73f9fe1da720cc9fe8bb215c823ebee636f87ee5
[master-thesis.git] / Parasitemia / ParasitemiaCore / ParasitesMarker.fs
1 module ParasitemiaCore.ParasitesMarker
2
3 open System.Drawing
4 open System.Linq
5
6 open Emgu.CV
7 open Emgu.CV.Structure
8
9 open Utils
10
11 type Result = {
12 darkStain: Image<Gray, byte>
13 infection: Image<Gray, byte>
14 stain: Image<Gray, byte> }
15
16 // Create three binary markers :
17 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
18 // * 'Stain' corresponds to the stain around the parasites.
19 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
20 let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
21 // We use the filtered image to find the dark stain.
22 let kmediansResults = KMedians.kmedians filteredGreen
23 let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
24 let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
25 darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
26 darkStain._And(fg)
27
28 let fgFloat = (fg / 255.0).Convert<Gray, float32>()
29 use greenWithoutBg = ImgTools.gaussianFilter green 1.0
30 greenWithoutBg.SetValue(Gray(0.0), fg.Not())
31
32 let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
33 use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
34 use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
35 let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
36 smears._And(fg)
37 smears
38
39 let tmp = filteredGreen.Convert<Gray, byte>()
40
41 { darkStain = darkStain;
42 stain = findSmears 10. 0.9
43 infection = findSmears 2.2 0.87 },
44 tmp,
45 tmp
46
47 // Create three binary markers :
48 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
49 // * 'Stain' corresponds to the stain around the parasites.
50 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
51 let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
52
53 let imgFilteredInfection = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
54 let filteredGreenWithoutInfection = imgFilteredInfection.Copy()
55 ImgTools.areaCloseF filteredGreenWithoutInfection (roundInt config.RBCRadius.NucleusArea)
56
57 (*
58 let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
59 ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea) *)
60
61 let darkStain =
62 // We use the filtered image to find the dark stain.
63 let _, mean_fg, mean_bg =
64 let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
65 ImgTools.otsu hist
66 filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
67
68 let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
69 let diff = img.Copy()
70 diff._Mul(level)
71 CvInvoke.Subtract(closed, diff, diff)
72 diff._ThresholdBinary(Gray(0.0), Gray(255.))
73 diff.Convert<Gray, byte>()
74
75 let infectionMarker = marker imgFilteredInfection filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
76
77 let imgFilteredStain = ImgTools.gaussianFilter img config.LPFStandardDeviationStain
78 let areaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
79 //ImgTools.areaOpenF imgFilteredStain areaOpening
80
81 let filteredGreenWithoutStain = imgFilteredStain.CopyBlank()
82 let kernelSize =
83 let size = roundInt (config.RBCRadius.Pixel / 5.f)
84 if size % 2 = 0 then size + 1 else size
85 use kernel =
86 if kernelSize <= 3
87 then
88 CvInvoke.GetStructuringElement(CvEnum.ElementShape.Rectangle, Size(3, 3), Point(-1, -1))
89 else
90 CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
91
92 CvInvoke.MorphologyEx(imgFilteredStain, filteredGreenWithoutStain, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
93 let stainMarker = marker (*filteredGreenWithoutInfection*) imgFilteredStain filteredGreenWithoutStain (1. / config.Parameters.cytoplasmSensitivity)
94
95 //
96 (*let blackTopHat = filteredGreenWithoutStain.CopyBlank()
97 CvInvoke.Subtract(filteredGreenWithoutStain, imgFilteredStain, blackTopHat)
98 ImgTools.saveImg blackTopHat "blackTopHat.png"*)
99
100 { darkStain = darkStain
101 infection = infectionMarker
102 stain = stainMarker },
103 filteredGreenWithoutStain,
104 filteredGreenWithoutInfection
105
106