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.scale = 1.0 then img else img.Resize(config.scale, CvEnum.Inter.Area)
  18
  19     use blue  = scaledImg.Item(0)
  20     use green = scaledImg.Item(1)
  21     use red = scaledImg.Item(2)
  22
  23     let greenFloat = green.Convert<Gray, float32>()
  24
  25     let filteredGreen = gaussianFilter green config.preFilterSigma
  26     logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
  27
  28     let RBCSize = Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
  29     let RBCSizeDelta = RBCSize / 3.0
  30
  31     let config = { config with minRBCSize = RBCSize - RBCSizeDelta ; maxRBCSize = RBCSize + RBCSizeDelta }
  32
  33     let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
  34
  35     use sobelKernel =
  36         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  37                                         [ 2.0f; 0.0f; -2.0f ]
  38                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  39
  40     use xEdges = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
  41     use yEdges = filteredGreenFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  42
  43     let xEdgesData = xEdges.Data
  44     let yEdgesData = yEdges.Data
  45     for r in 0..xEdges.Rows-1 do
  46         xEdgesData.[r, 0, 0] <- 0.0
  47         xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  48         yEdgesData.[r, 0, 0] <- 0.0
  49         yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  50
  51     for c in 0..xEdges.Cols-1 do
  52         xEdgesData.[0, c, 0] <- 0.0
  53         xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  54         yEdgesData.[0, c, 0] <- 0.0
  55         yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  56
  57     use magnitudes = new Matrix<float>(xEdges.Size)
  58     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  59
  60     let min = ref 0.0
  61     let minLocation = ref <| Point()
  62     let max = ref 0.0
  63     let maxLocation = ref <| Point()
  64     magnitudes.MinMax(min, max, minLocation, maxLocation)
  65
  66     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  67     use edges = new Matrix<byte>(xEdges.Size)
  68     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  69
  70     logTime "Finding edges" (fun() -> thin edges)
  71     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  72
  73     let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
  74
  75     let parasites = ParasitesMarker.find greenFloat filteredGreenFloat kmediansResults config
  76
  77     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  78         let matchingEllipses = Ellipse.find edges xEdges yEdges config
  79         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  80
  81     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
  82
  83     // Output pictures if debug flag is set.
  84     match config.debug with
  85     | DebugOn output ->
  86         let dirPath = System.IO.Path.Combine(output, name)
  87         System.IO.Directory.CreateDirectory dirPath |> ignore
  88
  89         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  90
  91         saveMat (edges * 255.0) (buildFileName " - edges.png")
  92
  93         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  94         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  95         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  96
  97         let imgAllEllipses = img.Copy()
  98         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
  99         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 100
 101         let imgEllipses = img.Copy()
 102         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
 103         saveImg imgEllipses (buildFileName " - ellipses.png")
 104
 105         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 106
 107         let imgCells = img.Copy()
 108         drawCells imgCells false cells
 109         saveImg imgCells (buildFileName " - cells.png")
 110
 111         let imgCells' = img.Copy()
 112         drawCells imgCells' true cells
 113         saveImg imgCells' (buildFileName " - cells - full.png")
 114
 115         let filteredGreenMaxima = gaussianFilter green config.preFilterSigma
 116         for m in ImgTools.findMaxima filteredGreenMaxima do
 117             ImgTools.drawPoints filteredGreenMaxima m 255uy
 118         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 119
 120         saveImg filteredGreen (buildFileName " - filtered.png")
 121         saveImg blue (buildFileName " - blue.png")
 122         saveImg green (buildFileName " - green.png")
 123         saveImg red (buildFileName " - red.png")
 124     | _ -> ()
 125
 126     cells