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 = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
+ 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 * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
+ 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)
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 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.areaClose filteredGreenWithoutStain (int config.StainArea)
-
- // We use the filtered image to find the dark stain.
-
- // With K-Means.
- let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0)
- let { KMeans.mean_bg = value_bg; KMeans.mean_fg = value_fg; KMeans.d_fg = d_fg } = kmeansResults
-
- // With K-Medians.
- (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting this again in MainAnalysis
- let { KMedians.median_bg = value_bg; KMedians.median_fg = value_fg; KMedians.d_fg = d_fg } = kmediansResults *)
-
- let darkStain = d_fg.Cmp(value_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
- darkStain._And(filteredGreenWithoutInfection.Cmp(value_fg, CvEnum.CmpType.LessThan))
-
- let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
- let diff = closed - (img * level)
+ ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.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
+ diff.Convert<Gray, byte>()
+
+ let infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
+ let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity)
- 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 },
- filteredGreenWithoutInfection,
filteredGreenWithoutStain
-
-
-
-
-
-