Parasitemia/ParasitemiaCore/Analysis.fs

   1 module ParasitemiaCore.Analysis
   2
   3 open System
   4 open System.Linq
   5
   6 open FSharp.Collections.ParallelSeq
   7
   8 open Emgu.CV
   9 open Emgu.CV.Structure
  10
  11 open Logger
  12
  13 open Utils
  14 open Morpho
  15 open ImgTools
  16 open Config
  17 open Types
  18
  19 let warningRatioDifferenceRBCDiameter = 1.2
  20
  21 /// <summary>
  22 /// Analyze the given image and detect reb blood cell (RBC) in it.
  23 /// </summary>
  24 /// <param name="img">The image</param>
  25 /// <param name="name">The name, used during logging</param>
  26 /// <param name="config">The configuration, must not be shared with another analysis</param>
  27 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
  28 ///     The first call returning 'false' will cancel the analysis.
  29 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
  30 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
  31 let doAnalysis (img : Image<Bgr, byte>) (name : string) (config : Config) (reportProgress : (int -> bool) option) : AnalysisResult option =
  32
  33     // To report the progress of this function from 0 to 100.
  34     // Return 'None' if the process must be aborted.
  35     let reportWithVal (percent : int) (value : 'a) : 'a option =
  36         match reportProgress with
  37         | Some f -> if f percent then Some value else None
  38         | _ -> Some value
  39
  40     let report (percent : int) : unit option =
  41         reportWithVal percent ()
  42
  43     let inline buildLogWithName (text : string) = sprintf "№ %s: %s" name text
  44     let logWithName mess = Log.Info "%s" (buildLogWithName mess)
  45     let inline logTimeWithName (text : string) (f : unit -> 'a option) : 'a option = Log.LogWithTime Severity.INFO f "%s" (buildLogWithName text)
  46
  47     // Monadic construction to be able to abort the progress when running.
  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] // Green.
  56         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
  57
  58         use img_parasites = img_float.[2] // Red.
  59         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
  60
  61         logWithName (sprintf "Nominal erythrocyte diameter: %O" 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
  70         let! radius = logTimeWithName "Granulometry (area)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
  71         //let! radius = logTimeWithName "Granulometry (morpho)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
  72         config.SetRBCRadius <| radius
  73
  74         logWithName (sprintf "Found erythrocyte diameter: %O" config.RBCRadius)
  75
  76         do! report 20
  77
  78         do!
  79             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  80             if secondAreaOpening > initialAreaOpening then
  81                 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
  82             else
  83                 report 30
  84
  85         // Remove pale centers from the parasites image.
  86         areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
  87
  88         // Removing parasites.
  89         areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
  90
  91         let! parasites, imgWhitoutParasite, imgWithoutNucleus =
  92             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
  93
  94         let! edges, xGradient, yGradient =
  95             logTimeWithName "Finding edges" (
  96                 fun () ->
  97                     let edges, xGradient, yGradient = Edges.find img_RBC_filtered
  98                     removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  99                     reportWithVal 50 (edges, xGradient, yGradient)
 100             )
 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         do
 109             if config.RBCRadiusByResolution.μm / config.RBCRadius.μm > warningRatioDifferenceRBCDiameter then
 110                 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)
 111             elif config.RBCRadius.μm / config.RBCRadiusByResolution.μm > warningRatioDifferenceRBCDiameter then
 112                 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)
 113
 114         logWithName "Analysis finished"
 115
 116         do
 117             // Output pictures if debug flag is set.
 118             match config.Debug with
 119             | DebugOn output ->
 120                 let dirPath = System.IO.Path.Combine (output, name)
 121                 System.IO.Directory.CreateDirectory dirPath |> ignore
 122
 123                 let buildFileName postfix = System.IO.Path.Combine (dirPath, name + postfix)
 124
 125                 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
 126
 127                 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
 128                 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
 129                 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 130
 131                 let imgAllEllipses = img_RBC_filtered.Copy ()
 132                 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray 200.0) 0.04
 133                 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 134
 135                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte> ()
 136                 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr (0.0, 240.0, 240.0)) 1.0
 137                 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
 138
 139                 let imgCells = img.Copy ()
 140                 Drawing.drawCells imgCells false cells
 141                 IO.saveImg imgCells (buildFileName " - cells.png")
 142
 143                 let imgCells' = img.Copy ()
 144                 Drawing.drawCells imgCells' true cells
 145                 IO.saveImg imgCells' (buildFileName " - cells - full.png")
 146
 147                 (* let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 148                 for m in findMaxima filteredRBCMaxima do
 149                     Drawing.drawPoints filteredRBCMaxima m 255.f
 150                 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png") *)
 151
 152                 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
 153                 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 154
 155                 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
 156                 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
 157
 158                 IO.saveImg img_float.[2] (buildFileName " - source - red.png")
 159                 IO.saveImg img_float.[1] (buildFileName " - source - green.png")
 160                 IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
 161             | _ -> ()
 162
 163         return
 164             {
 165                 Cells = cells
 166                 RBCSize_μm = config.RBCRadius.μm
 167                 RBCSize_px = config.RBCRadius.Pixel
 168             }
 169
 170         //return cells
 171     }
 172
 173 /// <summary>
 174 /// Do multiple analyses on the same time. The number of concurrent process depends on the number of the core.
 175 /// </summary>
 176 /// <param name="imgs">The images: (name * configuration * image)</param>
 177 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
 178 ///     The first call returning 'false' will cancel the analysis.
 179 ///     The 'int' parameter correspond to the progression from 0 to 100</param>
 180 /// <return>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name</return>
 181 let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) list) (reportProgress : (int -> bool) option) : (string * AnalysisResult) list option =
 182     let report (percent : int) : bool =
 183         match reportProgress with
 184         | Some f -> f percent
 185         | _ -> true
 186
 187     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int> ()
 188     let nbImgs = List.length imgs
 189
 190     let reportProgressImg (id : string) (progress : int) =
 191         progressPerAnalysis.AddOrUpdate (id, progress, (fun _ _ -> progress)) |> ignore
 192         report (progressPerAnalysis.Values.Sum () / nbImgs)
 193
 194     let n = Environment.ProcessorCount
 195
 196     let results =
 197         imgs
 198         |> PSeq.choose (
 199             fun (id, config, img) ->
 200                 try
 201                     match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
 202                     | Some result -> Some (id, result)
 203                     | None -> None
 204                 with
 205                 | ex ->
 206                     Log.Error "Analysis %s failed: %O" id ex
 207                     None
 208         )
 209         |> PSeq.withDegreeOfParallelism n
 210         |> PSeq.toList
 211
 212     // If one of the analyses has been aborted we return 'None'.
 213     if List.length results <> List.length imgs then
 214         None
 215     else
 216         Some results
 217