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 =
+ logWithName "Starting analysis ..."
- let imgFloat = img.Convert<Bgr, float32>()
- use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)
+ use green = img.Item(1)
+ let greenFloat = green.Convert<Gray, float32>()
+ let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
- use green = scaledImg.Item(1)
+ logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
- use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
+ 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)
- use sobelKernel =
- new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
- [ 2.0f; 0.0f; -2.0f ]
- [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
+ report 8
- use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
- use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+ 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 xEdgesData = xEdges.Data
- let yEdgesData = yEdges.Data
- for r in 0..xEdges.Rows-1 do
- xEdgesData.[r, 0, 0] <- 0.0
- xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
- yEdgesData.[r, 0, 0] <- 0.0
- yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
+ logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
- for c in 0..xEdges.Cols-1 do
- xEdgesData.[0, c, 0] <- 0.0
- xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
- yEdgesData.[0, c, 0] <- 0.0
- yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
+ report 24
- use magnitudes = new Matrix<float>(xEdges.Size)
- CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+ if secondAreaOpening > initialAreaOpening
+ then
+ logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
- let min = ref 0.0
- let minLocation = ref <| Point()
- let max = ref 0.0
- let maxLocation = ref <| Point()
- magnitudes.MinMax(min, max, minLocation, maxLocation)
+ let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+ //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
- use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
- use edges = new Matrix<byte>(xEdges.Size)
- CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
+ 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)
- logTime "Finding edges" (fun() -> thin edges)
- logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
+ let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () ->
+ let matchingEllipses = Ellipse.find edges xGradient yGradient config
+ matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
- let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
+ report 80
- let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
+ let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
- let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
- let matchingEllipses = Ellipse.find edges xEdges yEdges config
- matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
+ report 100
- let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
+ logWithName "Analysis finished"
// Output pictures if debug flag is set.
- match config.debug with
+ match config.Debug with
| DebugOn output ->
- let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
+ 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.infection (buildFileName " - parasites - infection.png")
let imgAllEllipses = img.Copy()
- drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
+ 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")
- saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.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 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