/// <summary>
/// This service calculates the spike-triggered covariance for given stimuli data and response spikes data.
/// </summary>
/// <param name="stimuli">
/// The stimuli that triggered spikes as 2-dimensional array with:
/// [?][ ] - List of stimuli frames.
/// [ ][?] - Stimulus data for the frame.</param>
/// <param name="spikes">
/// The detected spikes for the stimuli as 2-dimensional array with:
/// [?][ ][ ] - List of cells.
/// [ ][?][ ] - List of spike data for the cell.
/// [ ][ ][?] - Time when spike occurred.
/// </param>
/// <param name="roundStrategy">
/// The strategy for rounding the frame numbers.
/// </param>
/// <returns>Returns a vector containing the STA. </returns>
/// <remarks>
/// Calculation of STC:
///
/// N T
/// C = Σ [s(tn)-A][s(tn)-A]
/// n=1
/// -----------------------
/// N-1
///
/// N = total number of spikes
/// s = vector representing the stimuli
/// tn = time when the nth spike occurred
/// A = STA (spike-triggered average)
/// C = resulting covariance matrix
/// </remarks>
public static double[][] CalculateSTC(double[][] stimuli, double[][][] spikes, RoundStrategy roundStrategy)
{
var spikeTriggeredStimulusEnsemble = GetSpikeTriggeredStimulusEnsemble(stimuli, spikes, 0, roundStrategy);
var sta = CalculateSTA(stimuli, spikes, 0, roundStrategy);
var n = spikeTriggeredStimulusEnsemble.Length;
var stc =
Math.Divide(
Math.Sum(
Math.Subtract(spikeTriggeredStimulusEnsemble, sta).Select(stimulusReducedBySta =>
Math.Tensor(stimulusReducedBySta, stimulusReducedBySta)).ToArray()),
n - 1);
return stc;
}
/// <summary>
/// This method creates a list with all stimuli data that elicited spikes.
/// </summary>
/// <param name="stimuli">
/// The stimuli that triggered spikes as 2-dimensional array with:
/// [?][ ] - List of stimuli frames.
/// [ ][?] - Stimulus data for the frame.</param>
/// <param name="spikes">
/// The detected spikes for the stimuli as 2-dimensional array with:
/// [?][ ][ ] - List of cells.
/// [ ][?][ ] - List of spike data for the cell.
/// [ ][ ][?] - No. of frame which triggered the spike.
/// </param>
/// <param name="frameOffset">
/// The offset of the first frame which is taken for calculations. All other frames will be behind that frame.
/// </param>
/// <param name="roundStrategy">
/// The strategy for rounding the frame numbers.
/// </param>
/// <returns>Returns an array of the stimuli which triggered spikes. </returns>
public static double[][] GetSpikeTriggeredStimulusEnsemble(double[][] stimuli, double[][][] spikes, int frameOffset, RoundStrategy roundStrategy)
{
var spikeTriggeredStimulusEnsemble = new List<double[]>();
var spikesAndFrames = new double[0][][];
if (roundStrategy == RoundStrategy.Ceiling)
spikesAndFrames = Math.Ceiling(Math.Divide(spikes, Constants.STIMULI_FrameInterval));
else if (roundStrategy == RoundStrategy.Floor)
spikesAndFrames = Math.Floor(Math.Divide(spikes, Constants.STIMULI_FrameInterval));
else if (roundStrategy == RoundStrategy.Round)
spikesAndFrames = Math.Round(Math.Divide(spikes, Constants.STIMULI_FrameInterval));
foreach (double[][] cell in spikesAndFrames)
{
for (var spike = 0; spike < cell.Length; spike++)
{
var frame = (int)(cell[spike][0] - frameOffset);
if (frame > 0 && frame < stimuli.Length)
spikeTriggeredStimulusEnsemble.Add(stimuli[frame]);
}
}
return spikeTriggeredStimulusEnsemble.ToArray();
}
/// <summary>
/// This service calculates the spike-triggered average for given stimuli data and response spikes data.
/// </summary>
/// <param name="stimuli">
/// The stimuli that triggered spikes as 2-dimensional array with:
/// [?][ ] - List of stimuli frames.
/// [ ][?] - Stimulus data for the frame.</param>
/// <param name="spikes">
/// The detected spikes for the stimuli as 2-dimensional array with:
/// [?][ ][ ] - List of cells.
/// [ ][?][ ] - List of spike data for the cell.
/// [ ][ ][?] - Time when spike occurred.
/// </param>
/// <param name="frameOffset">
/// The offset of the first frame which is taken for calculations. All other frames will be behind that frame.
/// </param>
/// <param name="roundStrategy">
/// The strategy for rounding the frame numbers.
/// </param>
/// <returns>Returns a vector containing the STA. </returns>
/// <remarks>
/// Calculation of STA:
///
/// N
/// A = Σ s(tn)
/// n=1
/// ---------
/// N
///
/// N = total number of spikes
/// s = vector representing the stimuli
/// tn = time when the nth spike occurred
/// A = resulting STA (spike-triggered average)
/// </remarks>
public static double[] CalculateSTA(double[][] stimuli, double[][][] spikes, int frameOffset, RoundStrategy roundStrategy)
{
var spikeTriggeredStimulusEnsemble = GetSpikeTriggeredStimulusEnsemble(stimuli, spikes, frameOffset, roundStrategy);
var sta = Math.Subtract(Math.Mean(spikeTriggeredStimulusEnsemble), Math.Mean(stimuli));
return sta;
}