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 config.RBCRadius <- logTime
"Granulometry" (fun() -> Granulometry.findRadius
(filteredGreen.Convert<Gray, byte
>()) (10, 100) 0.3 |> float32
)
24 let secondAreaOpen = int <| config.RBCArea / 3.f
25 if secondAreaOpen > config.Parameters.initialAreaOpen
27 logTime
"areaOpen 2" (fun () -> ImgTools.areaOpenF
filteredGreen secondAreaOpen)
29 let parasites, filteredGreenWhitoutStain
= ParasitesMarker.find
filteredGreen config
30 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
32 let edges, xGradient
, yGradient
= logTime
"Finding edges" (fun () -> ImgTools.findEdges
filteredGreenWhitoutStain)
33 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges (config.RBCRadius ** 2.f
/ 50.f
|> int))
35 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
36 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
37 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
39 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
41 // Output pictures if debug flag is set.
42 match config.Debug with
44 let dirPath = System.IO.Path.Combine(output
, name
)
45 System.IO.Directory.CreateDirectory dirPath |> ignore
47 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
49 saveMat
(edges * 255.0) (buildFileName " - edges.png")
51 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
52 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
53 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
55 let imgAllEllipses = img
.Copy()
56 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
57 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
59 let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte
>()
60 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
61 saveImg
imgEllipses (buildFileName " - ellipses.png")
63 let imgCells = img
.Copy()
64 drawCells
imgCells false cells
65 saveImg
imgCells (buildFileName " - cells.png")
67 let imgCells' = img.Copy()
68 drawCells imgCells' true cells
69 saveImg
imgCells' (buildFileName " - cells - full.png")
71 let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
72 for m in ImgTools.findMaxima filteredGreenMaxima do
73 ImgTools.drawPoints filteredGreenMaxima m 255.f
74 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
76 saveImg filteredGreen (buildFileName " - filtered.png")
77 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
78 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
80 saveImg green (buildFileName " - green.png")
82 use blue = img.Item(0)
83 saveImg blue (buildFileName " - blue.png")
86 saveImg red (buildFileName " - red.png")