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     parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius.
  38
  39     minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  40     cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  41
  42     nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  43     infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive).
  44
  45     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
  46     minimumCellAreaFactor: float32 // Factor of the mean RBC area. A cell with an area below this will be rejected.
  47 }
  48
  49 let defaultParameters = {
  50     rbcDiameter = 8.<μm>
  51     resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
  52
  53     colorContribution_BG_RBC = (* 0., 1., 0. *) 0.16, 0.44, 0.4
  54     colorContribution_RBC_parasite = (* 1., 0., 0. *) 0.54, 0.41, 0.05
  55
  56     ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  57
  58     granulometryRange = 0.5f
  59
  60     minRbcRadius = -0.3f
  61     maxRbcRadius = 0.3f
  62
  63     LPFStandardDeviationParasite = 0.15<μm>
  64     LPFStandardDeviationStain = 0.15<μm> // 0.12
  65     LPFStandardDeviationRBC = 0.2<μm> // 8.5e-6<inch>. // 0.2<μm>
  66
  67     factorNbPick = 1.0
  68
  69     darkStainLevel = 0.25 // 0.3
  70     maxDarkStainRatio = 0.1 // 10 %
  71
  72     parasiteRadiusRatio = 0.5f // 40 %
  73
  74     minimumParasiteAreaRatio = 0.02f // 2 %
  75     cytoplasmSensitivity = 0.96 //  1) 0.91, 2) 0.92
  76
  77     nucleusAreaRatio = 0.01f // 1.0 %
  78     infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94
  79
  80     standardDeviationMaxRatio = 0.5 // 0.5
  81     minimumCellAreaFactor = 0.4f }
  82
  83 type RBCRadius (radius: float32, parameters: Parameters) =
  84     member this.Pixel = radius
  85     member this.μm : float<μm> =
  86         1.<px> * (float radius) / parameters.resolution |> inchToμm
  87
  88     member this.Min = radius + parameters.minRbcRadius * radius
  89     member this.Max = radius + parameters.maxRbcRadius * radius
  90
  91     member this.Area = PI * radius ** 2.f
  92     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  93
  94     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  95
  96     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
  97     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
  98
  99     override this.ToString() =
 100         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
 101
 102 type Config (param: Parameters) =
 103     let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float<ppi>) : float32 =
 104         let rbcRadiusInch: float<inch> = (μmToInch rbcDiameter) / 2.
 105         let rbcRadiusPx: float<px> = resolution * rbcRadiusInch
 106         float32 rbcRadiusPx
 107
 108     let mutable parameters: Parameters = param
 109     let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 110     let mutable rbcRadius = RBCRadius(0.f, parameters)
 111
 112     new () = Config(defaultParameters)
 113
 114     member this.Parameters
 115         with get() = parameters
 116         and set(param) =
 117             parameters <- param
 118             rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 119             rbcRadius <- RBCRadius(rbcRadius.Pixel, param)
 120
 121     member val Debug = DebugOff with get, set
 122
 123     member this.LPFStandardDeviationParasite =
 124         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 125         float stdDeviation
 126
 127     member this.LPFStandardDeviationStain =
 128         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationStain) * parameters.resolution
 129         float stdDeviation
 130
 131     member this.LPFStandardDeviationRBC =
 132         let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 133         float stdDeviation
 134
 135     member this.RBCRadiusByResolution = rbcRadiusByResolution
 136     member this.RBCRadius = rbcRadius
 137
 138     member this.SetRBCRadius (radiusPixel: float32) =
 139         rbcRadius <- RBCRadius(radiusPixel, parameters)
 140
 141     member this.Copy () =
 142         this.MemberwiseClone() :?> Config
 143