+++ /dev/null
-module ParasitemiaCore.Analysis
-
-open System
-open System.Linq
-open System.Drawing
-
-open FSharp.Collections.ParallelSeq
-
-open Emgu.CV
-open Emgu.CV.Structure
-
-open Logger
-
-open Utils
-open Morpho
-open ImgTools
-open Config
-open Types
-
-/// <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.
- // Return 'None' if the process must be aborted.
- let reportWithVal (percent: int) (value: 'a) : 'a option =
- match reportProgress with
- | Some f ->
- if f percent
- then Some value
- else None
- | _ -> Some value
-
- let report (percent: int) : unit option =
- reportWithVal percent ()
-
- 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)
-
- maybe {
- do! report 0
-
- logWithName "Starting analysis ..."
-
- use img_float = img.Convert<Bgr, float32>()
-
- 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
-
- 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 "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
-
- 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 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
-
- logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
-
- do! report 20
-
- 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
-
- // Removing parasites.
- areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
-
- let! parasites, imgWhitoutParasite, imgWithoutNucleus =
- logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
-
- 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! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
-
- let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
-
- let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
-
- logWithName "Analysis finished"
-
- 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
-
- let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
-
- IO.saveMat (edges * 255.0) (buildFileName " - edges.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 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 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()
- Drawing.drawCells imgCells false cells
- IO.saveImg imgCells (buildFileName " - cells.png")
-
- let imgCells' = img.Copy()
- Drawing.drawCells imgCells' true cells
- IO.saveImg imgCells' (buildFileName " - cells - full.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")
-
- IO.saveImg img_RBC_filtered (buildFileName " - filtered.png")
- IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
- IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
-
- IO.saveImg img_RBC (buildFileName " - source - RBC.png")
- IO.saveImg img_parasites (buildFileName " - source - parasites.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")
- | _ -> ()
-
- return cells }
-
-/// <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 reportProgressImg (id: string) (progress: int) =
- progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
- report (progressPerAnalysis.Values.Sum() / nbImgs)
-
- let n = Environment.ProcessorCount
-
- 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