let greenFloat = green.Convert<Gray, float32>()
let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
- logWithName (sprintf "Nominal erytrocyte diameter: %s" config.FormattedRadius)
+ logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
- let initialAreaOpening = int<| config.RBCArea * 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.
+ 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 8
+ report 10
let range =
- let delta = config.Parameters.granulometryRange * config.RBCRadius
- int <| config.RBCRadius - delta, int <| config.RBCRadius + delta
+ 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)
- let r2 = logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
- // log (sprintf "r1: %A, r2: %A" r1 r2)
- config.RBCRadius <- r2
+ config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
- logWithName (sprintf "Found erytrocyte diameter: %s" config.FormattedRadius)
+ logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
- report 24
+ report 20
- let secondAreaOpening = int <| config.RBCArea * config.Parameters.ratioAreaPaleCenter
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
if secondAreaOpening > initialAreaOpening
then
logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
- removeArea edges (config.RBCRadius ** 2.f / 50.f |> int)
+ removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
edges, xGradient, yGradient)
- let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () ->
- let matchingEllipses = Ellipse.find edges xGradient yGradient config
- matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
+ 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 ellipses parasites filteredGreenWhitoutStain config)
+ let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
report 100
saveImg parasites.infection (buildFileName " - parasites - infection.png")
let imgAllEllipses = img.Copy()
- drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
+ 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 ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
saveImg imgEllipses (buildFileName " - ellipses.png")
let imgCells = img.Copy()
progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
report (progressPerAnalysis.Values.Sum() / nbImgs)
- let nbConcurrentTaskLimit = 4
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.withDegreeOfParallelism n
|> PSeq.toList