Use float32 images instead of byte to improve the edge detection precision.

[master-thesis.git] / Parasitemia / Parasitemia / ParasitesMarker.fs

diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
index 44da901..9e46c23 100644 (file)
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker.fs
@@ -1,39 +1,88 @@
 module ParasitesMarker
 
 open System.Drawing
+open System.Linq
 
 open Emgu.CV
 open Emgu.CV.Structure
+open Utils
 
 type Result = {
     darkStain: Image<Gray, byte>
-    stain: Image<Gray, byte>
-    infection: Image<Gray, byte> }
+    infection: Image<Gray, byte>
+    stain: Image<Gray, byte> }
 
-let find (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result =
+
+// Create three binary markers :
+// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
+// * 'Stain' corresponds to the stain around the parasites.
+// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
+let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
 
     // We use the filtered image to find the dark stain.
-    let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = KMedians.kmedians filteredGreen 1.0
-    let darkStain = d_fg.Cmp(median_bg * config.darkStainLevel, CvEnum.CmpType.GreaterThan)
+    let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
+    let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
+    let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
     darkStain._And(fg)
-    
+
     let fgFloat = (fg / 255.0).Convert<Gray, float32>()
-    let greenWithoutBg = green.Copy()
+    use greenWithoutBg = ImgTools.gaussianFilter green 1.0
     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
 
-    let findSmears (sigma: float) (level: float) : Image<Gray, byte> =       
-        let greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
-        let fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
-
+    let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
+        use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
+        use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
         smears._And(fg)
-        smears    
+        smears
+
+    let tmp = filteredGreen.Convert<Gray, byte>()
 
     { darkStain = darkStain;
-      stain = findSmears config.stainSigma config.stainLevel
-      infection = findSmears config.infectionSigma config.infectionLevel }
-    
+      stain = findSmears 10. 0.9
+      infection = findSmears 2.2 0.87 },
+    tmp,
+    tmp
+
+
+// Create three binary markers :
+// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
+// * 'Stain' corresponds to the stain around the parasites.
+// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
+let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
+
+    let filteredGreenWithoutInfection = filteredGreen.Copy()
+    ImgTools.areaCloseF filteredGreenWithoutInfection (int config.InfectionArea)
+
+    let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
+    ImgTools.areaCloseF filteredGreenWithoutStain (int config.StainArea)
+
+    // We use the filtered image to find the dark stain.
+
+    // With K-Means.
+    let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0)
+    let { KMeans.mean_bg = value_bg; KMeans.mean_fg = value_fg; KMeans.d_fg = d_fg } = kmeansResults
+
+    // With K-Medians.
+    (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting this again in MainAnalysis
+    let { KMedians.median_bg = value_bg; KMedians.median_fg = value_fg; KMedians.d_fg = d_fg } = kmediansResults *)
+
+    let darkStain = d_fg.Cmp(value_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
+    darkStain._And(filteredGreenWithoutInfection.Cmp(value_fg, CvEnum.CmpType.LessThan))
+
+    let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
+        let diff = closed - (img * level)
+        diff._ThresholdBinary(Gray(0.0), Gray(255.))
+        diff.Convert<Gray, byte>()
+
+    let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
+    let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
 
+    { darkStain = darkStain
+      infection = infectionMarker
+      stain = stainMarker },
+    filteredGreenWithoutInfection,
+    filteredGreenWithoutStain