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     factorNbPick: float // The number of computed ellipse per edge pixel.
  28
  29     // Parasites detection.
  30     darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
  31     maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC.
  32
  33     parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius.
  34     minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  35
  36     cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  37
  38     nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  39     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  40
  41     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  42     minimumCellAreaFactor: float32 } // Factor of the mean RBC area. A cell with an area below this will be rejected.
  43
  44 let defaultParameters = {
  45     rbcDiameter = 7.5<μm>
  46     resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
  47
  48     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  49
  50     granulometryRange = 0.5f
  51
  52     minRbcRadius = -0.3f
  53     maxRbcRadius = 0.3f
  54
  55     LPFStandardDeviationParasite = 0.15<μm>
  56     LPFStandardDeviationRBC = 0.2<μm>
  57
  58     factorNbPick = 1.0
  59
  60     darkStainLevel = 0.25
  61     maxDarkStainRatio = 0.1 // 10 %
  62
  63     parasiteRadiusRatio = 0.5f // 40 %
  64
  65     minimumParasiteAreaRatio = 0.02f // 2 %
  66     cytoplasmSensitivity = 0.96
  67
  68     nucleusAreaRatio = 0.01f // 1.0 %
  69     infectionSensitivity = 0.92
  70
  71     standardDeviationMaxRatio = 0.6
  72     minimumCellAreaFactor = 0.4f }
  73
  74 type RBCRadius (radius: float32, parameters: Parameters) =
  75     member this.Pixel = radius
  76     member this.μm : float<μm> =
  77         1.<px> * (float radius) / parameters.resolution |> inchToμm
  78
  79     member this.Min = radius + parameters.minRbcRadius * radius
  80     member this.Max = radius + parameters.maxRbcRadius * radius
  81
  82     member this.Area = PI * radius ** 2.f
  83     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  84
  85     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  86
  87     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
  88     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
  89
  90     override this.ToString() =
  91         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
  92
  93 type Config (param: Parameters) =
  94     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
  95         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
  96         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
  97         float32 rbcRadiusPx
  98
  99     let mutable parameters: Parameters = param
 100     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 101     let mutable rbcRadius = RBCRadius(0.f, parameters)
 102
 103     new () = Config(defaultParameters)
 104
 105     member this.Parameters
 106         with get() = parameters
 107         and set(param) =
 108             parameters <- param
 109             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 110             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 111
 112     member val Debug = DebugOff with get, set
 113
 114     member this.LPFStandardDeviationParasite =
 115         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 116         float stdDeviation
 117
 118     member this.LPFStandardDeviationRBC =
 119         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 120         float stdDeviation
 121
 122     member this.RBCRadiusByResolution = rbcRadiusByResolution
 123     member this.RBCRadius = rbcRadius
 124
 125     member this.SetRBCRadius (radiusPixel: float32) =
 126         rbcRadius <- RBCRadius(radiusPixel, parameters)
 127
 128     member this.Copy () =
 129         this.MemberwiseClone() :?> Config
 130