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)
20 let greenFloat = green.Convert<Gray, float32
>()
21 let filteredGreen = gaussianFilter
greenFloat config.Parameters.preFilterSigma
23 logTime
"areaOpen 1" (fun () -> ImgTools.areaOpenF
filteredGreen config.Parameters.initialAreaOpen
)
25 config.RBCRadius <- logTime
"Granulometry" (fun() -> Granulometry.findRadius
(filteredGreen.Convert<Gray, byte
>()) (10, 100) 0.5 |> float)
27 let secondAreaOpen = int <| config.RBCArea / 3.
28 if secondAreaOpen > config.Parameters.initialAreaOpen
30 logTime
"areaOpen 2" (fun () -> ImgTools.areaOpenF
filteredGreen secondAreaOpen)
32 let parasites, filteredGreenWhitoutInfection
, filteredGreenWhitoutStain
= ParasitesMarker.find
filteredGreen config
33 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
35 let edges, xGradient
, yGradient
= logTime
"Finding edges" (fun () -> ImgTools.findEdges
filteredGreenWhitoutStain)
36 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
38 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
39 let matchingEllipses = Ellipse.find
edges xGradient yGradient
config
40 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
42 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
44 // Output pictures if debug flag is set.
45 match config.Debug with
47 let dirPath = System.IO.Path.Combine(output
, name
)
48 System.IO.Directory.CreateDirectory dirPath |> ignore
50 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
52 //saveImg canny (buildFileName " - canny.png")
54 saveMat
(edges * 255.0) (buildFileName " - edges.png")
56 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
57 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
58 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
60 let imgAllEllipses = img.Copy()
61 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
62 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
64 let imgEllipses = img.Copy()
65 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
66 saveImg
imgEllipses (buildFileName " - ellipses.png")
68 let imgCells = img.Copy()
69 drawCells
imgCells false cells
70 saveImg
imgCells (buildFileName " - cells.png")
72 let imgCells' = img.Copy()
73 drawCells imgCells' true cells
74 saveImg
imgCells' (buildFileName " - cells - full.png")
76 let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
77 for m in ImgTools.findMaxima filteredGreenMaxima do
78 ImgTools.drawPoints filteredGreenMaxima m 255.f
79 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
81 saveImg filteredGreen (buildFileName " - filtered.png")
82 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
83 saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
85 saveImg green (buildFileName " - green.png")
87 use blue = scaledImg.Item(0)
88 saveImg blue (buildFileName " - blue.png")
90 use red = scaledImg.Item(2)
91 saveImg red (buildFileName " - red.png")