Add a way to detect the membrane of a parasite in the ring stage.

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

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
index 4ab52d9..813d090 100644 (file)
--- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs
+++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
@@ -50,20 +50,28 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
         logWithName "Starting analysis ..."
 
-        use green = img.[1]
-        let greenFloat = green.Convert<Gray, float32>()
-        let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
+        use img_RBC =
+            use imgFloat = img.Convert<Bgr, float32>()
+            let redFactor, greenFactor, blueFactor = config.Parameters.colorContribution_BG_RBC
+            blueFactor * imgFloat.[0] + greenFactor * imgFloat.[1] + redFactor * imgFloat.[2]
+
+        let img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+
+        use img_parasites =
+            use imgFloat = img.Convert<Bgr, float32>()
+            let redFactor, greenFactor, blueFactor = config.Parameters.colorContribution_RBC_parasite
+            blueFactor * imgFloat.[0] + greenFactor * imgFloat.[1] + redFactor * imgFloat.[2]
 
         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.
-        do! logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening; report 10)
+        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 () -> ImgTools.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 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))
+        let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
         config.SetRBCRadius <| radius
 
         logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
@@ -74,15 +82,17 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
             let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
             if secondAreaOpening > initialAreaOpening
             then
-                logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30)
+                logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF img_RBC_filtered secondAreaOpening; report 30)
             else
                 report 30
 
-        let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+        ImgTools.areaCloseF img_RBC_filtered (config.RBCRadius.Area * 0.1f |> roundInt)
+
+        let parasites, filteredGreenWhitoutStain, filteredGreenWithoutInfection = ParasitesMarker.find img_parasites config
         //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
-            let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
+            let edges, xGradient, yGradient = ImgTools.findEdges img_RBC_filtered
             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
             reportWithVal 40 (edges, xGradient, yGradient))
 
@@ -90,7 +100,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
         let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
 
-        let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config))
+        let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
 
         logWithName "Analysis finished"
 
@@ -125,22 +135,17 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
                 drawCells imgCells' true cells
                 saveImg imgCells' (buildFileName " - cells - full.png")
 
-                let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
+                let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
                 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 img_RBC_filtered (buildFileName " - filtered.png")
                 saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
-                //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
-
-                saveImg green (buildFileName " - green.png")
-
-                use blue = img.Item(0)
-                saveImg blue (buildFileName " - blue.png")
+                saveImg filteredGreenWithoutInfection (buildFileName " - filtered closed infection.png")
 
-                use red = img.Item(2)
-                saveImg red (buildFileName " - red.png")
+                saveImg img_RBC (buildFileName " - source - RBC.png")
+                saveImg img_parasites (buildFileName " - source - parasites.png")
             | _ -> ()
 
         return cells }