Cleaning + renaming.

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

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
index 5a8e16d..9c85c7b 100644 (file)
--- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs
+++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
@@ -52,22 +52,20 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
         use img_float = img.Convert<Bgr, float32>()
 
-        // use img_RBC = mergeChannels img_float config.Parameters.colorContribution_BG_RBC
-        use img_RBC = mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
-        let img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+        use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
+        use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 
-        //use img_parasites = mergeChannels img_float config.Parameters.colorContribution_RBC_parasite
-        use img_parasites = mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
+        use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
+        use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
 
         logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
 
         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)
+        do! logTimeWithName "First area opening" (fun () -> 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 img_RBC_filtered range |> float32))
         config.SetRBCRadius <| radius
 
@@ -79,20 +77,20 @@ 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 img_RBC_filtered secondAreaOpening; report 30)
+                logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
             else
                 report 30
 
-        // Removing of parasites.
-        ImgTools.areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
+        // Removing parasites.
+        areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
 
-        let parasites, filteredGreenWhitoutStain, filteredGreenWithoutInfection = ParasitesMarker.find img_parasites config
-        //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+        let! parasites, imgWhitoutParasite, imgWithoutNucleus =
+            logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
 
         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
-            let edges, xGradient, yGradient = ImgTools.findEdges img_RBC_filtered
+            let edges, xGradient, yGradient = findEdges img_RBC_filtered
             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
-            reportWithVal 40 (edges, xGradient, yGradient))
+            reportWithVal 50 (edges, xGradient, yGradient))
 
         let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
 
@@ -114,7 +112,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
                 saveMat (edges * 255.0) (buildFileName " - edges.png")
 
                 saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
-                saveImg parasites.cytoplasm (buildFileName " - parasites - stain.png")
+                saveImg parasites.parasite (buildFileName " - parasites - stain.png")
                 saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 
                 let imgAllEllipses = img.Copy()
@@ -134,16 +132,20 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
                 saveImg imgCells' (buildFileName " - cells - full.png")
 
                 let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
-                for m in ImgTools.findMaxima filteredGreenMaxima do
-                    ImgTools.drawPoints filteredGreenMaxima m 255.f
+                for m in findMaxima filteredGreenMaxima do
+                    drawPoints filteredGreenMaxima m 255.f
                 saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 
                 saveImg img_RBC_filtered (buildFileName " - filtered.png")
-                saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
-                saveImg filteredGreenWithoutInfection (buildFileName " - filtered closed infection.png")
+                saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
+                saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 
                 saveImg img_RBC (buildFileName " - source - RBC.png")
                 saveImg img_parasites (buildFileName " - source - parasites.png")
+
+                saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
+                saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
+                saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
             | _ -> ()
 
         return cells }