From 000e7091983f20ef75d0eba9bf1c865c76483f24 Mon Sep 17 00:00:00 2001 From: Greg Burri Date: Mon, 1 Feb 2016 10:02:08 +0100 Subject: [PATCH] Change the way the dark stain is marked. --- Parasitemia/ParasitemiaCore/Config.fs | 9 ++++++--- Parasitemia/ParasitemiaCore/MatchingEllipses.fs | 5 +++-- Parasitemia/ParasitemiaCore/ParasitesMarker.fs | 6 ++++-- Parasitemia/ParasitemiaUI/State.fs | 9 +++++---- 4 files changed, 18 insertions(+), 11 deletions(-) diff --git a/Parasitemia/ParasitemiaCore/Config.fs b/Parasitemia/ParasitemiaCore/Config.fs index d50ab0e..21a36f9 100644 --- a/Parasitemia/ParasitemiaCore/Config.fs +++ b/Parasitemia/ParasitemiaCore/Config.fs @@ -35,6 +35,7 @@ type Parameters = { 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. + cytoplasmSizeRatio: float32 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. @@ -61,12 +62,13 @@ let defaultParameters = { factorNbValidPick = 0.06 //1.0 factorNbMaxPick = 4. - darkStainLevel = 0.25 + darkStainLevel = 1.1 maxDarkStainRatio = 0.1 // 10 % - parasiteRadiusRatio = 0.5f // 40 % - + parasiteRadiusRatio = 0.5f // 50 % minimumParasiteAreaRatio = 0.02f // 2 % + + cytoplasmSizeRatio = 1.f / 5.f cytoplasmSensitivity = 0.96 nucleusAreaRatio = 0.01f // 1.0 % @@ -87,6 +89,7 @@ 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 diff --git a/Parasitemia/ParasitemiaCore/MatchingEllipses.fs b/Parasitemia/ParasitemiaCore/MatchingEllipses.fs index af72e57..d4a6a41 100644 --- a/Parasitemia/ParasitemiaCore/MatchingEllipses.fs +++ b/Parasitemia/ParasitemiaCore/MatchingEllipses.fs @@ -12,8 +12,9 @@ open Utils // All ellipses with a score below this are removed. let matchingScoreThresholdPerRadiusUnit = 0.07f // For a radius of 1. // 0.25 let matchingScorePower = 20.f -let windowSizeRadiusFactor = 1.f / 2.f +let windowSizeRadiusFactor = 1.f / 2.f // Used when searching for neighbor ellipses. let minimumDistanceFromCenterRadiusFactor = 1.f / 3.f +let minimumAreaFactor = 1.1f; type private EllipseScoreFlaggedKd (matchingScore: float32, e: Ellipse) = let mutable matchingScore = matchingScore @@ -92,7 +93,7 @@ type MatchingEllipses (radius: float32) = else // Case where ellipses are overlapped. match EEOver.EEOverlapArea e.Ellipse other.Ellipse with - | Some (overlapArea, _, _) when e.Ellipse.Area < 1.1f * overlapArea || other.Ellipse.Area < 1.1f * overlapArea -> + | Some (overlapArea, _, _) when e.Ellipse.Area < minimumAreaFactor * overlapArea || other.Ellipse.Area < minimumAreaFactor * overlapArea -> other.Removed <- true | _ -> () diff --git a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs index 0d7c7ae..2b70682 100644 --- a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs +++ b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs @@ -27,7 +27,7 @@ let find (img: Image) (config: Config.Config) : Result * Image) (closed: Image) (level: float) : Image = let diff = img.Copy() @@ -36,11 +36,13 @@ let find (img: Image) (config: Config.Config) : Result * Image() + // Nucleus. let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity) + // Cytoplasm. let imgWithoutParasite = img.CopyBlank() let kernelSize = - let size = roundInt (config.RBCRadius.Pixel / 5.f) + let size = roundInt config.RBCRadius.CytoplasmSize if size % 2 = 0 then size + 1 else size use kernel = if kernelSize <= 3 diff --git a/Parasitemia/ParasitemiaUI/State.fs b/Parasitemia/ParasitemiaUI/State.fs index 5b6a91c..69662d5 100644 --- a/Parasitemia/ParasitemiaUI/State.fs +++ b/Parasitemia/ParasitemiaUI/State.fs @@ -136,7 +136,7 @@ type State (defaultConfig: ParasitemiaCore.Config.Config) = // To match with previously manually altered RBC. let manuallyAlteredPreviousRBCS = sourceImage.rbcs |> List.filter (fun rbc -> rbc.setManually) let tolerance = (float sourceImage.config.RBCRadius.Pixel) * 0.5 // +/-. - let getPreviousRBC (center: Point) : RBC option = + let getPreviousManuallyAlteredRBC (center: Point) : RBC option = manuallyAlteredPreviousRBCS |> List.tryFind (fun rbc -> rbc.center.X > center.X - tolerance && rbc.center.X < center.X + tolerance && rbc.center.Y > center.Y - tolerance && rbc.center.Y < center.Y + tolerance) @@ -146,9 +146,10 @@ type State (defaultConfig: ParasitemiaCore.Config.Config) = |> List.mapi (fun i cell -> let center = Point(float cell.center.X, float cell.center.Y) let infected, setManually = - match getPreviousRBC center with - | Some rbc -> rbc.infected, true - | _ -> cell.cellClass = ParasitemiaCore.Types.InfectedRBC, false + let infected = cell.cellClass = ParasitemiaCore.Types.InfectedRBC + match getPreviousManuallyAlteredRBC center with + | Some rbc when rbc.infected <> infected -> rbc.infected, true // If it has been previously manually changed and now match the result, the manually flag is removed. + | _ -> infected, false { num = i + 1 infected = infected -- 2.45.2