Comparative_MEA_dataset/Codes/MATLAB spike detection/FileRunner.m

classdef FileRunner
    %   Summary of this class goes here
    %   Detailed explanation goes here
    
    properties (SetAccess = private)
        files; % lista tiedostoista, jotka luetaan
        last_file; % viimeinen onnistunut, alotetaan 0:sta
        file_read_error; % alotetaan 0:sta
        
       
        
        type; % type of file reading now
        spkdetconf; % configuration for detecting spikes
        recordtime; % timestamp for the current recording
     
        duration; % duration of current file
        
        
        samplerate;
        
        file_finished; % alotetaan 1:st?
        
        % axionfileille OpenAxionFile-metodissa
        first_ch_col; % alotus 1
        final_ch_col; % luetaan maksimi tiedoston tiedoista
        first_ch_row; % alotus 1
        final_ch_row; % luetaan maksimi tiedoston tiedoista
        first_well_col; % alotus 1
        final_well_col; % luetaan maksimi tiedoston tiedoista
        first_well_row; % alotus 1
        final_well_row; % luetaan maksimi tiedoston tiedoista
        last_ch_col; % alotus 0
        last_ch_row; % alotus 0
        last_well_row; % alotus 0
        last_well_col; % alotus 0
        
        Plate_type
        T; %added by andrey table for csv
        csv_directory; %where to save the csv files
    end
    
    methods
        function obj = FileRunner(p_SpikeDetConfiguration, p_TargetFiles,csv_directory)
            obj.files = p_TargetFiles;
            obj.last_file = 0;
            
            obj.spkdetconf = p_SpikeDetConfiguration;
            obj.file_read_error = 0;       
            obj.file_finished = 1;
            obj.T=table;
            obj.csv_directory=csv_directory;
        end
        
        function r_fname = getCurrentFile(obj)
            % files; % lista tiedostoista, jotka luetaan
            % last_file; % viimeinen onnistunut, alotetaan 0:sta
            r_fname = obj.files{obj.last_file};
        end
        
        %function r_durr = getCurrentFileDuration(obj) %NOT IN USE ?!!!!!!!!!!!
            %r_durr = obj.duration;
        %end
        
        % onnistuiko,indexes,spikes,chlabel,duration,record_time,detection threshold,noise
        function [r_result, obj] = ReadSpikesFromNextChannel(obj) % palauttaa seuraavan kanavan indexes & waves etc
            %curr_well=strcat(char(64+obj.last_well_row+1),num2str(obj.last_well_col+1));
            %splitter=@(x) strsplit(x, '/'); 
            %while ~any(strcmp(cellfun(@(z) z{end}, cellfun(splitter,{h5info(obj.getCurrentFile()).Groups(1).Groups.Name}, 'UniformOutput',false), 'UniformOutput',false), curr_well)) 
                %fprintf([curr_well '_' 'seems to be excluded\n']);
                %obj = obj.JumpNextWell;
                %curr_well=strcat(char(64+obj.last_well_row+1),num2str(obj.last_well_col+1));
            %end
            % onko viel? elektrodeita, jotka pit?isi lukea
            if obj.file_finished &&...% jos oli viimeinen tai eka kanava
                obj.last_file >= length(obj.files) % ja jos ei ole tiedostoja jotka pit?isi lukea                        
                Finalcsv=sortrows(obj.T, 2);
                thefilenamefull=strsplit(obj.getCurrentFile(), '.');
                thefilename=strsplit(thefilenamefull{1}, '\');
                thefilename=thefilename{end};
                writetable(Finalcsv, strcat(obj.csv_directory, '\',thefilename,'_', 'spikes.csv'));
                disp('All files have been read from!');
                r_result = [];
            else % ei ole eka tai vika kanava, tai on tiedostoja joista pit?isi lukea
                % Tarvitseeko avata uusi tiedosto
                if obj.file_finished&&...
                    obj.last_file>0
                    Finalcsv=sortrows(obj.T, 2);
                    thefilenamefull=strsplit(obj.getCurrentFile(), '.');
                    thefilename=strsplit(thefilenamefull{1}, '\');
                    thefilename=thefilename{end};
                    writetable(Finalcsv, strcat(obj.csv_directory, '\',thefilename,'_', 'spikes.csv'));
                    obj.T=table; %zeroing the table
                    obj = obj.OpenNewFile();
                end
                
                if obj.file_finished
                    obj = obj.OpenNewFile(); %( obj.files(obj.last_file+1) );
                end
                
                %if ~obj.file_read_error
                %Reading the channel 

                
                [r_result.error,m_data, r_result.chlabel, obj] = obj.ReadAxionChannel();
                
                %disp(r_result.chlabel)
                
                obj = obj.SiirraOsoittimetSeuraavaan();
                if ~r_result.error
                    % check if the channel is behaving properly or if is noisy  
                    obj.spkdetconf.sr = obj.samplerate; 
                    [r_result.indexes, r_result.spikes, r_result.threshold, ~, r_result.noise, ~] = DetectSpikes_Amp(m_data, obj.spkdetconf);
                                                           
                    Time=r_result.indexes;                  
                    Channel=string(repmat(r_result.chlabel, numel(r_result.indexes),1));
                    %repeating the channel label as many times %as the number
                    %of the detected spikes. (For the table creation)
                    TT=table(Channel, Time);
                    obj.T=[obj.T; TT];
                end
                %end
            end
        end
     
               
                 
        function [errorread,data,chlabel, obj] = ReadAxionChannel(obj)
            
            %well does not exist jump to another and display...might be not
            %recorded or so
            %jump to the next
            %if channel (single)does not exist then display channel not recorded 
            %next
            disp(obj.getCurrentFile())
            data = []; %there in Meeri's code to return at least something with e.g. error=1
            %error = 0;
            %duration = [];
            m_well=strcat(char(64+obj.last_well_row+1),num2str(obj.last_well_col+1));
            
            splitter=@(x) strsplit(x, '/'); 
            while ~any(strcmp(cellfun(@(z) z{end}, cellfun(splitter,{h5info(obj.getCurrentFile()).Groups(1).Groups.Name}, 'UniformOutput',false), 'UniformOutput',false), m_well)) 
                fprintf([m_well '_' 'seems to be excluded\n']);
                obj = obj.JumpNextWell;
                m_well=strcat(char(64+obj.last_well_row+1),num2str(obj.last_well_col+1));
                if obj.file_finished == 1
                    errorread = 1;%to show that the file finished and nothing to readhere
                    chlabel=[];
                    return
                end
            end
            
            m_ch=strcat(num2str(obj.last_ch_col+1),num2str(obj.last_ch_row+1));
            chlabel = strcat(m_well,'_',m_ch); % which well which electrode
            disp(['now reading: ' chlabel]);
            try 
                
                data = h5read(obj.getCurrentFile(),['/Data/' m_well '/' m_ch]);
                %if isempty(obj.duration)
                    %duration = length(data)/obj.samplerate;
                    %obj.duration = duration;
                %else
                    %duration = obj.duration;%better when open file?????
                %end
                errorread = 0;
            catch %err
                errorread = 1;
                InactiveChannels=h5read(obj.getCurrentFile(), '/DataInfo/InactiveChannels');
                if any(contains(InactiveChannels, chlabel)) 
                    disp(['Channel' ' ' chlabel ' ' 'is inactive, it is not recorded in the initial analysed file.'])
                else
                    error(['Smth wrong with' ' ' chlabel ' ' 'channel reading!']); %ADDED
                end
          
            end 
        end
        
        function obj = SiirraOsoittimetSeuraavaan(obj)
            if obj.final_ch_row-1 <= obj.last_ch_row % viimeinen elektrodi, otetaan seuraavalta sarakkeelta
                obj.last_ch_row = obj.first_ch_row-1;
                if obj.final_ch_col-1 <= obj.last_ch_col % viimeinen sarake, otetaan seuraava kaivo
                    obj.last_ch_col = obj.first_ch_col-1;
                    if obj.final_well_col-1 <= obj.last_well_col % viimeinen kaivosarake, otetaan seuraavalta rivilt?
                        obj.last_well_col = obj.first_well_col-1;
                        if obj.final_well_row-1 <= obj.last_well_row
                            disp('All channels have been read from!');
                            obj.file_finished = 1;
                        else
                            obj.last_well_row = obj.last_well_row+1;
                        end
                    else
                        obj.last_well_col = obj.last_well_col+1;
                    end
                else
                    obj.last_ch_col = obj.last_ch_col+1;
                end                    
            else
                obj.last_ch_row = obj.last_ch_row+1; % riveitt?in seuraava electrodi
            end
            
        end
        
        
        function obj = OpenNewFile(obj)
            obj.file_finished = 0;
            obj.file_read_error = 1; %setting it to 1 if everything successful it will be switched to 0 during OpenAxionFile
            while obj.file_read_error && obj.last_file < length(obj.files) %&& obj.spkdetconf.MinTime > obj.duration
                disp(['Opening new file: ' obj.files{obj.last_file+1}]);
                obj.type = strsplit(obj.files{obj.last_file+1},'.');
                obj.type = cell2mat(obj.type(end));
                                                 
                %strcmp('raw',obj.type) % axion files
                obj = obj.OpenAxionFile(obj.files{obj.last_file+1});
              
                obj.last_file = obj.last_file+1;
                
            end
            if obj.file_read_error && obj.last_file == length(obj.files)
                error('NOT A SINGLE FILE WAS OPENED SUCCESSFULLY!')
            end
        end
        

  
        
        function obj = OpenAxionFile(obj, p_TargetFile) % sets also sample rate, voltageScale, recordtime
            try
                %obj.AxisFileData=AxisFile(p_TargetFile);
               
                obj.Plate_type=h5readatt(p_TargetFile, '/DataInfo/', 'Plate type');
                
                obj.first_ch_col = 1;
                obj.first_ch_row = 1;
                obj.first_well_col = 1;
                obj.first_well_row = 1;
                
                obj.last_ch_col = 0;
                obj.last_ch_row = 0;
                obj.last_well_row = 0;
                obj.last_well_col = 0;
                
                if strcmp(obj.Plate_type, '12-well plate')
                    obj.final_ch_col = 8;
                    obj.final_ch_row = 8;
                    obj.final_well_col = 4;
                    obj.final_well_row = 3;
                elseif strcmp(obj.Plate_type, '48-well plate')
                    obj.final_ch_col = 4;
                    obj.final_ch_row = 4;
                    obj.final_well_col = 8;
                    obj.final_well_row = 6;
                else
                    disp('Unknown MEA layout!')
                end
                 
                obj.duration = h5readatt(p_TargetFile, '/DataInfo/','DurationInSec');
                obj.samplerate = h5readatt(p_TargetFile, '/DataInfo/','SamplingFrequencyInHz');
                %obj.recordtime = ...;
                
                obj.file_read_error = 0;
            catch %err
                disp (['File ' p_TargetFile ' could not be opened successfully!']);
                obj.file_read_error = 1;
            end
        end
        
        
        function obj = JumpNextWell(obj)        
            if obj.final_well_col-1 <= obj.last_well_col 
                obj.last_well_col = obj.first_well_col-1;
                if obj.final_well_row-1 <= obj.last_well_row
                    disp('All channels have been read from!');
                    obj.file_finished = 1;
                else
                    obj.last_well_row = obj.last_well_row+1;
                end
            else
                obj.last_well_col = obj.last_well_col+1;
            end
        end
        
    end
end