Remove the parasite detection function from Ma.

[master-thesis.git] / Parasitemia / ParasitemiaCore / Config.fs

diff --git a/Parasitemia/ParasitemiaCore/Config.fs b/Parasitemia/ParasitemiaCore/Config.fs
index 9df9dc4..3089953 100644 (file)
--- a/Parasitemia/ParasitemiaCore/Config.fs
+++ b/Parasitemia/ParasitemiaCore/Config.fs
@@ -13,8 +13,9 @@ type Parameters = {
     rbcDiameter: float<μm>
     resolution: float<ppi>
 
-    colorContribution_BG_RBC: float * float * float // (R, G, B).
-    colorContribution_RBC_parasite: float * float * float // (R, G, B).
+    averageColor_BG: float32 * float32 * float32 // R * G * B.
+    averageColor_RBC: float32 * float32 * float32 // R * G * B.
+    averageColor_Parasite: float32 * float32 * float32 // R * G * B.
 
     ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
 
@@ -24,7 +25,6 @@ type Parameters = {
     maxRbcRadius: float32 // Factor of the mean RBC radius.
 
     LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
-    LPFStandardDeviationStain: float<μm>
     LPFStandardDeviationRBC: float<μm>
 
     // Ellipse.
@@ -34,11 +34,12 @@ type Parameters = {
     darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
     maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC.
 
-    stainArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
-    stainSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
-    maxStainRatio: float // A cell must own less than this ratio to be a RBC.
+    parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius.
+    minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
 
-    infectionArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
+    cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
+
+    nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
 
     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
@@ -49,8 +50,13 @@ let defaultParameters = {
     rbcDiameter = 8.<μm>
     resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
 
-    colorContribution_BG_RBC = 0.16, 0.44, 0.4
-    colorContribution_RBC_parasite = 0.54, 0.41, 0.05
+    averageColor_BG = 113.3f, 135.3f, 150.3f
+    averageColor_RBC = 94.7f, 80.7f, 99.3f
+    averageColor_Parasite = 76.f, 58.f, 94.f
+
+    (*averageColor_BG = 179.f, 148.f, 121.f
+    averageColor_RBC = 141.f, 96.f, 83.f
+    averageColor_Parasite = 123.f, 89.f, 83.f*)
 
     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
 
@@ -60,20 +66,20 @@ let defaultParameters = {
     maxRbcRadius = 0.3f
 
     LPFStandardDeviationParasite = 0.15<μm>
-    LPFStandardDeviationStain = 0.15<μm> // 0.12
-    LPFStandardDeviationRBC = 0.2<μm> // 8.5e-6<inch>. // 0.2<μm>
+    LPFStandardDeviationRBC = 0.2<μm>
 
     factorNbPick = 1.0
 
-    darkStainLevel = 0.25 // 0.3
+    darkStainLevel = 0.25
     maxDarkStainRatio = 0.1 // 10 %
 
-    infectionArea = 0.01f // 0.8 % // 0.012f
-    infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94
+    parasiteRadiusRatio = 0.5f // 40 %
+
+    minimumParasiteAreaRatio = 0.02f // 2 %
+    cytoplasmSensitivity = 0.96 //  1) 0.91, 2) 0.92
 
-    stainArea = 0.08f // 6 % // 0.08f
-    stainSensitivity = 0.96 //  1) 0.91, 2) 0.92
-    maxStainRatio = 0.12 // 12 %
+    nucleusAreaRatio = 0.01f // 1.0 %
+    infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94
 
     standardDeviationMaxRatio = 0.5 // 0.5
     minimumCellAreaFactor = 0.4f }
@@ -89,8 +95,10 @@ type RBCRadius (radius: float32, parameters: Parameters) =
     member this.Area = PI * radius ** 2.f
     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
 
-    member this.InfectionArea = parameters.infectionArea * this.Area
-    member this.StainArea = parameters.stainArea * this.Area
+    member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
+
+    member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
+    member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
 
     override this.ToString() =
         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
@@ -120,10 +128,6 @@ type Config (param: Parameters) =
         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
         float stdDeviation
 
-    member this.LPFStandardDeviationStain =
-        let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationStain) * parameters.resolution
-        float stdDeviation
-
     member this.LPFStandardDeviationRBC =
         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
         float stdDeviation