exportSpikesUMS.m

function spikes = exportSpikesUMS(obj,varargin)
% Export the detected spikes into UMS2000 style structs. Only input
% at present is 'channels', to set a subset of detected spikes to
% export by channel number. Defaults to all channels that have been
% read. Will automatically run spike detection on any channels that
% haven't been processed yet, with default settings in detectSpikes
% method. Returns the requested data in a struct array.
if ~exist('ss_default_params.m','file')
    error('Need the UltraMegaSort2000 toolbox on the path to export in their data format')
end
settings.channels = obj.loadedChannels;

settings = obj.parseInputs(varargin,settings);

% Required for preallocation. Kinda annoying. Because it's a
% struct array, of a different type than this class, it doesn't
% like other preallocation methods:
spikes = cell(1,length(settings.channels));

for c = 1:length(settings.channels)
    if length(obj.spikes) < settings.channels(c) ...
            || ~isfield(obj.spikes(settings.channels(c)),'loaded') ...
            || ~obj.spikes(settings.channels(c)).loaded
        disp(['Channel ' num2str(settings.channels(c)) ' has not had spikes extracted, doing so now'])
        obj.detectSpikes('channels',settings.channels(c));
    end
    if obj.spikes(settings.channels(c)).loaded
        ind = settings.channels(c);
        count = length(obj.spikes(ind).spiketimes);
        if count < 2
            disp([9 9 'Skipping ' num2str(settings.channels(c)) ': too few spikes'])
        else
            spikes{c} = ss_default_params(obj.Fs);

            spikes{c}.info.channel = ind;

            spikes{c}.info.detect.stds = obj.spikes(ind).sd;
            spikes{c}.info.detect.dur = obj.spikes(ind).duration;
            spikes{c}.info.detect.thresh = obj.spikes(ind).threshold;
            spikes{c}.info.detect.align_sample = floor(-obj.spikes(ind).window(1)*(obj.Fs/1e3)) + 1;
            spikes{c}.info.detect.event_channel = obj.spikes(ind).channel * ones(1,count);

            spikes{c}.waveforms = obj.spikes(ind).waveforms;
            spikes{c}.spiketimes = obj.spikes(ind).spiketimes;
            spikes{c}.trials = ones(1,count);
            spikes{c}.unwrapped_times = obj.spikes(ind).spiketimes;

            [pca.u,pca.s,pca.v] = svd(detrend(spikes{c}.waveforms(:,:),'constant'), 0);
            spikes{c}.info.pca = pca;
            spikes{c}.info.detect.cov = obj.spikes(ind).covariance;
            spikes{c}.info.align.aligned = 1; % this detection method is always aligned
        end
    end
end

spikes = [spikes{:}];