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     let imgFloat = img.Convert<Bgr, float32>()
  18     use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)
  19
  20     use green = scaledImg.Item(1)
  21
  22     use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
  23
  24     use sobelKernel =
  25         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  26                                         [ 2.0f; 0.0f; -2.0f ]
  27                                         [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
  28
  29     use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
  30     use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  31
  32     let xEdgesData = xEdges.Data
  33     let yEdgesData = yEdges.Data
  34     for r in 0..xEdges.Rows-1 do
  35         xEdgesData.[r, 0, 0] <- 0.0
  36         xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  37         yEdgesData.[r, 0, 0] <- 0.0
  38         yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
  39
  40     for c in 0..xEdges.Cols-1 do
  41         xEdgesData.[0, c, 0] <- 0.0
  42         xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  43         yEdgesData.[0, c, 0] <- 0.0
  44         yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
  45
  46     use magnitudes = new Matrix<float>(xEdges.Size)
  47     CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
  48
  49     let min = ref 0.0
  50     let minLocation = ref <| Point()
  51     let max = ref 0.0
  52     let maxLocation = ref <| Point()
  53     magnitudes.MinMax(min, max, minLocation, maxLocation)
  54
  55     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  56     use edges = new Matrix<byte>(xEdges.Size)
  57     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  58
  59     logTime "Finding edges" (fun() -> thin edges)
  60     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  61
  62     let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
  63
  64     let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
  65
  66     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  67         let matchingEllipses = Ellipse.find edges xEdges yEdges config
  68         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  69
  70     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
  71
  72     // Output pictures if debug flag is set.
  73     match config.debug with
  74     | DebugOn output ->
  75         let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
  76         saveMat (edges * 255.0) (buildFileName " - edges.png")
  77
  78         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  79         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  80         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  81
  82         let imgAllEllipses = img.Copy()
  83         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
  84         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  85
  86         let imgEllipses = img.Copy()
  87         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  88         saveImg imgEllipses (buildFileName " - ellipses.png")
  89
  90         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
  91
  92         let imgCells = img.Copy()
  93         drawCells imgCells false cells
  94         saveImg imgCells (buildFileName " - cells.png")
  95
  96         let imgCells' = img.Copy()
  97         drawCells imgCells' true cells
  98         saveImg imgCells' (buildFileName " - cells - full.png")
  99     | _ -> ()
 100
 101     cells