open Logger
open Utils
+open Morpho
open ImgTools
open Config
open Types
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
+/// <summary>
+/// Analyze the given image and detect reb blood cell (RBC) in it.
+/// </summary>
+/// <param name="img">The image</param>
+/// <param name="name">The name, used during logging</param>
+/// <param name="config">The configuration, must not be shared with another analysis</param>
+/// <param name="reportProgress">An optional function to report progress and/or cancel the process.
+/// The first call returning 'false' will cancel the analysis.
+/// The 'int' parameter correspond to the progression from 0 to 100</param>
+/// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
+let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
+
// To report the progress of this function from 0 to 100.
- let inline report (percent: int) =
+ // Return 'None' if the process must be aborted.
+ let reportWithVal (percent: int) (value: 'a) : 'a option =
match reportProgress with
- | Some f -> f percent
- | _ -> ()
+ | Some f ->
+ if f percent
+ then Some value
+ else None
+ | _ -> Some value
- let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
- let logWithName mess = Log.User(buildLogWithName mess)
- let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
+ let report (percent: int) : unit option =
+ reportWithVal percent ()
- logWithName "Starting analysis ..."
+ let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
+ let logWithName mess = Log.User(buildLogWithName mess)
+ let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
- use green = img.Item(1)
- let greenFloat = green.Convert<Gray, float32>()
- let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
+ maybe {
+ do! report 0
- logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
+ logWithName "Starting analysis ..."
- let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // 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.
- logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
+ use img_float = img.Convert<Bgr, float32>()
- report 10
+ use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
+ use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
- let range =
- let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
- int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
- //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
- config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
+ use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
+ use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
- logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
+ logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
- report 20
+ 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.
+ do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
- let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
- if secondAreaOpening > initialAreaOpening
- then
- logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
+ let range =
+ let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
+ int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
+ let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
+ config.SetRBCRadius <| radius
- let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
- //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+ logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
- let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
- let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
- removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
- edges, xGradient, yGradient)
+ do! report 20
- let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
+ do!
+ let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+ if secondAreaOpening > initialAreaOpening
+ then
+ logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
+ else
+ report 30
- report 60
+ // Removing parasites.
+ areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
- let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
+ let! parasites, imgWhitoutParasite, imgWithoutNucleus =
+ logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
- report 80
+ let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
+ let edges, xGradient, yGradient = Edges.find img_RBC_filtered
+ removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
+ reportWithVal 50 (edges, xGradient, yGradient))
- let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
+ let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
- report 100
+ let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
- logWithName "Analysis finished"
+ let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
- // Output pictures if debug flag is set.
- match config.Debug with
- | DebugOn output ->
- let dirPath = System.IO.Path.Combine(output, name)
- System.IO.Directory.CreateDirectory dirPath |> ignore
+ logWithName "Analysis finished"
- let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+ do
+ // Output pictures if debug flag is set.
+ match config.Debug with
+ | DebugOn output ->
+ let dirPath = System.IO.Path.Combine(output, name)
+ System.IO.Directory.CreateDirectory dirPath |> ignore
- saveMat (edges * 255.0) (buildFileName " - edges.png")
+ let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
- saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
- saveImg parasites.stain (buildFileName " - parasites - stain.png")
- saveImg parasites.infection (buildFileName " - parasites - infection.png")
+ IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
- let imgAllEllipses = img.Copy()
- drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
- saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+ IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+ IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
+ IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
- let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
- drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
- saveImg imgEllipses (buildFileName " - ellipses.png")
+ let imgAllEllipses = img.Copy()
+ Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
+ IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
- let imgCells = img.Copy()
- drawCells imgCells false cells
- saveImg imgCells (buildFileName " - cells.png")
+ let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
+ Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ IO.saveImg imgEllipses (buildFileName " - ellipses.png")
- let imgCells' = img.Copy()
- drawCells imgCells' true cells
- saveImg imgCells' (buildFileName " - cells - full.png")
+ let imgCells = img.Copy()
+ Drawing.drawCells imgCells false cells
+ IO.saveImg imgCells (buildFileName " - cells.png")
- let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
- for m in ImgTools.findMaxima filteredGreenMaxima do
- ImgTools.drawPoints filteredGreenMaxima m 255.f
- saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+ let imgCells' = img.Copy()
+ Drawing.drawCells imgCells' true cells
+ IO.saveImg imgCells' (buildFileName " - cells - full.png")
- saveImg filteredGreen (buildFileName " - filtered.png")
- saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
- //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+ let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+ for m in findMaxima filteredGreenMaxima do
+ Drawing.drawPoints filteredGreenMaxima m 255.f
+ IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
- saveImg green (buildFileName " - green.png")
+ IO.saveImg img_RBC_filtered (buildFileName " - filtered.png")
+ IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
+ IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
- use blue = img.Item(0)
- saveImg blue (buildFileName " - blue.png")
+ IO.saveImg img_RBC (buildFileName " - source - RBC.png")
+ IO.saveImg img_parasites (buildFileName " - source - parasites.png")
- use red = img.Item(2)
- saveImg red (buildFileName " - red.png")
- | _ -> ()
+ IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
+ IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
+ IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
+ | _ -> ()
- cells
+ return cells }
-// ID * cell list.
-let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
- let inline report (percent: int) =
+/// <summary>
+/// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
+/// </summary>
+/// <param name="imgs">The images: (name * configuration * image)</param>
+/// <param name="reportProgress">An optional function to report progress and/or cancel the process.
+/// The first call returning 'false' will cancel the analysis.
+/// The 'int' parameter correspond to the progression from 0 to 100</param>
+/// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
+let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
+ let report (percent: int) : bool =
match reportProgress with
| Some f -> f percent
- | _ -> ()
+ | _ -> true
let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
let nbImgs = List.length imgs
let n = Environment.ProcessorCount
- imgs
- |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
- |> PSeq.withDegreeOfParallelism n
- |> PSeq.toList
+ let results =
+ imgs
+ |> PSeq.choose (
+ fun (id, config, img) ->
+ match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
+ | Some result -> Some (id, result)
+ | None -> None)
+ |> PSeq.withDegreeOfParallelism n
+ |> PSeq.toList
+
+ // If one of the analyses has been aborted we return 'None'.
+ if List.length results <> List.length imgs
+ then None
+ else Some results
+
projects / master-thesis.git / blobdiff