X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=53429b234dd8589ea3423d149e0ed17cb386deaa;hb=81d1b86719a1ebaf649c1de4c1364603155a53e1;hp=7f55c7ca324449f65f26b1616e124db941b88d0c;hpb=4147bfad3c85dcf4fe7d291abf7d356379d88b4f;p=master-thesis.git

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index 7f55c7c..53429b2 100644
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -1,6 +1,7 @@
 module ImageAnalysis
 
 open System
+open System.Linq
 open System.Drawing
 
 open FSharp.Collections.ParallelSeq
@@ -20,42 +21,60 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
         | Some f -> f percent
         | _ -> ()
 
+    let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
+    let logWithName = buildLogWithName >> log
+    let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) f
+
+    logWithName "Starting analysis ..."
+
     use green = img.Item(1)
     let greenFloat = green.Convert<Gray, float32>()
     let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
 
-    let initialAreaOpening = int<| config.RBCArea * config.Parameters.ratioAreaPaleCenter
-    logTime "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
-    report 8
+    logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
+
+    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)
+
+    report 10
 
     let range =
-        let delta = config.Parameters.granulometryRange * config.RBCRadius
-        int <| config.RBCRadius - delta, int <| config.RBCRadius + delta
-    //let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
-    let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
-    // log (sprintf "r1: %A, r2: %A" r1 r2)
-    config.RBCRadius <- r2
-    report 24
-
-    let secondAreaOpening = int <| config.RBCArea * config.Parameters.ratioAreaPaleCenter
+        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)
+
+    logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
+
+    report 20
+
+    let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
     if secondAreaOpening > initialAreaOpening
     then
-        logTime "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
+        logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
 
     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
-    logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
+    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)
+
+    let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
+
+    report 60
+
+    let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
 
-    let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
-        let matchingEllipses = Ellipse.find edges xGradient yGradient config
-        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
     report 80
 
-    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
+    let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
+
     report 100
 
+    logWithName "Analysis finished"
+
     // Output pictures if debug flag is set.
     match config.Debug with
     | DebugOn output ->
@@ -71,11 +90,11 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 
         let imgAllEllipses = img.Copy()
-        drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
+        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 ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
+        drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
         saveImg imgEllipses (buildFileName " - ellipses.png")
 
         let imgCells = img.Copy()
@@ -106,28 +125,23 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
     cells
 
-// ID * cell radius * cell list.
-let doMultipleAnalysis (imgs: (string * Image<Bgr, byte>) list) (config : Config) (reportProgress: (int -> unit) option) : (string * float * Cell list) list =
+// 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) =
         match reportProgress with
         | Some f -> f percent
         | _ -> ()
 
-    let monitor = Object()
-    let mutable total = 0
+    let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
     let nbImgs = List.length imgs
-    let reportProgressImg =
-        (fun progress ->
-            lock monitor (fun () -> total <- total + progress)
-            report (total / nbImgs))
 
-    let nbConcurrentTaskLimit = 4
+    let reportProgressImg (id: string) (progress: int) =
+        progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
+        report (progressPerAnalysis.Values.Sum() / nbImgs)
+
     let n = Environment.ProcessorCount
 
     imgs
-    |> PSeq.map (fun (id, img) ->
-        let localConfig = config.Copy()
-        let cells = doAnalysis img id localConfig (Some reportProgressImg)
-        id, float localConfig.RBCRadius, cells)
-    |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
+    |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
+    |> PSeq.withDegreeOfParallelism n
     |> PSeq.toList