/// <summary>
/// Execute segmentation process of inner structures.
/// </summary>
public void Execute()
{
if (image != null)
{
Image <Bgr, byte> maskedImage = new Image <Bgr, byte>(image.Width, image.Height, new Bgr(255, 255, 255));
CvInvoke.cvCopy(image, maskedImage, particleMask);
Console.WriteLine("Image dimensions: " + image.Width + " / " + image.Height);
Console.WriteLine("Masked Image dimensions: " + maskedImage.Width + " / " + maskedImage.Height);
UMat temp = SegmentationUtils.IncreaseContrast(maskedImage.ToUMat(), 5.0, 8);
temp = SegmentationUtils.Blur(temp, 3, 1.0);
temp = SegmentationUtils.Sharp(temp);
Image <Bgr, byte> tempImage = new Image <Bgr, byte>(temp.Bitmap);
UMat uMatChannel = SegmentationUtils.GetColorChannelAsUMat(segmentationParameters.Colorspace, tempImage, segmentationParameters.Channel);
if (segmentationParameters.UseKmeans)
{
KmeansSegmentation(uMatChannel);
}
else
{
StandardSegmentation(uMatChannel);
}
}
}
/// <summary>
/// Execute segmentation process.
/// </summary>
public void Execute()
{
if (image != null)
{
UMat temp = SegmentationUtils.IncreaseContrast(image.ToUMat(), 5.0, 8);
temp = SegmentationUtils.Blur(temp, 3, 1.0);
temp = SegmentationUtils.Sharp(temp);
Image <Bgr, byte> tempImage = new Image <Bgr, byte>(temp.Bitmap);
UMat uMatChannel = SegmentationUtils.GetColorChannelAsUMat(segmentationParameters.Colorspace, tempImage, segmentationParameters.Channel);
UMat thresholded = null;
using (UMat copy = uMatChannel.Clone())
{
if (segmentationParameters.UseOtsu)
{
thresholded = SegmentationUtils.ThresholdOtsu(copy);
}
else
{
thresholded = SegmentationUtils.Threshold(copy, segmentationParameters.Threshold);
}
}
UMat closed = SegmentationUtils.Closing(thresholded, 5);
//UMat eroded = SegmentationUtils.Erode(closed, 15);
UMat dilated = SegmentationUtils.Dilate(closed, 10);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\dilated.png", dilated);
VectorOfVectorOfPoint contours = new VectorOfVectorOfPoint();
VectorOfVectorOfPoint contoursRelevant = new VectorOfVectorOfPoint();
CvInvoke.FindContours(dilated, contours, null, RetrType.External, ChainApproxMethod.ChainApproxSimple);
int autoMaxPixelSize = ImageUtils.GetPercentualImagePixelCount(image, 0.03f);
for (int i = 0; i < contours.Size; i++)
{
double area = CvInvoke.ContourArea(contours[i]);
if (IsContourRelevant(area, autoMaxPixelSize, segmentationParameters))
{
contoursRelevant.Push(contours[i]);
}
}
CvInvoke.DrawContours(image, contoursRelevant, -1, new MCvScalar(0, 0, 255));
mask = new Image <Gray, Byte>(image.Width, image.Height, new Gray(0.0));
CvInvoke.DrawContours(mask, contoursRelevant, -1, new MCvScalar(255.0), thickness: -1);
}
}
/// <summary>
/// Kmeans segmentation of given image.
/// 1. Do a kmeans clustering
/// 2. Find contours
/// 3. Classification of clusters (?)
/// </summary>
/// <param name="uMatChannel"></param>
private void KmeansSegmentation(UMat uMatChannel)
{
if (false)
{
Image <Bgr, byte> newImage = new Image <Bgr, byte>(uMatChannel.Bitmap);
Image <Bgr, byte> clusteredImage = SegmentationUtils.KMeansClustering <Bgr, byte, byte>(newImage.Clone(), 3, SegmentationUtils._clusterColors);
ReadWriteUtils.WriteUMatToFile(@"D:\testdata\_temp\kmeans.png", clusteredImage.ToUMat());
// TODO
// Find contours
// Classificate contours
}
throw new NotImplementedException();
}
/// <summary>
/// Standard segmentation of given image.
/// 1. Thresholding
/// 2. Morphological operations
/// 3. Find contours
/// 4. Calculate coefficients and classificate contours
/// </summary>
/// <param name="uMatChannel">image in UMat format</param>
private void StandardSegmentation(UMat uMatChannel)
{
// thresholding
UMat thresholded = null;
using (UMat copy = uMatChannel.Clone())
{
if (segmentationParameters.UseOtsu)
{
thresholded = SegmentationUtils.ThresholdOtsu(copy);
}
else
{
thresholded = SegmentationUtils.Threshold(copy, segmentationParameters.Threshold);
}
}
// morphological operations (todo: make kernel generic or depending on image size)
UMat opened = SegmentationUtils.Opening(thresholded, 5);
UMat dilated = SegmentationUtils.Dilate(opened, 5);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\dilated.png", dilated);
UMat inverted = new UMat();
CvInvoke.BitwiseNot(dilated, inverted);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\inverted.png", inverted);
VectorOfVectorOfPoint contours = new VectorOfVectorOfPoint();
VectorOfVectorOfPoint contoursRelevant = new VectorOfVectorOfPoint();
CvInvoke.FindContours(inverted, contours, null, RetrType.Ccomp, ChainApproxMethod.ChainApproxSimple);
int nonRelevantPixelSize = ImageUtils.GetPercentualImagePixelCount <UMat>(inverted, 0.005f);
Console.WriteLine("Non relevant pixel size: " + nonRelevantPixelSize);
Console.WriteLine("Number of contours: " + contours.Size);
ClassifyContours(uMatChannel, ref contours, ref contoursRelevant, nonRelevantPixelSize);
// debug: show image with found contours
//CvInvoke.DrawContours(image, contoursRelevant, -1, new MCvScalar(0, 255, 0));
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\image_with_contours.png", image.ToUMat());
// creat mask with rigid structures
Image <Gray, byte> mask = new Image <Gray, byte>(image.Width, image.Height, new Gray(0.0));
CvInvoke.DrawContours(mask, contoursRelevant, -1, new MCvScalar(255.0), thickness: -1);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\mask.png", mask.ToUMat());
UMat inv1 = new UMat();
CvInvoke.BitwiseNot(mask, inv1);
UMat convertedMask = new UMat();
inv1.ConvertTo(convertedMask, DepthType.Cv32F);
// create mask with non rigid structures
Image <Gray, byte> convMask = new Image <Gray, byte>(convertedMask.Bitmap);
Image <Gray, byte> mask2 = new Image <Gray, byte>(image.Width, image.Height, new Gray(255.0));
CvInvoke.Subtract(particleMask, convMask, mask2);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\INV_mask.png", mask2.ToUMat());
UMat inv2 = new UMat();
//CvInvoke.BitwiseNot(mask2, inv2);
CvInvoke.BitwiseAnd(mask2, mask, inv2);
inv2 = SegmentationUtils.Dilate(inv2, 10);
UMat convertedMask2 = new UMat();
inv2.ConvertTo(convertedMask2, DepthType.Cv32F);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\_mask1.png", convertedMask);
//ReadWriteUtils.WriteUMatToFile(ApplicationContext.OutputPath + "\\_mask2.png", convertedMask2);
// add masks to list
masks.Add(convertedMask);
masks.Add(convertedMask2);
}
