public static bool IsTissue(Bitmap image)
{
const double GRENZ_ENTROPIE = 0.5;
var bitmapProcessor = new BitmapProcessor(image);//liefert schnelleren Zugriff auf die Pixel-Werte, alternativ auch SharpAccessory.Imaging.Processors.GrayscaleProcessor
int[] greyArray = new int[256];
for (var y = 0; y < bitmapProcessor.Height; y++)
{
for (var x = 0; x < bitmapProcessor.Width; x++)
{
var r = bitmapProcessor.GetRed(x, y);
var g = bitmapProcessor.GetGreen(x, y);
var b = bitmapProcessor.GetBlue(x, y);
var grauwert = (int)(r + g + b) / 3;
greyArray[grauwert]++;
}
}
bitmapProcessor.Dispose();
//Calculate Shannon Entropie
return(calcEntropie(greyArray) > GRENZ_ENTROPIE);
}
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 }));
}
private static void Main(string[] args)
{
const double GRENZ_ENTROPIE = 0.1;
foreach (var slideName in Util.GetSlideFilenames(new string[] { args[0] }))
{
using (var slideCache = new SlideCache(slideName)){
// scale=1 -> baselayer , sollte so klein wie möglich sein um die Rechenzeit zu minimieren
// targetSize Größe der zu prozessierenden Bilder, hängt von der hardware ab und bestimmt die Auflösung der Heatmap, für niedrige scale-Werte sollte auch die Größe reduziert werden
// Auflösung: Breite=tissueSlidePartitioner.Columns Höhe=tissueSlidePartitioner.Rows
// var: implizit typisiert, tatsächlich stark typisiert da der Compiler den Typ kennt; RMT->Goto To Definition
// Empfehlung: http://shop.oreilly.com/product/0636920040323.do die 5.0 gibt es auch als pdf im Internet
var tissueSlidePartitioner = new SlidePartitioner <bool>(slideCache.Slide, 0.2f, new Size(500, 500)); //Nicht unbedingt auf dem Baselayerr arbeiten zB. 1f --> 0.1
using (var overViewImage = slideCache.Slide.GetImagePart(0, 0, slideCache.Slide.Size.Width, slideCache.Slide.Size.Height, tissueSlidePartitioner.Columns, tissueSlidePartitioner.Rows)){
//TODO falls die Gewebeerkennung auf dem Übersichtsbild stattfinden soll, dann hier
slideCache.SetImage("overview", overViewImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\...
}
//Multithreading
Parallel.ForEach(tissueSlidePartitioner.Values, (tile) =>
{
using (var tileImage = slideCache.Slide.GetImagePart(tile))
{
var containsTissue = false;
double entropie = 0.0;
#region hier sollte containsTissue richtig bestimmt werden
var bitmapProcessor = new BitmapProcessor(tileImage);//liefert schnelleren Zugriff auf die Pixel-Werte, alternativ auch SharpAccessory.Imaging.Processors.GrayscaleProcessor
int[] greyArray = new int[256];
for (var y = 0; y < bitmapProcessor.Height; y++)
{
for (var x = 0; x < bitmapProcessor.Width; x++)
{
var r = bitmapProcessor.GetRed(x, y);
var g = bitmapProcessor.GetGreen(x, y);
var b = bitmapProcessor.GetBlue(x, y);
var grauwert = (int)(r + g + b) / 3;
greyArray[grauwert]++;
}
}
bitmapProcessor.Dispose();
//Calculate Shannon Entropie
entropie = calcEntropie(greyArray);
//Contains Tissue ermitteln
if (0 == tile.Index.Y)
{
containsTissue = false;//oberste Reihe sollte kein Gewebe enthalten
}
else
{
//if (slideCache.Slide.GetAnnotationsInArea(tile.SourceArea).Any()) containsTissue = true;//Kacheln mit Annotationen enthalten Gewebe
if (entropie > GRENZ_ENTROPIE)
{
containsTissue = true;
}
}
#endregion
//Wert zur Kachel speichern
tile.Data = containsTissue;
//Only for Debug
var saveImage = false;
if (saveImage)
{
string path = args[1] + @"\" + slideCache.SlideName + @"\";
if (containsTissue)
{
path += @"isTissue\";
}
else
{
path += @"noTissue\";
}
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
tileImage.Save(path + tile.Index.X + "-" + tile.Index.Y + ".png");
//var tileCache = slideCache.GetTileCache(tile.Index);
//tileCache.SetImage("rgb",tileImage);//speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\[Index]\... ansonsten tileImage.Save("[uri].png")
}
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done - containsTissue: " + containsTissue.ToString() + " - entropie: " + entropie.ToString());
}
});
//true wird zu grün, false zu rot; syntax ist lambda (=>) mit einem conditional operator (?)
Func <bool, Color> f = b =>
{
if (b)
{
return(Color.Red);
}
else
{
return(Color.Green);
}
};
using (var heatMap = tissueSlidePartitioner.GenerateHeatMap(f))
{
slideCache.SetImage("tissueHeatMap", heatMap);
}
}
}
}
static void Main(string[] args)
{
#region init
if (0 == args.Length)
{
Console.WriteLine("no slide name");
return;
}
var slideName = args[0];
var processinHelper = new Processing(slideName);
var slide = processinHelper.Slide;
#endregion init
var part = new WsiPartitioner(new Rectangle(new Point(0, 0), slide.Size), new Size(1000, 1000), new Size(0, 0), 1.0);
var tissueData = new TiledProcessInformation<bool>(part, slideName);
#region global tissue detection
int overviewImageWidth = slide.Size.Width / OverviewTileSize;
int overviewImageHeight = slide.Size.Height / OverviewTileSize;
Bitmap overviewImage = slide.GetImagePart(0, 0, slide.Size.Width, slide.Size.Height, overviewImageWidth, overviewImageHeight);
var bitmapProcessor = new BitmapProcessor(overviewImage);
ObjectLayer overviewLayer = new TissueDetector().Execute(bitmapProcessor, Radius, NoiseLevel);
bitmapProcessor.Dispose();
DrawObjectsToImage(overviewImage, overviewLayer, Color.Black);
overviewImage.Save(processinHelper.DataPath + "tissueDetectionOverview.png");
#endregion global tissue detection
//part.Tiles[]
foreach (var tile in part)
{
#region global tissue detection
var rect = tile.SourceRect;
int overviewX = rect.X / OverviewTileSize;
int overviewY = rect.Y / OverviewTileSize;
int windowSize = rect.Width / OverviewTileSize;
bool tileInObject = true;
int partsOutside = 0;
for (int y = 0; y < windowSize; y++)
{
for (int x = 0; x < windowSize; x++)
{
int newX = overviewX + x;
int newY = overviewY + y;
if (newX < 0 || newX >= overviewLayer.Map.Width || newY < 0 || newY >= overviewLayer.Map.Height) { continue; }
uint id = overviewLayer.Map[newX, newY];
if (id != 0) continue;
partsOutside++;
if (!(partsOutside >= Math.Pow(windowSize + 1, 2) * 0.75)) continue;
tileInObject = false;
break;
}
if (!tileInObject) { break; }
}
tissueData.AddDataToCurrentTile(tileInObject);
#endregion global tissue detection
if (tileInObject) Console.WriteLine(tile.SourceRect + ":" + partsOutside);
}
tissueData.ToFile(processinHelper.DataPath + "tissueData.tpi");
using (Bitmap b = tissueData.GenerateHeatMap(tissue => tissue ? Color.Green : Color.Red))
b.Save(processinHelper.DataPath + "tissueData.png");
Console.WriteLine("done");
Console.ReadKey();
}
private static void processInput()
{
int Radius = 2;
int NoiseLevel = 10;
Console.WriteLine("Processing Input...");
foreach (var import in importItems)
{
Console.WriteLine();
Console.WriteLine(import.FileName);
Console.WriteLine("Slide extrahieren...");
var processingHelper = new Processing(import.FileName);
var slide = processingHelper.Slide;
Console.WriteLine("Ausschnitt aus Slide extrahieren mit originaler Auflösung...");
int partImageWidth = import.LowerRight.X - import.UpperLeft.X;
int partImageHeight = import.LowerRight.Y - import.UpperLeft.Y;
Bitmap partImage = slide.GetImagePart(
import.UpperLeft.X, import.UpperLeft.Y,
partImageWidth, partImageHeight,
partImageWidth, partImageHeight
);
#region global tissue detection
Console.WriteLine("Gewebe suchen und in separatem Layer speichern...");
var bitmapProcessor = new BitmapProcessor(partImage);
ObjectLayer overviewLayer = new TissueDetector().Execute(bitmapProcessor, Radius, NoiseLevel);
bitmapProcessor.Dispose();
Console.WriteLine("Gewebe-Layer in Ausschnitt zeichnen + speichern...");
DrawObjectsToImage(partImage, overviewLayer, Color.Black);
partImage.Save(processingHelper.DataPath + "ImagePartTissue.png");
#endregion global tissue detection
#region Deconvolution
Console.WriteLine("Execute deconvolution 3...");
var gpX = new ColorDeconvolution().Get3rdStain(partImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
gpX.Dispose();
Bitmap gpX_bmp = gpX.Bitmap;
gpX_bmp.Save(processingHelper.DataPath + "ImagePartColor3.png");
Console.WriteLine("Execute deconvolution 2...");
var gpE = new ColorDeconvolution().Get2ndStain(partImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
gpE.Dispose();
Bitmap gpE_bmp = gpE.Bitmap;
gpE_bmp.Save(processingHelper.DataPath + "ImagePartColor2.png");
Console.WriteLine("Execute deconvolution 1...");
var gpH = new ColorDeconvolution().Get1stStain(partImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
gpH.Dispose();
Bitmap gpH_bmp = gpH.Bitmap;
gpH_bmp.Save(processingHelper.DataPath + "ImagePartColor1.png");
#endregion Deconvolution
#region execute edge detection
Console.WriteLine("Execute edge detection...");
SobelResponse responseH = Filtering.ExecuteSobel(gpH_bmp);
SobelResponse responseE = Filtering.ExecuteSobel(gpE_bmp);
var substracted = new double[responseH.Size.Width, responseH.Size.Height];
var substractedRange = new Range<double>();
for (var x = 0; x < responseH.Size.Width; x++)
{
for (var y = 0; y < responseH.Size.Height; y++)
{
var value = Math.Max(0, responseE.Gradient[x, y] - responseH.Gradient[x, y]);
substracted[x, y] = value;
substractedRange.Add(value);
}
}
double[,] nonMaximumSupression = Filtering.ExecuteNonMaximumSupression(substracted, responseE.Orientation);
Bitmap edges = Visualization.Visualize(nonMaximumSupression, Visualization.CreateColorizing(substractedRange.Maximum));
edges.Save(processingHelper.DataPath + "ImagePartEdges.png");
#endregion execute edge detection
exportItems.Add(
new Ausgabe {
Identify = import.Identify,
Result = false,
Message = "kein Fehler"
}
);
}
}
