Ensemble_Sorting.m

% Script to sort  and merge for Rasters for Several Analized Conditions
% from script get_bayes_ensembles and from GUI NeuralNetworks (by JP)
% 
% Requirement: load a .mat File from FinderSpiker
% 
% Input
%   Raster_Analysis      Data Structure of Ensemble Anlysis
%   From Worksapce:
%       RASTER_Selected_Clean
%       XY_Selected
%       fs
%       Experiment ID
% Output @ .mat File
%   New_Order_Clustering:    Sorting by Ensemble 
%   XY_cluster:              Ensembled-Sorted Indexes
%   Features_Ensemble
%   Features_Condition
%   ColorState
% Output @ .csv File
%   Neural General Ensemble Features:
%   Neural Detailed Ensemble Features:
%   Functional Network List of NODES & EDGES to import to Gephi

%% Setup *****************************************************************

Import_FinderSpiker;
prepare_ensembles_data;

%% MAKE PLOTS ###########################################################

Plot_Neural_Ensembles;
 
%% IF ALL EXPERIMENT in ONE Analysis
NCplot=NC;
UniRMutiE=false; % Checker if all conditons are in one single analyzed raster
if CummFrames==TotalFrames && NC==1 && numel(Names_Conditions)>1
    disp('---------------------------------------------------------------')
    disp('>>>>>>>>>>>>>   Extracting Conditons from    <<<<<<<<<<<<<<<<<<')
    disp('>>>>>>>>>>>>>>>>   Whole Experiment   <<<<<<<<<<<<<<<<<<<<<<<<<')
    disp('---------------------------------------------------------------')
    NCplot=length(Names_Conditions);
    THRvector=repmat(THR,NCplot,1); % make it cell:
    for nth=1:numel(THRvector)
        THR{nth}=THRvector(nth);
    end
    UniRMutiE=true;
    NCupdate=length(Names_Conditions);
    cummFrames=1;
    intA=0; % Initialize Interval A
    intB=0; % Initialize Interval B
    % DISCLOSE IF WHOLE RASTER was ANALYZED
    for c=1:NCupdate
        Rasters{c}=R_Condition{c}';        % frames x cells
        [~,framesC]=size(R_Condition{c});  % frames of condition
        intB=intB+framesC;
        [SIG_FRAMES_UPD{c},indexSIG,~]=intersect(SIG_FRAMES{1},intA+1:intB);
        SIG_FRAMES_UPD{c}=SIG_FRAMES_UPD{c}-intA;
        % SIG_FRAMES_UPD{c}=SIG_FRAMES_UPD{c};
        labelsUPD{c}=LABELS{1}(indexSIG);           % Clustering Labels
        NGroupsUPD{c}=length(unique(labelsUPD{c})); % N groups
        intA=intB;
        cummFrames=cummFrames+framesC;              % Cummulative Frames
    end
    NameCond=Condition_Names;
    disp('------------------>>Conditions Extracted.')
else
    NameCond=Names_Conditions;
end
%% Exporting to GEPHI and Ensemble Data per Condition
Ncells=size(R_Condition{1},1);
% Ncells=sum(sum(R_Condition{1},2)>1);
% Select Sort of Color for Gephi Visualization
answer = questdlg('Make Node Colors for Gephi Visualization?', ...
	'Mix Color Ensembles', ...
	'MIX','EVEN','EVEN');

NG=0;
AuxC=0;
NetworkCondition=cell(NCplot,1);
Ensemble_Threshold=zeros(NCplot,1);
% Input: ColorState, from Clustering Analysis
for c=1:NCplot
    % Initialize Output
    % Max Links Between Neurons
    Network{c}.MaxSynLinks=0;
    % Max Links Between Neurons
    Network{c}.MaxCoupledPair=[0,0]; % Neurons A,B
    % Satitstics of Weights Connections (Synaptic Strength)
    Network{c}.SynStrengthStats=[0,0,0,0];
    % Get raw data **************************************************
    % R=Rasters{c}(:,IndexesActive);      % frames x cells
    R=Rasters{c};      % frames x cells
    ActNeu=find(sum(R,1)>0);         % Active Neurons in each Raster: ENS & NON ENS
    % CAG=sum(R,2);                   % CAG in each Condition
    % Get labels 
    if UniRMutiE         % IF ALL EXPERIMETN in ONE Analysis
        labels=labelsUPD{c};            % Clustering Labels
        sigframes=SIG_FRAMES_UPD{c};    % Significative Frames
        NG=NGroupsUPD{c};               % N ensembles @ condition
        LENGHTRASTER{c}=size(R,1);
    else                 % Conditons were anayzed separately
        labels=LABELS{c};               % Clustering Labels
        sigframes=SIG_FRAMES{c};        % Significative Frames
        NG=NGroups{c};                  % N Ensembles @ condition
    end
    % Get Neural Ensembles Data **************************************
    if NG>0    %% IF THERE'RE ENSEMBLES in the RASTER
        % Re-Sorting in each Condition:
        [OrderOneCondition,Neurons_State_Cluster]=OrderClusters(labels,sigframes,R,NG);
        % CS=ColorState;
        % SORTING CONDITION
        Index_Ensemble=Indexes(OrderOneCondition);          % Neurons Label Raster
        % Hebbian Sequences 
        % HebbSequence=Ensembles_Transitions(fs,labels,sigframes,CAG,ColorState,0); % ---> save
        % Save Network to Gephi**********************************
        switch answer
            case 'MIX'
                fNet=Get_Gephi_Network(R,Ncells,XY_selectedClean,Neurons_State_Cluster,OrderOneCondition,ColorState,labels,Experiment,1);
            case 'EVEN'
                fNet=Get_Gephi_Network(R,Ncells,XY_selectedClean,Neurons_State_Cluster,OrderOneCondition,ColorState,labels,Experiment);
            otherwise
                % fNet=Get_Gephi_Network(R,XY_selectedClean,Neurons_State_Cluster,OneCondition,ColorState,labels,Experiment);
        end
        %  Color Mode: Compensate:
        % fNet=Get_Gephi_Network(R,XY_selectedClean,Neurons_State_Cluster,OrderOneCondition,ColorState,labels,Experiment);
        %  Color Mode: MIXER:
        % fNet=Get_Gephi_Network(R,XY_selectedClean,Neurons_State_Cluster,OrderOneCondition,ColorState,labels,Experiment,1);
        
        
        NetworkCondition{c}=fNet;
        ShNeuron(c)=fNet.SharedNeruons/numel(ActNeu);
        % ************************************************************
        % Features  of Ensembles ########################
        Ensembled_Labels{c}=labels;
        Ensemble_Threshold(c)=THR{c};
    else       %% Non-Ensembles
        ShNeuron(c)=0;
        ActivityLength=0;
        % Features  of Ensembles ########################
        Ensembled_Labels{c}=[];
        Ensemble_Threshold(c)=THR{c};
    end
    % Update auxiliar variables
    if UniRMutiE
        AuxC=1;
    else
        AuxC=AuxC+NGroups{c};
    end

end
%% GET & SAVE NEURAL ENSEMBLE FEATURES
[Features_Ensemble,Features_Condition]=get_ensembles_features(Rasters,Ensemble_Threshold,Ensembled_Labels,fs,LENGHTRASTER);
Features_Condition.CoreNeurons=ShNeuron;
% Network Features
Features_Condition.Network=NetworkCondition;
save_features_ensembles(Experiment,Condition_Names,Features_Ensemble,Features_Condition);

%% Save SORTING,COORDINATES and COLOR ENSEMBLES
% Save this Only if it was Analyzed the whole enchilada
% if CummFrames==TotalFrames
    checkname=1;
    while checkname==1
        ActualDir=pwd;
        SlashesIndx=find(ActualDir=='\');
        DefaultPath=[ActualDir(1:SlashesIndx(end)),'Processed Data'];
        if exist(DefaultPath,'dir')==0
            DefaultPath=pwd; % Current Diretory of Finder Spiker
        end
        [FileName,PathName] = uigetfile('*.mat',[' Pick the Analysis File ',Experiment],...
            'MultiSelect', 'off',DefaultPath);
        % dotindex=find(FileName=='.');
        if strcmp(FileName(1:end-4),Experiment)
            checkname=0;
            % SAVE DATA
            disp('>>Updating .mat with Neural Ensemble Analysis...')
            save([PathName,FileName],'XY_cluster','New_Order_Clustering',...
                                    'Features_Ensemble','Features_Condition',...
                                    'ColorState','XY_selectedClean','-append');
            disp('>>Done.')
            disp('>>Saving Analysis...')
            % Save Selected Analysis Variables
            for c=1:NC
                fprintf('>> Saving %s Analysis ... ',NameCond{c,1});
                save([PathName,FileName],VarNames{c},...
                '-append');
                fprintf('Done \n');
            end
            disp([Experiment,'   -> UPDATED (Ensembles Sorting Data)'])
        elseif FileName==0
            checkname=0;
            disp('ENSEMBLES SORTING DISCARDED')
            disp('NOT SAVED')
        else
            disp('Not the same Experiment!')
            disp('Try again!')
        end
    end
% end
disp('>>END.')
%% END OF THE WORLD