15 let doAnalysis (img
: Image<Bgr, byte
>) (name
: string) (config
: Config) : Cell list =
16 use green = img
.Item(1)
17 let greenFloat = green.Convert<Gray, float32
>()
18 let filteredGreen = gaussianFilter
greenFloat (float config.Parameters.preFilterSigma
)
20 logTime
"areaOpen 1" (fun () -> ImgTools.areaOpenF
filteredGreen config.Parameters.initialAreaOpen
)
22 let r1 = logTime
"Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing
(filteredGreen.Convert<Gray, byte
>()) (10, 80) 0.5 |> float32
)
23 // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
24 // log (sprintf "r1: %A, r2: %A" r1 r2)
25 config.RBCRadius <- r1
27 let secondAreaOpen = int <| config.RBCArea / 3.f
29 if secondAreaOpen > config.Parameters.initialAreaOpen
31 logTime
"areaOpen 2" (fun () -> ImgTools.areaOpenF
filteredGreen secondAreaOpen)
33 let parasites, filteredGreenWhitoutStain
= ParasitesMarker.find
filteredGreen config
34 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
36 let edges, xGradient
, yGradient
= logTime
"Finding edges" (fun () -> ImgTools.findEdges
filteredGreenWhitoutStain)
37 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges (config.RBCRadius ** 2.f
/ 50.f
|> int))
39 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
40 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
41 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
43 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
45 // Output pictures if debug flag is set.
46 match config.Debug with
48 let dirPath = System.IO.Path.Combine(output
, name
)
49 System.IO.Directory.CreateDirectory dirPath |> ignore
51 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
53 saveMat
(edges * 255.0) (buildFileName " - edges.png")
55 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
56 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
57 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
59 let imgAllEllipses = img
.Copy()
60 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
61 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
63 let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte
>()
64 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
65 saveImg
imgEllipses (buildFileName " - ellipses.png")
67 let imgCells = img
.Copy()
68 drawCells
imgCells false cells
69 saveImg
imgCells (buildFileName " - cells.png")
71 let imgCells' = img.Copy()
72 drawCells imgCells' true cells
73 saveImg
imgCells' (buildFileName " - cells - full.png")
75 let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
76 for m in ImgTools.findMaxima filteredGreenMaxima do
77 ImgTools.drawPoints filteredGreenMaxima m 255.f
78 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
80 saveImg filteredGreen (buildFileName " - filtered.png")
81 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
82 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
84 saveImg green (buildFileName " - green.png")
86 use blue = img.Item(0)
87 saveImg blue (buildFileName " - blue.png")
90 saveImg red (buildFileName " - red.png")