Use real unit (um and ppi) instead of pixel in the parameters.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index ec2aabb..7f55c7c 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
 
@@ -11,22 +13,34 @@ open ImgTools
 open Config
 open Types
 
+let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
+    // To report the progress of this function from 0 to 100.
+    let inline report (percent: int) =
+        match reportProgress with
+        | Some f -> f percent
+        | _ -> ()
 
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
-    let scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
-
-    use green = scaledImg.Item(1)
+    use green = img.Item(1)
     let greenFloat = green.Convert<Gray, float32>()
-    let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
-
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
-
-    config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float32)
-
-    let secondAreaOpen = int <| config.RBCArea / 3.f
-    if secondAreaOpen > config.Parameters.initialAreaOpen
+    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
+
+    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
+    if secondAreaOpening > initialAreaOpening
     then
-        logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
+        logTime "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
@@ -37,8 +51,10 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     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)
+    report 100
 
     // Output pictures if debug flag is set.
     match config.Debug with
@@ -58,7 +74,7 @@ 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")
 
@@ -70,7 +86,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawCells imgCells' true cells
         saveImg imgCells' (buildFileName " - cells - full.png")
 
-        let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
+        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")
@@ -81,11 +97,37 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         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