X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FConfig.fs;h=e000d657334cdb0c044b2094dd54a32850b23c28;hp=1110096ea4d826ec40277263f4a5cd59fcec8d52;hb=2d712781def419c9acc98368f7102b19b064f16d;hpb=3b645f8ff5259f88a33ffbd9a63b10a8640c439f diff --git a/Parasitemia/ParasitemiaCore/Config.fs b/Parasitemia/ParasitemiaCore/Config.fs index 1110096..e000d65 100644 --- a/Parasitemia/ParasitemiaCore/Config.fs +++ b/Parasitemia/ParasitemiaCore/Config.fs @@ -9,78 +9,79 @@ type Debug = | DebugOff | DebugOn of string // Output directory. -type Parameters = { - rbcDiameter: float<μm> - resolution: float +type Parameters = + { + rbcDiameter : float<μm> + resolution : float - colorContribution_BG_RBC: float * float * float // (R, G, B). - colorContribution_RBC_parasite: float * float * float // (R, G, B). + ratioAreaPaleCenter : float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'. - ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'. + granulometryRange : float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius. - granulometryRange: float32 // The radius will be seeked from radius - granulometryRange * radius to radius + granulometryRange * radius. + minRbcRadius : float32 // Factor of the mean RBC radius. + maxRbcRadius : float32 // Factor of the mean RBC radius. - minRbcRadius: float32 // Factor of the mean RBC radius. - maxRbcRadius: float32 // Factor of the mean RBC radius. + LPFStandardDeviationParasite : float<μm> // Sigma parameter of the gaussian to remove the high frequency noise. + LPFStandardDeviationRBC : float<μm> - LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise. - LPFStandardDeviationStain: float<μm> - LPFStandardDeviationRBC: float<μm> + // Ellipse. + nbPickElementsMin : int + factorNbValidPick : float // The number of computed ellipse per edge pixel. + factorNbMaxPick : float - // Ellipse. - factorNbPick: float // The number of computed ellipse per edge pixel. + // Parasites detection. + darkStainLevel : float // Lower -> more sensitive. Careful about illumination on the borders. + maxDarkStainRatio : float // When a cell must own less than this ratio to be a RBC. - // Parasites detection. - darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders. - maxDarkStainRatio: float // When a cell must own less than this ratio to be a RBC. + parasiteRadiusRatio : float32 // The ratio of the parasite radius of the RBC radius. + minimumParasiteAreaRatio : float32 // Factor of a RBC area. 0.5 means the half of RBC area. - parasiteRadiusRatio: float32 // The ratio of the parasite radius of the RBC radius. + cytoplasmSizeRatio : float32 + cytoplasmSensitivity : float // between 0 (the least sensitive) and 1 (the most sensitive). - minimumParasiteAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area. - cytoplasmSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive). + nucleusAreaRatio : float32 // Factor of a RBC area. 0.5 means the half of RBC area. + infectionSensitivity : float // between 0 (the least sensitive) and 1 (the most sensitive). - nucleusAreaRatio: float32 // Factor of a RBC area. 0.5 means the half of RBC area. - infectionSensitivity: float // between 0 (the least sensitive) and 1 (the most sensitive). + // [] standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation + minimumCellAreaFactor : float32 // Factor of the mean RBC area. A cell with an area below this will be rejected. + } - standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation - minimumCellAreaFactor: float32 // Factor of the mean RBC area. A cell with an area below this will be rejected. -} +let defaultParameters = + { + rbcDiameter = 7.5<μm> + resolution = 230.e3 // 230.e3 Correspond to 50X. -let defaultParameters = { - rbcDiameter = 8.<μm> - resolution = 220.e3 // 220.e3 Correspond to 50X. + ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center. - colorContribution_BG_RBC = (* 0., 1., 0. *) 0.16, 0.44, 0.4 - colorContribution_RBC_parasite = (* 1., 0., 0. *) 0.54, 0.41, 0.05 + granulometryRange = 0.5f - ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center. + minRbcRadius = -0.23f + maxRbcRadius = 0.23f - granulometryRange = 0.5f + LPFStandardDeviationParasite = 0.15<μm> + LPFStandardDeviationRBC = 0.22<μm> - minRbcRadius = -0.3f - maxRbcRadius = 0.3f + nbPickElementsMin = 10 + factorNbValidPick = 0.06 //1.0 + factorNbMaxPick = 4. - LPFStandardDeviationParasite = 0.15<μm> - LPFStandardDeviationStain = 0.15<μm> // 0.12 - LPFStandardDeviationRBC = 0.2<μm> // 8.5e-6. // 0.2<μm> + darkStainLevel = 1. + maxDarkStainRatio = 0.1 // 10 % - factorNbPick = 1.0 + parasiteRadiusRatio = 0.5f // 50 % + minimumParasiteAreaRatio = 0.02f // 2 % - darkStainLevel = 0.25 // 0.3 - maxDarkStainRatio = 0.1 // 10 % + cytoplasmSizeRatio = 1.f / 5.f + cytoplasmSensitivity = 0.96 - parasiteRadiusRatio = 0.5f // 40 % + nucleusAreaRatio = 0.01f // 1.0 % + infectionSensitivity = 0.92 - minimumParasiteAreaRatio = 0.02f // 2 % - cytoplasmSensitivity = 0.96 // 1) 0.91, 2) 0.92 + // standardDeviationMaxRatio = 0.6 // Obsolete. + minimumCellAreaFactor = 0.4f + } - nucleusAreaRatio = 0.01f // 1.0 % - infectionSensitivity = 0.9 // 1) 0.93, 2) 0.94 - - standardDeviationMaxRatio = 0.5 // 0.5 - minimumCellAreaFactor = 0.4f } - -type RBCRadius (radius: float32, parameters: Parameters) = +type RBCRadius (radius : float32, parameters : Parameters) = member this.Pixel = radius member this.μm : float<μm> = 1. * (float radius) / parameters.resolution |> inchToμm @@ -92,52 +93,49 @@ type RBCRadius (radius: float32, parameters: Parameters) = member this.MinArea = parameters.minimumCellAreaFactor * this.Area member this.ParasiteRadius = parameters.parasiteRadiusRatio * radius + member this.CytoplasmSize = parameters.cytoplasmSizeRatio * radius member this.NucleusArea = parameters.nucleusAreaRatio * this.Area member this.MinimumParasiteArea = parameters.minimumParasiteAreaRatio * this.Area - override this.ToString() = + override this.ToString () = sprintf "%d px (%.1f μm)" (Utils.roundInt <| 2.f * radius) (2. * this.μm) -type Config (param: Parameters) = - let RBCadiusInPixels (rbcDiameter: float<μm>) (resolution: float) : float32 = - let rbcRadiusInch: float = (μmToInch rbcDiameter) / 2. - let rbcRadiusPx: float = resolution * rbcRadiusInch +type Config (param : Parameters) = + let RBCadiusInPixels (rbcDiameter : float<μm>) (resolution : float) : float32 = + let rbcRadiusInch : float = (μmToInch rbcDiameter) / 2. + let rbcRadiusPx : float = resolution * rbcRadiusInch float32 rbcRadiusPx - let mutable parameters: Parameters = param - let mutable rbcRadiusByResolution = RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters) - let mutable rbcRadius = RBCRadius(0.f, parameters) + let mutable parameters : Parameters = param + let mutable rbcRadiusByResolution = RBCRadius (RBCadiusInPixels parameters.rbcDiameter parameters.resolution, parameters) + let mutable rbcRadius = RBCRadius (0.f, parameters) - new () = Config(defaultParameters) + new () = Config defaultParameters member this.Parameters - with get() = parameters - and set(param) = + with get () = parameters + and set param = parameters <- param - rbcRadiusByResolution <- RBCRadius(RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param) - rbcRadius <- RBCRadius(rbcRadius.Pixel, param) + rbcRadiusByResolution <- RBCRadius (RBCadiusInPixels parameters.rbcDiameter parameters.resolution, param) + rbcRadius <- RBCRadius (rbcRadius.Pixel, param) member val Debug = DebugOff with get, set member this.LPFStandardDeviationParasite = - let stdDeviation: float = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution - float stdDeviation - - member this.LPFStandardDeviationStain = - let stdDeviation: float = (μmToInch parameters.LPFStandardDeviationStain) * parameters.resolution + let stdDeviation : float = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution float stdDeviation member this.LPFStandardDeviationRBC = - let stdDeviation: float = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution + let stdDeviation : float = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution float stdDeviation member this.RBCRadiusByResolution = rbcRadiusByResolution member this.RBCRadius = rbcRadius - member this.SetRBCRadius (radiusPixel: float32) = - rbcRadius <- RBCRadius(radiusPixel, parameters) + member this.SetRBCRadius (radiusPixel : float32) = + rbcRadius <- RBCRadius (radiusPixel, parameters) member this.Copy () = - this.MemberwiseClone() :?> Config + this.MemberwiseClone () :?> Config