then
[]
else
- let infection = parasites.infection.Copy() // To avoid to modify the parameter.
+ let infection = parasites.nucleus.Copy() // To avoid to modify the parameter.
// This is the minimum window size to check if other ellipses touch 'e'.
let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max)
let minX, minY, maxX, maxY = ellipseWindow e
let infectedPixels = List<Point>()
- let
stainPixels = List<Point>()
+ let
cytoplasmPixels = List<Point>()
//let mutable stainPixels = 0
let mutable darkStainPixels = 0
nbElement <- nbElement + 1
let infected = infection.Data.[y, x, 0] > 0uy
- let stain = parasites.stain.Data.[y, x, 0] > 0uy
+ let stain = parasites.cytoplasm.Data.[y, x, 0] > 0uy
let darkStain = parasites.darkStain.Data.[y, x, 0] > 0uy
if infected
if stain
then
- stainPixels.Add(Point(x, y))
+ cytoplasmPixels.Add(Point(x, y))
if darkStain
then
darkStainPixels <- darkStainPixels + 1
- let mutable stainArea = 0
+ let mutable cytoplasmArea = 0
if infectedPixels.Count > 0
then
- for stainPixel in stainPixels do
- if infectedPixels.Exists(fun p -> pown (p.X - stainPixel.X) 2 + pown (p.Y - stainPixel.Y) 2 <= perimeterParasiteSquared)
+ for cytoplasmPixel in cytoplasmPixels do
+ if infectedPixels.Exists(fun p -> pown (p.X - cytoplasmPixel.X) 2 + pown (p.Y - cytoplasmPixel.Y) 2 <= perimeterParasiteSquared)
then
- stainArea <- stainArea + 1
+ cytoplasmArea <- cytoplasmArea + 1
let cellClass =
then
Peculiar
- elif infectedPixels.Count > 0 && stainArea >= minimumParasiteArea
+ elif infectedPixels.Count > 0 && cytoplasmArea >= minimumParasiteArea
then
- let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
+ let infectionToRemove = ImgTools.connectedComponents parasites.cytoplasm infectedPixels
for p in infectionToRemove do
infection.Data.[p.Y, p.X, 0] <- 0uy
InfectedRBC
Some { cellClass = cellClass
center = Point(roundInt e.Cx, roundInt e.Cy)
- infectedArea = if cellClass = InfectedRBC then infectedPixels.Count else 0
- stainArea = stainArea
+ nucleusArea = if cellClass = InfectedRBC then infectedPixels.Count else 0
+ parasiteArea = cytoplasmArea
elements = elements })
rbcDiameter: float<μm>
resolution: float<ppi>
- colorContribution_BG_RBC: float * float * float // (R, G, B).
- colorContribution_RBC_parasite: float * float * float // (R, G, B).
+ averageColor_BG: float32 * float32 * float32 // R * G * B.
+ averageColor_RBC: float32 * float32 * float32 // R * G * B.
+ averageColor_Parasite: float32 * float32 * float32 // R * G * B.
ratioAreaPaleCenter: float32 // The area of the second opening is 'ratioSecondAreaOpen' * mean RBC area. It's applied only if greater than 'initialAreaOpen'.
maxRbcRadius: float32 // Factor of the mean RBC radius.
LPFStandardDeviationParasite: float<μm> // Sigma parameter of the gaussian to remove the high frequency noise.
- LPFStandardDeviationStain: float<μm>
LPFStandardDeviationRBC: float<μm>
// Ellipse.
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.
+
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.
rbcDiameter = 8.<μm>
resolution = 220.e3<ppi> // 220.e3<ppi> Correspond to 50X.
- colorContribution_BG_RBC = (* 0., 1., 0. *) 0.16, 0.44, 0.4
- colorContribution_RBC_parasite = (* 1., 0., 0. *) 0.54, 0.41, 0.05
+ averageColor_BG = 113.3f, 135.3f, 150.3f
+ averageColor_RBC = 94.7f, 80.7f, 99.3f
+ averageColor_Parasite = 76.f, 58.f, 94.f
+
+ (*averageColor_BG = 179.f, 148.f, 121.f
+ averageColor_RBC = 141.f, 96.f, 83.f
+ averageColor_Parasite = 123.f, 89.f, 83.f*)
ratioAreaPaleCenter = 2.f / 5.f // The ratio between an RBC area and the area of the its pale center.
maxRbcRadius = 0.3f
LPFStandardDeviationParasite = 0.15<μm>
- LPFStandardDeviationStain = 0.15<μm> // 0.12
- LPFStandardDeviationRBC = 0.2<μm> // 8.5e-6<inch>. // 0.2<μm>
+ LPFStandardDeviationRBC = 0.2<μm>
factorNbPick = 1.0
- darkStainLevel = 0.25 // 0.3
+ darkStainLevel = 0.25
maxDarkStainRatio = 0.1 // 10 %
parasiteRadiusRatio = 0.5f // 40 %
let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationParasite) * parameters.resolution
float stdDeviation
- member this.LPFStandardDeviationStain =
- let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationStain) * parameters.resolution
- float stdDeviation
-
member this.LPFStandardDeviationRBC =
let stdDeviation: float<px> = (μmToInch parameters.LPFStandardDeviationRBC) * parameters.resolution
float stdDeviation
use img_float = img.Convert<Bgr, float32>()
// use img_RBC = mergeChannels img_float config.Parameters.colorContribution_BG_RBC
- use img_RBC = mergeChannelsWithProjection img_float (94.7f, 80.7f, 99.3f) (113.3f, 135.3f, 150.3f) 255.
+ use img_RBC = mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
let img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
//use img_parasites = mergeChannels img_float config.Parameters.colorContribution_RBC_parasite
- use img_parasites = mergeChannelsWithProjection img_float (76.f, 58.f, 94.f) (94.7f, 80.7f, 99.3f) 255.
+ use img_parasites = mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
saveMat (edges * 255.0) (buildFileName " - edges.png")
saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
- saveImg parasites.stain (buildFileName " - parasites - stain.png")
- saveImg parasites.infection (buildFileName " - parasites - infection.png")
+ saveImg parasites.cytoplasm (buildFileName " - parasites - stain.png")
+ saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
let imgAllEllipses = img.Copy()
drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
open Utils
type Result = {
- darkStain: Image<Gray, byte>
- infection: Image<Gray, byte>
- stain: Image<Gray, byte> }
+ darkStain: Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
+ nucleus: Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
+ cytoplasm: Image<Gray, byte> } // Parasite cytoplasm.
-// Create three binary markers :
-// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
-// * 'Stain' corresponds to the stain around the parasites.
-// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
-let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
- // We use the filtered image to find the dark stain.
- let kmediansResults = KMedians.kmedians filteredGreen
- let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
- let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
- darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
- darkStain._And(fg)
-
- let fgFloat = (fg / 255.0).Convert<Gray, float32>()
- use greenWithoutBg = ImgTools.gaussianFilter green 1.0
- greenWithoutBg.SetValue(Gray(0.0), fg.Not())
-
- let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
- use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
- use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
- let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
- smears._And(fg)
- smears
-
- let tmp = filteredGreen.Convert<Gray, byte>()
-
- { darkStain = darkStain;
- stain = findSmears 10. 0.9
- infection = findSmears 2.2 0.87 },
- tmp,
- tmp
-
-// Create three binary markers :
-// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
-// * 'Stain' corresponds to the stain around the parasites.
-// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
- let imgFilteredInfection = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
- let filteredGreenWithoutInfection = imgFilteredInfection.Copy()
- ImgTools.areaCloseF filteredGreenWithoutInfection (roundInt config.RBCRadius.NucleusArea)
+ let imgFilteredParasite = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
- (*
- let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
- ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea) *)
+ let filteredGreenWithoutNucleus = imgFilteredParasite.Copy()
+ ImgTools.areaCloseF filteredGreenWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
let darkStain =
// We use the filtered image to find the dark stain.
let _, mean_fg, mean_bg =
- let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
+ let hist = ImgTools.histogramImg filteredGreenWithoutNucleus 300
ImgTools.otsu hist
- filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
+ filteredGreenWithoutNucleus.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
let diff = img.Copy()
diff._ThresholdBinary(Gray(0.0), Gray(255.))
diff.Convert<Gray, byte>()
- let infectionMarker = marker imgFilteredInfection filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
-
- let imgFilteredStain = ImgTools.gaussianFilter img config.LPFStandardDeviationStain
- let areaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
- //ImgTools.areaOpenF imgFilteredStain areaOpening
+ let nucleusMarker = marker imgFilteredParasite filteredGreenWithoutNucleus (1. / config.Parameters.infectionSensitivity)
- let filteredGreenWithoutStain = imgFilteredStain.CopyBlank()
+ let filteredGreenWithoutCytoplasm = imgFilteredParasite.CopyBlank()
let kernelSize =
let size = roundInt (config.RBCRadius.Pixel / 5.f)
if size % 2 = 0 then size + 1 else size
else
CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
- CvInvoke.MorphologyEx(imgFilteredStain, filteredGreenWithoutStain, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
- let stainMarker = marker (*filteredGreenWithoutInfection*) imgFilteredStain filteredGreenWithoutStain (1. / config.Parameters.cytoplasmSensitivity)
-
- //
- (*let blackTopHat = filteredGreenWithoutStain.CopyBlank()
- CvInvoke.Subtract(filteredGreenWithoutStain, imgFilteredStain, blackTopHat)
- ImgTools.saveImg blackTopHat "blackTopHat.png"*)
+ CvInvoke.MorphologyEx(imgFilteredParasite, filteredGreenWithoutCytoplasm, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
+ let cytoplasmMarker = marker imgFilteredParasite filteredGreenWithoutCytoplasm (1. / config.Parameters.cytoplasmSensitivity)
{ darkStain = darkStain
- infection = infectionMarker
- stain = stainMarker },
- filteredGreenWithoutStain,
- filteredGreenWithoutInfection
+ nucleus = nucleusMarker
+ cytoplasm = cytoplasmMarker },
+ filteredGreenWithoutCytoplasm,
+ filteredGreenWithoutNucleus
type Cell = {
cellClass: CellClass
center: Point
- infectedArea: int
- stainArea: int
+ nucleusArea: int
+ parasiteArea: int
elements: Matrix<byte> }
[<Struct>]
sourceImage.rbcs <- cells
|> List.filter (fun cell -> match cell.cellClass with ParasitemiaCore.Types.HealthyRBC | ParasitemiaCore.Types.InfectedRBC -> true | _ -> false )
- |> List.sortByDescending (fun cell -> cell.infectedArea, (w - cell.center.X) + (h - cell.center.Y))
+ |> List.sortByDescending (fun cell -> cell.nucleusArea, (w - cell.center.X) + (h - cell.center.Y))
|> List.mapi (fun i cell ->
let center = Point(float cell.center.X, float cell.center.Y)
let infected, setManually =
setManually = setManually
center = center
size = Size(float cell.elements.Width, float cell.elements.Height)
- infectedArea = cell.infectedArea })
+ infectedArea = cell.nucleusArea })
alteredSinceLastSave <- true
projects / master-thesis.git / commitdiff