1
module ParasitemiaCore.Analysis
7 open FSharp.Collections.ParallelSeq
10 open Emgu.CV.Structure
21 /// Analyze the given image and detect reb blood cell (RBC) in it.
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 =
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
-> if f percent
then Some value else None
39 let report (percent
: int) : unit option =
40 reportWithVal percent ()
42 let inline buildLogWithName
(text
: string) = sprintf
"№ %s: %s" name text
43 let logWithName mess
= Log.Info "%s" (buildLogWithName
mess)
44 let inline logTimeWithName
(text : string) (f
: unit -> 'a option) : 'a
option = Log.LogWithTime Severity.INFO f
"%s" (buildLogWithName
text)
46 // Monadic construction to be able to abort the progress when running.
50 logWithName "Starting analysis ..."
52 use img_float = img
.Convert<Bgr, float32
>()
54 use img_RBC = img_float.[1] // Green.
55 use img_RBC_filtered = gaussianFilter
img_RBC config
.LPFStandardDeviationRBC
57 use img_parasites = img_float.[2] // Red.
58 use img_parasites_filtered = gaussianFilter
img_parasites config.LPFStandardDeviationParasite
60 logWithName (sprintf
"Nominal erythrocyte diameter: %O" config.RBCRadiusByResolution)
62 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.
63 do! logTimeWithName
"First area opening" (fun () -> areaOpenF
img_RBC_filtered initialAreaOpening; report 10)
66 let delta = config.Parameters.granulometryRange
* config.RBCRadiusByResolution.Pixel
67 int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
69 let! radius = logTimeWithName
"Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing
img_RBC_filtered range |> float32
))
70 //let! radius = logTimeWithName "Granulometry (morpho)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
71 config.SetRBCRadius <| radius
73 logWithName (sprintf
"Found erythrocyte diameter: %O" config.RBCRadius)
78 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
79 if secondAreaOpening > initialAreaOpening then
80 logTimeWithName
"Second area opening" (fun () -> areaOpenF
img_RBC_filtered secondAreaOpening; report 30)
84 // Remove pale centers from the parasites image.
85 areaOpenF
img_parasites_filtered (int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter
)
87 // Removing parasites.
88 areaCloseF
img_RBC_filtered (roundInt
<| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f
)
90 let! parasites, imgWhitoutParasite
, imgWithoutNucleus
=
91 logTimeWithName
"Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find
img_parasites_filtered config))
93 let! edges
, xGradient
, yGradient
= logTimeWithName
"Finding edges" (fun () ->
94 let edges, xGradient
, yGradient
= Edges.find
img_RBC_filtered
95 removeArea
edges (config.RBCRadius.Pixel ** 2.f
/ 50.f
|> int)
96 reportWithVal 50 (edges, xGradient
, yGradient
))
98 let! matchingEllipses
= logTimeWithName
"Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find
edges xGradient yGradient
config))
100 let! prunedEllipses
= logTimeWithName
"Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses
.PrunedEllipses))
102 let! cells
= logTimeWithName
"Classifier" (fun () -> reportWithVal 100 (Classifier.findCells
prunedEllipses parasites img.Width img.Height config))
104 logWithName "Analysis finished"
107 // Output pictures if debug flag is set.
108 match config.Debug with
110 let dirPath = System.IO.Path.Combine(output
, name)
111 System.IO.Directory.CreateDirectory dirPath |> ignore
113 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name + postfix
)
115 IO.saveMat
(edges * 255.0) (buildFileName " - edges.png")
117 IO.saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
118 IO.saveImg
parasites.parasite
(buildFileName " - parasites - stain.png")
119 IO.saveImg
parasites.nucleus
(buildFileName " - parasites - infection.png")
121 let imgAllEllipses = img_RBC_filtered.Copy()
122 Drawing.drawEllipses
imgAllEllipses matchingEllipses
.Ellipses (Gray(200.0)) 0.04
123 IO.saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
125 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte
>()
126 Drawing.drawEllipses
imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
127 IO.saveImg
imgEllipses (buildFileName " - ellipses.png")
129 let imgCells = img.Copy()
130 Drawing.drawCells
imgCells false cells
131 IO.saveImg
imgCells (buildFileName " - cells.png")
133 let imgCells' = img.Copy()
134 Drawing.drawCells imgCells' true cells
135 IO.saveImg
imgCells' (buildFileName " - cells - full.png")
137 (* let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
138 for m in findMaxima filteredRBCMaxima do
139 Drawing.drawPoints filteredRBCMaxima m 255.f
140 IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png") *)
142 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
143 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
145 IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
146 IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.png")
148 IO.saveImg img_float.[2] (buildFileName " - source - red.png")
149 IO.saveImg img_float.[1] (buildFileName " - source - green.png")
150 IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
157 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
159 /// <param name="imgs">The images: (name * configuration * image)</param>
160 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
161 /// The first call returning 'false' will cancel the analysis.
162 /// The 'int' parameter correspond to the progression from 0 to 100</param>
163 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
164 let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) list) (reportProgress : (int -> bool) option) : (string * Cell list) list option =
165 let report (percent : int) : bool =
166 match reportProgress with
167 | Some f -> f percent
170 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
171 let nbImgs = List.length imgs
173 let reportProgressImg (id : string) (progress : int) =
174 progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
175 report (progressPerAnalysis.Values.Sum() / nbImgs)
177 let n = Environment.ProcessorCount
182 fun (id, config, img) ->
184 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
185 | Some result -> Some (id, result)
189 Log.Error "Analysis %s failed: %O" id ex
192 |> PSeq.withDegreeOfParallelism n
195 // If one of the analyses has been aborted we return 'None'.
196 if List.length results <> List.length imgs then