Use a maybe monad to be able abort an analysis.

diff --git a/Parasitemia/Logger/Logger.fs b/Parasitemia/Logger/Logger.fs
index 552e37d..1f029d5 100644 (file)
--- a/Parasitemia/Logger/Logger.fs
+++ b/Parasitemia/Logger/Logger.fs
@@ -139,12 +139,14 @@ type Log () =
     static member AddListener (listener: IListener) = instance.AddListener(listener)
     static member RmListener (listener: IListener) = instance.RmListener(listener)
 
-    static member LogWithTime (message: string, severity: Severity, f: unit -> 'a, [<ParamArray>] args: Object[]) : 'a =
+    static member LogWithTime (message: string, severity: Severity, f: unit -> 'a option, [<ParamArray>] args: Object[]) : 'a option =
         let sw = Stopwatch()
         sw.Start()
         let res = f ()
         sw.Stop()
-        instance.Write(String.Format(message, args) + sprintf " (time: %d ms)" sw.ElapsedMilliseconds, severity)
+        if res.IsSome
+        then
+            instance.Write(String.Format(message, args) + sprintf " (time: %d ms)" sw.ElapsedMilliseconds, severity)
         res
 
     static member Debug (message: string, [<ParamArray>] args: Object[]) =

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
index 0f368d8..be72a2b 100644 (file)
--- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs
+++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
@@ -16,123 +16,135 @@ open ImgTools
 open Config
 open Types
 
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
+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) =
+    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 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) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
-
-    logWithName "Starting analysis ..."
+    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 "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
+        use green = img.Item(1)
+        let greenFloat = green.Convert<Gray, float32>()
+        let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
 
-    report 10
+        logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
 
-    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)
+        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.
+        do! logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening; report 10)
 
-    logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
+        //do! report 10
 
-    report 20
+        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)
+        let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing filteredGreen range |> float32))
+        config.SetRBCRadius <| radius
 
-    let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
-    if secondAreaOpening > initialAreaOpening
-    then
-        logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
+        logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
 
-    let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
-    //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+        do! report 20
 
-    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!
+            let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
+            if secondAreaOpening > initialAreaOpening
+            then
+                logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30)
+            else
+                report 30
 
-    let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
+        let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+        //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    report 60
+        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)
+            reportWithVal 40 (edges, xGradient, yGradient))
 
-    let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
+        let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
 
-    report 80
+        let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
 
-    let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
+        let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config))
 
-    report 100
+        logWithName "Analysis finished"
 
-    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
 
-    // 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)
 
-        let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+                saveMat (edges * 255.0) (buildFileName " - edges.png")
 
-        saveMat (edges * 255.0) (buildFileName " - edges.png")
+                saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+                saveImg parasites.stain (buildFileName " - parasites - stain.png")
+                saveImg parasites.infection (buildFileName " - parasites - infection.png")
 
-        saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
-        saveImg parasites.stain (buildFileName " - parasites - stain.png")
-        saveImg parasites.infection (buildFileName " - parasites - infection.png")
+                let imgAllEllipses = img.Copy()
+                drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
+                saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 
-        let imgAllEllipses = img.Copy()
-        drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
-        saveImg imgAllEllipses (buildFileName " - ellipses - all.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 imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
-        drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
-        saveImg imgEllipses (buildFileName " - ellipses.png")
+                let imgCells = img.Copy()
+                drawCells imgCells false cells
+                saveImg imgCells (buildFileName " - cells.png")
 
-        let imgCells = img.Copy()
-        drawCells imgCells false cells
-        saveImg imgCells (buildFileName " - cells.png")
+                let imgCells' = img.Copy()
+                drawCells imgCells' true cells
+                saveImg imgCells' (buildFileName " - cells - full.png")
 
-        let imgCells' = img.Copy()
-        drawCells imgCells' true cells
-        saveImg imgCells' (buildFileName " - cells - full.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 filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
-        for m in ImgTools.findMaxima filteredGreenMaxima do
-            ImgTools.drawPoints filteredGreenMaxima m 255.f
-        saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+                saveImg filteredGreen (buildFileName " - filtered.png")
+                saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
+                //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 
-        saveImg filteredGreen (buildFileName " - filtered.png")
-        saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
-        //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+                saveImg green (buildFileName " - green.png")
 
-        saveImg green (buildFileName " - green.png")
+                use blue = img.Item(0)
+                saveImg blue (buildFileName " - blue.png")
 
-        use blue = img.Item(0)
-        saveImg blue (buildFileName " - blue.png")
+                use red = img.Item(2)
+                saveImg red (buildFileName " - red.png")
+            | _ -> ()
 
-        use red = img.Item(2)
-        saveImg red (buildFileName " - red.png")
-    | _ -> ()
+        return cells }
 
-    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"></param>
+/// <param name="reportProgress">An optional function to report progress. The process is aborted if the returned value is false</param>
+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
@@ -143,7 +155,18 @@ let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (report
 
     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
+

diff --git a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
index 22ea041..ffe0d14 100644 (file)
--- a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
+++ b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
@@ -6,8 +6,6 @@ open System.Linq
 open Emgu.CV
 open Emgu.CV.Structure
 
-open Logger
-
 open Utils
 
 type Result = {
@@ -21,7 +19,7 @@ type Result = {
 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
 let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
     // We use the filtered image to find the dark stain.
-    let kmediansResults = Log.LogWithTime("Finding fg/bg (k-medians)", Severity.USER, (fun () -> KMedians.kmedians filteredGreen))
+    let kmediansResults = KMedians.kmedians filteredGreen
     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
     let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))

diff --git a/Parasitemia/ParasitemiaCore/Types.fs b/Parasitemia/ParasitemiaCore/Types.fs
index 917e7d8..e2accb7 100644 (file)
--- a/Parasitemia/ParasitemiaCore/Types.fs
+++ b/Parasitemia/ParasitemiaCore/Types.fs
@@ -59,4 +59,29 @@ type Line (a: float32, b: float32) =
     member this.A = a
     member this.B = b
 
+type MaybeBuilder () =
+    member this.Bind (x, f) =
+        match x with
+        | None -> None
+        | Some a -> f a
 
+    member this.ReturnFrom (x) = x
+
+    member this.TryFinally (body, compensation) =
+        try this.ReturnFrom(body())
+        finally compensation()
+
+    member this.Using (disposable: 'a when 'a :> IDisposable, body) =
+        let body' = fun () -> body disposable
+        this.TryFinally(body', fun () ->
+            match disposable with
+            | null -> ()
+            | disp -> disp.Dispose())
+
+    member this.Zero () =
+        None
+
+    member this.Return (x) =
+        Some x
+
+let maybe = new MaybeBuilder()
\ No newline at end of file

diff --git a/Parasitemia/ParasitemiaUI/Analysis.fs b/Parasitemia/ParasitemiaUI/Analysis.fs
index 24f9adb..9b9ed51 100644 (file)
--- a/Parasitemia/ParasitemiaUI/Analysis.fs
+++ b/Parasitemia/ParasitemiaUI/Analysis.fs
@@ -117,30 +117,34 @@ let showWindow (parent: Window) (state: State.State) : bool =
             then
                 MessageBox.Show("No image selected", "Cannot start analysis", MessageBoxButton.OK, MessageBoxImage.Information) |> ignore
             else
+                stackSourceImagesSelection.IsEnabled <- false
                 analysisPerformed <- false
                 butStart.IsEnabled <- false
                 butClose.Content <- "Abort"
+
                 async {
-                    let results =
+                    let maybeResults =
                         ParasitemiaCore.Analysis.doMultipleAnalysis
                             imagesToProcess
-                            (Some (fun progress -> window.Root.Dispatcher.Invoke(fun () -> progressBar.Value <- float progress)))
+                            (Some (fun progress -> window.Root.Dispatcher.Invoke(fun () -> progressBar.Value <- float progress); not analysisCancelled))
 
                     lock monitor (
                         fun() ->
-                            if not analysisCancelled
-                            then
+                            match maybeResults with
+                            | Some results ->
                                 for id, cells in results do
                                     state.SetResult (int id) cells
 
                                 window.Root.Dispatcher.Invoke(fun () ->
+                                    stackSourceImagesSelection.IsEnabled <- true
                                     butStart.IsEnabled <- true
                                     butClose.Content <- "Close"
                                     updateSourceImages ())
 
                                 Logger.Log.User("All analyses terminated successfully")
                                 atLeastOneAnalysisPerformed <- true
-                                analysisPerformed <- true)
+                                analysisPerformed <- true
+                            | None -> ())
                 } |> Async.Start
         | _ -> ())
 

diff --git a/Parasitemia/ParasitemiaUI/GUI.fs b/Parasitemia/ParasitemiaUI/GUI.fs
index d30cb66..921654a 100644 (file)
--- a/Parasitemia/ParasitemiaUI/GUI.fs
+++ b/Parasitemia/ParasitemiaUI/GUI.fs
@@ -344,6 +344,10 @@ let run (defaultConfig: Config) (fileToOpen: string option) =
             if currentRemoved
             then
                 updateCurrentImage()
+
+            updateGlobalParasitemia()
+
+            // Update image numbers.
             stackPreviews.Children |> Seq.cast<Views.ImageSourcePreview> |> Seq.iter (fun imgPreview -> imgPreview.txtImageNumber.Text <- (imgPreview.Tag :?> SourceImage).num.ToString()))
 
         imgCtrl.Tag <- srcImg

diff --git a/Parasitemia/ParasitemiaUI/Program.fs b/Parasitemia/ParasitemiaUI/Program.fs
index 74f0d35..24e33cd 100644 (file)
--- a/Parasitemia/ParasitemiaUI/Program.fs
+++ b/Parasitemia/ParasitemiaUI/Program.fs
@@ -74,12 +74,15 @@ let main args =
                     let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), config.Copy(), new Image<Bgr, byte>(file) ]
 
                     Log.LogWithTime("Whole analyze", Severity.USER, (fun () ->
-                        let results = ParasitemiaCore.Analysis.doMultipleAnalysis images None
-
-                        for id, cells in results do
-                            let config = images |> List.pick (fun (id', config', _) -> if id' = id then Some config' else None)
-                            let total, infected = countCells cells
-                            fprintf resultFile "File: %s %d %d %.2f (diameter: %A)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius))
+                        match ParasitemiaCore.Analysis.doMultipleAnalysis images None with
+                        | Some results ->
+                            for id, cells in results do
+                                let config = images |> List.pick (fun (id', config', _) -> if id' = id then Some config' else None)
+                                let total, infected = countCells cells
+                                fprintf resultFile "File: %s %d %d %.2f (diameter: %A)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius
+                        | None ->
+                            fprintf resultFile "Analysis aborted"
+                        Some ())) |> ignore
 
                     Log.RmListener(listener)
                     0

diff --git a/Parasitemia/ParasitemiaUI/XAML/MainWindow.xaml b/Parasitemia/ParasitemiaUI/XAML/MainWindow.xaml
index 6037bc1..d8c1fc8 100644 (file)
--- a/Parasitemia/ParasitemiaUI/XAML/MainWindow.xaml
+++ b/Parasitemia/ParasitemiaUI/XAML/MainWindow.xaml
@@ -21,7 +21,7 @@
             <MenuItem x:Name="menuStartAnalysis" Header="_Show analysis window" />
          </MenuItem>
          <MenuItem x:Name="menuView" Header="_View">
-            <MenuItem x:Name="menuHightlightRBC" Header="_Highlight healthy erytrocytes" IsCheckable="True" />
+            <MenuItem x:Name="menuHightlightRBC" Header="_Highlight all erytrocytes" IsCheckable="True" />
          </MenuItem>
          <MenuItem x:Name="menuHelp" Header="_Help">
             <MenuItem x:Name="menuAbout" Header="_About" />