Parasitemia/Parasitemia/MainAnalysis.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
  15 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
  16
  17     use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
  18
  19     use green = scaledImg.Item(1)
  20
  21     let greenFloat = green.Convert<Gray, float32>()
  22
  23     let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
  24
  25     (*let maximaImg = filteredGreen.Copy()
  26     let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
  27     for m in maxima do
  28         ImgTools.drawPoints maximaImg m 255uy
  29
  30     let greenOpen1 = filteredGreen.Copy()
  31     logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
  32
  33     logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
  34
  35     config.RBCSize <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
  36
  37     let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
  38
  39     let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
  40
  41     let parasites, filteredGreenWhitoutParasites, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config
  42     let filteredGreenWhitoutParasitesFloat = filteredGreenWhitoutParasites.Convert<Gray, float32>()
  43
  44     use sobelKernel =
  45         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  46                                         [ 2.0f; 0.0f; -2.0f ]
  47                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  48
  49     use xEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel).Convert<Gray, float>()
  50     use yEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  51
  52     let xEdgesData = xEdges.Data
  53     let yEdgesData = yEdges.Data
  54     for r in 0..xEdges.Rows-1 do
  55         xEdgesData.[r, 0, 0] <- 0.0
  56         xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  57         yEdgesData.[r, 0, 0] <- 0.0
  58         yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  59
  60     for c in 0..xEdges.Cols-1 do
  61         xEdgesData.[0, c, 0] <- 0.0
  62         xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  63         yEdgesData.[0, c, 0] <- 0.0
  64         yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  65
  66     use magnitudes = new Matrix<float>(xEdges.Size)
  67     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  68
  69     let min = ref 0.0
  70     let minLocation = ref <| Point()
  71     let max = ref 0.0
  72     let maxLocation = ref <| Point()
  73     magnitudes.MinMax(min, max, minLocation, maxLocation)
  74
  75     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  76     use edges = new Matrix<byte>(xEdges.Size)
  77     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  78
  79     logTime "Finding edges" (fun() -> thin edges)
  80     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  81
  82     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  83         let matchingEllipses = Ellipse.find edges xEdges yEdges config
  84         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  85
  86     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutParasites config)
  87
  88     // Output pictures if debug flag is set.
  89     match config.Debug with
  90     | DebugOn output ->
  91         let dirPath = System.IO.Path.Combine(output, name)
  92         System.IO.Directory.CreateDirectory dirPath |> ignore
  93
  94         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  95
  96         saveMat (edges * 255.0) (buildFileName " - edges.png")
  97
  98         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  99         saveImg parasites.stain (buildFileName " - parasites - stain.png")
 100         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 101
 102         let imgAllEllipses = img.Copy()
 103         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
 104         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 105
 106         let imgEllipses = img.Copy()
 107         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
 108         saveImg imgEllipses (buildFileName " - ellipses.png")
 109
 110         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 111
 112         let imgCells = img.Copy()
 113         drawCells imgCells false cells
 114         saveImg imgCells (buildFileName " - cells.png")
 115
 116         let imgCells' = img.Copy()
 117         drawCells imgCells' true cells
 118         saveImg imgCells' (buildFileName " - cells - full.png")
 119
 120         let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
 121         for m in ImgTools.findMaxima filteredGreenMaxima do
 122             ImgTools.drawPoints filteredGreenMaxima m 255uy
 123         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 124
 125         saveImg filteredGreen (buildFileName " - filtered.png")
 126         saveImg filteredGreenWhitoutParasites (buildFileName " - filtered closed.png")
 127
 128         (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
 129         saveImg stainMarker (buildFileName " - stain (area closing).png")*)
 130
 131         saveImg green (buildFileName " - green.png")
 132
 133         use blue  = scaledImg.Item(0)
 134         saveImg blue (buildFileName " - blue.png")
 135
 136         use red = scaledImg.Item(2)
 137         saveImg red (buildFileName " - red.png")
 138     | _ -> ()
 139
 140     cells