module ImageAnalysis
open System
+open System.Linq
open System.Drawing
+open FSharp.Collections.ParallelSeq
+
open Emgu.CV
open Emgu.CV.Structure
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
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
- let scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
+ logWithName "Starting analysis ..."
- use green = scaledImg.Item(1)
+ use green = img.Item(1)
let greenFloat = green.Convert<Gray, float32>()
- let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
+ 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)
- logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
+ report 8
- config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float32)
+ 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)
+ // log (sprintf "r1: %A, r2: %A" r1 r2)
- let secondAreaOpen = int <| config.RBCArea / 3.f
- if secondAreaOpen > config.Parameters.initialAreaOpen
+ logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
+
+ report 24
+
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+ if secondAreaOpening > initialAreaOpening
then
- logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
+ 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 = 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 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 allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
+ let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () ->
let matchingEllipses = Ellipse.find edges xGradient yGradient config
matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
- let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
+ report 80
+
+ let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
+
+ report 100
+
+ logWithName "Analysis finished"
// Output pictures if debug flag is set.
match config.Debug with
drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
- let imgEllipses = img.Copy()
+ let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
saveImg imgEllipses (buildFileName " - ellipses.png")
drawCells imgCells' true cells
saveImg imgCells' (buildFileName " - cells - full.png")
- let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
+ 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 green (buildFileName " - green.png")
- use blue = scaledImg.Item(0)
+ use blue = img.Item(0)
saveImg blue (buildFileName " - blue.png")
- use red = scaledImg.Item(2)
+ 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 nbConcurrentTaskLimit = 4 // To reduce the memory taken.
+ let n = Environment.ProcessorCount
+
+ imgs
+ |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
+ |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
+ |> PSeq.toList
projects / master-thesis.git / blobdiff