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 filteredGreen = gaussianFilter green config.preFilterSigma
+ logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
+
+ let RBCSize = Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+ let RBCSizeDelta = RBCSize / 3.0
+
+ let config = { config with minRBCSize = RBCSize - RBCSizeDelta ; maxRBCSize = RBCSize + RBCSizeDelta }
+
+ let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
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))
- use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
- use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+ use xEdges = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
+ use yEdges = filteredGreenFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
let xEdgesData = xEdges.Data
let yEdgesData = yEdges.Data
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 filteredGreenFloat 1.0)
- let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
+ let parasites = ParasitesMarker.find greenFloat filteredGreenFloat 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)
+ // 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.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")
+
+ let filteredGreenMaxima = gaussianFilter green config.preFilterSigma
+ for m in ImgTools.findMaxima filteredGreenMaxima do
+ ImgTools.drawPoints filteredGreenMaxima m 255uy
+ saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+
+ saveImg filteredGreen (buildFileName " - filtered.png")
+ saveImg blue (buildFileName " - blue.png")
+ saveImg green (buildFileName " - green.png")
+ saveImg red (buildFileName " - red.png")
| _ -> ()
cells