15 let doAnalysis (img
: Image<Bgr, byte
>) (name
: string) (config
: Config) : Cell list =
17 let imgFloat = img
.Convert<Bgr, float32
>()
18 use scaledImg = if config
.scale
= 1.0 then imgFloat else imgFloat.Resize(config
.scale
, CvEnum.Inter.Area)
20 use green = scaledImg.Item(1)
22 use filteredGreen = (gaussianFilter
green config
.doGSigma1
) - config
.doGLowFreqPercentageReduction
* (gaussianFilter
green config
.doGSigma2
)
25 new ConvolutionKernelF(array2D
[[ 1.0f; 0.0f; -1.0f ]
27 [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
29 use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
30 use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
32 let xEdgesData = xEdges.Data
33 let yEdgesData = yEdges.Data
34 for r
in 0..xEdges.Rows-1 do
35 xEdgesData.[r
, 0, 0] <- 0.0
36 xEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
37 yEdgesData.[r
, 0, 0] <- 0.0
38 yEdgesData.[r
, xEdges.Cols-1, 0] <- 0.0
40 for c
in 0..xEdges.Cols-1 do
41 xEdgesData.[0, c
, 0] <- 0.0
42 xEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
43 yEdgesData.[0, c
, 0] <- 0.0
44 yEdgesData.[xEdges.Rows-1, c
, 0] <- 0.0
46 use magnitudes = new Matrix<float>(xEdges.Size)
47 CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
50 let minLocation = ref <| Point()
52 let maxLocation = ref <| Point()
53 magnitudes.MinMax(min, max, minLocation, maxLocation)
55 use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte
>() // Otsu from OpenCV only support 'byte'.
56 use edges = new Matrix<byte
>(xEdges.Size)
57 CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
59 logTime
"Finding edges" (fun() -> thin
edges)
60 logTime
"Removing small connected components from thinning" (fun () -> removeArea
edges 12)
63 let kmediansResults = KMedians.kmedians filteredGreen 1.0
65 let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
67 let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
68 let windowSize = roundInt (1.6 * (snd radiusRange))
69 let factorNbPick = 1.5
70 let ellipses = logTime "Finding ellipses" (fun () ->
71 Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
73 let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
77 // Output pictures if debug flag is set.
78 match config.debug
with
80 let buildFileName postfix
= System.IO.Path.Combine(output
, name
+ postfix
)
81 saveMat
(edges * 255.0) (buildFileName " - edges.png")
83 (*saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
84 saveImg parasites.stain (buildFileName " - parasites - stain.png")
85 saveImg parasites.infection (buildFileName " - parasites - infection.png")
87 let imgEllipses = img.Copy()
88 drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0))
89 saveImg imgEllipses (buildFileName " - ellipses.png")
91 saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
93 let imgCells = img.Copy()
94 drawCells imgCells false cells
95 saveImg imgCells (buildFileName " - cells.png")
97 let imgCells' = img.Copy()
98 drawCells imgCells' true cells
99 saveImg imgCells' (buildFileName " - cells - full.png")*)