protected override void OnLoad(EventArgs e)
{
base.OnLoad(e);
Accessory.RedirectAssemblyBinding(@"W:\_Uni\TissueClassification\packages\PicNetML.0.0.16\lib\net45\");
this.CreateTabContainer("Weka-PicNet");
this.TabContainer.Enabled = true;
(new Button {
Text = "apply classifier", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate {
var progressDialog = new ProgressDialog {
Message = "executing", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => {
if (null == this.classifier || null == this.dataSet)
{
if (!this.loadClassifier())
{
return;
}
}
if (null == this.SelectedLayer)
{
if (null == this.DisplayedImage)
{
return;
}
this.addLayer(createLayer(this.DisplayedImage), true);
}
var layer = this.SelectedLayer.CreateAbove(io => true);
foreach (var io in layer.Objects)
{
this.classifier.Classify(this.dataSet, io, n => this.classes[n]);
}
layer.Name = layer.Name + " classified";
this.addLayer(layer, true);
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
(new Button {
Text = "load classifier", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate { this.loadClassifier(); };
(new Button {
Text = "save and clear data set", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate {
if (null == this.dataSet)
{
return;
}
var progressDialog = new ProgressDialog {
Message = "executing", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => {
using (var saveFileDialog = new SaveFileDialog {
Filter = "WEKA Attribute-Relation File (*.arff)|*.arff"
}) if (DialogResult.OK == saveFileDialog.ShowDialog())
{
this.dataSet.SaveAsWekaArff(saveFileDialog.FileName);
}
this.dataSet = null;
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
(new Button {
Text = "add ground truth to data set", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate {
if (null == this.SelectedLayer)
{
return;
}
var progressDialog = new ProgressDialog {
Message = "executing", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => {
if (null == this.dataSet)
{
this.dataSet = Util.CreateInstances(this.classes.Keys, this.featureNames);
}
this.dataSet.AddImageObjects(this.SelectedLayer);
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
(new Button {
Text = "classify layer by ground truth", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate {
if (null == this.DisplayedImage)
{
return;
}
if (null == this.SelectedLayer)
{
return;
}
var roiFileName = this.ImageFile.Url + ".roi";
if (!File.Exists(roiFileName))
{
return;
}
var progressDialog = new ProgressDialog {
Message = "executing", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => {
var learningSampleFile = LearningSampleFile.FromFile(roiFileName);
var groundTruthPositives = learningSampleFile.Samples.Select(sample => new Point((int)sample.Features["x0"].Value, (int)sample.Features["y0"].Value)).ToList();
var io2GroundTruth = new Dictionary <uint, int>();
foreach (var p in groundTruthPositives)
{
var id = this.SelectedLayer.Map[p.X, p.Y];
if (!io2GroundTruth.ContainsKey(id))
{
io2GroundTruth.Add(id, 0);
}
io2GroundTruth[id]++;
}
foreach (var io in this.SelectedLayer.Objects)
{
if (io2GroundTruth.ContainsKey(io.Id))
{
io.Class = 1 == io2GroundTruth[io.Id]?this.classes["nuclei"]:this.classes["conglomerate"];
}
else
{
io.Class = this.classes["void"];
}
}
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
this.RefreshBuffer();
};
(new Button {
Text = "create layer", Parent = this.TabContainer, Dock = DockStyle.Top
}).Click += delegate {
if (null == this.DisplayedImage)
{
return;
}
var progressDialog = new ProgressDialog {
Message = "executing", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => this.addLayer(createLayer(this.DisplayedImage), true)
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
}
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);
};
}
protected override void OnLoad(EventArgs e)
{
base.OnLoad(e);
CreateTabContainer("Segmentation");
TabContainer.Enabled = true;
_debugBox = new RichTextBox {
Text = "Debug Output\n==============================================", Parent = TabContainer, Dock = DockStyle.Fill, Enabled = true, ReadOnly = true
};
(new Button {
Text = "execute segmentations", Parent = TabContainer, Dock = DockStyle.Top
}).Click += delegate {
if (null == DisplayedImage)
{
return;
}
var progressDialog = new ProgressDialog {
Message = "executing segmentations", ProgressBarStyle = ProgressBarStyle.Marquee, AllowCancel = false, BackgroundTask = () => {
ClearOutput();
LogOutput("Calc Layers:");
_cellCores = _createCoreObjectLayer();
//_lumina = _createLuminaObjectLayer();
_simpleLumina = _createSimpleLuminaObjectLayer();
LogOutput(ObjectLayerrUtils.GetFeatureValueList(_cellCores, "area").Count.ToString());
LogOutput("Calc center point cores...");
_newCellCores = ObjectLayerrUtils.SetClass(ObjectLayerrUtils.AddFeatureCenterPoint(ObjectLayerrUtils.AddFeatureFormFactor(_cellCores)), new Class("cellCores", Color.Red));
LogOutput("Calc cores in near for lumina");
_newLumina = (ObjectLayerrUtils.AddFeatureCoresInNear(ObjectLayerrUtils.AddFeatureFormFactor(_simpleLumina), _newCellCores));
SetLayers(new [] { _cellCores, /*_lumina,*/ _simpleLumina, _newCellCores, _newLumina, ObjectLayerrUtils.MergeObjectLayers(_newLumina, _newCellCores) });
LogOutput("FINISH");
}
};
progressDialog.CenterToScreen();
progressDialog.ShowDialog();
};
_createCoreObjectLayer = () => {
LogOutput("Create Layer Cores");
var process = new CellCoresHE();
var processResult = process.Execute(new ProcessExecutionParams(DisplayedImage));
var layer = processResult.Layers.Last();
LogOutput("Add area and range");
layer = ObjectLayerrUtils.AddFeatureRange(ObjectLayerrUtils.AddFeatureArea(layer));
layer.Name = "cores";
return(layer);
};
_createLuminaObjectLayer = () => {
LogOutput("Create Layer Lumina");
var process = new LuminaSegmentation();
var processResult = process.Execute(new ProcessExecutionParams(DisplayedImage));
var layer = processResult.Layers.Last();
LogOutput("Add area and range");
layer = ObjectLayerrUtils.AddFeatureRange(ObjectLayerrUtils.AddFeatureArea(layer));
layer.Name = "lumina";
return(layer);
};
_createSimpleLuminaObjectLayer = () => {
LogOutput("Create Layer simple Lumina");
var segmentation = new SimpleLuminaSegmentation();
var layer = segmentation.Execute(DisplayedImage);
LogOutput("Add area and range");
layer = ObjectLayerrUtils.AddFeatureRange(ObjectLayerrUtils.AddFeatureArea(layer));
LogOutput("Improve Segmentaion Lumina");
layer = segmentation.ImprObjectLayer(layer);
layer.Name = "simple lumina";
return(layer);
};
}
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());
};
}