open Emgu.CV
open Emgu.CV.Structure
-open Logger
-
open Utils
+open Histogram
+open Otsu
+open Morpho
+open ImgTools
-type Result = {
- darkStain: Image<Gray, byte>
- infection: Image<Gray, byte>
- stain: Image<Gray, byte> }
-
-// 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 = Log.LogWithTime("Finding fg/bg (k-medians)", Severity.USER, (fun () -> 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>()
+type Result =
+ {
+ 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.
+ parasite : Image<Gray, byte> // The whole parasites.
+ }
- { darkStain = darkStain;
- stain = findSmears 10. 0.9
- infection = findSmears 2.2 0.87 },
- tmp,
- tmp
+let find (img : Image<Gray, float32>) (config : Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
-// 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 (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> =
- use filteredGreenWithoutInfection = filteredGreen.Copy()
- ImgTools.areaCloseF filteredGreenWithoutInfection (int config.RBCRadius.InfectionArea)
-
- let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
- ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea)
+ let imgWithoutNucleus = img.Copy ()
+ areaCloseF imgWithoutNucleus (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
- ImgTools.otsu hist
- filteredGreenWithoutInfection.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._Mul(level)
- CvInvoke.Subtract(closed, diff, diff)
- diff._ThresholdBinary(Gray(0.0), Gray(255.))
- diff.Convert<Gray, byte>()
-
- let infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
- let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity)
-
- // TODO: comprendre pourquoi des valeurs sont negatives!?!?
- (*
- let blackTopHat = filteredGreen.CopyBlank()
- CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
- ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
- *)
-
- { darkStain = darkStain
- infection = infectionMarker
- stain = stainMarker },
- filteredGreenWithoutStain
+ let hist = histogramImg imgWithoutNucleus 300
+ otsu hist
+ imgWithoutNucleus.Cmp (float mean_fg - config.Parameters.darkStainLevel * float (mean_bg - 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._Mul level
+ CvInvoke.Subtract (closed, diff, diff)
+ diff._ThresholdBinary (Gray 0.0, Gray 255.)
+ diff.Convert<Gray, byte> ()
+
+ // Nucleus.
+ let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
+
+ // Cytoplasm.
+ let imgWithoutParasite = img.CopyBlank ()
+ let kernelSize =
+ let size = roundInt config.RBCRadius.CytoplasmSize
+ if size % 2 = 0 then size + 1 else size
+ use kernel =
+ if kernelSize <= 3 then
+ CvInvoke.GetStructuringElement (CvEnum.ElementShape.Rectangle, Size (3, 3), Point (-1, -1))
+ else
+ CvInvoke.GetStructuringElement (CvEnum.ElementShape.Ellipse, Size (kernelSize, kernelSize), Point (-1, -1))
+
+ CvInvoke.MorphologyEx (img, imgWithoutParasite, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
+ let parasiteMarker = marker img imgWithoutParasite (1. / config.Parameters.cytoplasmSensitivity)
+
+ {
+ darkStain = darkStain
+ nucleus = nucleusMarker
+ parasite = parasiteMarker
+ },
+ imgWithoutParasite,
+ imgWithoutNucleus
projects / master-thesis.git / blobdiff