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     (*
  63     let kmediansResults = KMedians.kmedians filteredGreen 1.0
  64
  65     let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
  66
  67     let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
  68     let windowSize = roundInt (1.6 * (snd radiusRange))
  69     let factorNbPick = 1.5
  70     let ellipses = logTime "Finding ellipses" (fun () ->
  71         Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
  72
  73     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
  74     *)
  75     let cells = []
  76
  77     // Output pictures if debug flag is set.
  78     match config.debug with
  79     | DebugOn output ->
  80         let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
  81         saveMat (edges * 255.0) (buildFileName " - edges.png")
  82
  83         (*saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  84         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  85         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  86
  87         let imgEllipses = img.Copy()
  88         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0))
  89         saveImg imgEllipses (buildFileName " - ellipses.png")
  90
  91         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
  92
  93         let imgCells = img.Copy()
  94         drawCells imgCells false cells
  95         saveImg imgCells (buildFileName " - cells.png")
  96
  97         let imgCells' = img.Copy()
  98         drawCells imgCells' true cells
  99         saveImg imgCells' (buildFileName " - cells - full.png")*)
 100     | _ -> ()
 101
 102     cells