926aeac5523dcf734cab8660809337e8eb8a6b32
[master-thesis.git] / Parasitemia / ParasitemiaCore / MainAnalysis.fs
1 module ParasitemiaCore.Analysis
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 Logger
13
14 open Utils
15 open Morpho
16 open ImgTools
17 open Config
18 open Types
19
20 /// <summary>
21 /// Analyze the given image and detect reb blood cell (RBC) in it.
22 /// </summary>
23 /// <param name="img">The image</param>
24 /// <param name="name">The name, used during logging</param>
25 /// <param name="config">The configuration, must not be shared with another analysis</param>
26 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
27 /// The first call returning 'false' will cancel the analysis.
28 /// The 'int' parameter correspond to the progression from 0 to 100</param>
29 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
30 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
31
32 // To report the progress of this function from 0 to 100.
33 // Return 'None' if the process must be aborted.
34 let reportWithVal (percent: int) (value: 'a) : 'a option =
35 match reportProgress with
36 | Some f ->
37 if f percent
38 then Some value
39 else None
40 | _ -> Some value
41
42 let report (percent: int) : unit option =
43 reportWithVal percent ()
44
45 let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
46 let logWithName mess = Log.User(buildLogWithName mess)
47 let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
48
49 maybe {
50 do! report 0
51
52 logWithName "Starting analysis ..."
53
54 use img_float = img.Convert<Bgr, float32>()
55
56 use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
57 use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
58
59 use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
60 use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
61
62 logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
63
64 let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.1f // 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.
65 do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
66
67 let range =
68 let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
69 int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
70 let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
71 config.SetRBCRadius <| radius
72
73 logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
74
75 do! report 20
76
77 do!
78 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
79 if secondAreaOpening > initialAreaOpening
80 then
81 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
82 else
83 report 30
84
85 // Removing parasites.
86 areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
87
88 let! parasites, imgWhitoutParasite, imgWithoutNucleus =
89 logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
90
91 let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
92 let edges, xGradient, yGradient = Edges.find img_RBC_filtered
93 removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
94 reportWithVal 50 (edges, xGradient, yGradient))
95
96 let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
97
98 let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
99
100 let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
101
102 logWithName "Analysis finished"
103
104 do
105 // Output pictures if debug flag is set.
106 match config.Debug with
107 | DebugOn output ->
108 let dirPath = System.IO.Path.Combine(output, name)
109 System.IO.Directory.CreateDirectory dirPath |> ignore
110
111 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
112
113 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
114
115 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
116 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
117 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
118
119 let imgAllEllipses = img.Copy()
120 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
121 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
122
123 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
124 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
125 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
126
127 let imgCells = img.Copy()
128 Drawing.drawCells imgCells false cells
129 IO.saveImg imgCells (buildFileName " - cells.png")
130
131 let imgCells' = img.Copy()
132 Drawing.drawCells imgCells' true cells
133 IO.saveImg imgCells' (buildFileName " - cells - full.png")
134
135 let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
136 for m in findMaxima filteredGreenMaxima do
137 Drawing.drawPoints filteredGreenMaxima m 255.f
138 IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
139
140 IO.saveImg img_RBC_filtered (buildFileName " - filtered.png")
141 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
142 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
143
144 IO.saveImg img_RBC (buildFileName " - source - RBC.png")
145 IO.saveImg img_parasites (buildFileName " - source - parasites.png")
146
147 IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
148 IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
149 IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
150 | _ -> ()
151
152 return cells }
153
154 /// <summary>
155 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
156 /// </summary>
157 /// <param name="imgs">The images: (name * configuration * image)</param>
158 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
159 /// The first call returning 'false' will cancel the analysis.
160 /// The 'int' parameter correspond to the progression from 0 to 100</param>
161 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
162 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
163 let report (percent: int) : bool =
164 match reportProgress with
165 | Some f -> f percent
166 | _ -> true
167
168 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
169 let nbImgs = List.length imgs
170
171 let reportProgressImg (id: string) (progress: int) =
172 progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
173 report (progressPerAnalysis.Values.Sum() / nbImgs)
174
175 let n = Environment.ProcessorCount
176
177 let results =
178 imgs
179 |> PSeq.choose (
180 fun (id, config, img) ->
181 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
182 | Some result -> Some (id, result)
183 | None -> None)
184 |> PSeq.withDegreeOfParallelism n
185 |> PSeq.toList
186
187 // If one of the analyses has been aborted we return 'None'.
188 if List.length results <> List.length imgs
189 then None
190 else Some results
191