* Add the analysis window.

[master-thesis.git] / Parasitemia / Parasitemia / MainAnalysis.fs

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index a240878..2be9be1 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -3,6 +3,8 @@
 open System
 open System.Drawing
 
+open FSharp.Collections.ParallelSeq
+
 open Emgu.CV
 open Emgu.CV.Structure
 
@@ -12,46 +14,44 @@ open Config
 open Types
 
 
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
-
-    use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
-
-    use green = scaledImg.Item(1)
+let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
+    let inline report (percent: int) =
+        match reportProgress with
+        | Some f -> f percent
+        | _ -> ()
 
+    use green = img.Item(1)
     let greenFloat = green.Convert<Gray, float32>()
+    let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
 
-    let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
-
-    (*let maximaImg = filteredGreen.Copy()
-    let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
-    for m in maxima do
-        ImgTools.drawPoints maximaImg m 255uy
-
-    let greenOpen1 = filteredGreen.Copy()
-    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
+    report 8
 
-    let initialAreaOpen = 2000
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)
+    let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) (10, 80) 0.5 |> float32)
+    // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
+    // log (sprintf "r1: %A, r2: %A" r1 r2)
+    config.RBCRadius <- r1
+    report 24
 
-    config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+    let secondAreaOpen = int <| config.RBCArea * config.Parameters.ratioSecondAreaOpen
 
-    let secondAreaOpen = int <| config.RBCArea / 3.
-    if secondAreaOpen > initialAreaOpen
+    if secondAreaOpen > config.Parameters.initialAreaOpen
     then
         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
 
-    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+    let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
-
-    logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
+    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 allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
         let matchingEllipses = Ellipse.find edges xGradient yGradient config
-        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
+        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
+    report 80
 
     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
+    report 100
 
     // Output pictures if debug flag is set.
     match config.Debug with
@@ -61,8 +61,6 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 
-        //saveImg canny (buildFileName " - canny.png")
-
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 
         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
@@ -73,7 +71,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 
-        let imgEllipses = img.Copy()
+        let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
         saveImg imgEllipses (buildFileName " - ellipses.png")
 
@@ -92,15 +90,42 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         saveImg filteredGreen (buildFileName " - filtered.png")
         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
-        saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+        //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 
         saveImg green (buildFileName " - green.png")
 
-        use blue  = scaledImg.Item(0)
+        use blue = img.Item(0)
         saveImg blue (buildFileName " - blue.png")
 
-        use red = scaledImg.Item(2)
+        use red = img.Item(2)
         saveImg red (buildFileName " - red.png")
     | _ -> ()
 
     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 =
+    let inline report (percent: int) =
+        match reportProgress with
+        | Some f -> f percent
+        | _ -> ()
+
+    let monitor = Object()
+    let mutable total = 0
+    let nbImgs = List.length imgs
+    let reportProgressImg =
+        (fun progress ->
+            lock monitor (fun () -> total <- total + progress)
+            report (total / nbImgs))
+
+    let nbConcurrentTaskLimit = 4
+    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.toList