+++ /dev/null
-module ImageAnalysis
-
-open System
-open System.Linq
-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<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 = buildLogWithName >> log
- let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) 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