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 let warningRatioDifferenceRBCDiameter = 1.2
  21
  22 /// <summary>
  23 /// Analyze the given image and detect reb blood cell (RBC) in it.
  24 /// </summary>
  25 /// <param name="img">The image</param>
  26 /// <param name="name">The name, used during logging</param>
  27 /// <param name="config">The configuration, must not be shared with another analysis</param>
  28 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
  29 ///     The first call returning 'false' will cancel the analysis.
  30 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
  31 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
  32 let doAnalysis (img : Image<Bgr, byte>) (name : string) (config : Config) (reportProgress : (int -> bool) option) : AnalysisResult option =
  33
  34     // To report the progress of this function from 0 to 100.
  35     // Return 'None' if the process must be aborted.
  36     let reportWithVal (percent : int) (value : 'a) : 'a option =
  37         match reportProgress with
  38         | Some f -> if f percent then Some value 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.Info "%s" (buildLogWithName mess)
  46     let inline logTimeWithName (text : string) (f : unit -> 'a option) : 'a option = Log.LogWithTime Severity.INFO f "%s" (buildLogWithName text)
  47
  48     // Monadic construction to be able to abort the progress when running.
  49     maybe {
  50         do! report 0
  51
  52         logWithName "Starting analysis ..."
  53
  54         use img_float = img.Convert<Bgr, float32> ()
  55
  56         use img_RBC = img_float.[1] // Green.
  57         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
  58
  59         use img_parasites = img_float.[2] // Red.
  60         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
  61
  62         logWithName (sprintf "Nominal erythrocyte diameter: %O" config.RBCRadiusByResolution)
  63
  64         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.
  65         do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
  66
  67         let range =
  68             let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  69             int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  70
  71         let! radius = logTimeWithName "Granulometry (area)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
  72         //let! radius = logTimeWithName "Granulometry (morpho)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
  73         config.SetRBCRadius <| radius
  74
  75         logWithName (sprintf "Found erythrocyte diameter: %O" config.RBCRadius)
  76
  77         do! report 20
  78
  79         do!
  80             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  81             if secondAreaOpening > initialAreaOpening then
  82                 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
  83             else
  84                 report 30
  85
  86         // Remove pale centers from the parasites image.
  87         areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
  88
  89         // Removing parasites.
  90         areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
  91
  92         let! parasites, imgWhitoutParasite, imgWithoutNucleus =
  93             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
  94
  95         let! edges, xGradient, yGradient =
  96             logTimeWithName "Finding edges" (
  97                 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
 103         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
 104
 105         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
 106
 107         let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img.Width img.Height config))
 108
 109         do
 110             if config.RBCRadiusByResolution.μm / config.RBCRadius.μm > warningRatioDifferenceRBCDiameter then
 111                 logWithName (sprintf "Warning: erythrocyte diameter found is too low compared to the nominal erythrocyte diameter, maybe the PPI image resolution is lesser than %.0f ppi" config.Parameters.resolution)
 112             elif config.RBCRadius.μm / config.RBCRadiusByResolution.μm > warningRatioDifferenceRBCDiameter then
 113                 logWithName (sprintf "Warning: erythrocyte diameter found is too high compared to the nominal erythrocyte diameter, maybe the PPI image resolution is higher than %.0f" config.Parameters.resolution)
 114
 115         logWithName "Analysis finished"
 116
 117         do
 118             // Output pictures if debug flag is set.
 119             match config.Debug with
 120             | DebugOn output ->
 121                 let dirPath = System.IO.Path.Combine (output, name)
 122                 System.IO.Directory.CreateDirectory dirPath |> ignore
 123
 124                 let buildFileName postfix = System.IO.Path.Combine (dirPath, name + postfix)
 125
 126                 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
 127
 128                 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 129                 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
 130                 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 131
 132                 let imgAllEllipses = img_RBC_filtered.Copy ()
 133                 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray 200.0) 0.04
 134                 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 135
 136                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte> ()
 137                 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr (0.0, 240.0, 240.0)) 1.0
 138                 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
 139
 140                 let imgCells = img.Copy ()
 141                 Drawing.drawCells imgCells false cells
 142                 IO.saveImg imgCells (buildFileName " - cells.png")
 143
 144                 let imgCells' = img.Copy ()
 145                 Drawing.drawCells imgCells' true cells
 146                 IO.saveImg imgCells' (buildFileName " - cells - full.png")
 147
 148                 (* let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 149                 for m in findMaxima filteredRBCMaxima do
 150                     Drawing.drawPoints filteredRBCMaxima m 255.f
 151                 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png") *)
 152
 153                 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
 154                 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 155
 156                 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
 157                 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
 158
 159                 IO.saveImg img_float.[2] (buildFileName " - source - red.png")
 160                 IO.saveImg img_float.[1] (buildFileName " - source - green.png")
 161                 IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
 162             | _ -> ()
 163
 164         return
 165             {
 166                 Cells = cells
 167                 RBCSize_μm = config.RBCRadius.μm
 168                 RBCSize_px = config.RBCRadius.Pixel
 169             }
 170
 171         //return cells
 172     }
 173
 174 /// <summary>
 175 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
 176 /// </summary>
 177 /// <param name="imgs">The images: (name * configuration * image)</param>
 178 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 179 ///     The first call returning 'false' will cancel the analysis.
 180 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 181 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
 182 let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) list) (reportProgress : (int -> bool) option) : (string * AnalysisResult) list option =
 183     let report (percent : int) : bool =
 184         match reportProgress with
 185         | Some f -> f percent
 186         | _ -> true
 187
 188     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int> ()
 189     let nbImgs = List.length imgs
 190
 191     let reportProgressImg (id : string) (progress : int) =
 192         progressPerAnalysis.AddOrUpdate (id, progress, (fun _ _ -> progress)) |> ignore
 193         report (progressPerAnalysis.Values.Sum () / nbImgs)
 194
 195     let n = Environment.ProcessorCount
 196
 197     let results =
 198         imgs
 199         |> PSeq.choose (
 200             fun (id, config, img) ->
 201                 try
 202                     match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 203                     | Some result -> Some (id, result)
 204                     | None -> None
 205                 with
 206                 | ex ->
 207                     Log.Error "Analysis %s failed: %O" id ex
 208                     None
 209         )
 210         |> PSeq.withDegreeOfParallelism n
 211         |> PSeq.toList
 212
 213     // If one of the analyses has been aborted we return 'None'.
 214     if List.length results <> List.length imgs then
 215         None
 216     else
 217         Some results
 218