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 img_float = img.Convert<Bgr, float32>()
  54
  55         use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
  56         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
  57
  58         use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
  59         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
  60
  61         logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
  62
  63         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.
  64         do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
  65
  66         let range =
  67             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  68             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  69         let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
  70         config.SetRBCRadius <| radius
  71
  72         logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
  73
  74         do! report 20
  75
  76         do!
  77             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  78             if secondAreaOpening > initialAreaOpening
  79             then
  80                 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
  81             else
  82                 report 30
  83
  84         // Removing parasites.
  85         areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
  86
  87         let! parasites, imgWhitoutParasite, imgWithoutNucleus =
  88             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
  89
  90         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  91             let edges, xGradient, yGradient = findEdges img_RBC_filtered
  92             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  93             reportWithVal 50 (edges, xGradient, yGradient))
  94
  95         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
  96
  97         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
  98
  99         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
 100
 101         logWithName "Analysis finished"
 102
 103         do
 104             // Output pictures if debug flag is set.
 105             match config.Debug with
 106             | DebugOn output ->
 107                 let dirPath = System.IO.Path.Combine(output, name)
 108                 System.IO.Directory.CreateDirectory dirPath |> ignore
 109
 110                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 111
 112                 saveMat (edges * 255.0) (buildFileName " - edges.png")
 113
 114                 saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 115                 saveImg parasites.parasite (buildFileName " - parasites - stain.png")
 116                 saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 117
 118                 let imgAllEllipses = img.Copy()
 119                 drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
 120                 saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 121
 122                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
 123                 drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 124                 saveImg imgEllipses (buildFileName " - ellipses.png")
 125
 126                 let imgCells = img.Copy()
 127                 drawCells imgCells false cells
 128                 saveImg imgCells (buildFileName " - cells.png")
 129
 130                 let imgCells' = img.Copy()
 131                 drawCells imgCells' true cells
 132                 saveImg imgCells' (buildFileName " - cells - full.png")
 133
 134                 let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 135                 for m in findMaxima filteredGreenMaxima do
 136                     drawPoints filteredGreenMaxima m 255.f
 137                 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 138
 139                 saveImg img_RBC_filtered (buildFileName " - filtered.png")
 140                 saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
 141                 saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 142
 143                 saveImg img_RBC (buildFileName " - source - RBC.png")
 144                 saveImg img_parasites (buildFileName " - source - parasites.png")
 145
 146                 saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
 147                 saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
 148                 saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
 149             | _ -> ()
 150
 151         return cells }
 152
 153 /// <summary>
 154 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 155 /// </summary>
 156 /// <param name="imgs">The images: (name * configuration * image)</param>
 157 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 158 ///     The first call returning 'false' will cancel the analysis.
 159 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 160 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
 161 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
 162     let report (percent: int) : bool =
 163         match reportProgress with
 164         | Some f -> f percent
 165         | _ -> true
 166
 167     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 168     let nbImgs = List.length imgs
 169
 170     let reportProgressImg (id: string) (progress: int) =
 171         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 172         report (progressPerAnalysis.Values.Sum() / nbImgs)
 173
 174     let n = Environment.ProcessorCount
 175
 176     let results =
 177         imgs
 178         |> PSeq.choose (
 179             fun (id, config, img) ->
 180                 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 181                 | Some result -> Some (id, result)
 182                 | None -> None)
 183         |> PSeq.withDegreeOfParallelism n
 184         |> PSeq.toList
 185
 186     // If one of the analyses has been aborted we return 'None'.
 187     if List.length results <> List.length imgs
 188     then None
 189     else Some results
 190