* Modify a bit the parasite nucleus detection sensibility.

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

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
index 9c85c7b..926aeac 100644 (file)
--- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs
+++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
@@ -12,6 +12,7 @@ open Emgu.CV.Structure
 open Logger
 
 open Utils
+open Morpho
 open ImgTools
 open Config
 open Types
@@ -58,7 +59,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
         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)
+        logWithName (sprintf "Nominal erythrocyte 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 () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10)
@@ -69,7 +70,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
         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)
+        logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
 
         do! report 20
 
@@ -88,7 +89,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
             logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config))
 
         let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
-            let edges, xGradient, yGradient = findEdges img_RBC_filtered
+            let edges, xGradient, yGradient = Edges.find img_RBC_filtered
             removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
             reportWithVal 50 (edges, xGradient, yGradient))
 
@@ -109,43 +110,43 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
                 let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 
-                saveMat (edges * 255.0) (buildFileName " - edges.png")
+                IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
 
-                saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
-                saveImg parasites.parasite (buildFileName " - parasites - stain.png")
-                saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
+                IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+                IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
+                IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
 
                 let imgAllEllipses = img.Copy()
-                drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
-                saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+                Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
+                IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 
                 let imgEllipses = img_RBC_filtered.Convert<Bgr, byte>()
-                drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
-                saveImg imgEllipses (buildFileName " - ellipses.png")
+                Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+                IO.saveImg imgEllipses (buildFileName " - ellipses.png")
 
                 let imgCells = img.Copy()
-                drawCells imgCells false cells
-                saveImg imgCells (buildFileName " - cells.png")
+                Drawing.drawCells imgCells false cells
+                IO.saveImg imgCells (buildFileName " - cells.png")
 
                 let imgCells' = img.Copy()
-                drawCells imgCells' true cells
-                saveImg imgCells' (buildFileName " - cells - full.png")
+                Drawing.drawCells imgCells' true cells
+                IO.saveImg imgCells' (buildFileName " - cells - full.png")
 
                 let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
                 for m in findMaxima filteredGreenMaxima do
-                    drawPoints filteredGreenMaxima m 255.f
-                saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+                    Drawing.drawPoints filteredGreenMaxima m 255.f
+                IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 
-                saveImg img_RBC_filtered (buildFileName " - filtered.png")
-                saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
-                saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
+                IO.saveImg img_RBC_filtered (buildFileName " - filtered.png")
+                IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
+                IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
 
-                saveImg img_RBC (buildFileName " - source - RBC.png")
-                saveImg img_parasites (buildFileName " - source - parasites.png")
+                IO.saveImg img_RBC (buildFileName " - source - RBC.png")
+                IO.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")
+                IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png")
+                IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png")
+                IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png")
             | _ -> ()
 
         return cells }