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)
21 let greenFloat = green.Convert<Gray, float32
>()
23 let filteredGreen = gaussianFilter
green config
.Parameters.preFilterSigma
25 (*let maximaImg = filteredGreen.Copy()
26 let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
28 ImgTools.drawPoints maximaImg m 255uy
30 let greenOpen1 = filteredGreen.Copy()
31 logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
33 logTime
"areaOpen" (fun () -> ImgTools.areaOpen
filteredGreen 2000)
35 config
.RBCRadius <- Granulometry.findRadius
filteredGreen (10, 100) 0.5 |> float
37 let filteredGreenFloat = filteredGreen.Convert<Gray, float32
>() // Is it neccessary?
39 let kmediansResults = logTime
"Finding foreground (k-medians)" (fun () -> KMedians.kmedians
filteredGreenFloat 1.0)
41 let parasites, filteredGreenWhitoutInfection
, filteredGreenWhitoutStain
= ParasitesMarker2.find
filteredGreen filteredGreenFloat kmediansResults config
42 let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection
.Convert<Gray, float32
>()
43 let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain
.Convert<Gray, float32
>()
46 new ConvolutionKernelF(array2D
[[ 1.0f; 0.0f; -1.0f ]
48 [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
50 use xEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert<Gray, float>()
51 use yEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
53 let xEdgesData = xEdges.Data
54 let yEdgesData = yEdges.Data
55 for r
in 0..xEdges.Rows-1 do
56 xEdgesData.[r
, 0, 0] <- 0.0
57 xEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
58 yEdgesData.[r
, 0, 0] <- 0.0
59 yEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
61 for c
in 0..xEdges.Cols-1 do
62 xEdgesData.[0, c
, 0] <- 0.0
63 xEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
64 yEdgesData.[0, c
, 0] <- 0.0
65 yEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
67 use magnitudes = new Matrix<float>(xEdges.Size)
68 CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
71 let minLocation = ref <| Point()
73 let maxLocation = ref <| Point()
74 magnitudes.MinMax(min, max, minLocation, maxLocation)
76 use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte
>() // Otsu from OpenCV only support 'byte'.
77 use edges = new Matrix<byte
>(xEdges.Size)
78 CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
80 logTime
"Finding edges" (fun() -> thin
edges)
81 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
83 let allEllipses, ellipses
= logTime
"Finding ellipses" (fun () ->
84 let matchingEllipses = Ellipse.find
edges xEdges yEdges config
85 matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
87 let cells = logTime
"Classifier" (fun () -> Classifier.findCells
ellipses parasites filteredGreenWhitoutStain config)
89 // Output pictures if debug flag is set.
90 match config.Debug with
92 let dirPath = System.IO.Path.Combine(output
, name
)
93 System.IO.Directory.CreateDirectory dirPath |> ignore
95 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name
+ postfix
)
97 saveMat
(edges * 255.0) (buildFileName " - edges.png")
99 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
100 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
101 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
103 let imgAllEllipses = img.Copy()
104 drawEllipses
imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
105 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
107 let imgEllipses = img.Copy()
108 drawEllipses
imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
109 saveImg
imgEllipses (buildFileName " - ellipses.png")
111 saveImg
(kmediansResults.fg
* 255.0) (buildFileName " - foreground.png")
113 let imgCells = img.Copy()
114 drawCells
imgCells false cells
115 saveImg
imgCells (buildFileName " - cells.png")
117 let imgCells' = img.Copy()
118 drawCells imgCells' true cells
119 saveImg
imgCells' (buildFileName " - cells - full.png")
121 let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
122 for m in ImgTools.findMaxima filteredGreenMaxima do
123 ImgTools.drawPoints filteredGreenMaxima m 255uy
124 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
126 saveImg filteredGreen (buildFileName " - filtered.png")
127 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed.png")
129 (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
130 saveImg stainMarker (buildFileName " - stain (area closing).png")*)
132 saveImg green (buildFileName " - green.png")
134 use blue = scaledImg.Item(0)
135 saveImg blue (buildFileName " - blue.png")
137 use red = scaledImg.Item(2)
138 saveImg red (buildFileName " - red.png")