order of recordings cell array

[akianzai]

I noticed that the order of recordings cell array (session.recordNodes{1,1}.recordings) does not necessarily match with the order of recordings. For example, suppose that a total of 21 recordings were made and the data were saved in 21 folders (recording1, recording2,...,recording21). If you create a session object, it will contain session.recordNodes{1,1}.recordings that is a 1x21 cell array. But the cell array index number does not match with the recording number. That is, recordings{1,1} contains data from recording1, recordings{1,2} contains data from recording10, recordings{1,3} from recording11, ..., recordings{1,12} from recording2, and so on. This is because the directory search using glob() returns a list of folders in this order. In fact, there is a comment in BinaryRecording.m right after each glob() that says "% sort", but sorting was never implemented. I'm not sure if this is on purpose or it was meant to be implemented. In any case, this is a problem for me, and I added a few lines of code to do the sorting as shown below (under "% sort" in detectRecordings). I use binary data format, so I only modified BinaryRecording.m. But I suspect that session objects created from the data in other formats have the same issue.

========================== BinaryRecording.m ========================== % MIT License

% Copyright (c) 2021 Open Ephys

% Permission is hereby granted, free of charge, to any person obtaining a copy % of this software and associated documentation files (the "Software"), to deal % in the Software without restriction, including without limitation the rights % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell % copies of the Software, and to permit persons to whom the Software is % furnished to do so, subject to the following conditions:

% The above copyright notice and this permission notice shall be included in all % copies or substantial portions of the Software.

% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE % SOFTWARE.

classdef BinaryRecording < Recording

properties

    info

end

methods 

    function self = BinaryRecording(directory, experimentIndex, recordingIndex) 

        self = self@Recording(directory, experimentIndex, recordingIndex);
        self.format = 'Binary';

        self.info = jsondecode(fileread(fullfile(self.directory,'structure.oebin')));

        self = self.loadContinuous();
        self = self.loadEvents();
        self = self.loadSpikes();

        self = self.loadMessages();

    end

    function self = loadContinuous(self)

        for i = 1:length(self.info.continuous)

            directory = fullfile(self.directory, 'continuous', self.info.continuous(i).folder_name);

            stream = {};

            stream.metadata.sampleRate = self.info.continuous(i).sample_rate;
            stream.metadata.numChannels = self.info.continuous(i).num_channels;
            stream.metadata.processorId = self.info.continuous(i).source_processor_id;
            stream.metadata.streamName = self.info.continuous(i).folder_name(1:end-1);

            stream.metadata.names = {};
            for j = 1:length(self.info.continuous(i).channels)
                stream.metadata.names{j} = self.info.continuous(i).channels(j).channel_name;
            end

            %Utils.log("Searching for start timestamp for stream: ");
            %Utils.log("    ", stream.metadata.streamName);

            stream.metadata.id = num2str(stream.metadata.streamName);

            stream.timestamps = readNPY(fullfile(directory, 'timestamps.npy'));

            stream.sampleNumbers = readNPY(fullfile(directory, 'sample_numbers.npy'));

            data = memmapfile(fullfile(directory, 'continuous.dat'), 'Format', 'int16');

            stream.samples = reshape(data.Data, [stream.metadata.numChannels, length(data.Data) / stream.metadata.numChannels]);

            stream.metadata.startTimestamp = stream.timestamps(1);

            self.continuous(stream.metadata.id) = stream;

        end

    end

    function self = loadEvents(self)

        ttlDirectories = glob(fullfile(self.directory, 'events', '*', 'TTL*'));

        streamIdx = 0;

        for i = 1:length(ttlDirectories)

            files = regexp(ttlDirectories{i},filesep,'split');

            % Assumes full stream name always in the form
            % <PROCESSOR_NAME>_<PROCESSOR_ID>.<STREAM_ID>
            fullStreamName = files{length(files)-2};

            stream = regexp(fullStreamName,'\.','split');

            processor = stream{1};
            streamName = stream{2};

            processorId = str2double(processor(length(processor)-2:end));

            lines = readNPY(fullfile(ttlDirectories{i}, 'states.npy'));
            sampleNumbers = readNPY(fullfile(ttlDirectories{i}, 'sample_numbers.npy'));
            timestamps = readNPY(fullfile(ttlDirectories{i}, 'timestamps.npy'));

            numEvents = length(lines);

            self.ttlEvents(fullStreamName) = DataFrame(abs(lines), sampleNumbers, timestamps, processorId*ones(numEvents,1), repmat(string(fullStreamName),numEvents,1), lines > 0, ...
                'VariableNames', {'line','sample_number','timestamp','processor_id', 'stream_name', 'state'});

            streamIdx = streamIdx + 1;

        end

        if length(self.ttlEvents.keys) > 0
            %TODO: Concatenate data frames?
        end

    end

    function self = loadMessages(self)

        msgDirectory = glob(fullfile(self.directory, 'events', 'MessageCenter'));

        messages = fullfile(msgDirectory, 'text.npy');
        messages = dir(messages{:});

        if messages.bytes > 128

            % Utils.log("Found message events");

            text = readNPY(fullfile(msgDirectory{1}, 'text.npy'));
            sampleNumbers = readNPY(fullfile(msgDirectory{1}, 'sample_numbers.npy'));
            timestamps = readNPY(fullfile(msgDirectory{1}, 'timestamps.npy'));

            self.messages('MessageCenter') = DataFrame(timestamps, sampleNumbers, text, ...
                'VariableNames', {'timestamps','sample_number','text'});

        end

    end

    function self = loadSpikes(self)

        for i = 1:length(self.info.spikes)

            directory = fullfile(self.directory, 'spikes', self.info.spikes(i).folder);

            spikes = {};

            spikes.id = self.info.spikes(i).folder(1:end-1);

            spikes.timestamps = readNPY(fullfile(directory, 'timestamps.npy'));
            spikes.electrodes = readNPY(fullfile(directory, 'electrode_indices.npy'));
            spikes.clusters = readNPY(fullfile(directory, 'clusters.npy'));
            spikes.sample_numbers = readNPY(fullfile(directory, 'sample_numbers.npy'));

            spikes.waveforms = permute(readNPY(fullfile(directory, 'waveforms.npy')), [3 2 1]);

            self.spikes(spikes.id) = spikes;  

        end

    end

    function syncMessages = loadSyncMessages(self)

        syncMessages = containers.Map();

        rawMessages = splitlines(fileread(fullfile(self.directory, 'sync_messages.txt')));

        for i = 1:length(rawMessages)-1

            message = strsplit(rawMessages{i});

            if message{1} == "Software"

                % Found system time for start of the recording
                % "Software Time (milliseconds since midnight Jan 1st 1970 UTC): 1660948389101"
                syncMessages("Software") = str2double(message{end});

            else

                % Found a processor string

                %(e.g. "Start Time for File Reader (100) - Source_Sim-110.0 @ 30000 Hz: 80182")
                % Stream name will be: File_Reader-100.Source_Sim-110.0

                idx = find(strcmp(message, '@'));
                node_name = strjoin({strjoin(message(4:(idx-4)),'_'),message{idx-3}(2:end-1)},'-');

                stream_name = message{idx-1};

                start_timestamp = str2double(message{end});

                syncMessages(strjoin({node_name, stream_name},'.')) = start_timestamp;

            end

        end

    end

end

methods (Static)

    function detectedFormat = detectFormat(directory)

        detectedFormat = false;

        binaryFiles = glob(fullfile(directory, 'experiment*', 'recording*'));

        if length(binaryFiles) > 0
            detectedFormat = true;
        end

    end

    function recordings = detectRecordings(directory)

        recordings = {};

        experimentDirectories = glob(fullfile(directory, 'experiment*'));
        %sort according to the experiment number
        match = regexp(experimentDirectories,'(?:experiment)(\d+)','tokens');
        experiment_numbers = cellfun(@str2double,[match{:}]);
        [~,exp_sort_idx] = sort(experiment_numbers);
        experimentDirectories = experimentDirectories(exp_sort_idx);

        for expIdx = 1:length(experimentDirectories)

            recordingDirectories = glob(fullfile(experimentDirectories{expIdx}, 'recording*'));
            %sort according to the recording number
            match = regexp(recordingDirectories,'(?:recording)(\d+)','tokens');
            recording_numbers = cellfun(@str2double,[match{:}]);
            [~,rec_sort_idx] = sort(recording_numbers);
            recordingDirectories = recordingDirectories(rec_sort_idx);

            for recIdx = 1:length(recordingDirectories)
                recordings{end+1} = BinaryRecording(recordingDirectories{recIdx}, expIdx, recIdx);
            end

        end

    end

end

end