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
>()
50 let canny = green.Canny(60., 40.)
53 let minLocation = ref <| Point()
55 let maxLocation = ref <| Point()
56 magnitudes.MinMax(min, max, minLocation, maxLocation)
58 use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
59 use edges = new Matrix<byte>(xEdges.Size)
60 CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
62 logTime "Finding edges" (fun() -> thin edges)*)
64 let edges, xGradient
, yGradient
= ImgTools.findEdges
filteredGreenWhitoutStainFloat
66 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
68 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
69 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
70 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
72 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
74 // Output pictures if debug flag is set.
75 match config.Debug with
77 let dirPath = System.IO.Path.Combine(output
, name
)
78 System.IO.Directory.CreateDirectory dirPath |> ignore
80 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
82 saveImg
canny (buildFileName " - canny.png")
84 saveMat
(edges * 255.0) (buildFileName " - edges.png")
86 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
87 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
88 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
90 let imgAllEllipses = img.Copy()
91 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
92 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
94 let imgEllipses = img.Copy()
95 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
96 saveImg
imgEllipses (buildFileName " - ellipses.png")
98 // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
100 let imgCells = img.Copy()
101 drawCells
imgCells false cells
102 saveImg
imgCells (buildFileName " - cells.png")
104 let imgCells' = img.Copy()
105 drawCells imgCells' true cells
106 saveImg
imgCells' (buildFileName " - cells - full.png")
108 let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
109 for m in ImgTools.findMaxima filteredGreenMaxima do
110 ImgTools.drawPoints filteredGreenMaxima m 255uy
111 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
113 saveImg filteredGreen (buildFileName " - filtered.png")
114 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
115 saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
117 (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
118 saveImg stainMarker (buildFileName " - stain (area closing).png")*)
120 saveImg green (buildFileName " - green.png")
122 use blue = scaledImg.Item(0)
123 saveImg blue (buildFileName " - blue.png")
125 use red = scaledImg.Item(2)
126 saveImg red (buildFileName " - red.png")