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.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
use green = scaledImg.Item(1)
+ let greenFloat = green.Convert<Gray, float32>()
+ let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
- use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
+ logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
- 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 <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float)
- use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
- use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+ let secondAreaOpen = int <| config.RBCArea / 3.
+ if secondAreaOpen > config.Parameters.initialAreaOpen
+ then
+ logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF 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 parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+ //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
- 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 minLocation = ref <| Point()
- let max = ref 0.0
- let maxLocation = ref <| Point()
- magnitudes.MinMax(min, max, minLocation, maxLocation)
-
- use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
- 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)
+ let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
- (*
- let kmediansResults = KMedians.kmedians filteredGreen 1.0
+ let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
+ let matchingEllipses = Ellipse.find edges xGradient yGradient config
+ matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
- let parasites = ParasitesMarker.find green 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 cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
- *)
- let cells = []
+ 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 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)
+
+ //saveImg canny (buildFileName " - canny.png")
+
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)) 0.05
+ 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 false cells
saveImg imgCells (buildFileName " - cells.png")
let imgCells' = img.Copy()
drawCells imgCells' true cells
- saveImg imgCells' (buildFileName " - cells - full.png")*)
+ saveImg imgCells' (buildFileName " - cells - full.png")
+
+ let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
+ for m in ImgTools.findMaxima filteredGreenMaxima do
+ ImgTools.drawPoints filteredGreenMaxima m 255.f
+ 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 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
projects / master-thesis.git / blobdiff