Change the way the parasites are detected.

[master-thesis.git] / Parasitemia / Parasitemia / ParasitesMarker2.fs

diff --git a/Parasitemia/Parasitemia/ParasitesMarker2.fs b/Parasitemia/Parasitemia/ParasitesMarker2.fs
index 03af2b6..42645b4 100644 (file)
--- a/Parasitemia/Parasitemia/ParasitesMarker2.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker2.fs
@@ -1,47 +1,66 @@
 module ParasitesMarker2
 
 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 (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
+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 { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResult
+    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(filteredGreenFloat.Cmp(median_fg, CvEnum.CmpType.LessThan))
+    darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
 
-    let marker (area: int) (threshold: float) : Image<Gray, byte> * Image<Gray, byte> =
-        let closed = filteredGreen.Copy()
-        ImgTools.areaClose closed area
-        let diff = closed - filteredGreen
+    let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
+        let diff = closed - img
 
         let min = ref [| 0. |]
         let minLocation = ref <| [| Point() |]
         let max = ref [| 0. |]
         let maxLocation = ref <| [| Point() |]
         diff.MinMax(min, max, minLocation, maxLocation)
+        let max = (!max).[0]
+
+        let threshold = 0.2 * max
+        let diff' = diff - threshold
+
+        let m = MathNet.Numerics.Statistics.StreamingStatistics.Mean(seq {
+                for m in ImgTools.findMaxima diff' do
+                    let p = m.First()
+                    yield diff'.Data.[p.Y, p.X, 0] |> float }) + threshold
+
+        let valueThreshold = m * level
 
-        diff._ThresholdBinary((!max).[0] * threshold |> Gray, Gray(255.))
-        diff, closed
+        diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
+        diff
 
-    let parasitesMarker, filteredGreenWithoutParasites  = marker (int config.ParasiteArea) config.Parameters.infectionLevel
-    let stainMarker, filteredGreenWithoutStain = marker (int config.StainArea) config.Parameters.stainLevel
+    let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
+    let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
 
     { darkStain = darkStain
-      stain = parasitesMarker
-      infection = stainMarker },
-    filteredGreenWithoutParasites,
+      infection = infectionMarker
+      stain = stainMarker },
+    filteredGreenWithoutInfection,
     filteredGreenWithoutStain