open Emgu.CV
open Emgu.CV.Structure
+open Utils
+
type Result = {
darkStain: Image<Gray, byte>
infection: Image<Gray, byte>
// * '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>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
+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 { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResult
+ 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(filteredGreenFloat.Cmp(median_fg, CvEnum.CmpType.LessThan))
+ darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
- let marker (area: int) (threshold: float) : Image<Gray, byte> * Image<Gray, byte> =
- let closed = filteredGreen.Copy()
- ImgTools.areaClose closed area
- let diff = closed - filteredGreen
+ let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (threshold: float) : Image<Gray, byte> =
+ let diff = closed - img
let min = ref [| 0. |]
let minLocation = ref <| [| Point() |]
let max = ref [| 0. |]
let maxLocation = ref <| [| Point() |]
diff.MinMax(min, max, minLocation, maxLocation)
+ let max = (!max).[0]
- let valueThreshold = if (!max).[0] * threshold < 0.1 * (median_bg - median_fg) then 0.1 * (median_bg - median_fg) else (!max).[0] * threshold
+ let limitThreshold = 0.1
+ let valueThreshold = (*if max < limitThreshold * (median_bg - median_fg) then max / 2. else *) max * threshold
diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
- diff, closed
+ diff
- let infectionMarker, filteredGreenWithoutInfection = marker (int config.InfectionArea) config.Parameters.infectionLevel
- let stainMarker, filteredGreenWithoutStain = marker (int config.StainArea) config.Parameters.stainLevel
+ let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
+ let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
{ darkStain = darkStain
infection = infectionMarker