public override ProcessResult Execute(ProcessExecutionParams p)
{
GrayscaleProcessor gpH = new ColorDeconvolution().Get1stStain(p.Bitmap, ColorDeconvolution.KnownStain.HaematoxylinEosin);
GrayscaleProcessor gp = new GrayscaleProcessor(p.Bitmap, RgbToGrayscaleConversion.JustReds);
GrayscaleProcessor gpSobel = (GrayscaleProcessor)gp.Clone();
new MeanFilter().Execute(gp, new Size(3, 3));
new SobelEdgeDetector().Execute(gpSobel);
new MinimumFilter().Execute(gpH, new Size(3, 3));
new PixelInverter().Execute(gpH);
ObjectLayer l1stLevel = this.Execute1stLevelSegmentation(gp, gpSobel, gpH);
float targetArea = this.GetTargetArea(l1stLevel);
ObjectLayer l2ndLevel = this.Execute2ndLevelSegmentation(gp, gpSobel, gpH, targetArea);
ObjectLayer l3rdLevel = this.Execute3rdLevelSegmentation(l2ndLevel, gpSobel, gpH, targetArea);
gpSobel.WriteBack = false;
gpH.WriteBack = false;
gp.WriteBack = false;
gpSobel.Dispose();
gpH.Dispose();
gp.Dispose();
gpSobel.Bitmap.Dispose();
gpH.Bitmap.Dispose();
l3rdLevel.Name = "Image Analysis";
return(new ProcessResult(new ObjectLayer[] { l3rdLevel }));
}
public override ProcessResult Execute(ProcessExecutionParams p)
{
GrayscaleProcessor gpH = new ColorDeconvolution().Get1stStain(p.Bitmap, ColorDeconvolution.KnownStain.HaematoxylinEosin);
GrayscaleProcessor gp = new GrayscaleProcessor(p.Bitmap, RgbToGrayscaleConversion.JustReds);
GrayscaleProcessor gpSobel = (GrayscaleProcessor)gp.Clone();
new MeanFilter().Execute(gp, new Size(3, 3));
new SobelEdgeDetector().Execute(gpSobel);
new MinimumFilter().Execute(gpH, new Size(3, 3));
new PixelInverter().Execute(gpH);
ObjectLayer l1stLevel = this.Execute1stLevelSegmentation(gp, gpSobel, gpH);
float targetArea = this.GetTargetArea(l1stLevel);
ObjectLayer l2ndLevel = this.Execute2ndLevelSegmentation(gp, gpSobel, gpH, targetArea);
ObjectLayer l3rdLevel = this.Execute3rdLevelSegmentation(l2ndLevel, gpSobel, gpH, targetArea);
gpSobel.WriteBack = false;
gpH.WriteBack = false;
gp.WriteBack = false;
gpSobel.Dispose();
gpH.Dispose();
gp.Dispose();
gpSobel.Bitmap.Dispose();
gpH.Bitmap.Dispose();
l3rdLevel.Name = "Image Analysis";
return new ProcessResult(new ObjectLayer[] { l3rdLevel });
}
protected override void OnLoad(EventArgs e)
{
base.OnLoad(e);
this.CreateTabContainer("StromaDetection");
this.TabContainer.Enabled = true;
(new Button
{
Text = "execute cell core segmentation",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.DisplayedImage) return;
ProcessResult result = null;
var progressDialog = new ProgressDialog { Message = "executing cell core segmentation", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false };
progressDialog.BackgroundTask += () =>
{
var segmentation = new CellCoreSegmentation();
var executionParams = new ProcessExecutionParams(this.DisplayedImage);
result = segmentation.Execute(executionParams);
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
this.SetLayers(result.Layers.ToArray());
};
(new Button
{
Text = "execute threshold segmentation",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.DisplayedImage) return;
var m = new Map(this.DisplayedImage.Width, this.DisplayedImage.Height);
using (var gp = new GrayscaleProcessor(this.DisplayedImage.Clone() as Bitmap, RgbToGrayscaleConversion.Mean))
{
for (var x = 0; x < this.DisplayedImage.Width; x++)
{
for (var y = 0; y < this.DisplayedImage.Height; y++)
{
m[x, y] = gp.GetPixel(x, y) < this.threshold.Value ? 1u : 0u;
}
}
}
var layer = new ConnectedComponentCollector().Execute(m);
layer.Name = "threshold " + this.threshold.Value + " segmentation";
var layers = this.GetLayers().ToList();
layers.Add(layer);
this.SetLayers(layers.ToArray());
};
this.threshold = new NumericUpDown
{
Parent = new GroupBox
{
Parent = this.TabContainer,
Dock = DockStyle.Top,
Text = "threshold",
Height = 40
},
Dock = DockStyle.Fill,
Minimum = 0,
Maximum = 255,
Increment = 16,
Value = 128,
DecimalPlaces = 0
};
(new Button
{
Text = "display edges",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
this.SetDisplayedImage(this.edges);
};
(new Button
{
Text = "execute edge detection",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.stainH || null == this.stainE) return;
this.responseH = Filtering.ExecuteSobel(this.stainH);
this.responseE = Filtering.ExecuteSobel(this.stainE);
var substracted = new double[this.responseH.Size.Width, this.responseH.Size.Height];
var substractedRange = new Range<double>();
for (var x = 0; x < this.responseH.Size.Width; x++)
{
for (var y = 0; y < this.responseH.Size.Height; y++)
{
var value = Math.Max(0, this.responseE.Gradient[x, y] - this.responseH.Gradient[x, y]);
substracted[x, y] = value;
substractedRange.Add(value);
}
}
this.nonMaximumSupression = Filtering.ExecuteNonMaximumSupression(substracted, this.responseE.Orientation);
this.edges = Visualization.Visualize(this.nonMaximumSupression, Visualization.CreateColorizing(substractedRange.Maximum));
this.SetDisplayedImage(this.edges);
};
(new Button
{
Text = "display haematoxylin",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
this.SetDisplayedImage(this.stainH);
};
(new Button {
Text = "display eosin",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
this.SetDisplayedImage(this.stainE);
};
(new Button {
Text = "display source",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
this.SetDisplayedImage(this.source);
};
(new Button {
Text = "execute deconvolution",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.DisplayedImage) return;
this.source = this.DisplayedImage;
var gpE = new ColorDeconvolution().Get2ndStain(this.DisplayedImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
gpE.Dispose();
this.stainE = gpE.Bitmap;
var gpH = new ColorDeconvolution().Get1stStain(this.DisplayedImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
gpH.Dispose();
this.stainH = gpH.Bitmap;
this.SetDisplayedImage(this.stainE);
};
}
public override ProcessResult Execute(ProcessExecutionParams p)
{
GrayscaleProcessor gp = new GrayscaleProcessor(new Bitmap(p.Bitmap), RgbToGrayscaleConversion.None);
BitmapProcessor bp = new BitmapProcessor(p.Bitmap.Clone() as Bitmap);
for (int dy = 0; dy < gp.Height; dy++)
{
for (int dx = 0; dx < gp.Width; dx++)
{
int pixel = (int)bp.GetPixel(dx, dy);
int r = (pixel & 0x00ff0000) >> 16;
int g = (pixel & 0x0000ff00) >> 08;
int b = (pixel & 0x000000ff) >> 00;
int max = Math.Max(Math.Max(r, g), b);
int min = Math.Min(Math.Min(r, g), b);
int range = max - min;
int level = (r + g + b) / 3;
int val = level - range;
if (val > 255)
{
val = 255;
}
if (val < 0)
{
val = 0;
}
gp.SetPixel(dx, dy, (UInt32)level);
}
}
GrayscaleProcessor gpSobel = (GrayscaleProcessor)gp.Clone();
new SobelEdgeDetector().Execute(gpSobel);
ObjectLayer l1stLevel = Execute1stLevelSegmentation(gp, gpSobel);
ObjectLayer l2ndLevel = Execute2ndLevelSegmentation(l1stLevel, gp);
gpSobel.WriteBack = false;
gp.WriteBack = false;
gpSobel.Dispose();
gp.Dispose();
bp.Dispose();
gpSobel.Bitmap.Dispose();
gp.Bitmap.Dispose();
bp.Bitmap.Dispose();
l1stLevel.Name = "1st Level";
l2ndLevel.Name = "2nd Level";
return(new ProcessResult(new ObjectLayer[] { l1stLevel, l2ndLevel }));
}
protected override void OnLoad(EventArgs e)
{
base.OnLoad(e);
this.CreateTabContainer("StromaDetection2");
this.TabContainer.Enabled = true;
RConnector.BinPath = @"C:\Program Files\R\R-3.1.0\bin\x64\";
(new Button {
Text = "cluster by roundness",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.SelectedLayer) return;
try { RConnector.Engine.Evaluate("library(\"mclust\")"); }
catch { throw new Exception("try install mclust"); }
var progressDialog = new ProgressDialog {
Message = "extracting features",
ProgressBarStyle = ProgressBarStyle.Marquee,
AllowCancel = false
};
progressDialog.BackgroundTask += () =>
{
var matrix = RConnector.Engine.CreateNumericMatrix(this.SelectedLayer.Objects.Count, 1);
for (var i = 0; i < this.SelectedLayer.Objects.Count; i++)
{
matrix[i, 0] = this.SelectedLayer.Objects[i].Features["AspectRatioOfBoundingEllipsoid"].Value;
}
var result = this.cluster(matrix);
this.drawClusters(result.Item1, result.Item2);
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
this.RefreshBuffer();
};
(new Button {
Text = "cluster by position",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.SelectedLayer) return;
try { RConnector.Engine.Evaluate("library(\"mclust\")"); }
catch { throw new Exception("try install mclust"); }
var progressDialog = new ProgressDialog {
Message = "extracting features",
ProgressBarStyle = ProgressBarStyle.Marquee,
AllowCancel = false
};
progressDialog.BackgroundTask += () =>
{
var matrix = RConnector.Engine.CreateNumericMatrix(this.SelectedLayer.Objects.Count, 2);
for (var i = 0; i < this.SelectedLayer.Objects.Count; i++)
{
var io = this.SelectedLayer.Objects[i];
matrix[i, 0] = io.Features["CentroidX"].Value;
matrix[i, 1] = io.Features["CentroidY"].Value;
}
var result = this.cluster(matrix);
this.drawClusters(result.Item1, result.Item2);
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
this.RefreshBuffer();
};
this.clusters = new NumericUpDown {
Parent = new GroupBox {
Parent = this.TabContainer,
Dock = DockStyle.Top,
Text = "clusters",
Height = 40
},
Dock = DockStyle.Fill,
Minimum = 0,
Maximum = 20,
Increment = 1,
Value = 0,
DecimalPlaces = 0
};
(new Button {
Text = "extract features",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.SelectedLayer) return;
var progressDialog = new ProgressDialog {
Message = "extracting features",
ProgressBarStyle = ProgressBarStyle.Marquee,
AllowCancel = false
};
progressDialog.BackgroundTask += () =>
{
Centroid.ProcessLayer(this.SelectedLayer);
foreach (var io in this.SelectedLayer.Objects)
{
var boundingEllipsoid = BoundingEllipsoid.FromContour(io.Contour);
if (!io.Features.Contains("AngleOfBoundingEllipsoid")) io.Features.Add(new AngleOfBoundingEllipsoid(boundingEllipsoid));
if (!io.Features.Contains("AspectRatioOfBoundingEllipsoid")) io.Features.Add(new AspectRatioOfBoundingEllipsoid(boundingEllipsoid));
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
(new Button {
Text = "execute cell core segmentation",
Parent = this.TabContainer,
Dock = DockStyle.Top
}).Click += delegate
{
if (null == this.DisplayedImage) return;
ProcessResult result = null;
var progressDialog = new ProgressDialog {
Message = "executing cell core segmentation",
ProgressBarStyle = ProgressBarStyle.Marquee,
AllowCancel = false
};
progressDialog.BackgroundTask += () =>
{
var segmentation = new CellCoreSegmentation();
var executionParams = new ProcessExecutionParams(this.DisplayedImage);
result = segmentation.Execute(executionParams);
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
this.SetLayers(result.Layers.ToArray());
};
}
