--- /dev/null
+module ParasitemiaCore.Analysis
+
+open System
+open System.Linq
+open System.Drawing
+
+open FSharp.Collections.ParallelSeq
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+open Logger
+
+open Utils
+open Morpho
+open ImgTools
+open Config
+open Types
+
+/// <summary>
+/// Analyze the given image and detect reb blood cell (RBC) in it.
+/// </summary>
+/// <param name="img">The image</param>
+/// <param name="name">The name, used during logging</param>
+/// <param name="config">The configuration, must not be shared with another analysis</param>
+/// <param name="reportProgress">An optional function to report progress and/or cancel the process.
+/// The first call returning 'false' will cancel the analysis.
+/// The 'int' parameter correspond to the progression from 0 to 100</param>
+/// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
+let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
+
+ // To report the progress of this function from 0 to 100.
+ // Return 'None' if the process must be aborted.
+ let reportWithVal (percent: int) (value: 'a) : 'a option =
+ match reportProgress with
+ | Some f ->
+ if f percent
+ then Some value
+ else None
+ | _ -> Some value
+
+ let report (percent: int) : unit option =
+ reportWithVal percent ()
+
+ let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
+ let logWithName mess = Log.User(buildLogWithName mess)
+ let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
+
+ maybe {
+ do! report 0
+
+ logWithName "Starting analysis ..."
+
+ use img_float = img.Convert<Bgr, float32>()
+
+ use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
+ use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+
+ use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
+ use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
+
+ logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
+
+ 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.
+ do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
+
+ let range =
+ let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
+ int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
+ let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
+ config.SetRBCRadius <| radius
+
+ logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
+
+ do! report 20
+
+ do!
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+ if secondAreaOpening > initialAreaOpening
+ then
+ logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
+ else
+ report 30
+
+ // Remove pale centers from the parasites image.
+ areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
+
+ // Removing parasites.
+ areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
+
+ let! parasites, imgWhitoutParasite, imgWithoutNucleus =
+ logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
+
+ let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
+ let edges, xGradient, yGradient = Edges.find img_RBC_filtered
+ removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
+ reportWithVal 50 (edges, xGradient, yGradient))
+
+ let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
+
+ let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
+
+ let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
+
+ logWithName "Analysis finished"
+
+ do
+ // Output pictures if debug flag is set.
+ match config.Debug with
+ | DebugOn output ->
+ let dirPath = System.IO.Path.Combine(output, name)
+ System.IO.Directory.CreateDirectory dirPath |> ignore
+
+ let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+
+ IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
+
+ IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+ IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
+ IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
+
+ let imgAllEllipses = img.Copy()
+ Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
+ IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+
+ let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
+ Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ IO.saveImg imgEllipses (buildFileName " - ellipses.png")
+
+ let imgCells = img.Copy()
+ Drawing.drawCells imgCells false cells
+ IO.saveImg imgCells (buildFileName " - cells.png")
+
+ let imgCells' = img.Copy()
+ Drawing.drawCells imgCells' true cells
+ IO.saveImg imgCells' (buildFileName " - cells - full.png")
+
+ let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+ for m in findMaxima filteredGreenMaxima do
+ Drawing.drawPoints filteredGreenMaxima m 255.f
+ IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+
+ IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
+ IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
+
+ IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
+ IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
+
+ IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
+ IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
+ IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
+ | _ -> ()
+
+ return cells }
+
+/// <summary>
+/// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
+/// </summary>
+/// <param name="imgs">The images: (name * configuration * image)</param>
+/// <param name="reportProgress">An optional function to report progress and/or cancel the process.
+/// The first call returning 'false' will cancel the analysis.
+/// The 'int' parameter correspond to the progression from 0 to 100</param>
+/// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
+let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
+ let report (percent: int) : bool =
+ match reportProgress with
+ | Some f -> f percent
+ | _ -> true
+
+ let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
+ let nbImgs = List.length imgs
+
+ let reportProgressImg (id: string) (progress: int) =
+ progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
+ report (progressPerAnalysis.Values.Sum() / nbImgs)
+
+ let n = Environment.ProcessorCount
+
+ let results =
+ imgs
+ |> PSeq.choose (
+ fun (id, config, img) ->
+ match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
+ | Some result -> Some (id, result)
+ | None -> None)
+ |> PSeq.withDegreeOfParallelism n
+ |> PSeq.toList
+
+ // If one of the analyses has been aborted we return 'None'.
+ if List.length results <> List.length imgs
+ then None
+ else Some results
+
projects / master-thesis.git / blobdiff