A (vis1 seul)
            type3A(numstade)=type3A(numstade)+1;
        elseif any(type==3)%c'est type 2 (aut seul)
            type2(numstade)=type2(numstade)+1;
        elseif any(type==7)%c'est type 3B (vis2 seul)
            type3B(numstade)=type3B(numstade)+1;
        end
    else %on a une somme
        if ~any(type==3 |type==8 | type==10 | type==15)%on a pas d'intervention de automatique dans la somme => type 3C ou 3D
            nbr_tras_de5vers12=length(find(type(1:end-1)==5 & type(2:end)==12));
            nbr_tras_de7vers12=length(find(type(1:end-1)==7 & type(2:end)==12));
            nbr_tras_de0vers12=length(find(type(1:end-1)==0 & type(2:end)==12));
            if (nbr_tras_de5vers12+nbr_tras_de7vers12+nbr_tras_de0vers12)>1 %on a des transition multiple=> type 3D
                type3D(numstade)=type3D(numstade)+1;
                nbr_vis1_multiple(numstade)=nbr_vis1_multiple(numstade)+length(find(cotation_reference.debut>=pos_deb_type(i)-1 & (cotation_reference.debut+cotation_reference.duree)<=pos_fin_type(i)+1));
                nbr_vis2_multiple(numstade)=nbr_vis2_multiple(numstade)+length(find(cotation_reference.debut2>=pos_deb_type(i)-1 & (cotation_reference.debut2+cotation_reference.duree2)<=pos_fin_type(i)+1));
            else %type 1
                type3C(numstade)=type3C(numstade)+1;
            end
        else%on a une somme où aut intervient
            if ~any(type==5 |type==12 |type==8 | type==15)%on n'a pas d'intervention de Vis1 => type 1B ou 5B
                nbr_tras_de3vers10=length(find(type(1:end-1)==3 & type(2:end)==10));
                nbr_tras_de5vers10=length(find(type(1:end-1)==5 & type(2:end)==10));
                nbr_tras_de0vers10=length(find(type(1:end-1)==0 & type(2:end)==10));
                if (nbr_tras_de3vers10+nbr_tras_de5vers10+nbr_tras_de0vers10)>1 %on a des transition multiple=> type 5B
                    type5B(numstade)=type5B(numstade)+1;
                    nbr_aut_multiple(numstade)=nbr_aut_multiple(numstade)+length(find(cotation_automatique.debut>=pos_deb_type(i)-1 & (cotation_automatique.debut+cotation_automatique.duree)<=pos_fin_type(i)+1));
                    nbr_vis2_multiple(numstade)=nbr_vis2_multiple(numstade)+length(find(cotation_reference.debut2>=pos_deb_type(i)-1 & (cotation_reference.debut2+cotation_reference.duree2)<=pos_fin_type(i)+1));

                else %type 1B
                    type1B(numstade)=type1B(numstade)+1;
                end
            else
                if ~any(type==7 |type==12 |type==10 | type==15)%on n'a pas d'intervention de Vis2 => type 1A ou 5A
                    nbr_tras_de3vers8=length(find(type(1:end-1)==3 & type(2:end)==8));
                    nbr_tras_de5vers8=length(find(type(1:end-1)==5 & type(2:end)==8));
                    nbr_tras_de0vers8=length(find(type(1:end-1)==0 & type(2:end)==8));
                    if (nbr_tras_de3vers8+nbr_tras_de5vers8+nbr_tras_de0vers8)>1 %on a des transition multiple=> type 5A
                        type5A(numstade)=type5A(numstade)+1;
                        nbr_vis1_multiple(numstade)=nbr_vis1_multiple(numstade)+length(find(cotation_reference.debut>=pos_deb_type(i)-1 & (cotation_reference.debut+cotation_reference.duree)<=pos_fin_type(i)+1));
                        nbr_aut_multiple(numstade)=nbr_aut_multiple(numstade)+length(find(cotation_automatique.debut>=pos_deb_type(i)-1 & (cotation_automatique.debut+cotation_automatique.duree)<=pos_fin_type(i)+1));
                    else %type 1A
                        type1A(numstade)=type1A(numstade)+1;
                    end
                else%type 1C ou C
                    nbr_cot_aut=length(find(cotation_automatique.debut>=pos_deb_type(i)-1 & (cotation_automatique.debut+cotation_automatique.duree)<=pos_fin_type(i)+1));
                    nbr_cot_vis1=length(find(cotation_reference.debut>=pos_deb_type(i)-1 & (cotation_reference.debut+cotation_reference.duree)<=pos_fin_type(i)+1));
                    nbr_cot_vis2=length(find(cotation_reference.debut2>=pos_deb_type(i)-1 & (cotation_reference.debut2+cotation_reference.duree2)<=pos_fin_type(i)+1));
                    if (nbr_cot_aut>1 | nbr_cot_vis1>1 | nbr_cot_vis2>1)%si on a au moins deux mouvement dans une cotation
                        type5C(numstade)=type5C(numstade)+1;
                        nbr_vis1_multiple(numstade)=nbr_vis1_multiple(numstade)+length(find(cotation_reference.debut>=pos_deb_type(i)-1 & (cotation_reference.debut+cotation_reference.duree)<=pos_fin_type(i)+1));
                        nbr_vis2_multiple(numstade)=nbr_vis2_multiple(numstade)+length(find(cotation_reference.debut2>=pos_deb_type(i)-1 & (cotation_reference.debut2+cotation_reference.duree2)<=pos_fin_type(i)+1));
                        nbr_aut_multiple(numstade)=nbr_aut_multiple(numstade)+length(find(cotation_automatique.debut>=pos_deb_type(i)-1 & (cotation_automatique.debut+cotation_automatique.duree)<=pos_fin_type(i)+1));
                    else
                        type1C(numstade)=type1C(numstade)+1;
                    end
                end
            end
        end
    end
end
type1A(7)=sum(type1A);
type1B(7)=sum(type1B);
type1C(7)=sum(type1C);
type2(7)=sum(type2);
type3A(7)=sum(type3A);
type3B(7)=sum(type3B);
type3C(7)=sum(type3C);
type3D(7)=sum(type3D);
type5A(7)=sum(type5A);
type5B(7)=sum(type5B);
type5C(7)=sum(type5C);
nbr_aut_multiple(7)=sum(nbr_aut_multiple);
nbr_vis1_multiple(7)=sum(nbr_vis1_multiple);
nbr_vis2_multiple(7)=sum(nbr_vis2_multiple);

nbr_types={};
nbr_types.nbrtot_scored_by_system=nombre_auto;
nbr_types.nbrtot_scored_by_visual1=nombre_visu1;
nbr_types.nbrtot_scored_by_visual2=nombre_visu2;
nbr_types.nbr_scored_only_by_sys__type2=type2;
nbr_types.nbr_scored_only_by_vis1__type3A=type3A;
nbr_types.nbr_scored_only_by_vis2__type3B=type3B;
nbr_types.nbr_scored_only_by_systEvis1__type1A=type1A;
nbr_types.nbr_scored_only_by_systEvis2__type1B=type1B;
nbr_types.nbr_scored_only_by_vis1Evis2__type3C=type3C;
nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C=type1C;
nbr_types.type3D=type3D;
nbr_types.type5A=type5A;
nbr_types.type5B=type5B;
nbr_types.type5C=type5C;
nbr_types.nbr_aut_multiple=nbr_aut_multiple;
nbr_types.nbr_vis1_multiple=nbr_vis1_multiple;
nbr_types.nbr_vis2_multiple=nbr_vis2_multiple;

%(Reference,'Aut/Vis1')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_only_by_systEvis1__type1A(7))+(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7)) ;
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_systEvis2__type1B(7))+(nbr_types.nbr_scored_only_by_sys__type2(7))    ;
syst_Reference(2,1)=(nbr_types.nbr_scored_only_by_vis1__type3A(7))+(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7));
syst_Reference(2,1)=syst_Reference(2,1)+(nbr_types.type3D(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5A(7));
syst_Reference(1,2)=syst_Reference(1,2)+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_aut_Vis1=syst_Reference;
%(Reference,'syst/Vis2')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_only_by_systEvis2__type1B(7)) +(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7))  ;
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_systEvis1__type1A(7)) +(nbr_types.nbr_scored_only_by_sys__type2(7))  ; 
syst_Reference(2,1)=(nbr_types.nbr_scored_only_by_vis2__type3B(7)) +(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7));
syst_Reference(2,1)=syst_Reference(2,1)+(nbr_types.type3D(7));
syst_Reference(1,2)=syst_Reference(1,2)+(nbr_types.type5A(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_aut_Vis2=syst_Reference;
%(Reference,'Vis1/Vis2')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7)) +(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7)) ; 
syst_Reference(2,1)=(nbr_types.nbr_scored_only_by_vis2__type3B(7)) +(nbr_types.nbr_scored_only_by_systEvis2__type1B(7))  ;  
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_vis1__type3A(7)) +(nbr_types.nbr_scored_only_by_systEvis1__type1A(7)) ;
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type3D(7));
syst_Reference(1,2)=syst_Reference(1,2)+(nbr_types.type5A(7));
syst_Reference(2,1)=syst_Reference(2,1)+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_Vis1_Vis2=syst_Reference;
% (Reference,'Vis2/Vis1')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7)) +(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7)) ; 
syst_Reference(2,1)=(nbr_types.nbr_scored_only_by_vis2__type3B(7)) +(nbr_types.nbr_scored_only_by_systEvis2__type1B(7))  ; 
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_vis1__type3A(7)) +(nbr_types.nbr_scored_only_by_systEvis1__type1A(7)) ;
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type3D(7));
syst_Reference(1,2)=syst_Reference(1,2)+(nbr_types.type5A(7));
syst_Reference(2,1)=syst_Reference(2,1)+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference=syst_Reference';
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_Vis2_Vis1=syst_Reference;
% (Reference,'syst/Vis1uVis2')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_only_by_systEvis1__type1A(7)) +(nbr_types.nbr_scored_only_by_systEvis2__type1B(7))+(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7)) ;
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_sys__type2(7))  ; 
syst_Reference(2,1)= (nbr_types.nbr_scored_only_by_vis1__type3A(7)) +(nbr_types.nbr_scored_only_by_vis2__type3B(7)) +(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7)) ;
syst_Reference(2,1)=syst_Reference(2,1)+(nbr_types.type3D(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5A(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_aut_Vis1uVis2=syst_Reference;

%(Reference,'syst/Vis1nVis2')
syst_Reference=zeros(2,2);
syst_Reference(1,1)=(nbr_types.nbr_scored_by_vis1Evis2Esyst__type1C(7)) ;
syst_Reference(1,2)=(nbr_types.nbr_scored_only_by_systEvis1__type1A(7))+(nbr_types.nbr_scored_only_by_systEvis2__type1B(7))+(nbr_types.nbr_scored_only_by_sys__type2(7));
syst_Reference(2,1)=(nbr_types.nbr_scored_only_by_vis1Evis2__type3C(7)) ;
syst_Reference(2,1)=syst_Reference(2,1)+ (nbr_types.type3D(7));
syst_Reference(1,2)=syst_Reference(1,2)+(nbr_types.type5A(7))+(nbr_types.type5B(7));
syst_Reference(1,1)=syst_Reference(1,1)+(nbr_types.type5C(7));
syst_Reference(2,2)=round((duree_enregistrement)/duration_event)-syst_Reference(1,1)-syst_Reference(1,2)-syst_Reference(2,1);
confusion_matrix_aut_Vis1nVis2=syst_Reference;