let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
- let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat config
+ 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 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))
+ let canny = green.Canny(60., 40.)
- 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
- 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
-
- 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
-
- use magnitudes = new Matrix<float>(xEdges.Size)
- CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
-
- 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 "Finding edges" (fun() -> thin edges)*)
+
+ let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat
+
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 filteredGreenWhitoutStain config)
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()