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
  24     let greenFloat = green.Convert<Gray, float32>()
  25
  26     let green = gaussianFilter green 1.5
  27
  28     // let RBCSize = Granulometry.findRadius green (10, 100) 0.5
  29
  30     match config.debug with
  31     | DebugOn output ->
  32         let dirPath = System.IO.Path.Combine(output, name)
  33         System.IO.Directory.CreateDirectory dirPath |> ignore
  34         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  35
  36         saveImg green (buildFileName " - green.png")
  37
  38         let greenMaxima = green.Copy()
  39         let maxima = ImgTools.findMaxima greenMaxima
  40         for m in maxima do
  41             for p in m do
  42                 greenMaxima.Data.[p.Y, p.X, 0] <- 255uy
  43
  44         saveImg greenMaxima (buildFileName " - maxima.png")
  45
  46         logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800)
  47         saveImg green (buildFileName " - green opened.png")
  48
  49     | _ -> ()
  50
  51     []
  52     (*
  53
  54     use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2)
  55
  56     use sobelKernel =
  57         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  58                                         [ 2.0f; 0.0f; -2.0f ]
  59                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  60
  61     use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
  62     use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  63
  64     let xEdgesData = xEdges.Data
  65     let yEdgesData = yEdges.Data
  66     for r in 0..xEdges.Rows-1 do
  67         xEdgesData.[r, 0, 0] <- 0.0
  68         xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  69         yEdgesData.[r, 0, 0] <- 0.0
  70         yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  71
  72     for c in 0..xEdges.Cols-1 do
  73         xEdgesData.[0, c, 0] <- 0.0
  74         xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  75         yEdgesData.[0, c, 0] <- 0.0
  76         yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  77
  78     use magnitudes = new Matrix<float>(xEdges.Size)
  79     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  80
  81     let min = ref 0.0
  82     let minLocation = ref <| Point()
  83     let max = ref 0.0
  84     let maxLocation = ref <| Point()
  85     magnitudes.MinMax(min, max, minLocation, maxLocation)
  86
  87     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  88     use edges = new Matrix<byte>(xEdges.Size)
  89     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  90
  91     logTime "Finding edges" (fun() -> thin edges)
  92     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  93
  94     let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
  95
  96     let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config
  97
  98     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  99         let matchingEllipses = Ellipse.find edges xEdges yEdges config
 100         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
 101
 102     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
 103
 104     // Output pictures if debug flag is set.
 105     match config.debug with
 106     | DebugOn output ->
 107         let dirPath = System.IO.Path.Combine(output, name)
 108         System.IO.Directory.CreateDirectory dirPath |> ignore
 109
 110         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 111
 112         saveMat (edges * 255.0) (buildFileName " - edges.png")
 113
 114         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 115         saveImg parasites.stain (buildFileName " - parasites - stain.png")
 116         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 117
 118         let imgAllEllipses = img.Copy()
 119         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
 120         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 121
 122         let imgEllipses = img.Copy()
 123         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
 124         saveImg imgEllipses (buildFileName " - ellipses.png")
 125
 126         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 127
 128         let imgCells = img.Copy()
 129         drawCells imgCells false cells
 130         saveImg imgCells (buildFileName " - cells.png")
 131
 132         let imgCells' = img.Copy()
 133         drawCells imgCells' true cells
 134         saveImg imgCells' (buildFileName " - cells - full.png")
 135
 136         saveImg (normalizeAndConvert filteredGreen) (buildFileName " - filtered.png")
 137         saveImg blue (buildFileName " - blue.png")
 138         saveImg green (buildFileName " - green.png")
 139         saveImg red (buildFileName " - red.png")
 140     | _ -> ()
 141
 142     cells*)