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     let initialAreaOpen = 2000
  34     logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
  35
  36     config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
  37
  38     let secondAreaOpen = int <| config.RBCArea / 3.
  39     if secondAreaOpen > initialAreaOpen
  40     then
  41         logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen)
  42
  43     let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
  44
  45     let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config
  46     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  47     let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
  48     let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
  49
  50     use sobelKernel =
  51         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  52                                         [ 2.0f; 0.0f; -2.0f ]
  53                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  54
  55     use xEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert<Gray, float>()
  56     use yEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  57
  58     let xEdgesData = xEdges.Data
  59     let yEdgesData = yEdges.Data
  60     for r in 0..xEdges.Rows-1 do
  61         xEdgesData.[r, 0, 0] <- 0.0
  62         xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  63         yEdgesData.[r, 0, 0] <- 0.0
  64         yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  65
  66     for c in 0..xEdges.Cols-1 do
  67         xEdgesData.[0, c, 0] <- 0.0
  68         xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  69         yEdgesData.[0, c, 0] <- 0.0
  70         yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  71
  72     use magnitudes = new Matrix<float>(xEdges.Size)
  73     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  74
  75     let min = ref 0.0
  76     let minLocation = ref <| Point()
  77     let max = ref 0.0
  78     let maxLocation = ref <| Point()
  79     magnitudes.MinMax(min, max, minLocation, maxLocation)
  80
  81     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  82     use edges = new Matrix<byte>(xEdges.Size)
  83     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  84
  85     logTime "Finding edges" (fun() -> thin edges)
  86     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  87
  88     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  89         let matchingEllipses = Ellipse.find edges xEdges yEdges config
  90         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  91
  92     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  93
  94     // Output pictures if debug flag is set.
  95     match config.Debug with
  96     | DebugOn output ->
  97         let dirPath = System.IO.Path.Combine(output, name)
  98         System.IO.Directory.CreateDirectory dirPath |> ignore
  99
 100         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 101
 102         saveMat (edges * 255.0) (buildFileName " - edges.png")
 103
 104         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 105         saveImg parasites.stain (buildFileName " - parasites - stain.png")
 106         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 107
 108         let imgAllEllipses = img.Copy()
 109         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
 110         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 111
 112         let imgEllipses = img.Copy()
 113         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
 114         saveImg imgEllipses (buildFileName " - ellipses.png")
 115
 116         // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 117
 118         let imgCells = img.Copy()
 119         drawCells imgCells false cells
 120         saveImg imgCells (buildFileName " - cells.png")
 121
 122         let imgCells' = img.Copy()
 123         drawCells imgCells' true cells
 124         saveImg imgCells' (buildFileName " - cells - full.png")
 125
 126         let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
 127         for m in ImgTools.findMaxima filteredGreenMaxima do
 128             ImgTools.drawPoints filteredGreenMaxima m 255uy
 129         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 130
 131         saveImg filteredGreen (buildFileName " - filtered.png")
 132         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 133         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 134
 135         (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
 136         saveImg stainMarker (buildFileName " - stain (area closing).png")*)
 137
 138         saveImg green (buildFileName " - green.png")
 139
 140         use blue  = scaledImg.Item(0)
 141         saveImg blue (buildFileName " - blue.png")
 142
 143         use red = scaledImg.Item(2)
 144         saveImg red (buildFileName " - red.png")
 145     | _ -> ()
 146
 147     cells