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) (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() 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()) 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() 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) 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() 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