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> }
+
// 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 (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result =
+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 } = kmediansResult
- let darkStain = d_fg.Cmp(median_bg * config.darkStainLevel, CvEnum.CmpType.GreaterThan)
+ let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
+ 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 * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
darkStain._And(fg)
smears._And(fg)
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, byte>) (filteredGreenFloat: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
+
+ let filteredGreenWithoutInfection = filteredGreen.Copy()
+ ImgTools.areaClose filteredGreenWithoutInfection (int config.InfectionArea)
+
+ let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
+ ImgTools.areaClose filteredGreenWithoutStain (int config.StainArea)
+
+ // We use the filtered image to find the dark stain.
+ let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting again this in MainAnalysis
+ 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 * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
+ darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
+
+ let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
+ let diff = closed - (img * level)
+ diff._ThresholdBinary(Gray(0.0), Gray(255.))
+ diff
+
+ let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
+ let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
+
+ { darkStain = darkStain
+ infection = infectionMarker
+ stain = stainMarker },
+ filteredGreenWithoutInfection,
+ filteredGreenWithoutStain
+
+
+
+