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