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     colorContribution_BG_RBC: float * float * float // (R, G, B).
  17     colorContribution_RBC_parasite: float * float * float // (R, G, B).
  18
  19     ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
  20
  21     granulometryRange: float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius.
  22
  23     minRbcRadius: float32 // Factor of the mean RBC radius.
  24     maxRbcRadius: float32 // Factor of the mean RBC radius.
  25
  26     LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
  27     LPFStandardDeviationStain: float<μm>
  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     stainArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  38     stainSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  39     maxStainRatio: float // A cell must own less than this ratio to be a RBC.
  40
  41     infectionArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  42     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  43
  44     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  45     minimumCellAreaFactor: float32 // Factor of the mean RBC area. A cell with an area below this will be rejected.
  46 }
  47
  48 let defaultParameters = {
  49     rbcDiameter = 8.<μm>
  50     resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
  51
  52     colorContribution_BG_RBC = 0.16, 0.44, 0.4
  53     colorContribution_RBC_parasite = 0.54, 0.41, 0.05
  54
  55     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  56
  57     granulometryRange = 0.5f
  58
  59     minRbcRadius = -0.3f
  60     maxRbcRadius = 0.3f
  61
  62     LPFStandardDeviationParasite = 0.15<μm>
  63     LPFStandardDeviationStain = 0.15<μm> // 0.12
  64     LPFStandardDeviationRBC = 0.2<μm> // 8.5e-6<inch>. // 0.2<μm>
  65
  66     factorNbPick = 1.0
  67
  68     darkStainLevel = 0.25 // 0.3
  69     maxDarkStainRatio = 0.1 // 10 %
  70
  71     infectionArea = 0.01f // 0.8 % // 0.012f
  72     infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94
  73
  74     stainArea = 0.08f // 6 % // 0.08f
  75     stainSensitivity = 0.96 //  1) 0.91, 2) 0.92
  76     maxStainRatio = 0.12 // 12 %
  77
  78     standardDeviationMaxRatio = 0.5 // 0.5
  79     minimumCellAreaFactor = 0.4f }
  80
  81 type RBCRadius (radius: float32, parameters: Parameters) =
  82     member this.Pixel = radius
  83     member this.μm : float<μm> =
  84         1.<px> * (float radius) / parameters.resolution |> inchToμm
  85
  86     member this.Min = radius + parameters.minRbcRadius * radius
  87     member this.Max = radius + parameters.maxRbcRadius * radius
  88
  89     member this.Area = PI * radius ** 2.f
  90     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  91
  92     member this.InfectionArea = parameters.infectionArea * this.Area
  93     member this.StainArea = parameters.stainArea * this.Area
  94
  95     override this.ToString() =
  96         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
  97
  98 type Config (param: Parameters) =
  99     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
 100         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
 101         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
 102         float32 rbcRadiusPx
 103
 104     let mutable parameters: Parameters = param
 105     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 106     let mutable rbcRadius = RBCRadius(0.f, parameters)
 107
 108     new () = Config(defaultParameters)
 109
 110     member this.Parameters
 111         with get() = parameters
 112         and set(param) =
 113             parameters <- param
 114             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 115             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 116
 117     member val Debug = DebugOff with get, set
 118
 119     member this.LPFStandardDeviationParasite =
 120         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 121         float stdDeviation
 122
 123     member this.LPFStandardDeviationStain =
 124         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationStain) * parameters.resolution
 125         float stdDeviation
 126
 127     member this.LPFStandardDeviationRBC =
 128         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 129         float stdDeviation
 130
 131     member this.RBCRadiusByResolution = rbcRadiusByResolution
 132     member this.RBCRadius = rbcRadius
 133
 134     member this.SetRBCRadius (radiusPixel: float32) =
 135         rbcRadius <- RBCRadius(radiusPixel, parameters)
 136
 137     member this.Copy () =
 138         this.MemberwiseClone() :?> Config
 139