public SegParamsInnerStructuresForm(List <string> imageFilenames, SegmentationParameters parametersWholeTissue, SegmentationParameters parametersInnerTissue)
{
InitializeComponent();
this.filenames = imageFilenames;
this.selectedFile = imageFilenames.FirstOrDefault();
this.image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(this.selectedFile);
this.segmentationParametersInnerTissue = parametersInnerTissue;
this.segmentationParametersWholeTissue = parametersWholeTissue;
}
private void buttonCalcCoef_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
string fixedImageFilename = registrationParameters.FixedImageFilename;
string movingImageFilename = comboBoxMovingImage.SelectedValue.ToString();
bool isInnerSeg = comboBoxSegmentationParams.SelectedIndex == 1;
// read images
Image <Bgr, byte> img01 = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(fixedImageFilename);
Image <Bgr, byte> img02 = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(movingImageFilename);
// whole particle seg
Image <Gray, byte> mask01w;
string mask01wFn = DoWholeTissueSegmentation(img01, out mask01w, "\\mask01w.png");
Image <Gray, byte> mask02w;
string mask02wFn = DoWholeTissueSegmentation(img02, out mask02w, "\\mask02w.png");
sitk.LabelOverlapMeasuresImageFilter overlapFilter = null;
if (isInnerSeg)
{
string mask01iFn = DoInnerTissueSegmentation(img01, mask01w, "\\mask01i.png");
string mask02iFn = DoInnerTissueSegmentation(img02, mask02w, "\\mask02i.png");
overlapFilter = GetOverlapImageFilter(mask01iFn, mask02iFn);
DeleteFile(mask01iFn);
DeleteFile(mask02iFn);
}
else
{
overlapFilter = GetOverlapImageFilter(mask01wFn, mask02wFn);
}
if (overlapFilter != null)
{
double diceCoef = overlapFilter.GetDiceCoefficient();
double falseNegative = overlapFilter.GetFalseNegativeError();
double falsePositive = overlapFilter.GetFalsePositiveError();
double jaccard = overlapFilter.GetJaccardCoefficient();
double meanOverlap = overlapFilter.GetMeanOverlap();
double unionOverlap = overlapFilter.GetUnionOverlap();
labelDice.Text = diceCoef.ToString("0.###");
labelJacc.Text = jaccard.ToString("0.###");
labelfalseNegPos.Text = string.Format("{0} / {1}", falseNegative.ToString("0.###"), falsePositive.ToString("0.###"));
labelMeanOverlap.Text = meanOverlap.ToString("0.###");
labelUnionOverlap.Text = unionOverlap.ToString("0.###");
}
DeleteFile(mask01wFn);
DeleteFile(mask02wFn);
Cursor.Current = Cursors.Default;
}
public SegParamsWholeTissueForm(List <string> imageFilnames, SegmentationParameters parameters)
{
InitializeComponent();
this.segmentationParameters = parameters;
this.filenames = imageFilnames;
this.selectedFile = imageFilnames.FirstOrDefault();
this.image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(this.selectedFile);
InitializeButtons();
}
private string GetWholeParticleMaskFilename(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
Image <Bgr, byte> image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(filename);
WholeTissueSegmentation segImage = new WholeTissueSegmentation(image, _parameters.WholeTissueSegParams);
segImage.Execute();
segImage.GetOutput().Save(outputFilename);
segImage.Dispose();
return(outputFilename);
}
private void buttonNextSlice_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
int index = filenames.IndexOf(selectedFile) + 1;
selectedFile = filenames.ElementAt(index);
image.Dispose();
image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(selectedFile);
ReloadForm();
buttonPreviousSlice.Enabled = index > 0;
buttonNextSlice.Enabled = index < filenames.Count - 1;
Cursor.Current = Cursors.Default;
}
/// <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);
}