1
module ParasitemiaCore.Analysis
7 open FSharp.Collections.ParallelSeq
10 open Emgu.CV.Structure
20 /// Analyze the given image and detect reb blood cell (RBC) in it.
22 /// <param name="img">The image</param>
23 /// <param name="name">The name, used during logging</param>
24 /// <param name="config">The configuration, must not be shared with another analysis</param>
25 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
26 /// The first call returning 'false' will cancel the analysis.
27 /// The 'int' parameter correspond to the progression from 0 to 100</param>
28 /// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
29 let doAnalysis (img
: Image<Bgr, byte
>) (name: string) (config
: Config) (reportProgress
: (int -> bool) option) : Cell list option =
31 // To report the progress of this function from 0 to 100.
32 // Return 'None' if the process must be aborted.
33 let reportWithVal (percent
: int) (value
: 'a) : 'a
option =
34 match reportProgress
with
41 let report (percent
: int) : unit option =
42 reportWithVal percent ()
44 let inline buildLogWithName
(text
: string) = sprintf
"(%s) %s" name text
45 let logWithName mess
= Log.User(buildLogWithName
mess)
46 let inline logTimeWithName
(text: string) (f
: unit -> 'a option) : 'a
option = Log.LogWithTime((buildLogWithName
text), Severity.USER, f
)
51 logWithName "Starting analysis ..."
54 use imgFloat = img
.Convert<Bgr, float32
>()
55 let redFactor, greenFactor
, blueFactor
= config
.Parameters.colorContribution_BG_RBC
56 blueFactor
* imgFloat.[0] + greenFactor
* imgFloat.[1] + redFactor * imgFloat.[2]
58 let img_RBC_filtered = gaussianFilter
img_RBC config
.LPFStandardDeviationRBC
61 use imgFloat = img
.Convert<Bgr, float32
>()
62 let redFactor, greenFactor
, blueFactor
= config
.Parameters.colorContribution_RBC_parasite
63 blueFactor
* imgFloat.[0] + greenFactor
* imgFloat.[1] + redFactor * imgFloat.[2]
65 logWithName (sprintf
"Nominal erytrocyte diameter: %A" config
.RBCRadiusByResolution)
67 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.
68 do! logTimeWithName
"First area opening" (fun () -> ImgTools.areaOpenF
img_RBC_filtered initialAreaOpening; report 10)
71 let delta = config.Parameters.granulometryRange
* config.RBCRadiusByResolution.Pixel
72 int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
73 //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
74 let! radius = logTimeWithName
"Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing
img_RBC_filtered range |> float32
))
75 config.SetRBCRadius <| radius
77 logWithName (sprintf
"Found erytrocyte diameter: %A" config.RBCRadius)
82 let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
83 if secondAreaOpening > initialAreaOpening
85 logTimeWithName
"Second area opening" (fun () -> ImgTools.areaOpenF
img_RBC_filtered secondAreaOpening; report 30)
89 ImgTools.areaCloseF
img_RBC_filtered (config.RBCRadius.Area * 0.1f |> roundInt
)
91 let parasites, filteredGreenWhitoutStain
, filteredGreenWithoutInfection
= ParasitesMarker.find
img_parasites config
92 //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
94 let! edges
, xGradient
, yGradient
= logTimeWithName
"Finding edges" (fun () ->
95 let edges, xGradient
, yGradient
= ImgTools.findEdges
img_RBC_filtered
96 removeArea
edges (config.RBCRadius.Pixel ** 2.f
/ 50.f
|> int)
97 reportWithVal 40 (edges, xGradient
, yGradient
))
99 let! matchingEllipses
= logTimeWithName
"Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find
edges xGradient yGradient
config))
101 let! prunedEllipses
= logTimeWithName
"Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses
.PrunedEllipses))
103 let! cells
= logTimeWithName
"Classifier" (fun () -> reportWithVal 100 (Classifier.findCells
prunedEllipses parasites img_RBC_filtered config))
105 logWithName "Analysis finished"
108 // Output pictures if debug flag is set.
109 match config.Debug with
111 let dirPath = System.IO.Path.Combine(output
, name)
112 System.IO.Directory.CreateDirectory dirPath |> ignore
114 let buildFileName postfix
= System.IO.Path.Combine(dirPath, name + postfix
)
116 saveMat
(edges * 255.0) (buildFileName " - edges.png")
118 saveImg
parasites.darkStain
(buildFileName " - parasites - dark stain.png")
119 saveImg
parasites.stain
(buildFileName " - parasites - stain.png")
120 saveImg
parasites.infection
(buildFileName " - parasites - infection.png")
122 let imgAllEllipses = img
.Copy()
123 drawEllipses
imgAllEllipses matchingEllipses
.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
124 saveImg
imgAllEllipses (buildFileName " - ellipses - all.png")
126 let imgEllipses = filteredGreenWhitoutStain
.Convert<Bgr, byte
>()
127 drawEllipses
imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
128 saveImg
imgEllipses (buildFileName " - ellipses.png")
130 let imgCells = img
.Copy()
131 drawCells
imgCells false cells
132 saveImg
imgCells (buildFileName " - cells.png")
134 let imgCells' = img.Copy()
135 drawCells imgCells' true cells
136 saveImg
imgCells' (buildFileName " - cells - full.png")
138 let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
139 for m in ImgTools.findMaxima filteredGreenMaxima do
140 ImgTools.drawPoints filteredGreenMaxima m 255.f
141 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
143 saveImg img_RBC_filtered (buildFileName " - filtered.png")
144 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
145 saveImg filteredGreenWithoutInfection (buildFileName " - filtered closed infection.png")
147 saveImg img_RBC (buildFileName " - source - RBC.png")
148 saveImg img_parasites (buildFileName " - source - parasites.png")
154 /// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
156 /// <param name="imgs">The images: (name * configuration * image)</param>
157 /// <param name="reportProgress">An optional function to report progress and/or cancel the process.
158 /// The first call returning 'false' will cancel the analysis.
159 /// The 'int' parameter correspond to the progression from 0 to 100</param>
160 /// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
161 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
162 let report (percent: int) : bool =
163 match reportProgress with
164 | Some f -> f percent
167 let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
168 let nbImgs = List.length imgs
170 let reportProgressImg (id: string) (progress: int) =
171 progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
172 report (progressPerAnalysis.Values.Sum() / nbImgs)
174 let n = Environment.ProcessorCount
179 fun (id, config, img) ->
180 match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
181 | Some result -> Some (id, result)
183 |> PSeq.withDegreeOfParallelism n
186 // If one of the analyses has been aborted we return 'None'.
187 if List.length results <> List.length imgs