67b9ce3df31bcbd23bbc1d0e1ac3546c524ccc82
[master-thesis.git] / 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 = 0.06 //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