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     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     LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
  24     LPFStandardDeviationRBC: float<μm>
  25
  26     // Ellipse.
  27     nbPickElementsMin: int
  28     factorNbValidPick: float // The number of computed ellipse per edge pixel.
  29     factorNbMaxPick: float
  30
  31     // Parasites detection.
  32     darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
  33     maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC.
  34
  35     parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius.
  36     minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  37
  38     cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  39
  40     nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  41     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  42
  43     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  44     minimumCellAreaFactor: float32 } // Factor of the mean RBC area. A cell with an area below this will be rejected.
  45
  46 let defaultParameters = {
  47     rbcDiameter = 7.5<μm>
  48     resolution = 230.e3<ppi> // 230.e3<ppi> Correspond to 50X.
  49
  50     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  51
  52     granulometryRange = 0.5f
  53
  54     minRbcRadius = -0.23f
  55     maxRbcRadius = 0.23f
  56
  57     LPFStandardDeviationParasite = 0.15<μm>
  58     LPFStandardDeviationRBC = 0.22<μm>
  59
  60     nbPickElementsMin = 10
  61     factorNbValidPick = 0.05 //1.0
  62     factorNbMaxPick = 2.
  63
  64     darkStainLevel = 0.25
  65     maxDarkStainRatio = 0.1 // 10 %
  66
  67     parasiteRadiusRatio = 0.5f // 40 %
  68
  69     minimumParasiteAreaRatio = 0.02f // 2 %
  70     cytoplasmSensitivity = 0.96
  71
  72     nucleusAreaRatio = 0.01f // 1.0 %
  73     infectionSensitivity = 0.92
  74
  75     standardDeviationMaxRatio = 0.6
  76     minimumCellAreaFactor = 0.4f }
  77
  78 type RBCRadius (radius: float32, parameters: Parameters) =
  79     member this.Pixel = radius
  80     member this.μm : float<μm> =
  81         1.<px> * (float radius) / parameters.resolution |> inchToμm
  82
  83     member this.Min = radius + parameters.minRbcRadius * radius
  84     member this.Max = radius + parameters.maxRbcRadius * radius
  85
  86     member this.Area = PI * radius ** 2.f
  87     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  88
  89     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  90
  91     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
  92     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
  93
  94     override this.ToString() =
  95         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
  96
  97 type Config (param: Parameters) =
  98     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
  99         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
 100         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
 101         float32 rbcRadiusPx
 102
 103     let mutable parameters: Parameters = param
 104     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 105     let mutable rbcRadius = RBCRadius(0.f, parameters)
 106
 107     new () = Config(defaultParameters)
 108
 109     member this.Parameters
 110         with get() = parameters
 111         and set(param) =
 112             parameters <- param
 113             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 114             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 115
 116     member val Debug = DebugOff with get, set
 117
 118     member this.LPFStandardDeviationParasite =
 119         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 120         float stdDeviation
 121
 122     member this.LPFStandardDeviationRBC =
 123         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 124         float stdDeviation
 125
 126     member this.RBCRadiusByResolution = rbcRadiusByResolution
 127     member this.RBCRadius = rbcRadius
 128
 129     member this.SetRBCRadius (radiusPixel: float32) =
 130         rbcRadius <- RBCRadius(radiusPixel, parameters)
 131
 132     member this.Copy () =
 133         this.MemberwiseClone() :?> Config
 134