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 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
  20     // To report the progress of this function from 0 to 100.
  21     let reportWithVal (percent: int) (value: 'a) : 'a option =
  22         match reportProgress with
  23         | Some f ->
  24             if f percent
  25             then Some value
  26             else None
  27         | _ -> Some value
  28
  29     let report (percent: int) : unit option =
  30         reportWithVal percent ()
  31
  32     let inline buildLogWithName (text:  string) = sprintf "(%s) %s" name text
  33     let logWithName mess = Log.User(buildLogWithName mess)
  34     let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
  35
  36     maybe {
  37         do! report 0
  38
  39         logWithName "Starting analysis ..."
  40
  41         use green = img.Item(1)
  42         let greenFloat = green.Convert<Gray, float32>()
  43         let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
  44
  45         logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
  46
  47         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.
  48         do! logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening; report 10)
  49
  50         //do! report 10
  51
  52         let range =
  53             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  54             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  55         //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
  56         let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing filteredGreen range |> float32))
  57         config.SetRBCRadius <| radius
  58
  59         logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
  60
  61         do! report 20
  62
  63         do!
  64             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  65             if secondAreaOpening > initialAreaOpening
  66             then
  67                 logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30)
  68             else
  69                 report 30
  70
  71         let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  72         //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  73
  74         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  75             let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
  76             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  77             reportWithVal 40 (edges, xGradient, yGradient))
  78
  79         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
  80
  81         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
  82
  83         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config))
  84
  85         logWithName "Analysis finished"
  86
  87         do
  88             // Output pictures if debug flag is set.
  89             match config.Debug with
  90             | DebugOn output ->
  91                 let dirPath = System.IO.Path.Combine(output, name)
  92                 System.IO.Directory.CreateDirectory dirPath |> ignore
  93
  94                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  95
  96                 saveMat (edges * 255.0) (buildFileName " - edges.png")
  97
  98                 saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  99                 saveImg parasites.stain (buildFileName " - parasites - stain.png")
 100                 saveImg parasites.infection (buildFileName " - parasites - infection.png")
 101
 102                 let imgAllEllipses = img.Copy()
 103                 drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
 104                 saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 105
 106                 let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
 107                 drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 108                 saveImg imgEllipses (buildFileName " - ellipses.png")
 109
 110                 let imgCells = img.Copy()
 111                 drawCells imgCells false cells
 112                 saveImg imgCells (buildFileName " - cells.png")
 113
 114                 let imgCells' = img.Copy()
 115                 drawCells imgCells' true cells
 116                 saveImg imgCells' (buildFileName " - cells - full.png")
 117
 118                 let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
 119                 for m in ImgTools.findMaxima filteredGreenMaxima do
 120                     ImgTools.drawPoints filteredGreenMaxima m 255.f
 121                 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 122
 123                 saveImg filteredGreen (buildFileName " - filtered.png")
 124                 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 125                 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 126
 127                 saveImg green (buildFileName " - green.png")
 128
 129                 use blue = img.Item(0)
 130                 saveImg blue (buildFileName " - blue.png")
 131
 132                 use red = img.Item(2)
 133                 saveImg red (buildFileName " - red.png")
 134             | _ -> ()
 135
 136         return cells }
 137
 138 /// <summary>
 139 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 140 /// </summary>
 141 /// <param name="imgs"></param>
 142 /// <param name="reportProgress">An optional function to report progress. The process is aborted if the returned value is false</param>
 143 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
 144     let report (percent: int) : bool =
 145         match reportProgress with
 146         | Some f -> f percent
 147         | _ -> true
 148
 149     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 150     let nbImgs = List.length imgs
 151
 152     let reportProgressImg (id: string) (progress: int) =
 153         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 154         report (progressPerAnalysis.Values.Sum() / nbImgs)
 155
 156     let n = Environment.ProcessorCount
 157
 158     let results =
 159         imgs
 160         |> PSeq.choose (
 161             fun (id, config, img) ->
 162                 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 163                 | Some result -> Some (id, result)
 164                 | None -> None)
 165         |> PSeq.withDegreeOfParallelism n
 166         |> PSeq.toList
 167
 168     // If one of the analyses has been aborted we return 'None'.
 169     if List.length results <> List.length imgs
 170     then None
 171     else Some results
 172