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 filteredGreen = gaussianFilter green config.preFilterSigma
- logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
+ let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
- let RBCSize = Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
- let RBCSizeDelta = RBCSize / 3.0
+ (*let maximaImg = filteredGreen.Copy()
+ let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
+ for m in maxima do
+ ImgTools.drawPoints maximaImg m 255uy
- let config = { config with minRBCSize = RBCSize - RBCSizeDelta ; maxRBCSize = RBCSize + RBCSizeDelta }
+ let greenOpen1 = filteredGreen.Copy()
+ logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
- let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
+ let initialAreaOpen = 2000
+ logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
- 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))
+ config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
- use xEdges = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
- use yEdges = filteredGreenFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+ let secondAreaOpen = int <| config.RBCArea / 3.
+ if secondAreaOpen > initialAreaOpen
+ then
+ logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen)
- 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
+ let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
- 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
+ let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config
+ //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+ let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
+ let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
- use magnitudes = new Matrix<float>(xEdges.Size)
- CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
+ let canny = green.Canny(60., 40.)
- let min = ref 0.0
+ (*let min = ref 0.0
let minLocation = ref <| Point()
let max = ref 0.0
let maxLocation = ref <| Point()
use edges = new Matrix<byte>(xEdges.Size)
CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
- logTime "Finding edges" (fun() -> thin edges)
- logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
+ logTime "Finding edges" (fun() -> thin edges)*)
- let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
+ let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat
- let parasites = ParasitesMarker.find greenFloat filteredGreenFloat kmediansResults config
+ logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
- let matchingEllipses = Ellipse.find edges xEdges yEdges config
+ let matchingEllipses = Ellipse.find edges xGradient yGradient 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
let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+ saveImg canny (buildFileName " - canny.png")
+
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()
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")
- let filteredGreenMaxima = gaussianFilter green config.preFilterSigma
+ 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 blue (buildFileName " - blue.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")
| _ -> ()