module ImageAnalysis open System open System.Drawing open FSharp.Collections.ParallelSeq open Emgu.CV open Emgu.CV.Structure 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 | _ -> () use green = img.Item(1) let greenFloat = green.Convert() let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation let initialAreaOpening = int<| config.RBCArea * config.Parameters.ratioAreaPaleCenter logTime "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening) report 8 let range = let delta = config.Parameters.granulometryRange * config.RBCRadius int <| config.RBCRadius - delta, int <| config.RBCRadius + delta //let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert()) range 1.0 |> float32) let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32) // log (sprintf "r1: %A, r2: %A" r1 r2) config.RBCRadius <- r2 report 24 let secondAreaOpening = int <| config.RBCArea * config.Parameters.ratioAreaPaleCenter if secondAreaOpening > initialAreaOpening then logTime "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 = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain) logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int)) let allEllipses, ellipses = logTime "Finding ellipses" (fun () -> let matchingEllipses = Ellipse.find edges xGradient yGradient config matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses) report 80 let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) report 100 // 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 allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05 saveImg imgAllEllipses (buildFileName " - ellipses - all.png") let imgEllipses = filteredGreenWhitoutStain.Convert() drawEllipses imgEllipses ellipses (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 radius * cell list. let doMultipleAnalysis (imgs: (string * Image) list) (config : Config) (reportProgress: (int -> unit) option) : (string * float * Cell list) list = let inline report (percent: int) = match reportProgress with | Some f -> f percent | _ -> () let monitor = Object() let mutable total = 0 let nbImgs = List.length imgs let reportProgressImg = (fun progress -> lock monitor (fun () -> total <- total + progress) report (total / nbImgs)) let nbConcurrentTaskLimit = 4 let n = Environment.ProcessorCount imgs |> PSeq.map (fun (id, img) -> let localConfig = config.Copy() let cells = doAnalysis img id localConfig (Some reportProgressImg) id, float localConfig.RBCRadius, cells) |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n) |> PSeq.toList