--- /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 ImgTools
+open Config
+open Types
+
+let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
+ // To report the progress of this function from 0 to 100.
+ let inline report (percent: int) =
+ match reportProgress with
+ | Some f -> f 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) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
+
+ logWithName "Starting analysis ..."
+
+ use green = img.Item(1)
+ let greenFloat = green.Convert<Gray, float32>()
+ let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
+
+ logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
+
+ let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // 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.
+ logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
+
+ report 10
+
+ let range =
+ let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
+ int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
+ //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
+ config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
+
+ logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
+
+ report 20
+
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+ if secondAreaOpening > initialAreaOpening
+ then
+ logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
+
+ let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+ //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+
+ let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
+ let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
+ removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
+ edges, xGradient, yGradient)
+
+ let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
+
+ report 60
+
+ let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
+
+ report 80
+
+ let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
+
+ report 100
+
+ logWithName "Analysis finished"
+
+ // 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)
+
+ saveMat (edges * 255.0) (buildFileName " - edges.png")
+
+ saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+ saveImg parasites.stain (buildFileName " - parasites - stain.png")
+ saveImg parasites.infection (buildFileName " - parasites - infection.png")
+
+ let imgAllEllipses = img.Copy()
+ drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
+ saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+
+ let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
+ drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ saveImg imgEllipses (buildFileName " - ellipses.png")
+
+ let imgCells = img.Copy()
+ drawCells imgCells false cells
+ saveImg imgCells (buildFileName " - cells.png")
+
+ let imgCells' = img.Copy()
+ drawCells imgCells' true cells
+ saveImg imgCells' (buildFileName " - cells - full.png")
+
+ let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
+ for m in ImgTools.findMaxima filteredGreenMaxima do
+ ImgTools.drawPoints filteredGreenMaxima m 255.f
+ saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+
+ saveImg filteredGreen (buildFileName " - filtered.png")
+ saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
+ //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+
+ saveImg green (buildFileName " - green.png")
+
+ use blue = img.Item(0)
+ saveImg blue (buildFileName " - blue.png")
+
+ use red = img.Item(2)
+ saveImg red (buildFileName " - red.png")
+ | _ -> ()
+
+ cells
+
+// ID * cell list.
+let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
+ let inline report (percent: int) =
+ match reportProgress with
+ | Some f -> f percent
+ | _ -> ()
+
+ 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
+
+ imgs
+ |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
+ |> PSeq.withDegreeOfParallelism n
+ |> PSeq.toList
projects / master-thesis.git / blobdiff