a40e463843bb3392c16bde1d7c27b8b85baeb881
1
module ParasitesMarker
11 darkStain
: Image<Gray, byte
>
12 infection
: Image<Gray, byte
>
13 stain
: Image<Gray, byte
> }
16 // Create three binary markers :
17 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
18 // * 'Stain' corresponds to the stain around the parasites.
19 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
20 let findMa (green
: Image<Gray, float32
>) (filteredGreen
: Image<Gray, float32
>) (config
: Config.Config) : Result * Image<Gray, byte
> * Image<Gray, byte
> =
21 // We use the filtered image to find the dark stain.
22 let kmediansResults = logTime
"Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians
filteredGreen)
23 let { KMedians.fg
= fg
; KMedians.median_bg
= median_bg
; KMedians.median_fg
= median_fg
; KMedians.d_fg
= d_fg
} = kmediansResults
24 let darkStain = d_fg
.Cmp(median_bg
* float config.Parameters.darkStainLevel
, CvEnum.CmpType.GreaterThan)
25 darkStain._And
(filteredGreen.Cmp(median_fg
, CvEnum.CmpType.LessThan))
28 let fgFloat = (fg
/ 255.0).Convert<Gray, float32
>()
29 use greenWithoutBg = ImgTools.gaussianFilter green
1.0
30 greenWithoutBg.SetValue(Gray(0.0), fg
.Not())
32 let findSmears (sigma
: float) (level
: float) : Image<Gray, byte
> =
33 use greenWithoutBgSmoothed = ImgTools.gaussianFilter
greenWithoutBg sigma
34 use fgSmoothed = ImgTools.gaussianFilter
fgFloat sigma
35 let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level
), CvEnum.CmpType.LessThan)
39 let tmp = filteredGreen.Convert<Gray, byte
>()
41 { darkStain = darkStain;
42 stain = findSmears 10. 0.9
43 infection
= findSmears 2.2
0.87 },
48 // Create three binary markers :
49 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
50 // * 'Stain' corresponds to the stain around the parasites.
51 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
52 let find (filteredGreen: Image<Gray, float32
>) (config: Config.Config) : Result * Image<Gray, float32
> =
53 use filteredGreenWithoutInfection = filteredGreen.Copy()
54 ImgTools.areaCloseF
filteredGreenWithoutInfection (int config.InfectionArea)
56 let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
57 ImgTools.areaCloseF
filteredGreenWithoutStain (int config.StainArea)
60 // We use the filtered image to find the dark stain.
61 let _, mean_fg
, mean_bg
=
62 let hist = ImgTools.histogramImg
filteredGreenWithoutInfection 300
64 filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel
+ (float mean_fg), CvEnum.CmpType.LessThan)
66 let marker (img
: Image<Gray, float32
>) (closed
: Image<Gray, float32
>) (level
: float) : Image<Gray, byte
> =
69 CvInvoke.Subtract(closed
, diff, diff)
70 diff._ThresholdBinary
(Gray(0.0), Gray(255.))
71 diff.Convert<Gray, byte
>()
73 let infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity
)
74 let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity
)
76 // TODO: comprendre pourquoi des valeurs sont negatives!?!?
78 let blackTopHat = filteredGreen.CopyBlank()
79 CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
80 ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
83 { darkStain = darkStain
84 infection
= infectionMarker
85 stain = stainMarker },
86 filteredGreenWithoutStain