private static void Main(string[] args)
{
foreach (var slideName in Util.GetSlideFilenames(args))
{
using (var slideCache = new SlideCache(slideName)){
var hValues = File.Exists(slideCache.DataPath + "hValues.xml")?SlidePartitioner <double> .Load(slideCache.DataPath + "hValues.xml"):new SlidePartitioner <double>(slideCache.Slide, 1f, new Size(2000, 2000));
var eValues = File.Exists(slideCache.DataPath + "eValues.xml")?SlidePartitioner <double> .Load(slideCache.DataPath + "eValues.xml"):hValues.Duplicate <double>();
var hRange = new Range <double>();
var eRange = new Range <double>();
foreach (var tile in hValues.Values)
{
using (Bitmap tileImage = slideCache.Slide.GetImagePart(tile), hImage = tileImage.Clone() as Bitmap, eImage = tileImage.Clone() as Bitmap){
var gpH = new ColorDeconvolution().Get1stStain(hImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
var gpE = new ColorDeconvolution().Get2ndStain(eImage, ColorDeconvolution.KnownStain.HaematoxylinEosin);
var hSum = 0u;
var eSum = 0u;
var cnt = 0;
foreach (var grayscalePixel in gpH.Pixels())
{
hSum += grayscalePixel.V;
eSum += gpE.GetPixel(grayscalePixel.X, grayscalePixel.Y);
cnt++;
}
var meanH = (double)hSum / (double)cnt;
tile.Data = meanH;
hRange.Add(meanH);
var meanE = (double)eSum / (double)cnt;
eValues[tile.Index].Data = meanE;
eRange.Add(meanE);
gpH.Dispose();
gpE.Dispose();
if (slideCache.Slide.GetAnnotationsInArea(tile.SourceArea).Any())
{
var tileCache = slideCache.GetTileCache(tile.Index);
tileCache.SetImage("rgb", tileImage);
tileCache.SetImage("h", gpH.Bitmap);
tileCache.SetImage("e", gpE.Bitmap);
}
}
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done");
}
var range = new Range <double> {
hRange.Minimum, hRange.Maximum, eRange.Minimum, eRange.Maximum
};
Func <double, Color> toColor = v => {
var c = (int)Math.Round(range.Normalize(v) * 255d);
return(Color.FromArgb(c, c, c));
};
slideCache.SetImage("hValues", hValues.GenerateHeatMap(toColor));
slideCache.SetImage("eValues", eValues.GenerateHeatMap(toColor));
slideCache.SetImage("overview", slideCache.Slide.GetImagePart(0, 0, slideCache.Slide.Size.Width, slideCache.Slide.Size.Height, hValues.Columns, hValues.Rows));
hValues.Save(slideCache.DataPath + "hValues.xml");
eValues.Save(slideCache.DataPath + "eValues.xml");
}
}
}
private static void DrawHeatMapAll(SlidePartitioner <Dictionary <String, TissuAnnotaionEnum> > tissueSlidePartitioner, SlideCache slideCache)
{
Func <Dictionary <String, TissuAnnotaionEnum>, Color> drawWekaClassificationBaggingFunc = classifyDic => TissuAnnotaionToColor(classifyDic["wekaClassifyBagging"]);
Func <Dictionary <String, TissuAnnotaionEnum>, Color> drawOwnClassificationJ48Func = classifyDic => TissuAnnotaionToColor(classifyDic["ownClassificationJ48"]);
Func <Dictionary <String, TissuAnnotaionEnum>, Color> drawOwnClassificationJRipFunc = classifyDic => TissuAnnotaionToColor(classifyDic["ownClassifyJRip"]);
/* using (var heatMap = tissueSlidePartitioner.GenerateHeatMap(drawWekaClassificationBaggingFunc))
* {
* slideCache.SetImage("ClassificationDetection_wekaClassifyBagging", heatMap);
* }*/
using (var heatMap = tissueSlidePartitioner.GenerateHeatMap(drawOwnClassificationJ48Func))
{
slideCache.SetImage("ClassificationDetection_ownClassifyJ48", heatMap);
}
using (var heatMap = tissueSlidePartitioner.GenerateHeatMap(drawOwnClassificationJRipFunc))
{
slideCache.SetImage("ClassificationDetection_ownClassifyJRip", heatMap);
}
}
private static void Main(string[] args)
{
foreach (var slideName in Util.GetSlideFilenames(args))
{
using (var slideCache = new SlideCache(slideName)){
var scale = 0.2f;
var tileSize = 200;
var slidePartitionerFileName = slideCache.DataPath + "BudDetection.Tissue.xml";
var slidePartitioner = File.Exists(slidePartitionerFileName)?SlidePartitioner <bool?> .Load(slidePartitionerFileName):new SlidePartitioner <bool?>(slideCache.Slide, scale, new Size(tileSize, tileSize));
using (var overViewImage = slideCache.Slide.GetImagePart(0, 0, slideCache.Slide.Size.Width, slideCache.Slide.Size.Height, slidePartitioner.Columns, slidePartitioner.Rows)){
slideCache.SetImage("overview", overViewImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\...
//ggf. heatmap hier erstellen
}
int i = 0;
int max = slidePartitioner.Count;
double percent = 0;
foreach (var tile in slidePartitioner.Values)
{
percent = 100.0 * i++ / max;
if (tile.Data.HasValue)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ":" + tile.Data.Value + " skipped " + percent + "%");
continue;
}
using (var tileImage = slideCache.Slide.GetImagePart(tile)){
if (false)
{
var tileCache = slideCache.GetTileCache(tile.Index);
tileCache.SetImage("rgb", tileImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\[Index]\... ansonsten tileImage.Save("[uri].png")
}
var r = BudDetection.MyColorDeconvolution.Execute(tileImage);
tile.Data = r.Value; //Wert zur Kachel speichern
}
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done " + percent + "%");
if (Console.KeyAvailable)
{
break;
}
}
slidePartitioner.Save(slidePartitionerFileName);
using (var heatMap = slidePartitioner.GenerateHeatMap(b => b.HasValue?(b.Value?Color.Green:Color.White):Color.Black)) slideCache.SetImage("tissueHeatMap", heatMap);
}
}
}
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);
}
}
}
}
private static void Main(string[] args)
{
Console.WriteLine("Start SlideProzessor");
Console.WriteLine(args);
foreach (var slideName in Util.GetSlideFilenames(args))
{
Console.WriteLine("progress: " + slideName);
using (var slideCache = new SlideCache(slideName)){
// Skalierung des Bildes
var scale = 0.5f; // 0.1
var tileSize = 100; // 100
// Partionierung und speichern
var slidePartitionerFileName = slideCache.DataPath + "BudDetection.Tissue.xml";
var slidePartitioner = File.Exists(slidePartitionerFileName)?SlidePartitioner <bool?> .Load(slidePartitionerFileName):new SlidePartitioner <bool?>(slideCache.Slide, scale, new Size(tileSize, tileSize));
using (var overViewImage = slideCache.Slide.GetImagePart(0, 0, slideCache.Slide.Size.Width, slideCache.Slide.Size.Height, slidePartitioner.Columns, slidePartitioner.Rows)){
slideCache.SetImage("overview", overViewImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\...
//ggf. heatmap hier erstellen
}
// über alle Kacheln
var counter = 0;
foreach (var tile in slidePartitioner.Values)
{
counter = counter + 1;
// ist bereits ein wert vorhanden, dann überspringen
if (tile.Data.HasValue)
{
if (counter % 100 == 0)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ":" + tile.Data.Value + " skipped");
}
continue;
}
// bitmap erzeugen aus der Kachel
using (var tileImage = slideCache.Slide.GetImagePart(tile)){
// für debugging zwecke
if (false)
{
var tileCache = slideCache.GetTileCache(tile.Index);
tileCache.SetImage("rgb", tileImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\[Index]\... ansonsten tileImage.Save("[uri].png")
}
// Wert Berechnung
var r = BudDetection.ColorDeconvolution.Execute(tileImage);
tile.Data = r.Value; //Wert zur Kachel speichern
}
if (counter % 100 == 0)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done");
}
// unterbrechbar via key eingabe
if (Console.KeyAvailable)
{
break;
}
}
// zustand der bearbeitng speichern
slidePartitioner.Save(slidePartitionerFileName);
using (var heatMap = slidePartitioner.GenerateHeatMap(b => b.HasValue?(b.Value?Color.Green:Color.White):Color.Black)) slideCache.SetImage("tissueHeatMap", heatMap);
}
}
}
private static void Main(string[] args)
{
foreach (var slideName in Util.GetSlideFilenames(args))
{
using (var slideCache = new SlideCache(slideName)){
var scale = 0.5f;
var tileSize = 500;
var slidePartitionerFileName = slideCache.DataPath + "BudDetection.Buds.xml";
var slidePartitioner = File.Exists(slidePartitionerFileName)?SlidePartitioner <int?>
.Load(slidePartitionerFileName):new SlidePartitioner <int?>(slideCache.Slide, scale, new Size(tileSize, tileSize));
var heatMapHelper = new HeatMapHelper(slideCache.GetImage("tissueHeatMap"));
var budCountRange = new Range <int>();
foreach (var tile in slidePartitioner.Values)
{
if (tile.Data.HasValue)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ":" + tile.Data.Value + " skipped");
budCountRange.Add(tile.Data.Value);
continue;
}
var colors = heatMapHelper.GetAffectedColors(slideCache.Slide.Size, tile.SourceArea);
var values = heatMapHelper.GetAffectedValues(slideCache.Slide.Size, tile.SourceArea);
if (values.All(v => 0 != v))
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ": no tissue");
continue;
}
using (var tileImage = slideCache.Slide.GetImagePart(tile)){
if (false)
{
var tileCache = slideCache.GetTileCache(tile.Index);
tileCache.SetImage("rgb", tileImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\[Index]\... ansonsten tileImage.Save("[uri].png")
}
var r = BudDetection.Detector.Execute(tileImage);
//var r = ColorDeconvolution.Detect(tileImage);
var layer = r.Value;
tile.Data = layer.Objects.Count;
budCountRange.Add(layer.Objects.Count);
foreach (var io in layer.Objects)
{
//var bb=io.Contour.FindBoundingBox();
var offset = tile.SourceArea.Location;
var sourcePoints = new List <Point>();
foreach (var contourPoint in io.Contour.GetPoints())
{
double x = Math.Round(contourPoint.X / scale + offset.X);
double y = Math.Round(contourPoint.Y / scale + offset.Y);
var sourcePoint = new Point((int)x, (int)y);
sourcePoints.Add(sourcePoint);
}
var annotation = slideCache.Slide.CreateAnnotation(AnnotationType.PolygonLine);
foreach (var point in sourcePoints)
{
annotation.AppendPoints(point);
}
annotation.Color = Color.OrangeRed;
annotation.Name = null == io.Class?"bud":io.Class.Name;
}
}
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done");
if (Console.KeyAvailable)
{
break;
}
}
slidePartitioner.Save(slidePartitionerFileName);
using (var heatMap = slidePartitioner.GenerateHeatMap(b => {
if (!b.HasValue)
{
return(Color.LightSeaGreen);
}
var c = (int)Math.Round(budCountRange.Normalize(b.Value) * 255d);
return(Color.FromArgb(c, c, c));
}))
slideCache.SetImage("budHeatMap", heatMap);
}
}
}
private static void Main(string[] args)
{
foreach (var slideName in Util.GetSlideFilenames(args))
{
using (var slideCache = new SlideCache(slideName)){
// var scale = 0.1f;
var scale = 0.5f; // besser so laut 19.07.2018
var tileSize = 100;
var slidePartitionerFileName = slideCache.DataPath + "BudDetection.Buds.xml";
var slidePartitioner = File.Exists(slidePartitionerFileName)?SlidePartitioner <int?> .Load(slidePartitionerFileName):new SlidePartitioner <int?>(slideCache.Slide, scale, new Size(tileSize, tileSize));
var heatMapHelper = new HeatMapHelper(slideCache.GetImage("tissueHeatMap"));
var budCountRange = new Range <int>();
var counter = 0;
foreach (var tile in slidePartitioner.Values)
{
// test, ob schon was für die kackel berechnet wurde
if (tile.Data.HasValue)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ":" + tile.Data.Value + " skipped");
budCountRange.Add(tile.Data.Value);
continue;
}
// soll kachel bearbeitet werden
var colors = heatMapHelper.GetAffectedColors(slideCache.Slide.Size, tile.SourceArea);
var values = heatMapHelper.GetAffectedValues(slideCache.Slide.Size, tile.SourceArea);
if (values.All(v => 255 == v)) // 255 weiß
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + ": no tissue");
continue;
}
using (var tileImage = slideCache.Slide.GetImagePart(tile)){
counter = counter + 1;
if (false)
{
var tileCache = slideCache.GetTileCache(tile.Index);
tileCache.SetImage("rgb", tileImage); //speichert unter C:\ProgramData\processingRepository\[slideCache.SlideName]\[Index]\... ansonsten tileImage.Save("[uri].png")
}
var r = BudDetection.Detector.Execute(tileImage); // importent call
var layer = r.Value;
tile.Data = layer.Objects.Count;
budCountRange.Add(layer.Objects.Count);
// für alle gefundene objekte wird eine annotation angelegt
foreach (var io in layer.Objects)
{
//var bb=io.Contour.FindBoundingBox();
var offset = tile.SourceArea.Location;
var sourcePoints = new List <Point>();
foreach (var contourPoint in io.Contour.GetPoints())
{
double x = Math.Round(contourPoint.X / scale + offset.X);
double y = Math.Round(contourPoint.Y / scale + offset.Y);
var sourcePoint = new Point((int)x, (int)y);
sourcePoints.Add(sourcePoint);
}
var annotation = slideCache.Slide.CreateAnnotation(AnnotationType.PolygonLine);
foreach (var point in sourcePoints)
{
annotation.AppendPoints(point);
}
annotation.Color = Color.PaleVioletRed;
annotation.Name = null == io.Class?"bud":io.Class.Name;
}
}
if (counter % 100 == 0)
{
Console.WriteLine(slideCache.SlideName + "-" + tile.Index + " done");
}
if (Console.KeyAvailable)
{
break;
}
}
slidePartitioner.Save(slidePartitionerFileName);
// normalisierung
using (var heatMap = slidePartitioner.GenerateHeatMap(b => {
if (!b.HasValue)
{
return(Color.LightSeaGreen);
}
var c = (int)Math.Round(budCountRange.Normalize(b.Value) * 255d);
return(Color.FromArgb(c, c, c)); // grauwert(hell == viele butts)
}))
slideCache.SetImage("budHeatMap", heatMap);
}
}
}