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     cytoplasmSizeRatio: float32
  39     cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  40
  41     nucleusAreaRatio: 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     // [<Obsolete>] 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 let defaultParameters = {
  48     rbcDiameter = 7.5<μm>
  49     resolution = 230.e3<ppi> // 230.e3<ppi> Correspond to 50X.
  50
  51     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  52
  53     granulometryRange = 0.5f
  54
  55     minRbcRadius = -0.23f
  56     maxRbcRadius = 0.23f
  57
  58     LPFStandardDeviationParasite = 0.15<μm>
  59     LPFStandardDeviationRBC = 0.22<μm>
  60
  61     nbPickElementsMin = 10
  62     factorNbValidPick = 0.06 //1.0
  63     factorNbMaxPick = 4.
  64
  65     darkStainLevel = 1.
  66     maxDarkStainRatio = 0.1 // 10 %
  67
  68     parasiteRadiusRatio = 0.5f // 50 %
  69     minimumParasiteAreaRatio = 0.02f // 2 %
  70
  71     cytoplasmSizeRatio = 1.f / 5.f
  72     cytoplasmSensitivity = 0.96
  73
  74     nucleusAreaRatio = 0.01f // 1.0 %
  75     infectionSensitivity = 0.92
  76
  77     // standardDeviationMaxRatio = 0.6 // Obsolete.
  78     minimumCellAreaFactor = 0.4f }
  79
  80 type RBCRadius (radius: float32, parameters: Parameters) =
  81     member this.Pixel = radius
  82     member this.μm : float<μm> =
  83         1.<px> * (float radius) / parameters.resolution |> inchToμm
  84
  85     member this.Min = radius + parameters.minRbcRadius * radius
  86     member this.Max = radius + parameters.maxRbcRadius * radius
  87
  88     member this.Area = PI * radius ** 2.f
  89     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  90
  91     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  92     member this.CytoplasmSize = parameters.cytoplasmSizeRatio * radius
  93
  94     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
  95     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
  96
  97     override this.ToString() =
  98         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
  99
 100 type Config (param: Parameters) =
 101     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
 102         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
 103         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
 104         float32 rbcRadiusPx
 105
 106     let mutable parameters: Parameters = param
 107     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 108     let mutable rbcRadius = RBCRadius(0.f, parameters)
 109
 110     new () = Config(defaultParameters)
 111
 112     member this.Parameters
 113         with get() = parameters
 114         and set(param) =
 115             parameters <- param
 116             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 117             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 118
 119     member val Debug = DebugOff with get, set
 120
 121     member this.LPFStandardDeviationParasite =
 122         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 123         float stdDeviation
 124
 125     member this.LPFStandardDeviationRBC =
 126         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 127         float stdDeviation
 128
 129     member this.RBCRadiusByResolution = rbcRadiusByResolution
 130     member this.RBCRadius = rbcRadius
 131
 132     member this.SetRBCRadius (radiusPixel: float32) =
 133         rbcRadius <- RBCRadius(radiusPixel, parameters)
 134
 135     member this.Copy () =
 136         this.MemberwiseClone() :?> Config
 137