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 -> if f percent then Some value else None
  37         | _ -> Some value
  38
  39     let report (percent : int) : unit option =
  40         reportWithVal percent ()
  41
  42     let inline buildLogWithName (text : string) = sprintf "№ %s: %s" name text
  43     let logWithName mess = Log.Info "%s" (buildLogWithName mess)
  44     let inline logTimeWithName (text : string) (f : unit -> 'a option) : 'a option = Log.LogWithTime Severity.INFO f "%s" (buildLogWithName text)
  45
  46     // Monadic construction to be able to abort the progress when running.
  47     maybe {
  48         do! report 0
  49
  50         logWithName "Starting analysis ..."
  51
  52         use img_float = img.Convert<Bgr, float32>()
  53
  54         use img_RBC = img_float.[1] // Green.
  55         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
  56
  57         use img_parasites = img_float.[2] // Red.
  58         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
  59
  60         logWithName (sprintf "Nominal erythrocyte diameter: %O" config.RBCRadiusByResolution)
  61
  62         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.
  63         do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
  64
  65         let range =
  66             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  67             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  68
  69         let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
  70         //let! radius = logTimeWithName "Granulometry (morpho)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
  71         config.SetRBCRadius <| radius
  72
  73         logWithName (sprintf "Found erythrocyte diameter: %O" config.RBCRadius)
  74
  75         do! report 20
  76
  77         do!
  78             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  79             if secondAreaOpening > initialAreaOpening then
  80                 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
  81             else
  82                 report 30
  83
  84         // Remove pale centers from the parasites image.
  85         areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
  86
  87         // Removing parasites.
  88         areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
  89
  90         let! parasites, imgWhitoutParasite, imgWithoutNucleus =
  91             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
  92
  93         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  94             let edges, xGradient, yGradient = Edges.find img_RBC_filtered
  95             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  96             reportWithVal 50 (edges, xGradient, yGradient))
  97
  98         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
  99
 100         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
 101
 102         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img.Width img.Height config))
 103
 104         logWithName "Analysis finished"
 105
 106         do
 107             // Output pictures if debug flag is set.
 108             match config.Debug with
 109             | DebugOn output ->
 110                 let dirPath = System.IO.Path.Combine(output, name)
 111                 System.IO.Directory.CreateDirectory dirPath |> ignore
 112
 113                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 114
 115                 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
 116
 117                 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 118                 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
 119                 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 120
 121                 let imgAllEllipses = img_RBC_filtered.Copy()
 122                 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray(200.0)) 0.04
 123                 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 124
 125                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
 126                 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 127                 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
 128
 129                 let imgCells = img.Copy()
 130                 Drawing.drawCells imgCells false cells
 131                 IO.saveImg imgCells (buildFileName " - cells.png")
 132
 133                 let imgCells' = img.Copy()
 134                 Drawing.drawCells imgCells' true cells
 135                 IO.saveImg imgCells' (buildFileName " - cells - full.png")
 136
 137                 (* let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 138                 for m in findMaxima filteredRBCMaxima do
 139                     Drawing.drawPoints filteredRBCMaxima m 255.f
 140                 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png") *)
 141
 142                 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
 143                 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 144
 145                 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
 146                 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
 147
 148                 IO.saveImg img_float.[2] (buildFileName " - source - red.png")
 149                 IO.saveImg img_float.[1] (buildFileName " - source - green.png")
 150                 IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
 151             | _ -> ()
 152
 153         return cells
 154     }
 155
 156 /// <summary>
 157 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 158 /// </summary>
 159 /// <param name="imgs">The images: (name * configuration * image)</param>
 160 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 161 ///     The first call returning 'false' will cancel the analysis.
 162 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 163 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
 164 let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) list) (reportProgress : (int -> bool) option) : (string * Cell list) list option =
 165     let report (percent : int) : bool =
 166         match reportProgress with
 167         | Some f -> f percent
 168         | _ -> true
 169
 170     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 171     let nbImgs = List.length imgs
 172
 173     let reportProgressImg (id : string) (progress : int) =
 174         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 175         report (progressPerAnalysis.Values.Sum() / nbImgs)
 176
 177     let n = Environment.ProcessorCount
 178
 179     let results =
 180         imgs
 181         |> PSeq.choose (
 182             fun (id, config, img) ->
 183                 try
 184                     match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 185                     | Some result -> Some (id, result)
 186                     | None -> None
 187                 with
 188                 | ex ->
 189                     Log.Error "Analysis %s failed: %O" id ex
 190                     None
 191         )
 192         |> PSeq.withDegreeOfParallelism n
 193         |> PSeq.toList
 194
 195     // If one of the analyses has been aborted we return 'None'.
 196     if List.length results <> List.length imgs then
 197         None
 198     else
 199         Some results
 200