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[master-thesis.git] / Parasitemia / Parasitemia / MainAnalysis.fs
1 module ImageAnalysis
2
3 open System
4 open System.Linq
5 open System.Drawing
6
7 open FSharp.Collections.ParallelSeq
8
9 open Emgu.CV
10 open Emgu.CV.Structure
11
12 open Utils
13 open ImgTools
14 open Config
15 open Types
16
17 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
18 // To report the progress of this function from 0 to 100.
19 let inline report (percent: int) =
20 match reportProgress with
21 | Some f -> f percent
22 | _ -> ()
23
24 let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
25 let logWithName = buildLogWithName >> log
26 let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) f
27
28 logWithName "Starting analysis ..."
29
30 use green = img.Item(1)
31 let greenFloat = green.Convert<Gray, float32>()
32 let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
33
34 logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
35
36 let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // We do an area opening a little larger to avoid to do a second one in the case the radius found is near the initial one.
37 logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
38
39 report 10
40
41 let range =
42 let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
43 int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
44 //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
45 config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
46
47 logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
48
49 report 20
50
51 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
52 if secondAreaOpening > initialAreaOpening
53 then
54 logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
55
56 let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
57 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
58
59 let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
60 let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
61 removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
62 edges, xGradient, yGradient)
63
64 let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
65
66 report 60
67
68 let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
69
70 report 80
71
72 let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
73
74 report 100
75
76 logWithName "Analysis finished"
77
78 // Output pictures if debug flag is set.
79 match config.Debug with
80 | DebugOn output ->
81 let dirPath = System.IO.Path.Combine(output, name)
82 System.IO.Directory.CreateDirectory dirPath |> ignore
83
84 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
85
86 saveMat (edges * 255.0) (buildFileName " - edges.png")
87
88 saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
89 saveImg parasites.stain (buildFileName " - parasites - stain.png")
90 saveImg parasites.infection (buildFileName " - parasites - infection.png")
91
92 let imgAllEllipses = img.Copy()
93 drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
94 saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
95
96 let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
97 drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
98 saveImg imgEllipses (buildFileName " - ellipses.png")
99
100 let imgCells = img.Copy()
101 drawCells imgCells false cells
102 saveImg imgCells (buildFileName " - cells.png")
103
104 let imgCells' = img.Copy()
105 drawCells imgCells' true cells
106 saveImg imgCells' (buildFileName " - cells - full.png")
107
108 let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
109 for m in ImgTools.findMaxima filteredGreenMaxima do
110 ImgTools.drawPoints filteredGreenMaxima m 255.f
111 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
112
113 saveImg filteredGreen (buildFileName " - filtered.png")
114 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
115 //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
116
117 saveImg green (buildFileName " - green.png")
118
119 use blue = img.Item(0)
120 saveImg blue (buildFileName " - blue.png")
121
122 use red = img.Item(2)
123 saveImg red (buildFileName " - red.png")
124 | _ -> ()
125
126 cells
127
128 // ID * cell list.
129 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
130 let inline report (percent: int) =
131 match reportProgress with
132 | Some f -> f percent
133 | _ -> ()
134
135 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
136 let nbImgs = List.length imgs
137
138 let reportProgressImg (id: string) (progress: int) =
139 progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
140 report (progressPerAnalysis.Values.Sum() / nbImgs)
141
142 let n = Environment.ProcessorCount
143
144 imgs
145 |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
146 |> PSeq.withDegreeOfParallelism n
147 |> PSeq.toList