Parasitemia/Parasitemia/Config.fs

   1 module 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     ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
  17
  18     granulometryRange: float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius.
  19
  20     minRbcRadius: float32 // Factor of the mean RBC radius.
  21     maxRbcRadius: float32 // Factor of the mean RBC radius.
  22
  23     LPFStandardDeviation: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
  24
  25     // Ellipse.
  26     factorNbPick: float // The number of computed ellipse per edge pixel.
  27
  28     // Parasites detection.
  29     darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
  30     maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC.
  31
  32     stainArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  33     stainSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  34     maxStainRatio: float // A cell must own less than this ratio to be a RBC.
  35
  36     infectionArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  37     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  38
  39     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  40     minimumCellAreaFactor: float32 // Factor of the mean RBC area. A cell with an area below this will be rejected.
  41 }
  42
  43 let defaultParameters = {
  44     rbcDiameter = 8.<μm>
  45     resolution = 200.e3<ppi> // Correspond to 50X.
  46
  47     ratioAreaPaleCenter = 1.f / 3.f // The ratio between an RBC area and the area of the its pale center.
  48
  49     granulometryRange = 0.5f
  50
  51     minRbcRadius = -0.3f
  52     maxRbcRadius = 0.3f
  53
  54     LPFStandardDeviation = 0.2<μm> // 8.5e-6<inch>.
  55
  56     factorNbPick = 1.0
  57
  58     darkStainLevel = 0.25 // 0.3
  59     maxDarkStainRatio = 0.1 // 10 %
  60
  61     infectionArea = 0.012f // 1.2 %
  62     infectionSensitivity = 0.9
  63
  64     stainArea = 0.08f // 8 %
  65     stainSensitivity = 0.9
  66     maxStainRatio = 0.12 // 12 %
  67
  68     standardDeviationMaxRatio = 0.5 // 0.5
  69     minimumCellAreaFactor = 0.4f }
  70
  71 type RBCRadius (radius: float32, parameters: Parameters) =
  72     member this.Pixel = radius
  73     member this.μm : float<μm> =
  74         1.<px> * (float radius) / parameters.resolution |> inchToμm
  75
  76     member this.Min = radius + parameters.minRbcRadius * radius
  77     member this.Max = radius + parameters.maxRbcRadius * radius
  78
  79     member this.Area = PI * radius ** 2.f
  80     member this.MinArea = parameters.minimumCellAreaFactor * radius
  81
  82     member this.InfectionArea = parameters.infectionArea * this.Area
  83     member this.StainArea = parameters.stainArea * this.Area
  84
  85     override this.ToString() =
  86         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
  87
  88
  89 type Config (param: Parameters) =
  90     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
  91         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
  92         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
  93         float32 rbcRadiusPx
  94
  95     let mutable parameters: Parameters = param
  96     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
  97     let mutable rbcRadius = RBCRadius(0.f, parameters)
  98
  99     new () = Config(defaultParameters)
 100
 101     member this.Parameters
 102         with get() = parameters
 103         and set(param) =
 104             parameters <- param
 105             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 106             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 107
 108     member val Debug = DebugOff with get, set
 109
 110     member this.LPFStandardDeviation =
 111         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviation) * parameters.resolution
 112         float stdDeviation
 113
 114     member this.RBCRadiusByResolution = rbcRadiusByResolution
 115     member this.RBCRadius = rbcRadius
 116
 117     member this.SetRBCRadius (radiusPixel: float32) =
 118         rbcRadius <- RBCRadius(radiusPixel, parameters)
 119
 120     member this.Copy () =
 121         this.MemberwiseClone() :?> Config
 122