/// <summary>
/// Get the coefficient map of inner structures of tissue for the transform rigidity penalty term.
/// </summary>
/// <param name="filename">image filename</param>
/// <returns>return coefficient map filename</returns>
private string GetInnerStructureSegmentationsAsCoefficientMap(string filename)
{
InnerTissueSegmentation innerSegImage = GetInnerStructureSegmentation(filename);
string filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteUMatToFile(filenameCoefficientMap, innerSegImage.GetOutput().FirstOrDefault());
innerSegImage.Dispose();
// rescale image
sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(filenameCoefficientMap);
sitk.CastImageFilter castFilter = new sitk.CastImageFilter();
castFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkFloat32);
img = castFilter.Execute(img);
sitk.RescaleIntensityImageFilter filter = new sitk.RescaleIntensityImageFilter();
filter.SetOutputMinimum(0.0);
filter.SetOutputMaximum(1.0);
sitk.Image coefficientMap = filter.Execute(img);
// save as mhd
filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteSitkImage(coefficientMap, filenameCoefficientMap);
coefficientMap.Dispose();
return(filenameCoefficientMap);
}
/// <summary>
/// Get filename of the inner structures mask of an image.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>filename of the masked image</returns>
private string GetInnerStructureSegmentationFilename(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
InnerTissueSegmentation seg = GetInnerStructureSegmentation(filename);
seg.GetOutput()[1].Save(filename);
seg.Dispose();
return(filename);
}
/// <summary>
/// Get image of the inner structures mask of an image.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>masked image</returns>
private sitk.Image GetInnerStructureMask(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
InnerTissueSegmentation seg = GetInnerStructureSegmentation(filename);
seg.GetOutput()[1].Save(outputFilename);
seg.Dispose();
sitk.Image mask = ReadWriteUtils.ReadITKImageFromFile(outputFilename);
return(mask);
}
private string DoInnerTissueSegmentation(Image <Bgr, byte> img, Image <Gray, byte> mask, string filename)
{
InnerTissueSegmentation seg = new InnerTissueSegmentation(img.Clone(), mask.Clone(), registrationParameters.InnerStructuresSegParams);
seg.Execute();
UMat innerMask = seg.GetOutput()[0].Clone();
seg.Dispose();
string filepathResult = registrationParameters.OutputDirectory + filename;
ReadWriteUtils.WriteUMatToFile(filepathResult, innerMask);
return(filepathResult);
}
/// <summary>
/// Do segmentation of inner structures of the tissue for a given image.
/// </summary>
/// <param name="filename">image filename</param>
/// <param name="parameters">registration parameters containing segmentation params</param>
/// <returns>returns the segmentation instance</returns>
private InnerTissueSegmentation GetInnerStructureSegmentation(string filename)
{
Image <Bgr, byte> image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(filename);
WholeTissueSegmentation segImage = new WholeTissueSegmentation(image, _parameters.WholeTissueSegParams);
segImage.Execute();
Image <Gray, byte> wholeMask = segImage.GetOutput().Clone();
segImage.Dispose();
InnerTissueSegmentation innerSegImage = new InnerTissueSegmentation(image, wholeMask, _parameters.InnerStructuresSegParams);
innerSegImage.Execute();
return(innerSegImage);
}
private void buttonPreview_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
if (image != null)
{
WholeTissueSegmentation segImage = new WholeTissueSegmentation(image, segmentationParametersWholeTissue);
segImage.Execute();
Image <Gray, byte> mask = segImage.GetOutput().Clone();
segImage.Dispose();
if (mask != null)
{
InnerTissueSegmentation seg = new InnerTissueSegmentation(image.Clone(), mask.Clone(), segmentationParametersInnerTissue);
seg.Execute();
List <UMat> result = seg.GetOutput();
UMat a = new UMat();
result[0].Clone().ConvertTo(a, Emgu.CV.CvEnum.DepthType.Cv8U);
UMat b = new UMat();
result[1].Clone().ConvertTo(b, Emgu.CV.CvEnum.DepthType.Cv8U);
seg.Dispose();
if (pictureBoxSegmentation1.Image != null)
{
this.Invoke(new MethodInvoker(delegate() {
pictureBoxSegmentation1.Image.Dispose();
pictureBoxSegmentation1.Image = null;
}));
}
pictureBoxSegmentation1.Image = a.Bitmap;
if (pictureBoxSegmentation2.Image != null)
{
this.Invoke(new MethodInvoker(delegate() {
pictureBoxSegmentation2.Image.Dispose();
pictureBoxSegmentation2.Image = null;
}));
}
pictureBoxSegmentation2.Image = b.Bitmap;
}
}
Cursor.Current = Cursors.Default;
}
