Parasitemia/Parasitemia/MainAnalysis.fs

   1 module ImageAnalysis
   2
   3 open System
   4 open System.Linq
   5 open System.Drawing
   6
   7 open FSharp.Collections.ParallelSeq
   8
   9 open Emgu.CV
  10 open Emgu.CV.Structure
  11
  12 open Utils
  13 open ImgTools
  14 open Config
  15 open Types
  16
  17 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
  18     // To report the progress of this function from 0 to 100.
  19     let inline report (percent: int) =
  20         match reportProgress with
  21         | Some f -> f percent
  22         | _ -> ()
  23
  24     let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
  25     let logWithName = buildLogWithName >> log
  26     let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) f
  27
  28     logWithName "Starting analysis ..."
  29
  30     use green = img.Item(1)
  31     let greenFloat = green.Convert<Gray, float32>()
  32     let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
  33
  34     logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
  35
  36     let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // We do an area opening a little larger to avoid to do a second one in the case the radius found is near the initial one.
  37     logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
  38
  39     report 8
  40
  41     let range =
  42         let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  43         int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  44     //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
  45     config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
  46     // log (sprintf "r1: %A, r2: %A" r1 r2)
  47
  48     logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
  49
  50     report 24
  51
  52     let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  53     if secondAreaOpening > initialAreaOpening
  54     then
  55         logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
  56
  57     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  58     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  59
  60     let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  61         let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
  62         removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  63         edges, xGradient, yGradient)
  64
  65     let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () ->
  66         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  67         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  68
  69     report 80
  70
  71     let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  72
  73     report 100
  74
  75     logWithName "Analysis finished"
  76
  77     // Output pictures if debug flag is set.
  78     match config.Debug with
  79     | DebugOn output ->
  80         let dirPath = System.IO.Path.Combine(output, name)
  81         System.IO.Directory.CreateDirectory dirPath |> ignore
  82
  83         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  84
  85         saveMat (edges * 255.0) (buildFileName " - edges.png")
  86
  87         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  88         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  89         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  90
  91         let imgAllEllipses = img.Copy()
  92         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  93         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  94
  95         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  96         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  97         saveImg imgEllipses (buildFileName " - ellipses.png")
  98
  99         let imgCells = img.Copy()
 100         drawCells imgCells false cells
 101         saveImg imgCells (buildFileName " - cells.png")
 102
 103         let imgCells' = img.Copy()
 104         drawCells imgCells' true cells
 105         saveImg imgCells' (buildFileName " - cells - full.png")
 106
 107         let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
 108         for m in ImgTools.findMaxima filteredGreenMaxima do
 109             ImgTools.drawPoints filteredGreenMaxima m 255.f
 110         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 111
 112         saveImg filteredGreen (buildFileName " - filtered.png")
 113         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 114         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 115
 116         saveImg green (buildFileName " - green.png")
 117
 118         use blue = img.Item(0)
 119         saveImg blue (buildFileName " - blue.png")
 120
 121         use red = img.Item(2)
 122         saveImg red (buildFileName " - red.png")
 123     | _ -> ()
 124
 125     cells
 126
 127 // ID * cell list.
 128 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
 129     let inline report (percent: int) =
 130         match reportProgress with
 131         | Some f -> f percent
 132         | _ -> ()
 133
 134     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 135     let nbImgs = List.length imgs
 136
 137     let reportProgressImg (id: string) (progress: int) =
 138         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 139         report (progressPerAnalysis.Values.Sum() / nbImgs)
 140
 141     let nbConcurrentTaskLimit = 4 // To reduce the memory taken.
 142     let n = Environment.ProcessorCount
 143
 144     imgs
 145     |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
 146     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 147     |> PSeq.toList