Doc + cleaning.

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

diff --git a/Parasitemia/ParasitemiaCore/Analysis.fs b/Parasitemia/ParasitemiaCore/Analysis.fs
index c894fc4..e83977a 100644 (file)
--- a/Parasitemia/ParasitemiaCore/Analysis.fs
+++ b/Parasitemia/ParasitemiaCore/Analysis.fs
@@ -46,6 +46,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
     let logWithName mess = Log.User(buildLogWithName mess)
     let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
 
+    // Monadic construction to be able to abort the progress when running.
     maybe {
         do! report 0
 
@@ -53,10 +54,10 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
 
         use img_float = img.Convert<Bgr, float32>()
 
-        use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255.
+        use img_RBC = img_float.[1] // Green.
         use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
 
-        use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255.
+        use img_parasites = img_float.[2] // Red.
         use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
 
         logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution)
@@ -137,10 +138,10 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportPr
                 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
-                    Drawing.drawPoints filteredGreenMaxima m 255.f
-                IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+                let filteredRBCMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC
+                for m in findMaxima filteredRBCMaxima do
+                    Drawing.drawPoints filteredRBCMaxima m 255.f
+                IO.saveImg filteredRBCMaxima (buildFileName " - filtered - maxima.png")
 
                 IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
                 IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
@@ -182,9 +183,14 @@ let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (report
         imgs
         |> PSeq.choose (
             fun (id, config, img) ->
-                match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
-                | Some result -> Some (id, result)
-                | None -> None)
+                try
+                    match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with
+                    | Some result -> Some (id, result)
+                    | None -> None
+                with
+                | ex ->
+                    Log.Error("Analysis {0} failed: {1}", id, ex)
+                    None)
         |> PSeq.withDegreeOfParallelism n
         |> PSeq.toList