let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
- let imgFloat = img.Convert<Bgr, float32>()
- use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)
+ use scaledImg = if config.scale = 1.0 then img else img.Resize(config.scale, CvEnum.Inter.Area)
+ use blue = scaledImg.Item(0)
use green = scaledImg.Item(1)
+ use red = scaledImg.Item(2)
- use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
+
+ let greenFloat = green.Convert<Gray, float32>()
+
+ let green = gaussianFilter green 1.5
+
+ // let RBCSize = Granulometry.findRadius green (10, 100) 0.5
+
+ 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)
+
+ saveImg green (buildFileName " - green.png")
+
+ let greenMaxima = green.Copy()
+ let maxima = ImgTools.findMaxima greenMaxima
+ for m in maxima do
+ for p in m do
+ greenMaxima.Data.[p.Y, p.X, 0] <- 255uy
+
+ saveImg greenMaxima (buildFileName " - maxima.png")
+
+ logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800)
+ saveImg green (buildFileName " - green opened.png")
+
+ | _ -> ()
+
+ []
+ (*
+
+ use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2)
use sobelKernel =
new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
logTime "Finding edges" (fun() -> thin edges)
logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
- (*
- let kmediansResults = KMedians.kmedians filteredGreen 1.0
+ let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
- let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
+ let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config
- let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
- let windowSize = roundInt (1.6 * (snd radiusRange))
- let factorNbPick = 1.5
- let ellipses = logTime "Finding ellipses" (fun () ->
- Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
+ let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
+ let matchingEllipses = Ellipse.find edges xEdges yEdges config
+ matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
- *)
- let cells = []
// Output pictures if debug flag is set.
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.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)) 0.1
+ saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+
let imgEllipses = img.Copy()
- drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0))
+ 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' true cells
- saveImg imgCells' (buildFileName " - cells - full.png")*)
+ saveImg imgCells' (buildFileName " - cells - full.png")
+
+ saveImg (normalizeAndConvert filteredGreen) (buildFileName " - filtered.png")
+ saveImg blue (buildFileName " - blue.png")
+ saveImg green (buildFileName " - green.png")
+ saveImg red (buildFileName " - red.png")
| _ -> ()
- cells
+ cells*)