%% Loads parameters
loadParameters;


%% Folders
for i_fold=1:length(folders)
    
    %% Build paths for images, excel, features and results
    folder=folders{i_fold};
    fichero=([directorio_im '/' camera{i_fold} '/imageSets/' folder]);
    path_excel = [directorio_im '/' camera{i_fold} '/GT/GT_' folder '.xls'];
    path_features = [directorio_im '/' camera{i_fold} '/CNNfeatures/CNNfeatures_' folder '.mat'];
    path_features_PCA = [directorio_im '/' camera{i_fold} '/CNNfeatures/CNNfeaturesPCA_' folder '.mat'];
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%     path2concepts = [directorio_im '/' camera{i_fold} '/IMAGGAfeatures/' folder '_Top_100_classes_Smoothed_Filtered.mat']; % this loads a variable called 'tag_matrix'
%     path2concepts = [directorio_im '/' camera{i_fold} '/IMAGGAfeatures/' folder '_All_classes.mat']; % this loads a variable called 'tag_matrix'
    path2concepts = [directorio_im '/' camera{i_fold} '/IMAGGAfeatures/' folder '_All_classes_Smoothed_Filtered.mat']; % this loads a variable called 'tag_matrix'
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    root_results = [directorio_results '/' folder];
    mkdir(root_results);
    
    %% Images
    files_aux=dir([fichero '/*' formats{i_fold}]);
    count = 1;
	files = struct('name', []);
    for n_files = 1:length(files_aux)
        if(files_aux(n_files).name(1) ~= '.')
            files(count).name = files_aux(n_files).name;
            count = count+1;
        end
    end
    Nframes=length(files);

    %% Excel
    [clust_man,clustersIdGT,cl_limGT, ~]=analizarExcel_Narrative(path_excel, files);
    delim=cl_limGT';
    if delim(1) == 1, delim=delim(2:end); end
    clust_manId = {};
    for i=1:length(clust_man)
         [a,b]=find(clustersIdGT==i);
         clust_manId{i,1}=b;
    end

    %% Features 
    if strcmp(paramsfeatures.type, 'MOPCNN') 
        load(path_features_MOPCNN);
        features = X;
        clearvars X;
    elseif strcmp(paramsfeatures.type, 'CNN') ||  strcmp(paramsfeatures.type, 'CNNconcepts') 
         load(path2concepts);%this loads a variable called 'tag_matrix'
	 
	 % TMP MODIFICATION!
	 % tag_matrix = tag_matrix(1:50, :);

         load(path_features);%this loads a variable called 'features'
         [features_norm] = signedRootNormalization(features);
        %PCA FEATURES of global CNN
        if(exist(path_features_PCA) > 0)
            load(path_features_PCA);
        else
            [ featuresPCA, ~, ~ ] = applyPCA( features_norm, paramsPCA ) ; 
            save(path_features_PCA, 'featuresPCA');
        end 
        if strcmp(paramsfeatures.type, 'CNNconcepts')
            composite_features = [featuresPCA, tag_matrix'];
        end
    end 
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   
   
   
   
    %% CLUSTERING 

    LH_Clus={};
    start_clus={};
    previousMethods = {};
            
    %% ADWIN
    if strcmp(clus_type,'Both1')||strcmp(clus_type,'Both2')

        disp(['Start ADWIN ' folder]);

        % PCA
        if(paramsPCA.usePCA_Adwin && strcmp(paramsfeatures.type, 'CNNconcepts'))          
            [labels,dist2mean] = runAdwin(composite_features, confidence, pnorm); 
        elseif( strcmp(paramsfeatures.type, 'MOPCNN'))
            [features_norm] = signedRootNormalization(features);
            [labels,dist2mean] = runAdwin(features_norm, confidence, pnorm); 
        elseif (strcmp(paramsfeatures.type, 'CNN') && paramsPCA.usePCA_Adwin)
            [labels,dist2mean] = runAdwin(featuresPCA, confidence, pnorm); 
        end

        index=1;
        automatic2 = [];
        for pos=1:length(labels)-1
            if (labels(pos)~=labels(pos+1))>0
                automatic2(index)=pos;
                index=index+1;
            end
        end
        if (exist('automatic2','var')==0)
            automatic2=0;
        end
        [~,~,~,fMeasure_Adwin]=Rec_Pre_Acc_Evaluation(delim,automatic2,Nframes,tol);


        % Normalize distances
        dist2mean = normalizeAll(dist2mean);
        %dist2mean = signedRootNormalization(dist2mean')';

        bound_GC{2}=automatic2;
        LH_Clus{2}=getLHFromDists(dist2mean);
        start_clus{2}=labels;
        previousMethods{2} = 'ADWIN';
    end % end Adwin
            
            
    %% Clustering
    if strcmp(clus_type,'Both1')||strcmp(clus_type,'Clustering')     
        %% PCA
        if( paramsPCA.usePCA_Clustering && strcmp(paramsfeatures.type, 'CNNconcepts'))
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            	
            similarities=pdist(composite_features,'cosine');
            
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
         elseif(strcmp(paramsfeatures.type, 'MOPCNN'))
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            similarities=pdist(features,'euclidean');
        elseif(paramsPCA.usePCA_Clustering &&   strcmp(paramsfeatures.type, 'CNN'))
            similarities=pdist(featuresPCA,'cosine');
        elseif(strcmp(paramsfeatures.type, 'CNN'))
            similarities=pdist(features_norm,'cosine');
        end  
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        
        for met_indx=1:length(methods_indx)
            
            method=methods_indx{met_indx};  
            
            %% Load Results file if exists
            if(evalType == 2)
                file_save=(['Results_' method '_Res_' clus_type '_' folder '.mat']);
%                 if(exist([root_results '/' file_save]) > 0)
%                     load([root_results '/' file_save]);
%                     offset_results = length(Results);
%                 else
                    offset_results = 0;
%                 end
            end
            

            %% Clustering 
            Z = linkage(similarities, method);

            %% Cut value
            for idx_cut=1:length(cut_indx)

                cut=cut_indx(idx_cut);
                disp(['Start Clustering ' folder ', method ' method ', cutval ' num2str(cut)]);

                clustersId = cluster(Z, 'cutoff', cut, 'criterion', 'distance');

                %% AFTER IDs EXTRACTION - Evaluation
%                 [JIndex , FM_Bound , FM_Clust , automatic]=evaluationClustIDs(clustersId,clustersIdGT,tol,delim,clust_manId,files);
                [JIndex,FM_Bound,automatic]=evaluationClustIDs(clustersId,tol,delim,clust_manId,files);

%                 RPAF_Clustering.clustersIDs = clustersId;
%                 RPAF_Clustering.fMeasure = fMeasure;
%                 RPAF_Clustering.JaccardIndex = JIndex;


                RPAF_Clustering.clustersIDs = clustersId;
                RPAF_Clustering.fMeasure_Clustering = FM_Bound;
%                 RPAF_Clustering.fMeasure_Events = FM_Clust;
                RPAF_Clustering.JaccardIndex = JIndex;
                
                if( strcmp(paramsfeatures.type, 'CNN'))    
                    P=getLHFromClustering(features_norm,clustersId);
                elseif(strcmp(paramsfeatures.type, 'CNNconcepts'))
                    P=getLHFromClustering(composite_features,clustersId);
                else
                    P=getLHFromClustering(features,clustersId);                
                end
                LH_Clus{1} = P;
                start_clus{1}=clustersId';
                bound_GC{1}=automatic;
                previousMethods{1} = 'AC';

                %% Graph Cut
                % Build and calculate the Graph-Cuts
                
                disp('Start GC');
                
                %% PCA
                if(paramsPCA.usePCA_GC && strcmp(paramsfeatures.type, 'CNN'))
                    features_GC = featuresPCA;
                elseif(~paramsPCA.usePCA_GC && strcmp(paramsfeatures.type, 'CNN'))
                    features_GC = features;
                elseif(paramsPCA.usePCA_GC && strcmp(paramsfeatures.type, 'CNNconcepts'))
                    features_GC = composite_features;
                else
                    features_GC = [features, tag_matrix'];
                end
                
                [features_GC, ~, ~] = normalize(features_GC);
                if(evalType == 2)
                    [ fig , num_clus_GC, fMeasure_GC, eventsIDs, W_u_tested, W_p_tested ] = doIterativeTest(LH_Clus, start_clus, bound_GC, window_len, features_GC, tol, delim,1, nUnaryDivisions, nPairwiseDivisions, previousMethods, plotFigResults);

                    %% Store results
                    
                    % Plot
                    if(plotFigResults)
                        if(~isempty(fig))
                            fig_save = ([method '_cutVal_' num2str(cut) '.fig']);
                        end
                        saveas(fig,[root_results '/' fig_save]);
                    end
                    
                    % Results Evaluation
                    Results{idx_cut+offset_results}.cut_value = cut;
                    Results{idx_cut+offset_results}.RPAF_Clustering = RPAF_Clustering; 
                    Results{idx_cut+offset_results}.num_clus_GC = num_clus_GC;
                    Results{idx_cut+offset_results}.Wunary_tested = W_u_tested;
                    Results{idx_cut+offset_results}.Wpairwise_tested = W_p_tested;
                    Results{idx_cut+offset_results}.eventsIDs = eventsIDs;
                    Results{idx_cut+offset_results}.fMeasure_GC = fMeasure_GC;
		    Results{idx_cut+offset_results}.segments = eventsIDs; % rows -> unary, columns -> pairwise

                    if strcmp(clus_type,'Both1')
                        Results{idx_cut+offset_results}.fMeasure_Adwin = fMeasure_Adwin;
                        Results{idx_cut+offset_results}.fMeasure_Clustering = FM_Bound;
                    end

                elseif(evalType == 1)
                    [ labels, start_GC ] = doSingleTest(LH_Clus, start_clus, bound_GC ,window_len, W_unary, W_pairwise, features_GC, tol, delim, doEvaluation, previousMethods);
                end % end GC

                close all;
             end%end cut


             %% SAVE
             if(evalType == 2)
                save([root_results '/' file_save], 'Results');
             end
             
        end %end method
        clearvars LH_Clus start_clus
    end %end if clustering || both1  

end %end folder