X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FParasitesMarker.fs;h=20dbf4c74292341f897061620ed69c4df0bf6a5d;hb=f9ee9f2c0c1194a6a8f7475ee2ca0b7076b32261;hp=e422b04d92fa4fbd92ea56b1d3b382cad4fc36f0;hpb=e76da913cd58078ad2479357b2430ed62a6e0777;p=master-thesis.git

diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
index e422b04..20dbf4c 100644
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker.fs
@@ -1,44 +1,86 @@
 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> }
+
 
 // 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 (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result =
-
-    let green = ImgTools.gaussianFilter green 1.0
+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 } = kmediansResult
-    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
-
+        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
 
+    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, byte>) (filteredGreenFloat: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
+
+    let filteredGreenWithoutInfection = filteredGreen.Copy()
+    ImgTools.areaClose filteredGreenWithoutInfection (int config.InfectionArea)
+
+    let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
+    ImgTools.areaClose filteredGreenWithoutStain (int config.StainArea)
+
+    // We use the filtered image to find the dark stain.
+    let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting again this in MainAnalysis
+    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(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
+
+    let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
+        let diff = closed - (img * level)
+        diff._ThresholdBinary(Gray(0.0), Gray(255.))
+        diff
+
+    let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
+    let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
+
+    { darkStain = darkStain
+      infection = infectionMarker
+      stain = stainMarker },
+    filteredGreenWithoutInfection,
+    filteredGreenWithoutStain
+
+
+
+