Parasitemia/Parasitemia/ImageAnalysis.fs

   1 module ImageAnalysis
   2
   3 open System
   4 open System.Drawing
   5
   6 open Emgu.CV
   7 open Emgu.CV.Structure
   8
   9 open Utils
  10 open ImgTools
  11 open Config
  12 open Types
  13
  14 type Result = {
  15     RBCPositions : Point list
  16     infectedRBCPositions : Point list
  17     img: Image<Bgr, byte>
  18 }
  19
  20 let doAnalysis (img: Image<Bgr, byte>) (config: Config) : Result =
  21
  22     let imgFloat = img.Convert<Bgr, float32>()
  23     use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)
  24
  25     (*use scaledImg =
  26         if config.scale = 1.0
  27         then
  28             img
  29         else
  30             let m = new Mat()
  31             CvInvoke.Resize(img, m, Size(roundInt (float img.Size.Width * config.scale), roundInt (float img.Size.Height * config.scale)))
  32             m*)
  33
  34     use green = scaledImg.Item(1)
  35
  36     //use green = new Matrix<byte>(scaledImg.Size)
  37     //CvInvoke.MixChannels(scaledImg, green, [| 1; 0 |])
  38
  39     //let greenMatrix = new Matrix<byte>(green.Height, green.Width, green.DataPointer)
  40
  41     //let test = greenMatrix.[10, 10]
  42
  43     use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
  44
  45     use sobelKernel =
  46         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  47                                         [ 2.0f; 0.0f; -2.0f ]
  48                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  49
  50     use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
  51     use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  52
  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
  60
  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
  66
  67     use magnitudes = new Matrix<float>(xEdges.Size)
  68     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  69
  70     let min = ref 0.0
  71     let minLocation = ref <| Point()
  72     let max = ref 0.0
  73     let maxLocation = ref <| Point()
  74     magnitudes.MinMax(min, max, minLocation, maxLocation)
  75
  76     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  77     use edges = new Matrix<byte>(xEdges.Size)
  78     let threshold = CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary)
  79
  80 //    let filteredGreenMat = new Matrix<float32>(filteredGreen.Size)
  81 //    filteredGreen.CopyTo(filteredGreenMat)
  82     let parasites = ParasitesMarker.find green filteredGreen config
  83
  84     saveImg parasites.darkStain "parasites_dark_stain.png"
  85     saveImg parasites.stain "parasites_stain.png"
  86     saveImg parasites.infection "parasites_infection.png"
  87
  88     logTime "Finding edges" (fun() ->
  89         thin edges)
  90
  91     logTime "Removing small connected components" (fun () ->
  92         removeArea edges 12)
  93
  94     saveMat (edges * 255.0) "edges.png"
  95
  96     let radiusRange = config.scale * 20.0, config.scale * 40.0
  97     let windowSize = roundInt (1.6 * (snd radiusRange))
  98     let factorNbPick = 1.5
  99     let ellipses = logTime "Finding ellipses" (fun () ->
 100         Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
 101
 102     drawEllipses img ellipses (Bgr(0.0, 255.0, 255.0))
 103     //saveImg img "ellipses.png"
 104
 105     { RBCPositions = []; infectedRBCPositions = []; img = img }
 106
 107     //
 108
 109     (*use imageHSV = scaledImage.Convert<Hsv, uint8>()
 110     let H, S = match imageHSV.Split() with // Warning: H is from 0 to 179°.
 111                 | [| H; S; _|] -> H, S
 112                 | _ -> failwith "unable to split the HSV channels"
 113
 114     let hueShiftValue = 175
 115     // Modulo operator doesn't exist on matrix thus we have to apply a function to every pixels.
 116     let correctedH : Image<Gray, byte> = H.Convert(fun b _ _ ->
 117         (255 - int(b) * 255 / 179 + hueShiftValue) % 256 |> byte
 118     )
 119
 120     let correctedS : Image<Gray, byte> = S.Not()
 121
 122     let filteredH = correctedH.SmoothMedian(5)
 123     let filteredS = correctedS.SmoothMedian(5)*)
 124
 125     //let greenChannel = scaledImage.Item(1)
 126
 127     //let filteredImage = (gaussianFilter greenChannel config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenChannel config.doGSigma2)
 128
 129     // let filteredImage = greenChannel.ThresholdAdaptive(Gray(255.), CvEnum.AdaptiveThresholdType.GaussianC, CvEnum.ThresholdType.Binary, 61, Gray(5.0))
 130     // let thresholdedImage = filteredImage.CopyBlank()
 131
 132     // CvInvoke.Threshold(filteredImage, thresholdedImage, 0., 255., CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.BinaryInv) |> ignore
 133
 134     // filteredImage <|