15 let doAnalysis (img
: Image<Bgr, byte
>) (name
: string) (config
: Config) : Cell list =
16 let scaledImg = if config
.Parameters.scale
= 1.0 then img
else img.Resize(config
.Parameters.scale
, CvEnum.Inter.Area)
18 use green = scaledImg.Item(1)
19 let greenFloat = green.Convert<Gray, float32
>()
20 let filteredGreen = gaussianFilter
greenFloat (float config.Parameters.preFilterSigma
)
22 logTime
"areaOpen 1" (fun () -> ImgTools.areaOpenF
filteredGreen config.Parameters.initialAreaOpen
)
24 config.RBCRadius <- logTime
"Granulometry" (fun() -> Granulometry.findRadius
(filteredGreen.Convert<Gray, byte
>()) (10, 100) 0.3 |> float32
)
26 let secondAreaOpen = int <| config.RBCArea / 3.f
27 if secondAreaOpen > config.Parameters.initialAreaOpen
29 logTime
"areaOpen 2" (fun () -> ImgTools.areaOpenF
filteredGreen secondAreaOpen)
31 let parasites, filteredGreenWhitoutStain
= ParasitesMarker.find
filteredGreen config
32 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
34 let edges, xGradient
, yGradient
= logTime
"Finding edges" (fun () -> ImgTools.findEdges
filteredGreenWhitoutStain)
35 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges (config.RBCRadius ** 2.f
/ 50.f
|> int))
37 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
38 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
39 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
41 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
43 // Output pictures if debug flag is set.
44 match config.Debug with
46 let dirPath = System.IO.Path.Combine(output
, name
)
47 System.IO.Directory.CreateDirectory dirPath |> ignore
49 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
51 saveMat
(edges * 255.0) (buildFileName " - edges.png")
53 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
54 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
55 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
57 let imgAllEllipses = img.Copy()
58 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
59 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
61 let imgEllipses = img.Copy()
62 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
63 saveImg
imgEllipses (buildFileName " - ellipses.png")
65 let imgCells = img.Copy()
66 drawCells
imgCells false cells
67 saveImg
imgCells (buildFileName " - cells.png")
69 let imgCells' = img.Copy()
70 drawCells imgCells' true cells
71 saveImg
imgCells' (buildFileName " - cells - full.png")
73 let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
74 for m in ImgTools.findMaxima filteredGreenMaxima do
75 ImgTools.drawPoints filteredGreenMaxima m 255.f
76 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
78 saveImg filteredGreen (buildFileName " - filtered.png")
79 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
80 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
82 saveImg green (buildFileName " - green.png")
84 use blue = scaledImg.Item(0)
85 saveImg blue (buildFileName " - blue.png")
87 use red = scaledImg.Item(2)
88 saveImg red (buildFileName " - red.png")