processSpikesForSorting.m

function status = processSpikesForSorting(file_path,file_prefix)
% processSpikesForSorting combines spike data from .nev files in file_path that match
%   file_prefix string.  Saves spike data to new file named '(file_prefix)-spikes.nev'.
%   After running, sort spikes in Plexon OfflineSorter and save as '(file_prefix)-spikes-s.nev'.
%   Run this script again after spike sorting to separate into independent 
%   .mat files.

    if ~exist(fullfile(file_path,[file_prefix '-spikes-metatags.mat']),'file')
        % Merge spike data
        NEVlist = dir(fullfile(file_path,[file_prefix '*.nev']));
        NEVlist = NEVlist(cellfun('isempty',(regexp({NEVlist(:).name},'-s'))));
        disp(['Merging ' num2str(length(NEVlist)) ' files.'])
        NEVNSx_all = cerebus2NEVNSx(file_path,file_prefix,'noanalog');
        NEVNSx_all.NEV = artifact_removal(NEVNSx_all.NEV,10,0.0005,1);
        
        % Strip digital data from NEV into new variable
        disp(['Stripping digital data.'])
        NEVdigital.TimeStamp = NEVNSx_all.NEV.Data.SerialDigitalIO.TimeStamp;
        NEVdigital.TimeStampSec = NEVNSx_all.NEV.Data.SerialDigitalIO.TimeStampSec;
        NEVdigital.InsertionReason = NEVNSx_all.NEV.Data.SerialDigitalIO.InsertionReason;
        NEVdigital.UnparsedData = NEVNSx_all.NEV.Data.SerialDigitalIO.UnparsedData;
        NEVNSx_all.NEV.Data.SerialDigitalIO.TimeStamp=[];
        NEVNSx_all.NEV.Data.SerialDigitalIO.TimeStampSec=[];
        NEVNSx_all.NEV.Data.SerialDigitalIO.InsertionReason=[];
        NEVNSx_all.NEV.Data.SerialDigitalIO.UnparsedData=[];
        save(fullfile(file_path,[file_prefix '-digital']),'NEVdigital');
        
        % Save spikes only data
        disp('Saving merged NEV')
        saveNEVSpikesLimblab(NEVNSx_all.NEV, file_path, [file_prefix '-spikes.nev'])
        
        % Save metatags for unmerging
        disp('Saving metatags')
        MetaTags = NEVNSx_all.MetaTags;
        save(fullfile(file_path,[file_prefix '-spikes-metatags']),'MetaTags')
        
        % done
        disp('Merged.')
        status = 'merged spikes';
    else
        % Un-merge
        load(fullfile(file_path,[file_prefix '-spikes-metatags']),'MetaTags')
        if exist(fullfile(file_path,[file_prefix '-spikes-s.nev']),'file')
            NEV_sorted = openNEVLimblab('read',fullfile(file_path,[file_prefix '-spikes-s.nev']));
            if exist(fullfile(file_path,[file_prefix '-digital.mat']),'file')
                disp('Re-integrating digital data.')
                load(fullfile(file_path,[file_prefix '-digital']),'NEVdigital')
                NEV_sorted.Data.SerialDigitalIO.TimeStamp = NEVdigital.TimeStamp;
                NEV_sorted.Data.SerialDigitalIO.TimeStampSec = NEVdigital.TimeStampSec;
                NEV_sorted.Data.SerialDigitalIO.InsertionReason = NEVdigital.InsertionReason;
                NEV_sorted.Data.SerialDigitalIO.UnparsedData = NEVdigital.UnparsedData;
                delete(fullfile(file_path,[file_prefix '-digital.mat']))
            end
            
            disp(['Separating ' num2str(length(MetaTags.NEVlist) ) ' files.'])
            for iFile = 1:length(MetaTags.NEVlist) 
                t_offset = (MetaTags.FileStartSec(iFile))*30000;
                NEV_spikes_struct = NEV_sorted.Data.Spikes;
                first_idx = find(NEV_sorted.Data.Spikes.TimeStamp >= MetaTags.FileStartSec(iFile)*30000,1,'first');
                if iFile < length(MetaTags.NEVlist)
                    last_idx = find(NEV_sorted.Data.Spikes.TimeStamp < MetaTags.FileStartSec(iFile+1)*30000,1,'last');
                else
                    last_idx = length(NEV_sorted.Data.Spikes.TimeStamp);
                end
                NEV_spikes_struct.TimeStamp =  NEV_spikes_struct.TimeStamp(first_idx:last_idx) - t_offset;
                NEV_spikes_struct.Electrode =  NEV_spikes_struct.Electrode(first_idx:last_idx);
                NEV_spikes_struct.Unit =  NEV_spikes_struct.Unit(first_idx:last_idx);
                NEV_spikes_struct.Waveform =  NEV_spikes_struct.Waveform(:,first_idx:last_idx);
                NEV = openNEVLimblab('read', fullfile(file_path,MetaTags.NEVlist{iFile}),'nosave');
                NEV.Data.Spikes = NEV_spikes_struct;
                save(fullfile(file_path,MetaTags.NEVlist{iFile}(1:end-4)),'NEV')
            end
            delete(fullfile(file_path,[file_prefix '-spikes-metatags.mat']))
            status = 'processed';
        else
            status = 'merged spikes';
        end
    end