15 let doAnalysis (img
: Image<Bgr, byte
>) (name
: string) (config
: Config) : Cell list =
17 use scaledImg = if config
.scale
= 1.0 then img
else img.Resize(config
.scale
, CvEnum.Inter.Area)
19 use blue = scaledImg.Item(0)
20 use green = scaledImg.Item(1)
21 use red = scaledImg.Item(2)
23 let greenFloat = green.Convert<Gray, float32
>()
25 let filteredGreen = gaussianFilter
green config
.preFilterSigma
26 logTime
"areaOpen" (fun () -> ImgTools.areaOpen
filteredGreen 2000)
28 let RBCSize = Granulometry.findRadius
filteredGreen (10, 100) 0.5 |> float
29 let RBCSizeDelta = RBCSize / 3.0
31 let config = { config with minRBCSize
= RBCSize - RBCSizeDelta ; maxRBCSize
= RBCSize + RBCSizeDelta }
33 let filteredGreenFloat = filteredGreen.Convert<Gray, float32
>() // Is it neccessary?
36 new ConvolutionKernelF(array2D
[[ 1.0f; 0.0f; -1.0f ]
38 [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
40 use xEdges = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
41 use yEdges = filteredGreenFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
43 let xEdgesData = xEdges.Data
44 let yEdgesData = yEdges.Data
45 for r
in 0..xEdges.Rows-1 do
46 xEdgesData.[r
, 0, 0] <- 0.0
47 xEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
48 yEdgesData.[r
, 0, 0] <- 0.0
49 yEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
51 for c
in 0..xEdges.Cols-1 do
52 xEdgesData.[0, c
, 0] <- 0.0
53 xEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
54 yEdgesData.[0, c
, 0] <- 0.0
55 yEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
57 use magnitudes = new Matrix<float>(xEdges.Size)
58 CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
61 let minLocation = ref <| Point()
63 let maxLocation = ref <| Point()
64 magnitudes.MinMax(min, max, minLocation, maxLocation)
66 use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte
>() // Otsu from OpenCV only support 'byte'.
67 use edges = new Matrix<byte
>(xEdges.Size)
68 CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
70 logTime
"Finding edges" (fun() -> thin
edges)
71 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
73 let kmediansResults = logTime
"Finding foreground (k-medians)" (fun () -> KMedians.kmedians
filteredGreenFloat 1.0)
75 let parasites = ParasitesMarker.find
greenFloat filteredGreenFloat kmediansResults config
77 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
78 let matchingEllipses = Ellipse.find
edges xEdges yEdges config
79 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
81 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites kmediansResults.fg
config)
83 // Output pictures if debug flag is set.
84 match config.debug
with
86 let dirPath = System.IO.Path.Combine(output
, name
)
87 System.IO.Directory.CreateDirectory dirPath |> ignore
89 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
91 saveMat
(edges * 255.0) (buildFileName " - edges.png")
93 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
94 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
95 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
97 let imgAllEllipses = img.Copy()
98 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
99 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
101 let imgEllipses = img.Copy()
102 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
103 saveImg
imgEllipses (buildFileName " - ellipses.png")
105 saveImg
(kmediansResults.fg
* 255.0) (buildFileName " - foreground.png")
107 let imgCells = img.Copy()
108 drawCells
imgCells false cells
109 saveImg
imgCells (buildFileName " - cells.png")
111 let imgCells' = img.Copy()
112 drawCells imgCells' true cells
113 saveImg
imgCells' (buildFileName " - cells - full.png")
115 let filteredGreenMaxima = gaussianFilter green config.preFilterSigma
116 for m in ImgTools.findMaxima filteredGreenMaxima do
117 ImgTools.drawPoints filteredGreenMaxima m 255uy
118 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
120 saveImg filteredGreen (buildFileName " - filtered.png")
121 saveImg blue (buildFileName " - blue.png")
122 saveImg green (buildFileName " - green.png")
123 saveImg red (buildFileName " - red.png")