let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
- use scaledImg = if config.scale = 1.0 then img else img.Resize(config.scale, CvEnum.Inter.Area)
+ use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
- use blue = scaledImg.Item(0)
use green = scaledImg.Item(1)
- use red = scaledImg.Item(2)
-
let greenFloat = green.Convert<Gray, float32>()
- let green = gaussianFilter green 1.5
+ let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
- // let RBCSize = Granulometry.findRadius green (10, 100) 0.5
+ (*let maximaImg = filteredGreen.Copy()
+ let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
+ for m in maxima do
+ ImgTools.drawPoints maximaImg m 255uy
- 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)
+ let greenOpen1 = filteredGreen.Copy()
+ logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
- 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
+ let initialAreaOpen = 2000
+ logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
- saveImg greenMaxima (buildFileName " - maxima.png")
+ config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
- logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800)
- saveImg green (buildFileName " - green opened.png")
-
- | _ -> ()
+ let secondAreaOpen = int <| config.RBCArea / 3.
+ if secondAreaOpen > initialAreaOpen
+ then
+ logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen)
- []
- (*
+ let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
- use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2)
+ let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat config
+ let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
+ let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
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 = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert<Gray, float>()
+ use yEdges = filteredGreenWhitoutStainFloat.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 = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
-
- let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config
-
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 = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
// Output pictures if debug flag is set.
- match config.debug with
+ match config.Debug with
| DebugOn output ->
let dirPath = System.IO.Path.Combine(output, name)
System.IO.Directory.CreateDirectory dirPath |> ignore
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")
+ // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
let imgCells = img.Copy()
drawCells imgCells false cells
drawCells imgCells' true cells
saveImg imgCells' (buildFileName " - cells - full.png")
- saveImg (normalizeAndConvert filteredGreen) (buildFileName " - filtered.png")
- saveImg blue (buildFileName " - blue.png")
+ let filteredGreenMaxima = gaussianFilter green config.Parameters.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 filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
+ saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+
+ (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
+ saveImg stainMarker (buildFileName " - stain (area closing).png")*)
+
saveImg green (buildFileName " - green.png")
+
+ use blue = scaledImg.Item(0)
+ saveImg blue (buildFileName " - blue.png")
+
+ use red = scaledImg.Item(2)
saveImg red (buildFileName " - red.png")
| _ -> ()
- cells*)
+ cells