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 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
TiledProcessInformation<uint[]> haematoxylinHistogram;
TiledProcessInformation<uint[]> eosinHistogram;
if (!File.Exists(processinHelper.DataPath + "haematoxylinHistogram.tpi") || !File.Exists(processinHelper.DataPath + "eosinHistogram.tpi"))
{
if (!Directory.Exists(processinHelper.DataPath + "deconvolution")) Directory.CreateDirectory(processinHelper.DataPath + "deconvolution");
var tissueData = TiledProcessInformation<bool>.FromFile(processinHelper.DataPath + "tissueData.tpi");
haematoxylinHistogram = new TiledProcessInformation<uint[]>(tissueData.Partitioner, tissueData.WsiUri);
eosinHistogram = new TiledProcessInformation<uint[]>(tissueData.Partitioner, tissueData.WsiUri);
var partitioner = tissueData.Partitioner;
var dict = new Dictionary<Point, WsiRect>();
foreach (var tile in tissueData.Partitioner)
dict.Add(tissueData.Partitioner.CurrentIndices, tile);
var stopwatch = new Stopwatch();
foreach (var tile in partitioner)
{
var tissueTile = dict[partitioner.CurrentIndices];
if (!tissueData[tissueTile]) continue;
stopwatch.Start();
using (var tileImage = slide.GetImagePart(tile))
{
var hHistogramValue = new uint[256];
var hValues = new List<double>();
using (var gpH = new ColorDeconvolution().Get1stStain(tileImage, ColorDeconvolution.KnownStain.HaematoxylinEosin))
{
foreach (var intensity in gpH.GetPixels())
{
hHistogramValue[intensity]++;
hValues.Add(intensity);
}
haematoxylinHistogram.AddDataToCurrentTile(hHistogramValue);
gpH.Dispose();
gpH.Bitmap.Save(processinHelper.DataPath + "deconvolution\\" + partitioner.CurrentIndices + ".h.png");
}
var eHistogramValue = new uint[256];
var eValues = new List<double>();
using (var gpE = new ColorDeconvolution().Get2ndStain(tileImage, ColorDeconvolution.KnownStain.HaematoxylinEosin))
{
foreach (var intensity in gpE.GetPixels())
{
eHistogramValue[intensity]++;
eValues.Add(intensity);
}
eosinHistogram.AddDataToCurrentTile(eHistogramValue);
gpE.Dispose();
gpE.Bitmap.Save(processinHelper.DataPath + "deconvolution\\" + partitioner.CurrentIndices + ".e.png");
}
NumericVector hHistogram = RConnector.Engine.CreateNumericVector(hValues);
RConnector.Engine.SetSymbol("hHistogram", hHistogram);
NumericVector eHistogram = RConnector.Engine.CreateNumericVector(eValues);
RConnector.Engine.SetSymbol("eHistogram", eHistogram);
var handle = RConnector.StartOutput();
RConnector.Engine.Evaluate("hist(eHistogram, col=rgb(1,0,0,0.5),xlim=c(0,255), main=\"" + partitioner.CurrentIndices + "\", xlab=\"HE\")");
RConnector.Engine.Evaluate("hist(hHistogram, col=rgb(0,0,1,0.5), add=T)");
var output = RConnector.EndOutput(handle);
output.Save(processinHelper.DataPath + "deconvolution\\histogram" + partitioner.CurrentIndices + ".png");
}
stopwatch.Stop();
Console.WriteLine(partitioner.CurrentIndices + ":" + (stopwatch.ElapsedMilliseconds / 1000d) + "s");
stopwatch.Reset();
}
haematoxylinHistogram.ToFile(processinHelper.DataPath + "haematoxylinHistogram.tpi");
eosinHistogram.ToFile(processinHelper.DataPath + "eosinHistogram.tpi");
}
else
{
haematoxylinHistogram = TiledProcessInformation<uint[]>.FromFile(processinHelper.DataPath + "haematoxylinHistogram.tpi");
eosinHistogram = TiledProcessInformation<uint[]>.FromFile(processinHelper.DataPath + "eosinHistogram.tpi");
}
var hRange = new Range<uint>();
foreach (var tile in haematoxylinHistogram.Partitioner)
{
if (null == haematoxylinHistogram[tile]) continue;
uint sum = 0;
for (uint i = 0; i < 256; i++)
{
sum += haematoxylinHistogram[tile][i] * (255 - i);
}
hRange.Add(sum);
}
Func<uint[], Color> h2pixel = h =>
{
if (null == h) return Color.Gray;
uint sum = 0;
for (uint i = 0; i < 256; i++)
{
sum += h[i] * (255 - i);
}
var ratio = (double)sum / hRange.Maximum;
return Color.FromArgb(0, 0, (int)Math.Round(255.0 * ratio));
};
var eRange = new Range<uint>();
foreach (var tile in eosinHistogram.Partitioner)
{
if (null == eosinHistogram[tile]) continue;
uint sum = 0;
for (uint i = 0; i < 256; i++)
{
sum += eosinHistogram[tile][i] * (255 - i);
}
eRange.Add(sum);
}
Func<uint[], Color> e2pixel = e =>
{
if (null == e) return Color.Gray;
uint sum = 0;
for (uint i = 0; i < 256; i++)
{
sum += e[i] * (255 - i);
}
var ratio = (double)sum / eRange.Maximum;
return Color.FromArgb((int)Math.Round(255.0 * ratio), 0, 0);
};
using (Bitmap b = haematoxylinHistogram.GenerateHeatMap(h2pixel))
b.Save(processinHelper.DataPath + "haematoxylinHistogram.png");
using (Bitmap b = eosinHistogram.GenerateHeatMap(e2pixel))
b.Save(processinHelper.DataPath + "eosinHistogram.png");
Console.WriteLine("done");
Console.ReadKey();
}