Remove useless 'yield'
[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 let warningRatioDifferenceRBCDiameter = 1.2
21
22 /// <summary>
23 /// Analyze the given image and detect reb blood cell (RBC) in it.
24 /// </summary>
25 /// <param name="img">The image</param>
26 /// <param name="name">The name, used during logging</param>
27 /// <param name="config">The configuration, must not be shared with another analysis</param>
28 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
29 /// The first call returning 'false' will cancel the analysis.
30 /// The 'int' parameter correspond to the progression from 0 to 100</param>
31 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
32 let doAnalysis (img : Image<Bgr, byte>) (name : string) (config : Config) (reportProgress : (int -> bool) option) : AnalysisResult option =
33
34 // To report the progress of this function from 0 to 100.
35 // Return 'None' if the process must be aborted.
36 let reportWithVal (percent : int) (value : 'a) : 'a option =
37 match reportProgress with
38 | Some f -> if f percent then Some value else None
39 | _ -> Some value
40
41 let report (percent : int) : unit option =
42 reportWithVal percent ()
43
44 let inline buildLogWithName (text : string) = sprintf "№ %s: %s" name text
45 let logWithName mess = Log.Info "%s" (buildLogWithName mess)
46 let inline logTimeWithName (text : string) (f : unit -> 'a option) : 'a option = Log.LogWithTime Severity.INFO f "%s" (buildLogWithName text)
47
48 // Monadic construction to be able to abort the progress when running.
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] // Green.
57 use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
58
59 use img_parasites = img_float.[2] // Red.
60 use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
61
62 logWithName (sprintf "Nominal erythrocyte diameter: %O" 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
71 let! radius = logTimeWithName "Granulometry (area)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
72 //let! radius = logTimeWithName "Granulometry (morpho)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
73 config.SetRBCRadius <| radius
74
75 logWithName (sprintf "Found erythrocyte diameter: %O" config.RBCRadius)
76
77 do! report 20
78
79 do!
80 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
81 if secondAreaOpening > initialAreaOpening then
82 logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
83 else
84 report 30
85
86 // Remove pale centers from the parasites image.
87 areaOpenF img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter)
88
89 // Removing parasites.
90 areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
91
92 let! parasites, imgWhitoutParasite, imgWithoutNucleus =
93 logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
94
95 let! edges, xGradient, yGradient =
96 logTimeWithName "Finding edges" (
97 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
103 let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
104
105 let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
106
107 let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img.Width img.Height config))
108
109 do
110 if config.RBCRadiusByResolution.μm / config.RBCRadius.μm > warningRatioDifferenceRBCDiameter then
111 logWithName (sprintf "Warning: erythrocyte diameter found is too low compared to the nominal erythrocyte diameter, maybe the PPI image resolution is lesser than %.0f ppi" config.Parameters.resolution)
112 elif config.RBCRadius.μm / config.RBCRadiusByResolution.μm > warningRatioDifferenceRBCDiameter then
113 logWithName (sprintf "Warning: erythrocyte diameter found is too high compared to the nominal erythrocyte diameter, maybe the PPI image resolution is higher than %.0f" config.Parameters.resolution)
114
115 logWithName "Analysis finished"
116
117 do
118 // Output pictures if debug flag is set.
119 match config.Debug with
120 | DebugOn output ->
121 let dirPath = System.IO.Path.Combine (output, name)
122 System.IO.Directory.CreateDirectory dirPath |> ignore
123
124 let buildFileName postfix = System.IO.Path.Combine (dirPath, name + postfix)
125
126 IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
127
128 IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
129 IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
130 IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
131
132 let imgAllEllipses = img_RBC_filtered.Copy ()
133 Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray 200.0) 0.04
134 IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
135
136 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte> ()
137 Drawing.drawEllipses imgEllipses prunedEllipses (Bgr (0.0, 240.0, 240.0)) 1.0
138 IO.saveImg imgEllipses (buildFileName " - ellipses.png")
139
140 let imgCells = img.Copy ()
141 Drawing.drawCells imgCells false cells
142 IO.saveImg imgCells (buildFileName " - cells.png")
143
144 let imgCells' = img.Copy ()
145 Drawing.drawCells imgCells' true cells
146 IO.saveImg imgCells' (buildFileName " - cells - full.png")
147
148 (* let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
149 for m in findMaxima filteredRBCMaxima do
150 Drawing.drawPoints filteredRBCMaxima m 255.f
151 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png") *)
152
153 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
154 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
155
156 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
157 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
158
159 IO.saveImg img_float.[2] (buildFileName " - source - red.png")
160 IO.saveImg img_float.[1] (buildFileName " - source - green.png")
161 IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
162 | _ -> ()
163
164 return
165 {
166 Cells = cells
167 RBCSize_μm = config.RBCRadius.μm
168 RBCSize_px = config.RBCRadius.Pixel
169 }
170
171 //return cells
172 }
173
174 /// <summary>
175 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
176 /// </summary>
177 /// <param name="imgs">The images: (name * configuration * image)</param>
178 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
179 /// The first call returning 'false' will cancel the analysis.
180 /// The 'int' parameter correspond to the progression from 0 to 100</param>
181 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
182 let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) list) (reportProgress : (int -> bool) option) : (string * AnalysisResult) list option =
183 let report (percent : int) : bool =
184 match reportProgress with
185 | Some f -> f percent
186 | _ -> true
187
188 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int> ()
189 let nbImgs = List.length imgs
190
191 let reportProgressImg (id : string) (progress : int) =
192 progressPerAnalysis.AddOrUpdate (id, progress, (fun _ _ -> progress)) |> ignore
193 report (progressPerAnalysis.Values.Sum () / nbImgs)
194
195 let n = Environment.ProcessorCount
196
197 let results =
198 imgs
199 |> PSeq.choose (
200 fun (id, config, img) ->
201 try
202 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
203 | Some result -> Some (id, result)
204 | None -> None
205 with
206 | ex ->
207 Log.Error "Analysis %s failed: %O" id ex
208 None
209 )
210 |> PSeq.withDegreeOfParallelism n
211 |> PSeq.toList
212
213 // If one of the analyses has been aborted we return 'None'.
214 if List.length results <> List.length imgs then
215 None
216 else
217 Some results
218