e83977ab6fde91e83aafb695b002871cd394546d
[master-thesis.git] / Parasitemia / ParasitemiaCore / Analysis.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 // Monadic construction to be able to abort the progress when running.
50 maybe {
51 do! report 0
52
53 logWithName "Starting analysis ..."
54
55 use img_float = img.Convert<Bgr, float32>()
56
57 use img_RBC = img_float.[1] // Green.
58 use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
59
60 use img_parasites = img_float.[2] // Red.
61 use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
62
63 logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
64
65 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.
66 do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
67
68 let range =
69 let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
70 int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
71
72 let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
73 //let! radius = logTimeWithName "Granulometry (morpho)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
74 config.SetRBCRadius <| radius
75
76 logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
77
78 do! report 20
79
80 do!
81 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
82 if secondAreaOpening > initialAreaOpening
83 then
84 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
85 else
86 report 30
87
88 // Remove pale centers from the parasites image.
89 areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
90
91 // Removing parasites.
92 areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
93
94 let! parasites, imgWhitoutParasite, imgWithoutNucleus =
95 logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
96
97 let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
98 let edges, xGradient, yGradient = Edges.find img_RBC_filtered
99 removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
100 reportWithVal 50 (edges, xGradient, yGradient))
101
102 let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
103
104 let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
105
106 let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
107
108 logWithName "Analysis finished"
109
110 do
111 // Output pictures if debug flag is set.
112 match config.Debug with
113 | DebugOn output ->
114 let dirPath = System.IO.Path.Combine(output, name)
115 System.IO.Directory.CreateDirectory dirPath |> ignore
116
117 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
118
119 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
120
121 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
122 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
123 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
124
125 let imgAllEllipses = img_RBC_filtered.Copy()
126 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray(200.0)) 0.04
127 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
128
129 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
130 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
131 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
132
133 let imgCells = img.Copy()
134 Drawing.drawCells imgCells false cells
135 IO.saveImg imgCells (buildFileName " - cells.png")
136
137 let imgCells' = img.Copy()
138 Drawing.drawCells imgCells' true cells
139 IO.saveImg imgCells' (buildFileName " - cells - full.png")
140
141 let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
142 for m in findMaxima filteredRBCMaxima do
143 Drawing.drawPoints filteredRBCMaxima m 255.f
144 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png")
145
146 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
147 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
148
149 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
150 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
151
152 IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
153 IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
154 IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
155 | _ -> ()
156
157 return cells }
158
159 /// <summary>
160 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
161 /// </summary>
162 /// <param name="imgs">The images: (name * configuration * image)</param>
163 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
164 /// The first call returning 'false' will cancel the analysis.
165 /// The 'int' parameter correspond to the progression from 0 to 100</param>
166 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
167 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
168 let report (percent: int) : bool =
169 match reportProgress with
170 | Some f -> f percent
171 | _ -> true
172
173 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
174 let nbImgs = List.length imgs
175
176 let reportProgressImg (id: string) (progress: int) =
177 progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
178 report (progressPerAnalysis.Values.Sum() / nbImgs)
179
180 let n = Environment.ProcessorCount
181
182 let results =
183 imgs
184 |> PSeq.choose (
185 fun (id, config, img) ->
186 try
187 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
188 | Some result -> Some (id, result)
189 | None -> None
190 with
191 | ex ->
192 Log.Error("Analysis {0} failed: {1}", id, ex)
193 None)
194 |> PSeq.withDegreeOfParallelism n
195 |> PSeq.toList
196
197 // If one of the analyses has been aborted we return 'None'.
198 if List.length results <> List.length imgs
199 then None
200 else Some results
201