Parasitemia/ParasitemiaCore/Analysis.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 Morpho
  16 open ImgTools
  17 open Config
  18 open Types
  19
  20 /// <summary>
  21 /// Analyze the given image and detect reb blood cell (RBC) in it.
  22 /// </summary>
  23 /// <param name="img">The image</param>
  24 /// <param name="name">The name, used during logging</param>
  25 /// <param name="config">The configuration, must not be shared with another analysis</param>
  26 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
  27 ///     The first call returning 'false' will cancel the analysis.
  28 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
  29 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
  30 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
  31
  32     // To report the progress of this function from 0 to 100.
  33     // Return 'None' if the process must be aborted.
  34     let reportWithVal (percent: int) (value: 'a) : 'a option =
  35         match reportProgress with
  36         | Some f ->
  37             if f percent
  38             then Some value
  39             else None
  40         | _ -> Some value
  41
  42     let report (percent: int) : unit option =
  43         reportWithVal percent ()
  44
  45     let inline buildLogWithName (text: string) = sprintf "№ %s: %s" name text
  46     let logWithName mess = Log.User(buildLogWithName mess)
  47     let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
  48
  49     // Monadic construction to be able to abort the progress when running.
  50     maybe {
  51         do! report 0
  52
  53         logWithName "Starting analysis ..."
  54
  55         use img_float = img.Convert<Bgr, float32>()
  56
  57         use img_RBC = img_float.[1] // Green.
  58         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
  59
  60         use img_parasites = img_float.[2] // Red.
  61         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
  62
  63         logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
  64
  65         let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.1f // 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.
  66         do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
  67
  68         let range =
  69             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  70             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  71
  72         let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
  73         //let! radius = logTimeWithName "Granulometry (morpho)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
  74         config.SetRBCRadius <| radius
  75
  76         logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
  77
  78         do! report 20
  79
  80         do!
  81             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  82             if secondAreaOpening > initialAreaOpening
  83             then
  84                 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
  85             else
  86                 report 30
  87
  88         // Remove pale centers from the parasites image.
  89         areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
  90
  91         // Removing parasites.
  92         areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
  93
  94         let! parasites, imgWhitoutParasite, imgWithoutNucleus =
  95             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
  96
  97         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  98             let edges, xGradient, yGradient = Edges.find img_RBC_filtered
  99             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
 100             reportWithVal 50 (edges, xGradient, yGradient))
 101
 102         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
 103
 104         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
 105
 106         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img.Width img.Height config))
 107
 108         logWithName "Analysis finished"
 109
 110         do
 111             // Output pictures if debug flag is set.
 112             match config.Debug with
 113             | DebugOn output ->
 114                 let dirPath = System.IO.Path.Combine(output, name)
 115                 System.IO.Directory.CreateDirectory dirPath |> ignore
 116
 117                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 118
 119                 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
 120
 121                 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 122                 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
 123                 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 124
 125                 let imgAllEllipses = img_RBC_filtered.Copy()
 126                 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray(200.0)) 0.04
 127                 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 128
 129                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
 130                 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 131                 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
 132
 133                 let imgCells = img.Copy()
 134                 Drawing.drawCells imgCells false cells
 135                 IO.saveImg imgCells (buildFileName " - cells.png")
 136
 137                 let imgCells' = img.Copy()
 138                 Drawing.drawCells imgCells' true cells
 139                 IO.saveImg imgCells' (buildFileName " - cells - full.png")
 140
 141                 let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 142                 for m in findMaxima filteredRBCMaxima do
 143                     Drawing.drawPoints filteredRBCMaxima m 255.f
 144                 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png")
 145
 146                 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
 147                 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 148
 149                 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
 150                 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
 151
 152                 IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
 153                 IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
 154                 IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
 155             | _ -> ()
 156
 157         return cells }
 158
 159 /// <summary>
 160 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 161 /// </summary>
 162 /// <param name="imgs">The images: (name * configuration * image)</param>
 163 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 164 ///     The first call returning 'false' will cancel the analysis.
 165 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 166 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
 167 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
 168     let report (percent: int) : bool =
 169         match reportProgress with
 170         | Some f -> f percent
 171         | _ -> true
 172
 173     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 174     let nbImgs = List.length imgs
 175
 176     let reportProgressImg (id: string) (progress: int) =
 177         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 178         report (progressPerAnalysis.Values.Sum() / nbImgs)
 179
 180     let n = Environment.ProcessorCount
 181
 182     let results =
 183         imgs
 184         |> PSeq.choose (
 185             fun (id, config, img) ->
 186                 try
 187                     match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 188                     | Some result -> Some (id, result)
 189                     | None -> None
 190                 with
 191                 | ex ->
 192                     Log.Error("Analysis {0} failed: {1}", id, ex)
 193                     None)
 194         |> PSeq.withDegreeOfParallelism n
 195         |> PSeq.toList
 196
 197     // If one of the analyses has been aborted we return 'None'.
 198     if List.length results <> List.length imgs
 199     then None
 200     else Some results
 201