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 2be9be1..7f55c7c 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -13,8 +13,8 @@ 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
@@ -22,22 +22,25 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
     use green = img.Item(1)
     let greenFloat = green.Convert<Gray, float32>()
-    let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
+    let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
 
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
+    let initialAreaOpening = int<| config.RBCArea * config.Parameters.ratioAreaPaleCenter
+    logTime "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
     report 8
 
-    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)
+    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 <- r1
+    config.RBCRadius <- r2
     report 24
 
-    let secondAreaOpen = int <| config.RBCArea * config.Parameters.ratioSecondAreaOpen
-
-    if secondAreaOpen > config.Parameters.initialAreaOpen
+    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
@@ -83,7 +86,7 @@ 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.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")
@@ -103,7 +106,6 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
     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) =