15 let doAnalysis (img
: Image<Bgr, byte
>) (name
: string) (config
: Config) : Cell list =
17 use scaledImg = if config
.Parameters.scale
= 1.0 then img
else img.Resize(config
.Parameters.scale
, CvEnum.Inter.Area)
19 use green = scaledImg.Item(1)
21 let greenFloat = green.Convert<Gray, float32
>()
23 let filteredGreen = gaussianFilter
green config
.Parameters.preFilterSigma
25 (*let maximaImg = filteredGreen.Copy()
26 let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
28 ImgTools.drawPoints maximaImg m 255uy
30 let greenOpen1 = filteredGreen.Copy()
31 logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
33 let initialAreaOpen = 2000
34 logTime
"areaOpen 1" (fun () -> ImgTools.areaOpen
filteredGreen 2000)
36 config
.RBCRadius <- Granulometry.findRadius
filteredGreen (10, 100) 0.5 |> float
38 let secondAreaOpen = int <| config.RBCArea / 3.
39 if secondAreaOpen > initialAreaOpen
41 logTime
"areaOpen 2" (fun () -> ImgTools.areaOpen
filteredGreen secondAreaOpen)
43 let filteredGreenFloat = filteredGreen.Convert<Gray, float32
>() // Is it neccessary?
45 let parasites, filteredGreenWhitoutInfection
, filteredGreenWhitoutStain
= ParasitesMarker.find
filteredGreen filteredGreenFloat config
46 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
47 let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection
.Convert<Gray, float32
>()
48 let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain
.Convert<Gray, float32
>()
51 let minLocation = ref <| Point()
53 let maxLocation = ref <| Point()
54 magnitudes.MinMax(min, max, minLocation, maxLocation)
56 use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
57 use edges = new Matrix<byte>(xEdges.Size)
58 CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
60 logTime "Finding edges" (fun() -> thin edges)*)
62 let edges, xGradient
, yGradient
= ImgTools.findEdges
filteredGreenWhitoutStainFloat
64 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
66 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
67 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
68 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
70 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
72 // Output pictures if debug flag is set.
73 match config.Debug with
75 let dirPath = System.IO.Path.Combine(output
, name
)
76 System.IO.Directory.CreateDirectory dirPath |> ignore
78 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
80 saveMat
(edges * 255.0) (buildFileName " - edges.png")
82 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
83 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
84 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
86 let imgAllEllipses = img.Copy()
87 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
88 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
90 let imgEllipses = img.Copy()
91 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
92 saveImg
imgEllipses (buildFileName " - ellipses.png")
94 // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
96 let imgCells = img.Copy()
97 drawCells
imgCells false cells
98 saveImg
imgCells (buildFileName " - cells.png")
100 let imgCells' = img.Copy()
101 drawCells imgCells' true cells
102 saveImg
imgCells' (buildFileName " - cells - full.png")
104 let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
105 for m in ImgTools.findMaxima filteredGreenMaxima do
106 ImgTools.drawPoints filteredGreenMaxima m 255uy
107 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
109 saveImg filteredGreen (buildFileName " - filtered.png")
110 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
111 saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
113 (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
114 saveImg stainMarker (buildFileName " - stain (area closing).png")*)
116 saveImg green (buildFileName " - green.png")
118 use blue = scaledImg.Item(0)
119 saveImg blue (buildFileName " - blue.png")
121 use red = scaledImg.Item(2)
122 saveImg red (buildFileName " - red.png")