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
projects / master-thesis.git / blobdiff