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     {
  14         rbcDiameter : float<μm>
  15         resolution : float<ppi>
  16
  17         ratioAreaPaleCenter : float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
  18
  19         granulometryRange : float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius.
  20
  21         minRbcRadius : float32 // Factor of the mean RBC radius.
  22         maxRbcRadius : float32 // Factor of the mean RBC radius.
  23
  24         LPFStandardDeviationParasite : float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
  25         LPFStandardDeviationRBC : float<μm>
  26
  27         // Ellipse.
  28         nbPickElementsMin : int
  29         factorNbValidPick : float // The number of computed ellipse per edge pixel.
  30         factorNbMaxPick : float
  31
  32         // Parasites detection.
  33         darkStainLevel : float // Lower -> more sensitive. Careful about illumination on the borders.
  34         maxDarkStainRatio : float // When a cell must own less than this ratio to be a RBC.
  35
  36         parasiteRadiusRatio : float32 // The ratio of the parasite radius of the RBC radius.
  37         minimumParasiteAreaRatio : float32 // Factor of a RBC area. 0.5 means the half of RBC area.
  38
  39         cytoplasmSizeRatio : float32
  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         // [<Obsolete>] 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     {
  51         rbcDiameter = 7.5<μm>
  52         resolution = 230.e3<ppi> // 230.e3<ppi> Correspond to 50X.
  53
  54         ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
  55
  56         granulometryRange = 0.5f
  57
  58         minRbcRadius = -0.23f
  59         maxRbcRadius = 0.23f
  60
  61         LPFStandardDeviationParasite = 0.15<μm>
  62         LPFStandardDeviationRBC = 0.22<μm>
  63
  64         nbPickElementsMin = 10
  65         factorNbValidPick = 0.06 //1.0
  66         factorNbMaxPick = 4.
  67
  68         darkStainLevel = 1.
  69         maxDarkStainRatio = 0.1 // 10 %
  70
  71         parasiteRadiusRatio = 0.5f // 50 %
  72         minimumParasiteAreaRatio = 0.02f // 2 %
  73
  74         cytoplasmSizeRatio = 1.f / 5.f
  75         cytoplasmSensitivity = 0.96
  76
  77         nucleusAreaRatio = 0.01f // 1.0 %
  78         infectionSensitivity = 0.92
  79
  80         // standardDeviationMaxRatio = 0.6 // Obsolete.
  81         minimumCellAreaFactor = 0.4f
  82     }
  83
  84 type RBCRadius (radius : float32, parameters : Parameters) =
  85     member this.Pixel = radius
  86     member this.μm : float<μm> =
  87         1.<px> * (float radius) / parameters.resolution |> inchToμm
  88
  89     member this.Min = radius + parameters.minRbcRadius * radius
  90     member this.Max = radius + parameters.maxRbcRadius * radius
  91
  92     member this.Area = PI * radius ** 2.f
  93     member this.MinArea = parameters.minimumCellAreaFactor * this.Area
  94
  95     member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius
  96     member this.CytoplasmSize = parameters.cytoplasmSizeRatio * radius
  97
  98     member this.NucleusArea = parameters.nucleusAreaRatio * this.Area
  99     member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area
 100
 101     override this.ToString () =
 102         sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm)
 103
 104 type Config (param : Parameters) =
 105     let RBCadiusInPixels (rbcDiameter : float<μm>) (resolution : float<ppi>) : float32 =
 106         let rbcRadiusInch : float<inch> = (μmToInch rbcDiameter) / 2.
 107         let rbcRadiusPx : float<px> = resolution * rbcRadiusInch
 108         float32 rbcRadiusPx
 109
 110     let mutable parameters : Parameters = param
 111     let mutable rbcRadiusByResolution = RBCRadius (RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters)
 112     let mutable rbcRadius = RBCRadius (0.f, parameters)
 113
 114     new () = Config defaultParameters
 115
 116     member this.Parameters
 117         with get () = parameters
 118         and set param =
 119             parameters <- param
 120             rbcRadiusByResolution <- RBCRadius (RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param)
 121             rbcRadius <- RBCRadius (rbcRadius.Pixel, param)
 122
 123     member val Debug = DebugOff with get, set
 124
 125     member this.LPFStandardDeviationParasite =
 126         let stdDeviation : float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
 127         float stdDeviation
 128
 129     member this.LPFStandardDeviationRBC =
 130         let stdDeviation : float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
 131         float stdDeviation
 132
 133     member this.RBCRadiusByResolution = rbcRadiusByResolution
 134     member this.RBCRadius = rbcRadius
 135
 136     member this.SetRBCRadius (radiusPixel : float32) =
 137         rbcRadius <- RBCRadius (radiusPixel, parameters)
 138
 139     member this.Copy () =
 140         this.MemberwiseClone () :?> Config
 141
 142     override this.ToString () =
 143         $"{{{nameof Config}: " +
 144         $"{nameof this.LPFStandardDeviationParasite} = {this.LPFStandardDeviationParasite}, " +
 145         $"{nameof this.LPFStandardDeviationRBC} = {this.LPFStandardDeviationRBC}, " +
 146         $"{nameof this.RBCRadiusByResolution} = {this.RBCRadiusByResolution}, " +
 147         $"{nameof this.RBCRadius} = {this.RBCRadius}, " +
 148         $"{nameof this.Parameters} = {this.Parameters}}}"