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.RBCRadius <- 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, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config
  42     let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
  43     let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
  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 = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert<Gray, float>()
  51     use yEdges = filteredGreenWhitoutStainFloat.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     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  79
  80     logTime "Finding edges" (fun() -> thin edges)
  81     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  82
  83     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  84         let matchingEllipses = Ellipse.find edges xEdges yEdges config
  85         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  86
  87     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  88
  89     // Output pictures if debug flag is set.
  90     match config.Debug with
  91     | DebugOn output ->
  92         let dirPath = System.IO.Path.Combine(output, name)
  93         System.IO.Directory.CreateDirectory dirPath |> ignore
  94
  95         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  96
  97         saveMat (edges * 255.0) (buildFileName " - edges.png")
  98
  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")
 102
 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")
 106
 107         let imgEllipses = img.Copy()
 108         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
 109         saveImg imgEllipses (buildFileName " - ellipses.png")
 110
 111         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 112
 113         let imgCells = img.Copy()
 114         drawCells imgCells false cells
 115         saveImg imgCells (buildFileName " - cells.png")
 116
 117         let imgCells' = img.Copy()
 118         drawCells imgCells' true cells
 119         saveImg imgCells' (buildFileName " - cells - full.png")
 120
 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")
 125
 126         saveImg filteredGreen (buildFileName " - filtered.png")
 127         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed.png")
 128
 129         (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
 130         saveImg stainMarker (buildFileName " - stain (area closing).png")*)
 131
 132         saveImg green (buildFileName " - green.png")
 133
 134         use blue  = scaledImg.Item(0)
 135         saveImg blue (buildFileName " - blue.png")
 136
 137         use red = scaledImg.Item(2)
 138         saveImg red (buildFileName " - red.png")
 139     | _ -> ()
 140
 141     cells