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 initialAreaOpen = 2000
+ logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
+
+ config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+
+ 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?
+ 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))
- use xEdges = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
- use yEdges = filteredGreenFloat.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 filteredGreenFloat 1.0)
-
- let parasites = ParasitesMarker.find greenFloat filteredGreenFloat 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")
- 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")
| _ -> ()