Parasitemia/ParasitemiaCore/MainAnalysis.fs

   1 module ParasitemiaCore.Analysis
   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 Logger
  13
  14 open Utils
  15 open ImgTools
  16 open Config
  17 open Types
  18
  19 /// <summary>
  20 /// Analyze the given image and detect reb blood cell (RBC) in it.
  21 /// </summary>
  22 /// <param name="img">The image</param>
  23 /// <param name="name">The name, used during logging</param>
  24 /// <param name="config">The configuration, must not be shared with another analysis</param>
  25 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
  26 ///     The first call returning 'false' will cancel the analysis.
  27 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
  28 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
  29 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
  30
  31     // To report the progress of this function from 0 to 100.
  32     // Return 'None' if the process must be aborted.
  33     let reportWithVal (percent: int) (value: 'a) : 'a option =
  34         match reportProgress with
  35         | Some f ->
  36             if f percent
  37             then Some value
  38             else None
  39         | _ -> Some value
  40
  41     let report (percent: int) : unit option =
  42         reportWithVal percent ()
  43
  44     let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
  45     let logWithName mess = Log.User(buildLogWithName mess)
  46     let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
  47
  48     maybe {
  49         do! report 0
  50
  51         logWithName "Starting analysis ..."
  52
  53         use green = img.[1]
  54         let greenFloat = green.Convert<Gray, float32>()
  55         let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
  56
  57         logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
  58
  59         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.
  60         do! logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening; report 10)
  61
  62         let range =
  63             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  64             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  65         //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
  66         let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing filteredGreen range |> float32))
  67         config.SetRBCRadius <| radius
  68
  69         logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
  70
  71         do! report 20
  72
  73         do!
  74             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  75             if secondAreaOpening > initialAreaOpening
  76             then
  77                 logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30)
  78             else
  79                 report 30
  80
  81         let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  82         //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  83
  84         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  85             let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
  86             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  87             reportWithVal 40 (edges, xGradient, yGradient))
  88
  89         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
  90
  91         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
  92
  93         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config))
  94
  95         logWithName "Analysis finished"
  96
  97         do
  98             // Output pictures if debug flag is set.
  99             match config.Debug with
 100             | DebugOn output ->
 101                 let dirPath = System.IO.Path.Combine(output, name)
 102                 System.IO.Directory.CreateDirectory dirPath |> ignore
 103
 104                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 105
 106                 saveMat (edges * 255.0) (buildFileName " - edges.png")
 107
 108                 saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 109                 saveImg parasites.stain (buildFileName " - parasites - stain.png")
 110                 saveImg parasites.infection (buildFileName " - parasites - infection.png")
 111
 112                 let imgAllEllipses = img.Copy()
 113                 drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
 114                 saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 115
 116                 let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
 117                 drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 118                 saveImg imgEllipses (buildFileName " - ellipses.png")
 119
 120                 let imgCells = img.Copy()
 121                 drawCells imgCells false cells
 122                 saveImg imgCells (buildFileName " - cells.png")
 123
 124                 let imgCells' = img.Copy()
 125                 drawCells imgCells' true cells
 126                 saveImg imgCells' (buildFileName " - cells - full.png")
 127
 128                 let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
 129                 for m in ImgTools.findMaxima filteredGreenMaxima do
 130                     ImgTools.drawPoints filteredGreenMaxima m 255.f
 131                 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 132
 133                 saveImg filteredGreen (buildFileName " - filtered.png")
 134                 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 135                 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 136
 137                 saveImg green (buildFileName " - green.png")
 138
 139                 use blue = img.Item(0)
 140                 saveImg blue (buildFileName " - blue.png")
 141
 142                 use red = img.Item(2)
 143                 saveImg red (buildFileName " - red.png")
 144             | _ -> ()
 145
 146         return cells }
 147
 148 /// <summary>
 149 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 150 /// </summary>
 151 /// <param name="imgs">The images: (name * configuration * image)</param>
 152 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 153 ///     The first call returning 'false' will cancel the analysis.
 154 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 155 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
 156 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
 157     let report (percent: int) : bool =
 158         match reportProgress with
 159         | Some f -> f percent
 160         | _ -> true
 161
 162     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 163     let nbImgs = List.length imgs
 164
 165     let reportProgressImg (id: string) (progress: int) =
 166         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 167         report (progressPerAnalysis.Values.Sum() / nbImgs)
 168
 169     let n = Environment.ProcessorCount
 170
 171     let results =
 172         imgs
 173         |> PSeq.choose (
 174             fun (id, config, img) ->
 175                 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 176                 | Some result -> Some (id, result)
 177                 | None -> None)
 178         |> PSeq.withDegreeOfParallelism n
 179         |> PSeq.toList
 180
 181     // If one of the analyses has been aborted we return 'None'.
 182     if List.length results <> List.length imgs
 183     then None
 184     else Some results
 185