convert2nwbEcephysMatNnx/convert2nwb.m

% Convert to NWB
%
% Run this script to convert derived data generated by the Brain-wide
% infra-slow dynamics study at UoL to the Neurodata Without Borders (NWB)
% file format.
%
% The script works by loading general, animal, and recording session
% metadata from nwbParams, nwbAnimalParams, nwbSessionParams, respectively.
% It then locates the derived data MAT files for each animal and converts
% them into derived data NWB files dividing the data per recording session.
% The derived data include spiking, waveform, pupil area size fluctuation,
% and total facial movement data.
%
% The conversion pipeline depends on the specific structure of derived data
% MAT files used in this study. The way the pipeline is organised is
% dictated by the fact that the conversion procedure was adopted late in
% the study. Ideally NWB file format should be adopted early in the study.
%
% You can use this pipeline to get an idea of how to convert your own
% ecephys data to the NWB file format to store spiking and behavioural
% data combined with some metadata.

cleanUp

% Load general NWB parameters
nwbParams

% Load animal-specific parameters
nwbAnimalParams

% Load session-specific parameters
nwbSessionParams

% Generate Matlab classes from NWB core schema files
generateCore;

% Generate NWB files for every recording session
if ~exist(animalDerivedDataFolderNWB, 'file')
  mkdir(animalDerivedDataFolderNWB) % Folder to store animal's converted NWB data
end
derivedData = animalDerivedDataFile;
for iSess = 1:numel(sessionID)
  % Assign NWB file fields
  nwb = NwbFile( ...
    'session_description', sessionDescription{iSess},...
    'identifier', [animalID '_' sessionID{iSess}], ...
    'session_start_time', sessionStartTime{iSess}, ...
    'general_experimenter', experimenter, ... % optional
    'general_session_id', sessionID{iSess}, ... % optional
    'general_institution', institution, ... % optional
    'general_related_publications', publications, ... % optional
    'general_notes', sessionNotes{iSess}, ... % optional
    'general_lab', lab); % optional
  
  % Create subject object
  subject = types.core.Subject( ...
    'subject_id', animalID, ...
    'age', age, ...
    'description', description, ...
    'species', species, ...
    'sex', sex);
  nwb.general_subject = subject;
  
  % Create electrode tables: Info about each recording channel
  input.iElectrode = 1;
  input.electrodeDescription = electrodeDescription{iSess};
  input.electrodeManufacturer = electrodeManufacturer{iSess};
  input.nShanks = nShanks{iSess};
  input.nChannelsPerShank = nChannelsPerShank{iSess};
  input.electrodeLocation = electrodeLocation{iSess};
  input.electrodeCoordinates = electrodeCoordinates{iSess};
  input.sessionID = sessionID{iSess};
  input.electrodeLabel = electrodeLabel{iSess};
  if probeInserted{iSess}{input.iElectrode} && ~isempty(endCh{iSess}{1})
    tbl1 = createElectrodeTable(nwb, input);
  else
    tbl1 = [];
  end
  
  input.iElectrode = 2;
  if probeInserted{iSess}{input.iElectrode} && ~isempty(endCh{iSess}{2})
    tbl2 = createElectrodeTable(nwb, input);
  else
    tbl2 = [];
  end
  
  tbl = [tbl1; tbl2];
  electrode_table = util.table2nwb(tbl, 'all electrodes');
  nwb.general_extracellular_ephys_electrodes = electrode_table;
  
  % Load spike times from the MAT file
  [spikes, metadata, derivedData] = getSpikes(derivedData, animalID, sessionID{iSess}, tbl);
  [spike_times_vector, spike_times_index] = util.create_indexed_column(spikes);
  spike_times_vector.description = 'Session spike times';
  spike_times_index.description = 'Indices dividing spike times into units';
  
  % Load and reshape unit waveforms
  waveformsFile1 = [electrodeFolder{iSess}{1} filesep 'waveforms.mat'];
  if exist(waveformsFile1, 'file')
    waveformsProbe1 = load(waveformsFile1);
  else
    waveformsProbe1 = [];
    waveformsProbe1.maxWaveforms = [];
  end
  if probeInserted{iSess}{1} && ~isempty(spikes)
    [waveformMat1, waveformVecGrp1, waveformVec1, waveformMeans1, nWaveformSamples1] = reshapeWaveforms(waveformsProbe1, 1, metadata, nCh{iSess}{1});
  else
    waveformMat1 = []; waveformVecGrp1 = {}; waveformVec1 = {}; waveformMeans1 = {}; nWaveformSamples1 = 0;
  end
  waveformsFile2 = [electrodeFolder{iSess}{2} filesep 'waveforms.mat'];
  if exist(waveformsFile2, 'file')
    waveformsProbe2 = load(waveformsFile2);
  else
    waveformsProbe2 = [];
    waveformsProbe2.maxWaveforms = [];
  end
  if probeInserted{iSess}{2} && ~isempty(spikes)
    [waveformMat2, waveformVecGrp2, waveformVec2, waveformMeans2, nWaveformSamples2] = reshapeWaveforms(waveformsProbe2, 2, metadata, nCh{iSess}{2});
  else
    waveformMat2 = []; waveformVecGrp2 = {}; waveformVec2 = {}; waveformMeans2 = {}; nWaveformSamples2 = 0;
  end
  maxWaveforms = [waveformsProbe1.maxWaveforms; waveformsProbe2.maxWaveforms];
  waveformMat = [waveformMat1; waveformMat2];
  waveformVec = [waveformVec1; waveformVec2];
  waveformMeans = [waveformMeans1; waveformMeans2];
  nWaveformSamples = max([nWaveformSamples1 nWaveformSamples2]);
  for iWave = 1:numel(waveformMeans)
    if isempty(waveformMeans{iWave})
      waveformMeans{iWave} = nan(1,nWaveformSamples);
    end
  end
  
  % Create waveform indices
  % These indices are not used as our waveform array has a different form and meaning than the one used in the NWB file.
  % We only store mean waveforms on maximum amplitude channels.
  % More on ragged array indexing used in NWB files see https://nwb-schema.readthedocs.io/en/latest/format_description.html
  [waveforms, waveformIndex] = util.create_indexed_column(waveformVec');
  waveformIndexIndex = {};
  if ~isempty(waveformVec1)
    waveformIndexIndex1 = reshape(waveformIndex.data(1:size(waveformVec1,1)),nCh{iSess}{1},size(waveformVec1,1)/nCh{iSess}{1})';
    for iUnit = 1:size(waveformVecGrp1,1)
      waveformIndexIndex = [waveformIndexIndex; waveformIndexIndex1(iUnit,:)];
    end
  end
  if ~isempty(waveformVec2)
    waveformIndexIndex2 = reshape(waveformIndex.data(size(waveformVec1,1)+1:end),nCh{iSess}{2},size(waveformVec2,1)/nCh{iSess}{2})';
    for iUnit = 1:size(waveformVecGrp2,1)
      waveformIndexIndex = [waveformIndexIndex; waveformIndexIndex2(iUnit,:)];
    end
  end
  [inds, waveformIndexIndex] = util.create_indexed_column(waveformIndexIndex');
  
  % Store spiking and waveform data inside the nwb object
  % see https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/Units.html
  if ~isempty(spikes)
    nwb.units = types.core.Units( ...
      'colnames', {'cluster_id','local_cluster_id','type',...
      'peak_channel_index','peak_channel_id',... % Provide the column order. All column names have to be defined below
      'local_peak_channel_id','rel_horz_pos','rel_vert_pos',...
      'isi_violations','isolation_distance','area','probe_id',...
      'electrode_group','spike_times','spike_times_index'}, ...
      'description', 'Units table', ...
      'id', types.hdmf_common.ElementIdentifiers( ...
      'data', int64(0:length(spikes) - 1)), ...
      'cluster_id', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,1}), ...
      'description', 'Unique cluster id'), ...
      'local_cluster_id', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,2}), ...
      'description', 'Local cluster id on the probe'), ...
      'type', types.hdmf_common.VectorData( ...
      'data', metadata{:,3}, ...
      'description', 'Cluster type: unit vs mua'), ...
      'peak_channel_index', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,4}), ...
      'description', 'Peak channel row index in the electrode table'), ...
      'peak_channel_id', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,5}), ...
      'description', 'Unique ID of the channel with the largest cluster waveform amplitude'), ...
      'local_peak_channel_id', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,6}), ...
      'description', 'Local probe channel with the largest cluster waveform amplitude'), ...
      'rel_horz_pos', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,7})./1000, ...
      'description', 'Probe-relative horizontal position in mm'), ...
      'rel_vert_pos', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,8})./1000, ...
      'description', 'Probe tip-relative vertical position in mm'), ...
      'isi_violations', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,9}), ...
      'description', 'Interstimulus interval violations (unit quality measure)'), ...
      'isolation_distance', types.hdmf_common.VectorData( ...
      'data', cell2mat(metadata{:,10}), ...
      'description', 'Cluster isolation distance (unit quality measure)'), ...
      'area', types.hdmf_common.VectorData( ...
      'data', metadata{:,11}, ...
      'description', ['Brain area where the unit is located. Internal thalamic ' ...
      'nuclei divisions are not precise, because they are derived from unit locations on the probe.']), ...
      'probe_id', types.hdmf_common.VectorData( ...
      'data', metadata{:,12}, ...
      'description', 'Probe id where the unit is located'), ...
      'spike_times', spike_times_vector, ...
      'spike_times_index', spike_times_index, ...
      'electrode_group', types.hdmf_common.VectorData( ...
      'data', metadata{:,13}, ...
      'description', 'Recording channel groups'), ...
      'waveform_mean', types.hdmf_common.VectorData( ...
      'data', cell2mat(waveformMeans), ...
      'description', ['Mean waveforms on the probe channel with the largest waveform amplitude. ' ...
      'MUA waveforms are excluded. The order that waveforms are stored match the order of units in the unit table.']) ...
    );
  end
  
  % Add behavioural data: Pupil area size
  % see https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/TimeSeries.html
  % and https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/PupilTracking.html
  if isfield(derivedData.dataStruct, 'eyeData') && isfield(derivedData.dataStruct.eyeData, [animalID '_s' sessionID{iSess}])
    acceptablePeriod = derivedData.dataStruct.eyeData.([animalID '_s' sessionID{iSess}]).period; % Acceptable quality range in seconds
    videoFrameTimes = derivedData.dataStruct.eyeData.([animalID '_s' sessionID{iSess}]).frameTimes; % seconds
    acceptableSamples = markQualitySamples(acceptablePeriod, videoFrameTimes);
    pupilAreaSize = derivedData.dataStruct.eyeData.([animalID '_s' sessionID{iSess}]).pupilArea; % pixels^2
    pupilAreaSize = types.core.TimeSeries( ...
      'data', pupilAreaSize, ...
      'timestamps', videoFrameTimes, ...
      'data_unit', 'pixels^2', ...
      'starting_time_rate', videoFrameRate,...
      'control', uint8(acceptableSamples),...
      'control_description', {'low quality samples that should be excluded from analyses';...
      'acceptable quality samples'},...
      'description', ['Pupil area size over the recording session measured in pixels^2. ' ...
      'Acceptable quality period starting and ending times are given by data_continuity parameter. ' ...
      'The full data range can be divided into multiple acceptable periods.'] ...
      );
    
    pupilTracking = types.core.PupilTracking('TimeSeries', pupilAreaSize);
    behaviorModule = types.core.ProcessingModule('description', 'contains behavioral data');
    behaviorModule.nwbdatainterface.set('PupilTracking', pupilTracking);
  else
    behaviorModule = [];
  end
  
  % Add behavioural data: Total movement of the facial area
  % see https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/TimeSeries.html
  % and https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/BehavioralTimeSeries.html
  if isfield(derivedData.dataStruct, 'motionData') && isfield(derivedData.dataStruct.motionData, [animalID '_s' sessionID{iSess}])
    acceptablePeriod = derivedData.dataStruct.motionData.([animalID '_s' sessionID{iSess}]).period; % Acceptable quality range in seconds
    videoFrameTimes = derivedData.dataStruct.motionData.([animalID '_s' sessionID{iSess}]).frameTimes; % seconds
    acceptableSamples = markQualitySamples(acceptablePeriod, videoFrameTimes);
    totalFaceMovement = derivedData.dataStruct.motionData.([animalID '_s' sessionID{iSess}]).sa; % z-scored change in the frame pixels' content with respect to the previous frame
    totalFaceMovement = types.core.TimeSeries( ...
      'data', totalFaceMovement, ...
      'timestamps', videoFrameTimes, ...
      'data_unit', 'a.u.', ...
      'control', uint8(acceptableSamples),...
      'control_description', {'low quality samples that should be excluded from analyses';...
      'acceptable quality samples'},...
      'description', ['Z-scored change in the frame pixels'' content with respect to the previous frame. ' ...
      'It measures the total movement of objects inside the video.'] ...
      );
    
    behavioralTimeSeries = types.core.BehavioralTimeSeries('TimeSeries', totalFaceMovement);
    if ~exist('behaviorModule', 'var') || isempty(behaviorModule)
      behaviorModule = types.core.ProcessingModule('description', 'contains behavioral data');
    end
    behaviorModule.nwbdatainterface.set('BehavioralTimeSeries', behavioralTimeSeries);
  end
  
  if exist('behaviorModule', 'var') && ~isempty(behaviorModule)
    nwb.processing.set('behavior', behaviorModule);
  end
  
  % Save the NWB file for the session
  % If you encounter an hdf5lib2 error, you may need make sure that you are
  % not storing cell arrays of numbers in VectorData and that you delete
  % old NWB files rather than try overwriting them. For more details see
  % https://github.com/NeurodataWithoutBorders/matnwb/issues/462
  if iSess < 10
    nwbExport(nwb, [animalDerivedDataFolderNWB filesep 'ecephys_session_0' num2str(iSess) '.nwb']);
  else
    nwbExport(nwb, [animalDerivedDataFolderNWB filesep 'ecephys_session_' num2str(iSess) '.nwb']);
  end
end

% Read the NWB file
% nwb2 = nwbRead('ecephys_session_01.nwb');
% a = nwb2.units.getRow(1);



%% Local functions
function tbl = createElectrodeTable(nwb, input)
% tbl = createElectrodeTable(nwb, input)
%
% Function creates an electrode table with the following columns:
%   channel_id: a unnique probe channel ID formed by combining session ID,
%               probe reference number, and channel number relative to the
%               tip of the probe.
%   channel_local_index: channel index relative to the tip of the probe.
%                        Channel indices are only unique within a probe.
%   x: channel AP brain surface coordinate (probe inisertion location; mm).
%   y: channel ML brain surface coordinate (probe inisertion location; mm).
%   z: channel location relative to the tip of the probe in mm.
%   imp: channel impedance.
%   location: channel brain area location.
%   filtering: type of LFP filtering applied.
%   group: channel electrode group (e.g., shank 1). NWB documentation on
%          ElectrodeGroup datatype is provided in the following links:
%          https://nwb-schema.readthedocs.io/en/latest/format.html#electrodegroup
%          https://nwb-schema.readthedocs.io/en/latest/format.html#sec-electrodegroup-src
%   channel_label
%   probe_label.
% The rows of the table correspond to individual recording channels.
%
%   Input: nwb - nwb object.
%          input - structure with the following fields:
%            iElectrode: electrode reference number.
%            electrodeDescription: a cell array (n probes) with probe
%                                  desciptions.
%            electrodeManufacturer: a cell array of electrode manufacturers.
%            nShanks: a cell array of number of shanks.
%            nChannelsPerShank: a cell array of electrode number of
%                               recording channels per shank.
%            electrodeLocation: a cell array (n channels) of channel brain
%                               area locations.
%            electrodeCoordinates: a cell array (n probes) with recording
%                                  channel coordinate arrays (n channels by
%                                  3).
%            sessionID: a string with the session ID.
%            electrodeLabel: a cell array (n probes) with probe labels.
%
%   Output: tbl - a Matlab table object with rows and columns as described
%                 above.

% Parse input
iEl = input.iElectrode;
nSh = input.nShanks;
nCh = input.nChannelsPerShank;

% Create a table with given column labels
variables = {'channel_id', 'channel_local_index', 'x', 'y', 'z', 'imp', 'location', 'filtering', 'group', 'channel_label', 'probe_label'};
tbl = cell2table(cell(0, length(variables)), 'VariableNames', variables);

% Register the probe device
device = types.core.Device(...
  'description', input.electrodeDescription{iEl}, ...
  'manufacturer', input.electrodeManufacturer{iEl} ...
  );
nwb.general_devices.set(['probe' num2str(iEl)], device);

for iShank = 1:nSh{iEl}
  
  % Register a shank electrode group (only one because this is a single shank probe)
  electrode_group = types.core.ElectrodeGroup( ...
    'description', ['electrode group for probe' num2str(iEl)], ...
    'location', input.electrodeLocation{iEl}{end}, ...
    'device', types.untyped.SoftLink(device), ...
    'position', table(input.electrodeCoordinates{iEl}(1,1), ...
    input.electrodeCoordinates{iEl}(1,2), ...
    input.electrodeCoordinates{iEl}(1,3), ...
    'VariableNames',{'x','y','z'}) ...
    );
  nwb.general_extracellular_ephys.set(['probe' num2str(iEl)], electrode_group);
  group_object_view = types.untyped.ObjectView(electrode_group);
  
  % Populate the electrode table
  for iCh = 1:nCh{iEl}
    if iCh < 10
      channelID = str2double([input.sessionID num2str(iEl) '00' num2str(iCh)]);
    elseif iCh < 99
      channelID = str2double([input.sessionID num2str(iEl) '0' num2str(iCh)]);
    else
      channelID = str2double([input.sessionID num2str(iEl) num2str(iCh)]);
    end
    channel_label = ['probe' num2str(iEl) 'shank' num2str(iShank) 'elec' num2str(iCh)];
    tbl = [tbl; ...
      {channelID, iCh, input.electrodeCoordinates{iEl}(iCh, 1), input.electrodeCoordinates{iEl}(iCh, 2), input.electrodeCoordinates{iEl}(iCh, 3),...
      NaN, input.electrodeLocation{iEl}{iCh}, 'unknown', group_object_view, channel_label, input.electrodeLabel{iEl}}]; %#ok<*AGROW>
  end
end
end

function [spikes, metadataTbl, derivedData] = getSpikes(animalDerivedDataFile, animalID, sessionID, electrodeTbl)
% [spikes, metadataTbl, derivedData] = getSpikes(animalDerivedDataFile, animalID, sessionID, electrodeTbl)
%
% Function loads Neuronexus spiking data from a MAT file with a custom data
% structure. Input:
%   animalDerivedDataFile - a string with derived data file name or already
%                           loaded data.
%   animalID - an animal ID string.
%   sessionID - a session of interest ID string.
%   electrodeTbl - a Matlab table with electrode information generated by
%                  the function createElectrodeTable.
% Output: spikes - a 1-by-n cell array (n units) with unit spike times in
%                  seconds.
%         metadataTbl - a Matlab table with rows corresponding to
%                       individual clusters (units) and columns to:
%           cluster_id: a unique cluster ID formed by combining session
%                       ID, probe reference number, and unit cluster ID.
%           local_cluster_id: a unit cluster ID. This is only unique
%                             within the probe.
%           type - activity type: single unit (unit) or multi-unit (mua).
%           channel_index: recording channel with the highest unit peak
%                          index relative to the tip of the probe.
%           channel_id: a corresponding unnique probe channel ID formed by
%                       combining session ID, probe reference number, and
%                       channel number relative to the tip of the probe.
%           local_channel_id: a corresponding channel index relative to the
%                             tip of the probe. Channel indices are only
%                             unique within a probe.
%           rel_horz_position: relative horizontal position in um.
%           rel_vert_position: probe tip-relative vertical position in um.
%           isi_violations: interspike interval violations, a cluster
%                           quality measure.
%           isolation_distance: cluster isolation distance, a cluster
%                           quality measure.
%           area: unit brain area location.
%           probe_id: probe label.
%           electrode_group: channel electrode group (e.g., shank 1). NWB
%                            documentation on ElectrodeGroup datatype is
%                            provided in the following links:
%                            https://nwb-schema.readthedocs.io/en/latest/format.html#electrodegroup
%                            https://nwb-schema.readthedocs.io/en/latest/format.html#sec-electrodegroup-src
%         derivedData - animal data loaded from the MAT derived data file.

% Data series names with different brain areas
if ~isstruct(animalDerivedDataFile)
  derivedData = load(animalDerivedDataFile);
else
  derivedData = animalDerivedDataFile;
end
dataSeriesNames = {};
for iSeries = 1:11
  dataSeriesNames{iSeries} = [animalID '_s' sessionID num2str(iSeries)];
end
dataSeriesNames{iSeries+1} = [animalID '_s' sessionID];

% Series data
seriesDerivedData = {};
for iSeries = 1:numel(dataSeriesNames)
  if isfield(derivedData.dataStruct.seriesData, dataSeriesNames{iSeries})
    seriesDerivedData{iSeries} = derivedData.dataStruct.seriesData.(dataSeriesNames{iSeries});
    srData = seriesDerivedData{iSeries}.conf.samplingParams.srData;
  else
    seriesDerivedData{iSeries} = [];
  end
end

% Series unit data
seriesDerivedUnitData = {};
for iSeries = 1:numel(dataSeriesNames)
  if ~isempty(seriesDerivedData{iSeries})
    seriesDerivedUnitData{iSeries} = seriesDerivedData{iSeries}.shankData.shank1;
  else
    seriesDerivedUnitData{iSeries} = [];
  end
end

% Series population data
seriesDerivedPopulationData = {};
for iSeries = 1:numel(dataSeriesNames)
  if ~isempty(seriesDerivedData{iSeries})
    seriesDerivedPopulationData{iSeries} = seriesDerivedData{iSeries}.popData;
  else
    seriesDerivedPopulationData{iSeries} = [];
  end
end

% Spike array
sparseSpikes = [];
for iSeries = 1:numel(dataSeriesNames)
  if ~isempty(seriesDerivedPopulationData{iSeries})
    sparseSpikes = concatenateMat(sparseSpikes, seriesDerivedPopulationData{iSeries}.spkDB);
  end
end

% Spike times
nRows = size(sparseSpikes,1);
if nRows
  timeVector = (1:size(sparseSpikes,2))./srData;
  for iUnit = 1:nRows
    spikes{iUnit} = timeVector(logical(full(sparseSpikes(iUnit,:)))); %#ok<*SAGROW>
  end
else
  spikes = [];
end

% Unit metadata: [local_unit_id type local_probe_channel horizontal_position vertical_position ...
%                 isi_violations isolation_distance anterior_posterior_ccf_coordinate ...
%                 dorsal_ventral_ccf_coordinate left_right_ccf_coordinate]
metadata = [];
if nRows
  for iSeries = 1:numel(dataSeriesNames)
    if ~isempty(seriesDerivedPopulationData{iSeries})
      metadata = concatenateMat(metadata, seriesDerivedPopulationData{iSeries}.muaMetadata);
    end
  end
end

% Unit metadata: [metadata area]
if nRows
  areas = {};
  for iSeries = 1:numel(dataSeriesNames)
    if ~isempty(seriesDerivedPopulationData{iSeries})
      if iSeries == 1
        areas = [areas; repmat({'S1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 2
        areas = [areas; repmat({'VB'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 3
        areas = [areas; repmat({'Po'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 4
        areas = [areas; repmat({'LP'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 5
        areas = [areas; repmat({'DG'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 6
        areas = [areas; repmat({'CA1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 7
        areas = [areas; repmat({'RSC'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 8
        areas = [areas; repmat({'VB'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 9
        areas = [areas; repmat({'LP'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 10
        areas = [areas; repmat({'LGN'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 11
        areas = [areas; repmat({'CA3'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 12
        areas = [areas; repmat({'VB'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      end
    end
  end
  metadata = [num2cell(metadata) areas];
end

% Unit metadata: correct unit type
if nRows
  type = {};
  for iSeries = 1:numel(dataSeriesNames)
    if ~isempty(seriesDerivedPopulationData{iSeries})
      units = ismember(seriesDerivedPopulationData{iSeries}.spkDB_units, seriesDerivedUnitData{iSeries}.units);
      typeArea = repmat({'mua'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1);
      typeArea(units) = {'unit'};
      type = [type; typeArea];
    end
  end
  metadata(:,2) = type;
end

% Unit metadata: [metadata probe_id]
if nRows
  probeLabel = {};
  for iSeries = 1:numel(dataSeriesNames)
    if ~isempty(seriesDerivedPopulationData{iSeries})
      if iSeries == 1
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 2
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 3
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 4
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 5
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 6
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 7
        probeLabel = [probeLabel; repmat({'probe2'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 8
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 9
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 10
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 11
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      elseif iSeries == 12
        probeLabel = [probeLabel; repmat({'probe1'}, size(seriesDerivedPopulationData{iSeries}.muaMetadata,1), 1)];
      end
    end
  end
  metadata = [metadata probeLabel];
end

% Unit metadata: [unit_id metadata]
if nRows
  unitIDs = zeros(nRows,1);
  for iUnit = 1:nRows
    if strcmpi(metadata{iUnit, end}, 'probe1')
      unitID = [num2str(sessionID) '1'];
    else
      unitID = [num2str(sessionID) '2'];
    end
    if metadata{iUnit, 1} < 9
      unitID = [unitID '000' num2str(metadata{iUnit, 1})];
    elseif metadata{iUnit, 1} < 99
      unitID = [unitID '00' num2str(metadata{iUnit, 1})];
    elseif metadata{iUnit, 1} < 999
      unitID = [unitID '0' num2str(metadata{iUnit, 1})];
    else
      unitID = [unitID num2str(metadata{iUnit, 1})];
    end
    unitIDs(iUnit) = str2double(unitID);
  end
  metadata = [num2cell(unitIDs) metadata];
end

% Unit metadata: [metadata(:,1:3) probe_channel_index probe_channel_id metadata(:,4:end)]
if nRows
  channelIndices = zeros(nRows,1);
  channelIDs = zeros(nRows,1);
  electrodeGroups = {};
  for iUnit = 1:nRows
    ind = table2array(electrodeTbl(:,2)) == cell2mat(metadata(iUnit,4)) &...
      contains(table2array(electrodeTbl(:,end)), metadata(iUnit,end));
    channelIndices(iUnit) = find(ind);
    channelIDs(iUnit) = table2array(electrodeTbl(ind,1));
    electrodeGroups = [electrodeGroups; table2array(electrodeTbl(ind,9))];
  end
  metadata = [metadata(:,1:3) num2cell(channelIndices) num2cell(channelIDs) metadata(:,4:end)];
end

% Unit metadata: [metadata electrode_group]
if nRows
  metadataTbl = table(metadata(:,1), metadata(:,2), metadata(:,3), metadata(:,4), ...
    metadata(:,5), metadata(:,6), metadata(:,7), metadata(:,8), ...
    metadata(:,9), metadata(:,10), metadata(:,11), metadata(:,12), electrodeGroups, ...
    'VariableNames', {'cluster_id', 'local_cluster_id', 'type',...
    'channel_index', 'channel_id', 'local_channel_id',...
    'rel_horz_pos', 'rel_vert_pos', 'isi_violations',...
    'isolation_distance', 'area', 'probe_id', 'electrode_group'});
else
  metadataTbl = [];
end
end

function [reshapedWaveformsMat, reshapedWaveformsVecGrp, reshapedWaveformsVec, waveformsMean, nWaveformSamples] = reshapeWaveforms(waveforms, iEl, metadata, nCh)
% [reshapedWaveformsMat, reshapedWaveformsVecGrp, reshapedWaveformsVec, waveformsMean, nWaveformSamples] = reshapeWaveforms(waveforms, iEl, metadata, nCh)
%
% Function extracts relevant waveform information and reshapes the waveform
% array which is 3-dimensional with the first dimension being the unit, the
% second being the sample point, and the third one being the recording
% channel.
% Input: waveforms - a strucuture loaded from the waveforms MAT file.
%                    Relevant fields are waveforms (described above),
%                    maxWaveforms (same as waveforms but excluding all
%                    channels except for the maximum amplitude one), and
%                    cluIDs (unit cluster IDs corresponding to the
%                    dimension one in waveforms and maxWaveforms).
%        iEl - probe reference number.
%        metadata - a Matlab unit table produced by the function
%                   getSpikes.
%        nCh - number of recording channels with waveforms for the same
%              unit.
% Output: reshapedWaveformsMat - a 2D array reshaping waveforms.waveforms
%                                array by collapsing the third dimension
%                                and stacking all waveforms vertically one
%                                unit after another.
%         reshapedWaveformsVecGrp - a column cell array reshaping
%                                   waveforms.waveforms array and grouping
%                                   all waveforms from the same unit
%                                   together. Cell array entries correspond
%                                   to individual units. The missing MUAs
%                                   correspond to empty cell arrays.
%         reshapedWaveformsVec - a cell array with rows from
%                                reshapedWaveformsMat. Missing MUAs are
%                                also included as empty cells times the
%                                number of recording channels.
%         waveformsMean - waveforms.waveforms converted into a cell column
%                         array. MUAs are NaNs.
%         nWaveformSamples - a total number of data sample points forming a
%                            single waveform.

nWaveformSamples = size(waveforms.maxWaveforms,2);

if isfield(waveforms, 'waveforms')
  reshapedWaveformsMat = zeros(size(waveforms.waveforms,1)*size(waveforms.waveforms,3),size(waveforms.waveforms,2));
else
  reshapedWaveformsMat = [];
end
reshapedWaveformsVecGrp = {};
reshapedWaveformsVec = {};
waveformsMean = {};
metadataInds = ismember(table2cell(metadata(:,12)), ['probe' num2str(iEl)]);
metadata = metadata(metadataInds,:);
for iUnit = 1:size(metadata,1)
  if isfield(waveforms, 'cluIDs')
    row = find(ismember(waveforms.cluIDs, cell2mat(table2cell(metadata(iUnit,2)))));
  else
    row = [];
  end
  if isfield(waveforms, 'cluIDs') && sum(ismember(waveforms.cluIDs, cell2mat(table2cell(metadata(iUnit,2)))))
    unitWaveformMat = squeeze(waveforms.waveforms(row,:,:))';
    reshapedWaveformsMat((row-1)*size(waveforms.waveforms,3)+1:row*size(waveforms.waveforms,3),:) = unitWaveformMat;
    reshapedWaveformsVecGrp = [reshapedWaveformsVecGrp; {unitWaveformMat}];
    for iWave = 1:size(unitWaveformMat,1)
      reshapedWaveformsVec = [reshapedWaveformsVec; {unitWaveformMat(iWave,:)}];
    end
    waveformsMean = [waveformsMean; {waveforms.maxWaveforms(row,:)}];
  else
    reshapedWaveformsVecGrp = [reshapedWaveformsVecGrp; {[]}];
    if isfield(waveforms, 'waveforms')
      for iWave = 1:size(waveforms.waveforms,3)
        reshapedWaveformsVec = [reshapedWaveformsVec; {[]}];
      end
    else
      for iWave = 1:nCh
        reshapedWaveformsVec = [reshapedWaveformsVec; {[]}];
      end
    end
    waveformsMean = [waveformsMean; {nan(1,size(waveforms.maxWaveforms,2))}];
  end
end
end

function acceptableSamples = markQualitySamples(acceptablePeriod, videoFrameTimes)
% acceptableSamples = markQualitySamples(acceptablePeriod, videoFrameTimes)
%
% Function marks acceptable behavioural samples given the sample times and
% the range of acceptable time periods.
% Input: acceptablePeriod - a vector or a cell array of vectors marking the
%                           beginning and end of acceptable time periods.
%        videoFrameTimes - a vector with sample times.
% Ouptut: acceptableSamples - a logical vector marking acceptable samples
%                             by ones.

if isempty(acceptablePeriod) || isempty(videoFrameTimes)
  acceptableSamples = [];
else
  acceptableSamples = false(size(videoFrameTimes));
  if iscell(acceptablePeriod)
    for iPeriod = 1:numel(acceptablePeriod)
      acceptableSamples(videoFrameTimes >= acceptablePeriod{iPeriod}(1) & videoFrameTimes <= acceptablePeriod{iPeriod}(2)) = true;
    end
  else
    acceptableSamples(videoFrameTimes >= acceptablePeriod(1) & videoFrameTimes <= acceptablePeriod(2)) = true;
  end
end
end