Parasitemia/ParasitemiaCore/Config.fs

   1 module ParasitemiaCore.Config
   2
   3 open System
   4
   5 open Const
   6 open UnitsOfMeasure
   7
   8 type Debug =
   9     | DebugOff
  10     | DebugOn of string // Output directory.
  11
  12 type Parameters = {
  13     rbcDiameter: float<μm>
  14     resolution: float<ppi>
  15
  16     averageColor_BG: float32 * float32 * float32 // R * G * B.
  17     averageColor_RBC: float32 * float32 * float32 // R * G * B.
  18     averageColor_Parasite: float32 * float32 * float32 // R * G * B.
  19
  20     ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
  21
  22     granulometryRange: float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius.
  23
  24     minRbcRadius: float32 // Factor of the mean RBC radius.
  25     maxRbcRadius: float32 // Factor of the mean RBC radius.
  26
  27     LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
  28     LPFStandardDeviationRBC: float<μm>
  29
  30     // Ellipse.
  31     factorNbPick: float // The number of computed ellipse per edge pixel.
  32
  33     // Parasites detection.
  34     darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
  35     maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC.
  36
  37     parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius.
  38     minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  39
  40     cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  41
  42     nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  43     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  44
  45     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  46     minimumCellAreaFactor: float32 // Factor of the mean RBC area. A cell with an area below this will be rejected.
  47 }
  48
  49 let defaultParameters = {
  50     rbcDiameter = 8.<μm>
  51     resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
  52
  53     averageColor_BG = 113.3f, 135.3f, 150.3f
  54     averageColor_RBC = 94.7f, 80.7f, 99.3f
  55     averageColor_Parasite = 76.f, 58.f, 94.f
  56
  57     (*averageColor_BG = 179.f, 148.f, 121.f
  58     averageColor_RBC = 141.f, 96.f, 83.f
  59     averageColor_Parasite = 123.f, 89.f, 83.f*)
  60
  61     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  62
  63     granulometryRange = 0.5f
  64
  65     minRbcRadius = -0.3f
  66     maxRbcRadius = 0.3f
  67
  68     LPFStandardDeviationParasite = 0.15<μm>
  69     LPFStandardDeviationRBC = 0.2<μm>
  70
  71     factorNbPick = 1.0
  72
  73     darkStainLevel = 0.25
  74     maxDarkStainRatio = 0.1 // 10 %
  75
  76     parasiteRadiusRatio = 0.5f // 40 %
  77
  78     minimumParasiteAreaRatio = 0.02f // 2 %
  79     cytoplasmSensitivity = 0.96 //  1) 0.91, 2) 0.92
  80
  81     nucleusAreaRatio = 0.01f // 1.0 %
  82     infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94
  83
  84     standardDeviationMaxRatio = 0.5 // 0.5
  85     minimumCellAreaFactor = 0.4f }
  86
  87 type RBCRadius (radius: float32, parameters: Parameters) =
  88     member this.Pixel = radius
  89     member this.μm : float<μm> =
  90         1.<px> * (float radius) / parameters.resolution |> inchToμm
  91
  92     member this.Min = radius + parameters.minRbcRadius * radius
  93     member this.Max = radius + parameters.maxRbcRadius * radius
  94
  95     member this.Area = PI * radius ** 2.f
  96     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  97
  98     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  99
 100     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
 101     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
 102
 103     override this.ToString() =
 104         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
 105
 106 type Config (param: Parameters) =
 107     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
 108         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
 109         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
 110         float32 rbcRadiusPx
 111
 112     let mutable parameters: Parameters = param
 113     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 114     let mutable rbcRadius = RBCRadius(0.f, parameters)
 115
 116     new () = Config(defaultParameters)
 117
 118     member this.Parameters
 119         with get() = parameters
 120         and set(param) =
 121             parameters <- param
 122             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 123             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 124
 125     member val Debug = DebugOff with get, set
 126
 127     member this.LPFStandardDeviationParasite =
 128         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 129         float stdDeviation
 130
 131     member this.LPFStandardDeviationRBC =
 132         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 133         float stdDeviation
 134
 135     member this.RBCRadiusByResolution = rbcRadiusByResolution
 136     member this.RBCRadius = rbcRadius
 137
 138     member this.SetRBCRadius (radiusPixel: float32) =
 139         rbcRadius <- RBCRadius(radiusPixel, parameters)
 140
 141     member this.Copy () =
 142         this.MemberwiseClone() :?> Config
 143