From 962440dfe579569ba7e3ebba6f878cb575d1fc02 Mon Sep 17 00:00:00 2001
From: Greg Burri <greg.burri@gmail.com>
Date: Sun, 3 Jan 2016 22:21:55 +0100
Subject: [PATCH] Cleaning.

---
 Parasitemia/Parasitemia/Config.fs          |  2 ++
 Parasitemia/Parasitemia/MainAnalysis.fs    | 20 ++++----------------
 Parasitemia/Parasitemia/ParasitesMarker.fs |  4 ++--
 Parasitemia/Parasitemia/Program.fs         |  2 ++
 4 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/Parasitemia/Parasitemia/Config.fs b/Parasitemia/Parasitemia/Config.fs
index 5740e8b..7f841c4 100644
--- a/Parasitemia/Parasitemia/Config.fs
+++ b/Parasitemia/Parasitemia/Config.fs
@@ -9,6 +9,8 @@ type Debug =
 type Parameters = {
     scale: float
 
+    initialAreaOpen: int
+
     minRbcRadius: float
     maxRbcRadius: float
 
diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index a240878..167e618 100644
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -17,34 +17,22 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
 
     use green = scaledImg.Item(1)
-
     let greenFloat = green.Convert<Gray, float32>()
-
     let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
 
-    (*let maximaImg = filteredGreen.Copy()
-    let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
-    for m in maxima do
-        ImgTools.drawPoints maximaImg m 255uy
-
-    let greenOpen1 = filteredGreen.Copy()
-    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
 
-    let initialAreaOpen = 2000
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)
-
-    config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+    config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.5 |> float)
 
     let secondAreaOpen = int <| config.RBCArea / 3.
-    if secondAreaOpen > initialAreaOpen
+    if secondAreaOpen > config.Parameters.initialAreaOpen
     then
         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
 
     let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
-
+    let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
index 9e46c23..71c15a9 100644
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker.fs
@@ -61,11 +61,11 @@ let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result
     // We use the filtered image to find the dark stain.
 
     // With K-Means.
-    let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0)
+    let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection) 1.0)
     let { KMeans.mean_bg = value_bg; KMeans.mean_fg = value_fg; KMeans.d_fg = d_fg } = kmeansResults
 
     // With K-Medians.
-    (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting this again in MainAnalysis
+    (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection) 1.0) // FIXME: avoid converting this again in MainAnalysis
     let { KMedians.median_bg = value_bg; KMedians.median_fg = value_fg; KMedians.d_fg = d_fg } = kmediansResults *)
 
     let darkStain = d_fg.Cmp(value_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index dffc8fd..94d2999 100644
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -61,6 +61,8 @@ let main args =
             Config(
               { scale = 1.
 
+                initialAreaOpen = 2000
+
                 minRbcRadius = -0.32
                 maxRbcRadius = 0.32
 
-- 
2.43.0