X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;fp=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=0000000000000000000000000000000000000000;hb=23466ba92c5595f6c0b9f97c86a221a4e5ffebe9;hp=926aeac5523dcf734cab8660809337e8eb8a6b32;hpb=e588f9c954a54cb259b2c1f6f9e8d9dbd4639269;p=master-thesis.git

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
deleted file mode 100644
index 926aeac..0000000
--- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs
+++ /dev/null
@@ -1,191 +0,0 @@
-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
-