1
module ParasitemiaCore.ParasitesMarker
14 darkStain
: Image<Gray, byte
>
15 infection
: Image<Gray, byte
>
16 stain
: Image<Gray, byte
> }
18 // Create three binary markers :
19 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
20 // * 'Stain' corresponds to the stain around the parasites.
21 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
22 let findMa (green
: Image<Gray, float32
>) (filteredGreen
: Image<Gray, float32
>) (config
: Config.Config) : Result * Image<Gray, byte
> * Image<Gray, byte
> =
23 // We use the filtered image to find the dark stain.
24 let kmediansResults = Log.LogWithTime("Finding fg/bg (k-medians)", Severity.USER, (fun () -> KMedians.kmedians
filteredGreen))
25 let { KMedians.fg
= fg
; KMedians.median_bg
= median_bg
; KMedians.median_fg
= median_fg
; KMedians.d_fg
= d_fg
} = kmediansResults
26 let darkStain = d_fg
.Cmp(median_bg
* float config.Parameters.darkStainLevel
, CvEnum.CmpType.GreaterThan)
27 darkStain._And
(filteredGreen.Cmp(median_fg
, CvEnum.CmpType.LessThan))
30 let fgFloat = (fg
/ 255.0).Convert<Gray, float32
>()
31 use greenWithoutBg = ImgTools.gaussianFilter green
1.0
32 greenWithoutBg.SetValue(Gray(0.0), fg
.Not())
34 let findSmears (sigma
: float) (level
: float) : Image<Gray, byte
> =
35 use greenWithoutBgSmoothed = ImgTools.gaussianFilter
greenWithoutBg sigma
36 use fgSmoothed = ImgTools.gaussianFilter
fgFloat sigma
37 let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level
), CvEnum.CmpType.LessThan)
41 let tmp = filteredGreen.Convert<Gray, byte
>()
43 { darkStain = darkStain;
44 stain = findSmears 10. 0.9
45 infection
= findSmears 2.2
0.87 },
49 // Create three binary markers :
50 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
51 // * 'Stain' corresponds to the stain around the parasites.
52 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
53 let find (filteredGreen: Image<Gray, float32
>) (config: Config.Config) : Result * Image<Gray, float32
> =
54 use filteredGreenWithoutInfection = filteredGreen.Copy()
55 ImgTools.areaCloseF
filteredGreenWithoutInfection (int config.RBCRadius.InfectionArea)
57 let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
58 ImgTools.areaCloseF
filteredGreenWithoutStain (int config.RBCRadius.StainArea)
61 // We use the filtered image to find the dark stain.
62 let _, mean_fg
, mean_bg
=
63 let hist = ImgTools.histogramImg
filteredGreenWithoutInfection 300
65 filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel
+ (float mean_fg), CvEnum.CmpType.LessThan)
67 let marker (img
: Image<Gray, float32
>) (closed
: Image<Gray, float32
>) (level
: float) : Image<Gray, byte
> =
70 CvInvoke.Subtract(closed
, diff, diff)
71 diff._ThresholdBinary
(Gray(0.0), Gray(255.))
72 diff.Convert<Gray, byte
>()
74 let infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity
)
75 let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity
)
77 // TODO: comprendre pourquoi des valeurs sont negatives!?!?
79 let blackTopHat = filteredGreen.CopyBlank()
80 CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
81 ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
84 { darkStain = darkStain
85 infection
= infectionMarker
86 stain = stainMarker },
87 filteredGreenWithoutStain