public Tracker90mmDish(int imageWidth, int imageHeight)
{
_foreground = new Image8(imageWidth, imageHeight);
_calc = new Image8(imageWidth, imageHeight);
_labelMarkers = new Image8(imageWidth, imageHeight);
int bufferSize = 0;
IppHelper.IppCheckCall(cv.ippiLabelMarkersGetBufferSize_8u_C1R(new IppiSize(imageWidth, imageHeight), &bufferSize));
_markerBuffer = (byte *)Marshal.AllocHGlobal(bufferSize);
fixed(IppiMomentState_64s **ppState = &_momentState)
{
//let ipp decide whether to give accurate or fast results
IppHelper.IppCheckCall(ip.ippiMomentInitAlloc_64s(ppState, IppHintAlgorithm.ippAlgHintNone));
}
_frame = 0;
//populate tracking parameters with default values
_threshold = 5;
_minArea = 10;
_maxArea = 300;
_fullTrustMinArea = 20;
_imageROI = new IppiROI(0, 0, imageWidth, imageHeight);
//The following calculation for FramesInBackground means that after ~30s of movie
//a stationary object will have dissappeared into the background (at 63% level)
FramesInBackground = (int)((30 * 240));
FramesInitialBackground = 2 * FramesInBackground;
}
/// <summary>
/// Method for parallelized tracking - depending on index
/// performs tracking on an image chunk
/// </summary>
/// <param name="index">The chunk's index</param>
private void TrackChunk(int index)
{
//each chunk has its own image region with its own wells to take care of
//currently, only 4 chunks on a 24-well plate are supported
if (index >= _parallelChunks)
{
System.Diagnostics.Debug.WriteLine("Fatal parallel tracking error. Tried to access non-existing chunk.");
}
//do image filtering, thresholding and closing
if (DoMedianFiltering)
{
IppHelper.IppCheckCall(ip.ippiFilterMedianWeightedCenter3x3_8u_C1R(_calc[_parallelImageRegions[index].X + 1, _parallelImageRegions[index].Y + 1], _calc.Stride,
_foreground[_parallelImageRegions[index].X + 1, _parallelImageRegions[index].Y + 1], _foreground.Stride,
new IppiSize(_parallelImageRegions[index].Width - 2, _parallelImageRegions[index].Height - 2), 1));
}
Im2Bw(_foreground, _parallelImageRegions[index]);
Close3x3(_foreground, _parallelImageRegions[index]);
//loop over the wells that belong to our region, extract the fish
//and put into our result structure
//Important: Need to put into the chunks section of the results section!
var ourWells = _parallelChunkWells[index];
for (int i = 0; i < ourWells.Count; i++)
{
_parallelTrackResults[i + _parallelCumWellCount[index]] = ExtractWellParallel(ourWells[i], index);
}
}
public Tracker90mmDish(int imageWidth, int imageHeight, IppiPoint dishCenter)
{
_foreground = new Image8(imageWidth, imageHeight);
_bgSubtracted = new Image8(imageWidth, imageHeight);
_calc = new Image8(imageWidth, imageHeight);
_dishCenter = dishCenter;
int bufferSize = 0;
IppHelper.IppCheckCall(cv.ippiLabelMarkersGetBufferSize_8u_C1R(new IppiSize(imageWidth, imageHeight), &bufferSize));
_markerBuffer = (byte *)Marshal.AllocHGlobal(bufferSize);
int momentSize = 0;
IppHelper.IppCheckCall(ip.ippiMomentGetStateSize_64f(IppHintAlgorithm.ippAlgHintNone, &momentSize));
_momentState = (IppiMomentState_64f *)Marshal.AllocHGlobal(momentSize);
//let ipp decide whether to give accurate or fast results
IppHelper.IppCheckCall(ip.ippiMomentInit_64f(_momentState, IppHintAlgorithm.ippAlgHintNone));
_frame = 0;
//populate tracking parameters with default values
_threshold = 6;
_minArea = 11;
_maxAllowedArea = 120;
_minEccentricity = 0.3;
_fullTrustMinArea = 20;
_imageROI = new IppiROI(0, 0, imageWidth, imageHeight);
_searchRegionSize = 90;
_removeCMOSISBrightLineArtefact = false;
_strel3x3 = Morphology.Generate3x3Mask(_foreground.Size);
//The following calculation for FramesInBackground means that after ~30s of movie
//a stationary object will have dissappeared into the background (at 63% level)
FramesInBackground = (int)((30 * 250));
FramesInitialBackground = 2 * 30 * 250;
BGUpdateEvery = 2;
}
/// <summary>
/// Computes instants speeds from a coordinate trace and stores the result
/// in the provided buffer
/// </summary>
/// <param name="path">The movement path</param>
/// <param name="frameRate">The framerate at acquisition</param>
/// <param name="isb">The buffer to store the speed in</param>
public void ComputeInstantSpeeds(CentroidBuffer path, int frameRate, InstantSpeedBuffer isb)
{
if (IsDisposed)
{
throw new ObjectDisposedException(this.ToString());
}
if (isb.Size.width != path.Size.width)
{
throw new ArgumentException("Path length and size of speed buffer must be the same!");
}
//Check that our buffers are present and match, otherwise fix
if (_calc1 == null)
{
_calc1 = new CentroidBuffer(path.Size.width);
_calc2 = new CentroidBuffer(path.Size.width);
}
else if (_calc1.Size.width != path.Size.width)
{
_calc1.Dispose();
_calc2.Dispose();
_calc1 = new CentroidBuffer(path.Size.width);
_calc2 = new CentroidBuffer(path.Size.width);
}
//compute difference trace subtracting the position at t from the position at t+1 by subtracting the unshifted input buffer from its shifted version
//the result gets stored in calc1 with the first value being 0
ip.ippiSet_32f_C1R(0, _calc1.Buffer, _calc1.Stride, _calc1.Size);
IppHelper.IppCheckCall(ip.ippiSub_32f_C1R(path.Buffer, path.Stride, (float *)((byte *)path.Buffer + 4), path.Stride, (float *)((byte *)_calc1.Buffer + 4), _calc1.Stride, new IppiSize(path.Size.width - 1, 2)));
//square the difference trace, storing the result in _calc2
IppHelper.IppCheckCall(ip.ippiSqr_32f_C1R(_calc1.Buffer, _calc1.Stride, _calc2.Buffer, _calc2.Stride, _calc1.Size));
//Add the values of the x and y coordinates, storing the sum of squares in the first row of _calc1
IppHelper.IppCheckCall(ip.ippiAdd_32f_C1R(_calc2.Buffer, _calc2.Stride, (float *)((byte *)_calc2.Buffer + _calc2.Stride), _calc2.Stride, _calc1.Buffer, _calc1.Stride, new IppiSize(_calc1.Size.width, 1)));
//Compute the square root of the sum-of-squares and copy the result to the first row of _calc2
IppHelper.IppCheckCall(ip.ippiSqrt_32f_C1R(_calc1.Buffer, _calc1.Stride, _calc2.Buffer, _calc2.Stride, new IppiSize(_calc1.Size.width, 1)));
//Multiply the distances by the framerate and store the result in our instant speed buffer
IppHelper.IppCheckCall(ip.ippiMulC_32f_C1R(_calc2.Buffer, _calc2.Stride, frameRate, isb.Buffer, isb.Stride, isb.Size));
}
/// <summary>
/// Extracts a fish (candidate) from an image by performing background subtraction, noise filtering, thresholding and closing to obtain a foreground
/// followed by marker extraction.
/// </summary>
/// <param name="im">The image to extract the fish from</param>
/// <param name="region">The ROI to search</param>
/// <returns>The most likely fish blob or null if no suitable candidate was found</returns>
protected BlobWithMoments ExtractFish(/*Image8 im,*/ IppiROI region)
{
int nMarkers = 0;
BlobWithMoments[] blobsDetected;
//Copy foreground to marker and label connected components
//IppHelper.IppCheckCall(ip.ippiCopy_8u_C1R(_foreground[region.TopLeft], _foreground.Stride, _labelMarkers[region.TopLeft], _labelMarkers.Stride, region.Size));
IppHelper.IppCheckCall(cv.ippiLabelMarkers_8u_C1IR(_foreground[region.TopLeft], _foreground.Stride, region.Size, 1, 254, IppiNorm.ippiNormInf, &nMarkers, _markerBuffer));
//loop over returned markers and use ipp to extract blobs
if (nMarkers > 0)
{
if (nMarkers > 254)
{
nMarkers = 254;
}
blobsDetected = new BlobWithMoments[nMarkers];
for (int i = 1; i <= nMarkers; i++)
{
//label all pixels with the current marker as 255 and others as 0
IppHelper.IppCheckCall(ip.ippiCompareC_8u_C1R(_foreground[region.TopLeft], _foreground.Stride, (byte)i, _calc[region.TopLeft], _calc.Stride, region.Size, IppCmpOp.ippCmpEq));
//calculate image moments
IppHelper.IppCheckCall(ip.ippiMoments64s_8u_C1R(_calc[region.TopLeft], _calc.Stride, region.Size, _momentState));
//retrieve moments
long m00 = 0;
long m10 = 0;
long m01 = 0;
long m20 = 0;
long m02 = 0;
long m11 = 0;
long m30 = 0;
long m03 = 0;
long m21 = 0;
long m12 = 0;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 0, 0, new IppiPoint(region.X, region.Y), &m00, 0);
//since our input image is not 0s and 1s but 0s and 255s we have to divide by 255 in order to re-normalize our moments
System.Diagnostics.Debug.Assert(m00 % 255 == 0, "M00 was not a multiple of 255");
m00 /= 255;
//only retrieve other moments if this is a "fish candidate"
if (m00 > MinArea && m00 <= MaxArea)
{
ip.ippiGetSpatialMoment_64s(_momentState, 1, 0, 0, new IppiPoint(region.X, region.Y), &m10, 0);
m10 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 1, 0, new IppiPoint(region.X, region.Y), &m01, 0);
m01 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 2, 0, 0, new IppiPoint(region.X, region.Y), &m20, 0);
m20 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 2, 0, new IppiPoint(region.X, region.Y), &m02, 0);
m02 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 1, 1, 0, new IppiPoint(region.X, region.Y), &m11, 0);
m11 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 3, 0, 0, new IppiPoint(region.X, region.Y), &m30, 0);
m30 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 3, 0, new IppiPoint(region.X, region.Y), &m03, 0);
m03 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 2, 1, 0, new IppiPoint(region.X, region.Y), &m21, 0);
m21 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 1, 2, 0, new IppiPoint(region.X, region.Y), &m12, 0);
m12 /= 255;
blobsDetected[i - 1] = new BlobWithMoments(m00, m10, m01, m20, m11, m02, m30, m03, m21, m12);
//Determine bounding box of the blob. The following seems kinda retarded as Ipp must already
//have obtained that information before so maybe there is some way to actually retrieve it??
//Do linescans using ipp's sum function starting from the blobs centroid until we hit a line
//the sum of which is 0
int xStart, xEnd, yStart, yEnd;
double sum = 1;
IppiPoint centroid = blobsDetected[i - 1].Centroid;
xStart = centroid.x - 5;
xEnd = centroid.x + 5;
yStart = centroid.y - 5;
yEnd = centroid.y + 5;
//in the following loops we PRE-increment, whence we stop the loop if we are at one coordinate short of the ends
//find xStart
while (sum > 0 && xStart > region.X + 4)
{
xStart -= 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, region.Y], _calc.Stride, new IppiSize(1, region.Height), &sum));
}
xStart += 1;//we have a sum of 0, so go back one line towards the centroid
//find xEnd
sum = 1;
while (sum > 0 && xEnd < region.X + region.Width - 6)
{
xEnd += 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xEnd, region.Y], _calc.Stride, new IppiSize(1, region.Height), &sum));
}
xEnd -= 1;//we have sum of 0, so go back one line towards the centroid
//find yStart - we can limit our x-search-space as we already have those boundaries
sum = 1;
while (sum > 0 && yStart > region.Y + 4)
{
yStart -= 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, yStart], _calc.Stride, new IppiSize(xEnd - xStart + 1, 1), &sum));
}
yStart += 1;
//find yEnd - again limit summation to x-search-space
sum = 1;
while (sum > 0 && yEnd < region.Y + region.Height - 6)
{
yEnd += 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, yEnd], _calc.Stride, new IppiSize(xEnd - xStart + 1, 1), &sum));
}
yEnd -= 1;
blobsDetected[i - 1].BoundingBox = new IppiRect(xStart, yStart, xEnd - xStart + 1, yEnd - yStart + 1);
}
else
{
blobsDetected[i - 1] = new BlobWithMoments();
}
}
}
else
{
return(null);
}
long maxArea = 0;
int maxIndex = -1;
for (int i = 0; i < blobsDetected.Length; i++)
{
if (blobsDetected[i] == null)
{
break;
}
//Simply note down the largest blob
if (blobsDetected[i].Area > maxArea)
{
maxArea = blobsDetected[i].Area;
maxIndex = i;
}
}
if (maxArea < MinArea)
{
return(null);
}
else
{
return(blobsDetected[maxIndex]);
}
}
/// <summary>
/// Performs a 3x3 closing operation on an image
/// </summary>
/// <param name="im">The (thresholded) image to close</param>
/// <param name="region">The ROI in which to perform the operation</param>
protected void Close3x3(Image8 im, IppiROI region)
{
IppHelper.IppCheckCall(ip.ippiDilate3x3_8u_C1IR(im[region.TopLeft.x + 1, region.TopLeft.y + 1], im.Stride, new IppiSize(region.Width - 2, region.Height - 2)));
IppHelper.IppCheckCall(ip.ippiErode3x3_8u_C1IR(im[region.TopLeft.x + 1, region.TopLeft.y + 1], im.Stride, new IppiSize(region.Width - 2, region.Height - 2)));
}
/// <summary>
/// Implements a "greater than" threshold like MATLABS
/// im2bw function
/// </summary>
/// <param name="im">The image to threshold</param>
/// <param name="region">The ROI in which to perform the operation</param>
/// <param name="threshold">The threshold to apply</param>
protected void Im2Bw(Image8 im, IppiROI region)
{
IppHelper.IppCheckCall(ip.ippiThreshold_LTVal_8u_C1IR(im[region.TopLeft], im.Stride, region.Size, (byte)(_threshold + 1), 0));
IppHelper.IppCheckCall(ip.ippiThreshold_GTVal_8u_C1IR(im[region.TopLeft], im.Stride, region.Size, _threshold, 255));
}
/// <summary>
/// Tracks fish on a multiwell plate
/// </summary>
/// <param name="image">The current image to track and update the background with</param>
/// <param name="updateBackground">If true the current image will be used to update the background</param>
/// <param name="forceFullFrame">If set to true background updates won't exclude fish locations</param>
/// <returns>A list of fish-blobs, one for each well or null if no fish was detected</returns>
public BlobWithMoments[] TrackMultiWell(Image8 image, bool updateBackground = true, bool forceFullFrame = false)
{
if (_frame == 0)
{
ip.ippiSet_8u_C1R(0, Foreground.Image, Foreground.Stride, Foreground.Size);
ip.ippiSet_8u_C1R(0, _calc.Image, _calc.Stride, _calc.Size);
}
BlobWithMoments[] currentFish = new BlobWithMoments[_wellnumber];
if (_frame > FramesInitialBackground && !forceFullFrame)
{
//do global stuff (everything except labelMarkers if we don't do parallel tracking otherwise only the inherently parallel background subtraction)
//cache 8-bit representation of the background
Image8 bg = _bgModel.Background;
//Perform background subtraction
if (DoMedianFiltering)
{
IppHelper.IppCheckCall(cv.ippiAbsDiff_8u_C1R(image.Image, image.Stride, bg.Image, bg.Stride, _calc.Image, _calc.Stride, image.Size));
}
else
{
IppHelper.IppCheckCall(cv.ippiAbsDiff_8u_C1R(image.Image, image.Stride, bg.Image, bg.Stride, _foreground.Image, _foreground.Stride, image.Size));
}
if (_trackMethod == TrackMethods.Parallel && _parallelChunks > 1)
{
if (!Parallel.For(0, _parallelChunks, TrackChunk).IsCompleted)
{
System.Diagnostics.Debug.WriteLine("Error in parallel tracking. Not all regions completed");
}
//copy our result into currentFish
for (int i = 0; i < _wellnumber; i++)
{
currentFish[i] = _parallelTrackResults[i];
}
}
else
{
if (DoMedianFiltering)
{
//remove noise via median filtering
IppHelper.IppCheckCall(ip.ippiFilterMedianWeightedCenter3x3_8u_C1R(_calc[1, 1], _calc.Stride,
_foreground[1, 1], _foreground.Stride, new IppiSize(image.Width - 2, image.Height - 2), 1));
}
//Threshold and close
Im2Bw(_foreground, new IppiROI(new IppiPoint(0, 0), image.Size));
Close3x3(_foreground, new IppiROI(new IppiPoint(0, 0), image.Size));
//label markers and extract - depending on the method selector
//we label components on the whole image (new) or individual wells(old)
if (_trackMethod == TrackMethods.OnWholeImage)
{
currentFish = ExtractAll();
}
else
{
for (int i = 0; i < _wellnumber; i++)
{
currentFish[i] = ExtractFish(_wells[i]);
}
}
}
}//If We are past initial background frames
//create/update background and advance frame counter
if (_frame == 0)
{
_bgModel = new SelectiveUpdateBGModel(image, 1.0f / FramesInBackground);
}
else if (updateBackground || _frame <= FramesInitialBackground)//only allow reduction of background update rate AFTER initial background has been created
{
if (currentFish == null || forceFullFrame)
{
_bgModel.UpdateBackground(image);
}
else
{
_bgModel.UpdateBackground(image, currentFish);
}
}
_frame++;
return(currentFish);
}
/// <summary>
/// Extracts for each well the most likely fish-blob or null if no suitable candidate was found
/// </summary>
/// <returns>All fish blobs found in the image</returns>
private BlobWithMoments[] ExtractAll()
{
int nMarkers = 0;
//we have fixed bounding boxes for each fish that are square and 1.5 times the typical fish-length
//with the fishes centroid centered in the box
int bbOffset = (int)(_typicalFishLength * 0.75);
int bbSize = (int)(_typicalFishLength * 1.5);
//Copy foreground to marker and label connected components
//IppHelper.IppCheckCall(ip.ippiCopy_8u_C1R(_foreground.Image, _foreground.Stride, _labelMarkers.Image, _labelMarkers.Stride, _foreground.Size));
IppHelper.IppCheckCall(cv.ippiLabelMarkers_8u_C1IR(_foreground.Image, _foreground.Stride, _foreground.Size, 1, 254, IppiNorm.ippiNormInf, &nMarkers, _markerBuffer));
if (nMarkers > 254)
{
nMarkers = 254;
}
//fish are identified by looping over all wells and computing the histogram of pixel values for each well. This will effectively tell us
//which marker is the most abundant in the given well => this would be the fish by our general detection logic
//The maximum value that ippiLabelMarkers has used is equal to nMarkers. Therefore, when we compute our histogram, we supply
//(nMarkers+2) as the nLevels parameter - this will give us (nMarkers+1) bins containing the counts from 0->nMarkers with 0 being our background
//loop over wells
for (int i = 0; i < _wellnumber; i++)
{
IppiROI well = _wells[i];
//get well-specific maxvalue
//byte maxVal = 0;
//IppHelper.IppCheckCall(ip.ippiMax_8u_C1R(_labelMarkers[well.TopLeft], _labelMarkers.Stride, well.Size, &maxVal));
//compute histogram in this well - from 0 until maxval
IppHelper.IppCheckCall(ip.ippiHistogramRange_8u_C1R(_foreground[well.TopLeft], _foreground.Stride, well.Size, _hist, _histogramLevels, nMarkers + 2));
//_hist now contains in position i the abundance of marker i => by looping over it from 1->nMarkers we can find the largest blob. If this blob is
//larger than our minimum size, we compute the moments and initialize a BlobWithMoments structure for it
int maxCount = 0;
int maxIndex = -1;
for (int j = 1; j <= nMarkers; j++)
{
if (_hist[j] > maxCount && _hist[j] > _minArea && _hist[j] <= _maxArea)
{
maxCount = _hist[j];
maxIndex = j;
}
}
if (maxIndex == -1)//no suitable fish found
{
_allFish[i] = null;
}
else
{
//compare and compute moments
//label all pixels with the current marker as 255 and others as 0
IppHelper.IppCheckCall(ip.ippiCompareC_8u_C1R(_foreground[well.TopLeft], _foreground.Stride, (byte)maxIndex, _wellCompare.Image, _wellCompare.Stride, well.Size, IppCmpOp.ippCmpEq));
//calculate image moments
IppHelper.IppCheckCall(ip.ippiMoments64s_8u_C1R(_wellCompare.Image, _wellCompare.Stride, well.Size, _momentState));
//retrieve moments
long m00 = 0;
long m10 = 0;
long m01 = 0;
long m20 = 0;
long m02 = 0;
long m11 = 0;
long m30 = 0;
long m03 = 0;
long m21 = 0;
long m12 = 0;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 0, 0, well.TopLeft, &m00, 0);
m00 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 1, 0, 0, well.TopLeft, &m10, 0);
m10 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 1, 0, well.TopLeft, &m01, 0);
m01 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 2, 0, 0, well.TopLeft, &m20, 0);
m20 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 2, 0, well.TopLeft, &m02, 0);
m02 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 1, 1, 0, well.TopLeft, &m11, 0);
m11 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 3, 0, 0, well.TopLeft, &m30, 0);
m30 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 0, 3, 0, well.TopLeft, &m03, 0);
m03 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 2, 1, 0, well.TopLeft, &m21, 0);
m21 /= 255;
ip.ippiGetSpatialMoment_64s(_momentState, 1, 2, 0, well.TopLeft, &m12, 0);
m12 /= 255;
_allFish[i] = new BlobWithMoments(m00, m10, m01, m20, m11, m02, m30, m03, m21, m12);
//assign bounding box
IppiRect bBox = new IppiRect(_allFish[i].Centroid.x - bbOffset, _allFish[i].Centroid.y - bbOffset, bbSize, bbSize);
if (bBox.x < well.X)
{
bBox.x = well.X;
}
if (bBox.y < well.Y)
{
bBox.y = well.Y;
}
if (bBox.x + bBox.width > well.X + well.Width)
{
bBox.width = well.X + well.Width - bBox.x;
}
if (bBox.y + bBox.height > well.Y + well.Height)
{
bBox.height = well.Y + well.Height - bBox.y;
}
_allFish[i].BoundingBox = bBox;
}
}//end looping over all wells
return(_allFish);
}
/// <summary>
/// Constructs a new multi-well tracker
/// </summary>
/// <param name="imageWidth">The total width of the image we want to track</param>
/// <param name="imageHeight">The total height of the image we want to track</param>
/// <param name="plate_index">This index is appended to the ROI file name to load file for proper plate</param>
/// <param name="parallelChunks">The number of parallel chunks to track</param>
public TrackerMultiWell(int imageWidth, int imageHeight, int plate_index, int parallelChunks = 2) : base(imageWidth, imageHeight)
{
_typicalFishLength = 30;
_trackMethod = TrackMethods.PerWell;//default to per-well tracking method
//Load ROIs - the following way to assess how many lines we have and hence how many
//ROIs we are dealing with is ugly but what the heck its quick to think up
_wellnumber = 0;
var assembly = Assembly.GetExecutingAssembly();
StreamReader roiStream = null;
string fileToOpen = string.Format("SleepTracker.ROI_defs_{0}.txt", plate_index);
//open for prescanning
var s = assembly.GetManifestResourceStream(fileToOpen);
roiStream = new StreamReader(s);
while (!roiStream.EndOfStream)
{
string line = roiStream.ReadLine();
string[] values = line.Split('\t');
if (values.Length == 4)
{
_wellnumber++;
}
}
roiStream.Dispose();
//reopen to load wells
s = assembly.GetManifestResourceStream(fileToOpen);
roiStream = new StreamReader(s);
_wells = new IppiROI[_wellnumber];
//we use the following hash-table to keep track of wells belonging
//to each row. This will give us the number of rows and their boundaries
//for later parallel chunk boundary determination as well as which wells
//should be tracked in which chunk
Dictionary <int, List <IppiROI> > wellsPerRow = new Dictionary <int, List <IppiROI> >();
Dictionary <int, int> columnStarts = new Dictionary <int, int>();
for (int i = 0; i < _wellnumber; i++)
{
System.Diagnostics.Debug.Assert(!roiStream.EndOfStream, "Unexpectedly reached end of ROI file");
string line = roiStream.ReadLine();
string[] values = line.Split('\t');
System.Diagnostics.Debug.Assert(values.Length == 4, "Found line in ROI file that does not contain 4 tab-separated strings");
int[] numValues = new int[4];
for (int j = 0; j < 4; j++)
{
numValues[j] = int.Parse(values[j]);
}
_wells[i] = new IppiROI(numValues[1], numValues[0], numValues[2], numValues[3]);
if (wellsPerRow.ContainsKey(_wells[i].Y))
{
wellsPerRow[_wells[i].Y].Add(_wells[i]);
}
else
{
//create a new list for this row and append our first well
wellsPerRow[_wells[i].Y] = new List <IppiROI>();
wellsPerRow[_wells[i].Y].Add(_wells[i]);
}
if (columnStarts.ContainsKey(_wells[i].X))
{
columnStarts[_wells[i].X]++;
}
else
{
columnStarts[_wells[i].X] = 1;
}
}
roiStream.Dispose();
//can't have more parallel regions than we have rows of wells
if (parallelChunks > wellsPerRow.Count)
{
parallelChunks = wellsPerRow.Count;
}
_allFish = new BlobWithMoments[_wellnumber];
//initialize our histogram bin boundaries (=histogram levels)
//the following assignment will allow us to study marker values from 0 to 254
//since: h[k] = countof(pLevels[k] <= pixels(x,y) < pLevels[k+1])
_histogramLevels = (int *)Marshal.AllocHGlobal(sizeof(int) * 256);
for (int i = 0; i < 256; i++)
{
_histogramLevels[i] = i;
}
_hist = (int *)Marshal.AllocHGlobal(sizeof(int) * 255);
//assume all wells have the same size
_wellCompare = new Image8(_wells[1].Size.width, _wells[1].Size.height);
_parallelChunks = parallelChunks;
//Initialize result array for parallel tracking
_parallelTrackResults = new BlobWithMoments[_wellnumber];
//Set up image regions for parallel tracking
_parallelImageRegions = new IppiROI[_parallelChunks];
//populate image regions and parallel buffers if _parallelChunks is larger 1
if (_parallelChunks > 1)
{
_parallelMarkerBuffers = new byte *[_parallelChunks];
_parallelMomentStates = new IppiMomentState_64s *[_parallelChunks];
//determine the number of rows in each chunk - integer division and last chunk get's the remainder tucked on
int nPerChunk = wellsPerRow.Count / _parallelChunks;
int nLastChunk = wellsPerRow.Count - (_parallelChunks - 1) * nPerChunk;
//obtain all our row-starting coordinates and sort ascending
var rowCoordinates = wellsPerRow.Keys.ToArray();
Array.Sort(rowCoordinates);
//do the same for column starting coordinates
var colCoordinates = columnStarts.Keys.ToArray();
Array.Sort(colCoordinates);
//Inititalize our parallel-well list array
_parallelChunkWells = new List <IppiROI> [_parallelChunks];
for (int i = 0; i < _parallelChunks; i++)
{
//for each chunk initialize it's well-list
_parallelChunkWells[i] = new List <IppiROI>();
int startRowInChunk = i * nPerChunk;
int endRowInChunk;
//are we dealing with the last chunk - this one potentially has a different number of rows!
if (i == _parallelChunks - 1)
{
endRowInChunk = startRowInChunk + nLastChunk - 1;
}
else
{
endRowInChunk = startRowInChunk + nPerChunk - 1;
}
//add all wells of this chunk to the list by looping over rows
//finding their start coordinate and using that to index into
//our dictionary. Then loop over the list in the dictionary
for (int j = startRowInChunk; j <= endRowInChunk; j++)
{
foreach (IppiROI wr in wellsPerRow[rowCoordinates[j]])
{
_parallelChunkWells[i].Add(wr);
}
}
//determine top-left corner as well as width and height of this chunk
int y_top = wellsPerRow[rowCoordinates[0]][0].Y;
int y_bottom = wellsPerRow[rowCoordinates[endRowInChunk]][0].Y + wellsPerRow[rowCoordinates[endRowInChunk]][0].Height - 1;
int height = y_bottom - y_top + 1;
System.Diagnostics.Debug.Assert(height > 1);
int x_left = colCoordinates[0];
int x_right = colCoordinates[colCoordinates.Length - 1] + wellsPerRow[rowCoordinates[0]][0].Width - 1;
int width = x_right - x_left + 1;
System.Diagnostics.Debug.Assert(width > 1);
_parallelImageRegions[i] = new IppiROI(x_left, y_top, width, height);
//Initialize marker buffer for this chunk
int bufferSize = 0;
IppHelper.IppCheckCall(cv.ippiLabelMarkersGetBufferSize_8u_C1R(_parallelImageRegions[i].Size, &bufferSize));
_parallelMarkerBuffers[i] = (byte *)Marshal.AllocHGlobal(bufferSize);
//initialize moment state for this chunk
fixed(IppiMomentState_64s **ppState = &_parallelMomentStates[i])
{
//let ipp decide whether to give accurate or fast results
IppHelper.IppCheckCall(ip.ippiMomentInitAlloc_64s(ppState, IppHintAlgorithm.ippAlgHintNone));
}
}
//determine each chunks start index in the fish output array based on the number of wells
//in lower chunks
_parallelCumWellCount = new int[_parallelChunks];
for (int i = 1; i < _parallelChunks; i++)
{
_parallelCumWellCount[i] = _parallelCumWellCount[i - 1] + _parallelChunkWells[i - 1].Count;
}
}
}
/// <summary>
/// Extracts a fish (candidate) from an image by performing background subtraction, noise filtering, thresholding and closing to obtain a foreground
/// followed by marker extraction.
/// </summary>
/// <param name="im">The image to extract the fish from</param>
/// <param name="region">The ROI to search</param>
/// <returns>The most likely fish blob or null if no suitable candidate was found</returns>
BlobWithMoments ExtractFish(Image8 im, IppiROI region)
{
int nMarkers = 0;
//Perform background subtraction - CASH BACKGROUND IMAGE POINTER - otherwise we actually do the whole costly
//32f conversion twice - once for accessing the actual image, and once for accessing the stride...
var bg = _bgModel.Background;
IppHelper.IppCheckCall(cv.ippiAbsDiff_8u_C1R(im[region.TopLeft], im.Stride, bg[region.TopLeft], bg.Stride, _calc[region.TopLeft], _calc.Stride, region.Size));
//remove noise via median filtering
_mFiltSize.width = region.Width - 2;
_mFiltSize.height = region.Height - 2;
IppHelper.IppCheckCall(ip.ippiFilterMedianWeightedCenter3x3_8u_C1R(_calc[region.X + 1, region.Y + 1], _calc.Stride,
_bgSubtracted[region.X + 1, region.Y + 1], _bgSubtracted.Stride, _mFiltSize, 1));
//Threshold and close
Im2Bw(_bgSubtracted, _foreground, region);
//Do as two step to get information back into _foreground
_strel3x3.Dilate(_foreground, _calc, region);
_strel3x3.Erode(_calc, _foreground, region);
//Label connected components
IppHelper.IppCheckCall(cv.ippiLabelMarkers_8u_C1IR(_foreground[region.TopLeft], _foreground.Stride, region.Size, 1, 254, IppiNorm.ippiNormInf, &nMarkers, _markerBuffer));
//loop over returned markers and use ipp to extract blobs
if (nMarkers > 0)
{
if (nMarkers > 254)
{
nMarkers = 254;
}
//create or update our intermediate blob storage to store the required number of marker representations
if (_blobsDetected == null || _blobsDetected.Length < nMarkers)
{
_blobsDetected = new BlobWithMoments[nMarkers];
}
for (int i = 1; i <= nMarkers; i++)
{
//label all pixels with the current marker as 255 and others as 0
IppHelper.IppCheckCall(ip.ippiCompareC_8u_C1R(_foreground[region.TopLeft], _foreground.Stride, (byte)i, _calc[region.TopLeft], _calc.Stride, region.Size, IppCmpOp.ippCmpEq));
//calculate image moments
IppHelper.IppCheckCall(ip.ippiMoments64f_8u_C1R(_calc[region.TopLeft], _calc.Stride, region.Size, _momentState));
//retrieve moments
double m00 = 0;
double m10 = 0;
double m01 = 0;
double m20 = 0;
double m02 = 0;
double m11 = 0;
double m30 = 0;
double m03 = 0;
double m21 = 0;
double m12 = 0;
ip.ippiGetSpatialMoment_64f(_momentState, 0, 0, 0, region.TopLeft, &m00);
//since our input image is not 0s and 1s but 0s and 255s we have to divide by 255 in order to re-normalize our moments
//System.Diagnostics.Debug.Assert(m00 % 255 == 0, "M00 was not a multiple of 255");
m00 /= 255;
//only retrieve other moments if this is a "fish candidate"
if (m00 >= MinArea)
{
ip.ippiGetSpatialMoment_64f(_momentState, 1, 0, 0, region.TopLeft, &m10);
m10 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 0, 1, 0, region.TopLeft, &m01);
m01 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 2, 0, 0, region.TopLeft, &m20);
m20 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 0, 2, 0, region.TopLeft, &m02);
m02 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 1, 1, 0, region.TopLeft, &m11);
m11 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 3, 0, 0, region.TopLeft, &m30);
m30 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 0, 3, 0, region.TopLeft, &m03);
m03 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 2, 1, 0, region.TopLeft, &m21);
m21 /= 255;
ip.ippiGetSpatialMoment_64f(_momentState, 1, 2, 0, region.TopLeft, &m12);
m12 /= 255;
if (_blobsDetected[i - 1] == null)
{
_blobsDetected[i - 1] = new BlobWithMoments((long)m00, (long)m10, (long)m01,
(long)m20, (long)m11, (long)m02, (long)m30, (long)m03, (long)m21, (long)m12);
}
else
{
_blobsDetected[i - 1].UpdateBlob((long)m00, (long)m10, (long)m01, (long)m20,
(long)m11, (long)m02, (long)m30, (long)m03, (long)m21, (long)m12);
}
//Determine bounding box of the blob. The following seems kinda retarded as Ipp must already
//have obtained that information before so maybe there is some way to actually retrieve it??
//Do linescans using ipp's sum function starting from the blobs centroid until we hit a line
//the sum of which is 0
int xStart, xEnd, yStart, yEnd;
double sum = 1;
IppiPoint centroid = _blobsDetected[i - 1].Centroid;
xStart = centroid.x - 1;
xEnd = centroid.x + 1;
yStart = centroid.y - 1;
yEnd = centroid.y + 1;
//in the following loops we PRE-increment, whence we stop the loop if we are at one coordinate short of the ends
//find xStart
_bboxScan.width = 1;
_bboxScan.height = region.Height;
while (sum > 0 && xStart > (region.X + 4))
{
xStart -= 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, region.Y], _calc.Stride, _bboxScan, &sum));
}
xStart += 1;//we have a sum of 0, so go back one line towards the centroid
//find xEnd
sum = 1;
while (sum > 0 && xEnd < region.X + region.Width - 5)
{
xEnd += 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xEnd, region.Y], _calc.Stride, _bboxScan, &sum));
}
xEnd -= 1;//we have sum of 0, so go back one line towards the centroid
//find yStart - we can limit our x-search-space as we already have those boundaries
_bboxScan.width = xEnd - xStart + 1;
_bboxScan.height = 1;
sum = 1;
while (sum > 0 && yStart > (region.Y + 4))
{
yStart -= 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, yStart], _calc.Stride, _bboxScan, &sum));
}
yStart += 1;
//find yEnd - again limit summation to x-search-space
sum = 1;
while (sum > 0 && yEnd < region.Y + region.Height - 5)
{
yEnd += 5;
IppHelper.IppCheckCall(ip.ippiSum_8u_C1R(_calc[xStart, yEnd], _calc.Stride, _bboxScan, &sum));
}
yEnd -= 1;
_blobsDetected[i - 1].UpdateBoundingBox(xStart, yStart, xEnd - xStart + 1, yEnd - yStart + 1);
}
else
{
if (_blobsDetected[i - 1] == null)
{
_blobsDetected[i - 1] = new BlobWithMoments();
}
else
{
_blobsDetected[i - 1].ResetBlob();
}
}
}
}
else
{
return(null);
}
//decide which of the detected objects is the fish
//usually we pick the larger blob - however to avoid
//tracking reflections on the wall, if the largest blob
//and second largest blob are of comparable size
//we pick the one which is closer to the center (as reflections
//are always more eccentric)
long maxArea = 0;
long secondMaxArea = 0;
int maxIndex = -1;
int secondMaxIndex = -1;
for (int i = 0; i < nMarkers; i++)
{
if (_blobsDetected[i] == null)
{
break;
}
//Note down the largest and second-largest blob - but only if those blobs aren't larger than the maxArea and if they eccentricity is at least MinEccentricity
//this comparison allows that if we find two exactly same-sized blobs to consider both but to not consider any further blobs of this size (which we hopefully never have anyways)
//Eccentricity and MaxAllowedArea checks removed at this point as they were mainly concieved to not track the laser.
if (_blobsDetected[i].Area >= maxArea && _blobsDetected[i].Area > secondMaxArea /*&& blobsDetected[i].Area<=MaxAllowedArea && blobsDetected[i].Eccentricity>=MinEccentricity*/)
{
secondMaxArea = maxArea;
maxArea = _blobsDetected[i].Area;
secondMaxIndex = maxIndex;
maxIndex = i;
}
}
if (maxArea < MinArea)
{
return(null);
}
else
{
//if our second-largest blob is at least two-thirds the size
//of the largest blob we also consider distance and swap accordingly
if ((float)secondMaxArea * 1.5 >= (float)maxArea)
{
double distMax, distSecondMax;
distMax = Distance.Euclidian(_blobsDetected[maxIndex].Centroid, DishCenter);
distSecondMax = Distance.Euclidian(_blobsDetected[secondMaxIndex].Centroid, DishCenter);
if (distMax > distSecondMax)
{
maxIndex = secondMaxIndex;
}
}
return(_blobsDetected[maxIndex]);
}
}
/// <summary>
/// Implements a "greater than" threshold like MATLABS
/// im2bw function
/// </summary>
/// <param name="imIn">The image to threshold</param>
/// <param name="imThresh">The image after thresholding</param>
/// <param name="region">The ROI in which to perform the operation</param>
/// <param name="threshold">The threshold to apply</param>
void Im2Bw(Image8 imIn, Image8 imThresh, IppiROI region)
{
IppHelper.IppCheckCall(ip.ippiCompareC_8u_C1R(imIn[region.TopLeft], imIn.Stride, _threshold, imThresh[region.TopLeft], imThresh.Stride, region.Size, IppCmpOp.ippCmpGreater));
}
/// <summary>
/// Tracks the tailsegments on the supplied image and returns
/// the angles and distances of each segment from the tailstart
/// </summary>
/// <param name="image">The image on which to id the tail</param>
/// <returns>NSegments number of TailPoints</returns>
public TailSegment[] TrackTail(Image8 image)
{
lock (_regionLock)
{
//CURRENTLY ONLY DOWNWARD FACING TAILS ARE PROPERLY VERIFIED!!!
//Generate background by morphology operation - 10 times a second or whenever our coordinates changed
//in the default case where the tail is darker than the background, using closing operation otherwise opening
if (_frameNumber % (_frameRate / 10) == 0 || !_bgValid)
{
if (!_bgValid)
{
//if our regions changed, reblank our images!
ip.ippiSet_8u_C1R(0, _background.Image, _background.Stride, _background.Size);
ip.ippiSet_8u_C1R(0, _foreground.Image, _foreground.Stride, _foreground.Size);
ip.ippiSet_8u_C1R(0, _thresholded.Image, _thresholded.Stride, _thresholded.Size);
}
if (_lightOnDark)
{
BWImageProcessor.Open(image, _background, _calc1, _strel, _trackRegionOuter);
}
else
{
BWImageProcessor.Close(image, _background, _calc1, _strel, _trackRegionOuter);
}
_bgValid = true;
}
//Compute foreground
IppHelper.IppCheckCall(cv.ippiAbsDiff_8u_C1R(_background[_trackRegionInner.TopLeft], _background.Stride, image[_trackRegionInner.TopLeft], image.Stride, _foreground[_trackRegionInner.TopLeft], _foreground.Stride, _trackRegionInner.Size));
//Threshold
BWImageProcessor.Im2Bw(_foreground, _thresholded, _trackRegionInner, _threshold);
//Fill small holes
BWImageProcessor.Close3x3(_thresholded, _thresholded, _calc1, _trackRegionOuter);
}
//Tracking concept: We track the angle of each segment end (TailStart+SegmentLength:TailEnd)
//as the angular displacement from the previous segment end
//To do this we define one full-circle with radius SegmentLength and an angle step corresponding
//to ~1 Pixel. Then for each angle we pre-compute in InitializeScanPoints the corresponding x
//and y offsets. From the full circle set we track -90 to +90 degrees around the angle of the
//previous segment - for the initial segment that angle will be 0. For each segment we will return
//the segment angle and its associated end-point coordinate
var retval = new TailSegment[_nSegments];
lock (_scanPointLock)
{
//The index of the absolute angle of the previous segment in our angle sweep array
//determines which angles we sweep over for the next segment
int prevAngleIndex = _scanAngles.Length / 2;
int nAnglesPerHalfPi = prevAngleIndex / 2;//this is the number of entries in the array that we have to walk to cover 90 degrees
//we scan beginning with one segment length away from tail start and then walk
//down the tail rather than using circles fixed arount the tailstart
IppiPoint prevSegmentEnd = TailStart;
//loop over tail segments
for (int i = 0; i < _nSegments; i++)
{
//loop over scan-points from -pi/2 to +pi/2 (i.e. nAnglesPerHalfPi) around previous segment angle
//interpreting the scan points as offsets around the previous tail segment
//end point
//then find tail angle of this segment
int pointsFound = 0;//the number of non-zero pixels identified
for (int j = -1 * nAnglesPerHalfPi; j < nAnglesPerHalfPi + 1; j++)
{
//Determine the index to scan - usually this will simply be "prevAngleIndex+j" however we
//have to loop around our angle array properly in case we screen more extreme angles
int currIndex = prevAngleIndex + j;
if (currIndex >= _scanAngles.Length)
{
currIndex = currIndex % _scanAngles.Length;
}
else if (currIndex < 0)
{
currIndex = currIndex + _scanAngles.Length;
}
//If current point is outside of the image, ignore it
IppiPoint pt = new IppiPoint(_coordinateOffsets[currIndex].x + prevSegmentEnd.x, _coordinateOffsets[currIndex].y + prevSegmentEnd.y);
if (pt.x < 0 || pt.y < 0 || pt.x >= _imageSize.width || pt.y >= _imageSize.height)
{
continue;
}
//if the value at the current point >0 we mark that angle as valid
//by storing the index in our anglestore
if (*_thresholded[pt] > 0)
{
_angleStore[pointsFound] = currIndex;
pointsFound++;
}
}
//find the median point in our angle store if we have more than 2 points stored
//the value in our angle store will directly give us the absolute screen angle of the segment
//as well as the coordinate offset which we can used together with the previous segment endpoint
//to compute the tail segment end coordinate - to get the delta angle we need to get the difference
//between the stored index and the previously stored index, prevAngleIndex
//after computing the appropriate return values we update prevAngleIndex with the index from the angle store
//and prevSegmentEnd with the returned coordinate of the current tail segment
double deltaTailAngle;
IppiPoint coordinate;
int pos; //the index in the angle store that we determine to be the tail-center
if (pointsFound == 0) //we have lost the tail - no reason to keep tracking - fill remaining positions in array with NaNs for their angle
{
for (int k = i; k < _nSegments; k++)
{
deltaTailAngle = double.NaN;
coordinate = new IppiPoint();
retval[k] = new TailSegment(deltaTailAngle, coordinate);
}
break;
}
else if (pointsFound < 3)
{
pos = _angleStore[0];
}
else
{
//we want the angle at the median position of valid points
//we don't compute intermediate positions however (we should be able to afford this since our angle step is so small), so in case
//of an even number of points, the top of the lower half currently
//wins - since array indexing is zero based, we have to subtract 1
//from the computed median position
pos = _angleStore[(int)(Math.Ceiling(pointsFound / 2.0) - 1)];
}
coordinate = new IppiPoint(prevSegmentEnd.x + _coordinateOffsets[pos].x, prevSegmentEnd.y + _coordinateOffsets[pos].y);
deltaTailAngle = (pos - prevAngleIndex) * _angleStep;
//the condition above of wrapping around the "angle circle":if (currIndex >= _scanAngles.Length)....
//results in one very large (close to +360 or -360) angle of opposite sign at the switch point
//however, since we usually only scan over offsets from +90 to -90 this case is easy to spot
//and remedy:
if (deltaTailAngle > 90)
{
deltaTailAngle = deltaTailAngle - 360;//this should create the appropriate tail angle btw. 0 and -90
}
else if (deltaTailAngle < -90)
{
deltaTailAngle = 360 + deltaTailAngle;//this should create the appropriate tail angle btw. 0 and +90
}
prevAngleIndex = pos;
prevSegmentEnd = coordinate;
retval[i] = new TailSegment(deltaTailAngle, coordinate);
}//loop over tail segments
}
_frameNumber++;
return(retval);
}
/// <summary>
/// Implements coordinate smoothing analogous to using filtfilt in matlab with a step function kernel
/// (moving average with no peak displacement)
/// </summary>
/// <param name="src">The source track to smoothen</param>
/// <param name="dst">The destination buffer for the smoothened track</param>
/// <param name="windowSize">The windowsize for averaging</param>
public void SmoothenTrack(CentroidBuffer src, CentroidBuffer dst, int windowSize)
{
if (IsDisposed)
{
throw new ObjectDisposedException(this.ToString());
}
if (src.Size.width != dst.Size.width)
{
throw new ArgumentException("Source and destination buffers need to have the same size!");
}
//For the internal buffers we require a size that fits both the coordinate buffer we
//intend to filter as well as the border pixels required for filtering
int borderSize = (int)Math.Ceiling(windowSize / 2.0);
int reqSize = src.Size.width + borderSize * 2;
//Adjust internal buffers if necessary
if (_calc1 == null)
{
_calc1 = new CentroidBuffer(reqSize);
_calc2 = new CentroidBuffer(reqSize);
}
else if (_calc1.Size.width != reqSize)
{
_calc1.Dispose();
_calc2.Dispose();
_calc1 = new CentroidBuffer(reqSize);
_calc2 = new CentroidBuffer(reqSize);
}
if (_kernel == null)
{
_kernelSize = windowSize;
_kernel = (float *)Marshal.AllocHGlobal(_kernelSize * 4);
int i = 0;
while (i < _kernelSize)
{
_kernel[i++] = 1 / (float)_kernelSize;
}
}
else if (_kernelSize != windowSize)
{
Marshal.FreeHGlobal((IntPtr)_kernel);
_kernelSize = windowSize;
_kernel = (float *)Marshal.AllocHGlobal(_kernelSize * 4);
int i = 0;
while (i < _kernelSize)
{
_kernel[i++] = 1 / (float)_kernelSize;
}
}
//filter parameters
IppiSize regionSize = new IppiSize(src.Size.width, 1);
IppiPoint anchor = new IppiPoint(borderSize, 0);
IppiSize kernelSize = new IppiSize(_kernelSize, 1);
float * calc1XStart = (float *)((byte *)_calc1.Buffer + borderSize * 4);
float * calc1YStart = (float *)((byte *)_calc1.Buffer + borderSize * 4 + _calc1.Stride);
float * calc2XStart = (float *)((byte *)_calc2.Buffer + borderSize * 4);
float * calc2YStart = (float *)((byte *)_calc2.Buffer + borderSize * 4 + _calc2.Stride);
//Copy src buffer adding borders
IppHelper.IppCheckCall(ip.ippiCopyConstBorder_32f_C1R(src.Buffer, src.Stride, src.Size, _calc1.Buffer, _calc1.Stride, _calc1.Size, 0, borderSize, 0));
//Fill calc2 to have borders ready after filtering
IppHelper.IppCheckCall(ip.ippiSet_32f_C1R(0, _calc2.Buffer, _calc2.Stride, _calc2.Size));
//filter x-coordinates with our kernel
IppHelper.IppCheckCall(ip.ippiFilter_32f_C1R(calc1XStart, _calc1.Stride, calc2XStart, _calc2.Stride, regionSize, _kernel, kernelSize, anchor));
//filter y-coordinates with our kernel
IppHelper.IppCheckCall(ip.ippiFilter_32f_C1R(calc1YStart, _calc1.Stride, calc2YStart, _calc2.Stride, regionSize, _kernel, kernelSize, anchor));
//invert buffer - mirror on vertical axis
IppHelper.IppCheckCall(ip.ippiMirror_32f_C1R(_calc2.Buffer, _calc2.Stride, _calc1.Buffer, _calc1.Stride, _calc2.Size, IppiAxis.ippAxsVertical));
//filter x-coordinates with our kernel - now on inverted buffer
IppHelper.IppCheckCall(ip.ippiFilter_32f_C1R(calc1XStart, _calc1.Stride, calc2XStart, _calc2.Stride, regionSize, _kernel, kernelSize, anchor));
//filter y-coordinates with our kernel - now on inverted buffer
IppHelper.IppCheckCall(ip.ippiFilter_32f_C1R(calc1YStart, _calc1.Stride, calc2YStart, _calc2.Stride, regionSize, _kernel, kernelSize, anchor));
//flip buffer back
IppHelper.IppCheckCall(ip.ippiMirror_32f_C1R(_calc2.Buffer, _calc2.Stride, _calc1.Buffer, _calc1.Stride, _calc2.Size, IppiAxis.ippAxsVertical));
//copy to dest
IppHelper.IppCheckCall(ip.ippiCopy_32f_C1R(calc1XStart, _calc1.Stride, dst.Buffer, dst.Stride, dst.Size));
}