public PointAnalysis(Bout bout, IppiPoint coordinate, IppiPoint_32f smoothenedCoordinate, float instantSpeed)
{
CompletedBout = bout;
OriginalCoordinate = coordinate;
SmoothenedCoordinate = smoothenedCoordinate;
InstantSpeed = instantSpeed;
}
/// <summary>
/// Detects bouts and returns summary information
/// </summary>
/// <param name="isb">The instant speed trace</param>
/// <param name="speedThreshold">Speeds below this threshold will be set to 0</param>
/// <param name="minFramesPerBout">For a movement to be called a bout we require at least this number of frames</param>
/// <param name="maxFramesAtPeak">Bouts should have clearly defined peaks. Bouts with a peak longer than this number get rejected</param>
/// <param name="frameRate">The framerate used for acquisition</param>
/// <returns>A bout summary info structure</returns>
public BoutSummary AnalyzeBouts(InstantSpeedBuffer isb, float speedThreshold, int minFramesPerBout, int maxFramesAtPeak, int frameRate)
{
if (IsDisposed)
{
throw new ObjectDisposedException(this.ToString());
}
if (_isCalc == null)
{
_isCalc = new InstantSpeedBuffer(isb.Size.width);
}
else if (_isCalc.Size.width != isb.Size.width)
{
_isCalc.Dispose();
_isCalc = new InstantSpeedBuffer(isb.Size.width);
}
BoutSummary retval = new BoutSummary();
Bout b = new Bout();
int i = 0;
//threshold the speed trace - copy result into our calculation buffer
ip.ippiThreshold_LTVal_32f_C1R(isb.Buffer, isb.Stride, _isCalc.Buffer, _isCalc.Stride, isb.Size, speedThreshold, 0);
while (i < _isCalc.Size.width)
{
if (_isCalc[i] == 0)
{
i++;
continue;
}
else//found potential bout start since speed above threshold
{
int peaklength = 0;
b.BoutStart = i;
b.PeakSpeed = _isCalc[i];
b.BoutPeak = i;
b.TotalDisplacement = _isCalc[i] / frameRate;
//loop over following frames collecting all frames that belong to the bout
while (i < _isCalc.Size.width && _isCalc[i] > 0)
{
if (_isCalc[i] > b.PeakSpeed)
{
b.PeakSpeed = _isCalc[i];
b.BoutPeak = i;
peaklength = 0; //new peakspeed found, reset peaklength
}
else if (_isCalc[i] == b.PeakSpeed) //another frame with the same speed as our peak
{
peaklength++;
}
b.TotalDisplacement += _isCalc[i] / frameRate;
i++;
}
b.BoutEnd = i - 1;
//check our bout criteria
if ((b.BoutEnd - b.BoutStart + 1) >= minFramesPerBout && peaklength <= maxFramesAtPeak)
{
//we have a valid bout
if (b.BoutStart == b.BoutPeak)
{
b.BoutStart--;
}
retval.NumberOfBouts++;
retval.AverageDisplacement += b.TotalDisplacement;
retval.AveragePeakSpeed += b.PeakSpeed;
retval.AverageLength += (b.BoutEnd - b.BoutStart + 1);
}
}//found potential bout
}
retval.AverageDisplacement /= retval.NumberOfBouts;
retval.AveragePeakSpeed /= retval.NumberOfBouts;
retval.AverageLength /= retval.NumberOfBouts;
return(retval);
}
/// <summary>
/// Processes the next point, filtering its position
/// computing speeds and detecting bouts
/// </summary>
/// <param name="coordinate">The coordinate to analyze</param>
/// <returns>The analysis of the given coordinate</returns>
public PointAnalysis ProcessNextPoint(IppiPoint coordinate)
{
//set up locals for processing
float x = coordinate.x;
float y = coordinate.y;
float xSmooth, ySmooth, speed;
xSmooth = ySmooth = speed = 0;
//optional filtered speed
float spdSmooth = 0;
//filter x-coordinate
sp.ippsFIR_32f(&x, &xSmooth, 1, _filterStateX);
//filter y-coordinate
sp.ippsFIR_32f(&y, &ySmooth, 1, _filterStateY);
//compute instant speed
speed = (float)Math.Sqrt((xSmooth - _lastX) * (xSmooth - _lastX) + (ySmooth - _lastY) * (ySmooth - _lastY));
speed *= 240;
//if requested, also filter the instant-speed value
if (_spdTapLength > 0)
{
sp.ippsFIR_32f(&speed, &spdSmooth, 1, _filterStateSpd);
}
else
{
spdSmooth = speed;
}
//update last coordinates
_lastX = xSmooth;
_lastY = ySmooth;
//Bout detection
if (_boutDetectionState.InPutativeBout) //we are currently adding frames to a new putative bout
{
if (spdSmooth < _speedThreshold) //putative bout is finished
{
_boutDetectionState.InPutativeBout = false; //reset
if (_boutDetectionState.FramesInBout >= _minFramesPerBout && _boutDetectionState.FramesAtPeak <= _maxFramesAtPeak) //bout was valid, fill bout structure and return it
{
Bout bout = new Bout();
bout.BoutEnd = _index - 1;
bout.BoutStart = _boutDetectionState.StartFrame;
bout.BoutPeak = _boutDetectionState.PeakFrame;
if (bout.BoutPeak == bout.BoutStart)
{
bout.BoutStart--;//don't start bout on peakframe
}
bout.PeakSpeed = _boutDetectionState.PeakSpeed;
bout.TotalDisplacement = _boutDetectionState.TotalDisplacement;
bout.StartingCoordinate = _boutDetectionState.StartingCoordinate;
bout.FinishCoordinate = new IppiPoint_32f(xSmooth, ySmooth);
//don't forget to update the index before we return
_index++;
return(new PointAnalysis(bout, coordinate, new IppiPoint_32f(xSmooth, ySmooth), spdSmooth));
}
}
else//putative bout continues
{
_boutDetectionState.FramesInBout++;
_boutDetectionState.TotalDisplacement += spdSmooth / _frameRate;
if (spdSmooth > _boutDetectionState.PeakSpeed)//new peak-speed detected
{
_boutDetectionState.PeakSpeed = spdSmooth;
_boutDetectionState.PeakFrame = _index;
_boutDetectionState.FramesAtPeak = 1; //reset
}
else if (spdSmooth == _boutDetectionState.PeakSpeed) //maybe not the best criterion - equality of float values very unlikely
{
_boutDetectionState.FramesAtPeak++;
}
}
}
else//currently the fish is stationary
{
if (spdSmooth > _speedThreshold)//we should start a new putative bout
{
_boutDetectionState.StartBout(spdSmooth, _index, _frameRate);
_boutDetectionState.StartingCoordinate.x = xSmooth;
_boutDetectionState.StartingCoordinate.y = ySmooth;
}
}
//advance index
_index++;
//return our analysis
return(new PointAnalysis(coordinate, new IppiPoint_32f(xSmooth, ySmooth), spdSmooth));
}
