module ParasitesMarker
open System.Drawing
+open System.Linq
open Emgu.CV
open Emgu.CV.Structure
+open Utils
type Result = {
darkStain: Image<Gray, byte>
- stain: Image<Gray, byte>
- infection: Image<Gray, byte> }
+ infection: Image<Gray, byte>
+ stain: Image<Gray, byte> }
-let find (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result =
+// 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 { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = KMedians.kmedians filteredGreen 1.0
- let darkStain = d_fg.Cmp(median_bg * config.darkStainLevel, CvEnum.CmpType.GreaterThan)
+ let kmediansResults = logTime "Finding fg/bg (k-medians)" (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>()
- let greenWithoutBg = green.Copy()
+ use greenWithoutBg = ImgTools.gaussianFilter green 1.0
greenWithoutBg.SetValue(Gray(0.0), fg.Not())
- let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
- let greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
- let fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
-
+ 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
+ smears
+
+ let tmp = filteredGreen.Convert<Gray, byte>()
{ darkStain = darkStain;
- stain = findSmears config.stainSigma config.stainLevel
- infection = findSmears config.infectionSigma config.infectionLevel }
-
+ 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 (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> =
+ use filteredGreenWithoutInfection = filteredGreen.Copy()
+ ImgTools.areaCloseF filteredGreenWithoutInfection (int config.InfectionArea)
+
+ let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
+ ImgTools.areaCloseF filteredGreenWithoutStain (int config.StainArea)
+
+ 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 config.Parameters.infectionLevel
+ let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
+
+ // 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