* Try another approach to remove false ellipses without success (commented).

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

diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
index 71c15a9..720488d 100644 (file)
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker.fs
@@ -18,11 +18,10 @@ type Result = {
 // * '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 kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
+    let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen)
     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)
+    let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
     darkStain._And(fg)
 
@@ -50,29 +49,24 @@ let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (
 // * '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()
+let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> =
+    use 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.
+    let _, mean_fg, mean_bg =
+        let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
+        ImgTools.otsu hist
 
-    // With K-Means.
-    let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection) 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) 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 darkStain = filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
 
     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
-        let diff = closed - (img * level)
+        let diff = img.Copy()
+        diff._Mul(level)
+        CvInvoke.Subtract(closed, diff, diff)
         diff._ThresholdBinary(Gray(0.0), Gray(255.))
         diff.Convert<Gray, byte>()
 
@@ -82,7 +76,6 @@ let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result
     { darkStain = darkStain
       infection = infectionMarker
       stain = stainMarker },
-    filteredGreenWithoutInfection,
     filteredGreenWithoutStain