X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FAnalysis.fs;h=1ba273c0c0bc278de9c0dcc393e14b81f51e373c;hb=refs%2Ftags%2F1.0.13;hp=7f58463110cb4d3becb2474623a7c53cc21b4421;hpb=04d4504e7b248a82ddfc1a41d325e59d24146590;p=master-thesis.git
diff --git a/Parasitemia/ParasitemiaCore/Analysis.fs b/Parasitemia/ParasitemiaCore/Analysis.fs
index 7f58463..1ba273c 100644
--- a/Parasitemia/ParasitemiaCore/Analysis.fs
+++ b/Parasitemia/ParasitemiaCore/Analysis.fs
@@ -2,7 +2,6 @@
open System
open System.Linq
-open System.Drawing
open FSharp.Collections.ParallelSeq
@@ -17,6 +16,8 @@ open ImgTools
open Config
open Types
+let warningRatioDifferenceRBCDiameter = 1.2
+
///
/// Analyze the given image and detect reb blood cell (RBC) in it.
///
@@ -27,39 +28,37 @@ open Types
/// The first call returning 'false' will cancel the analysis.
/// The 'int' parameter correspond to the progression from 0 to 100
/// A list of detected cells or nothing if the process has been cancelled
-let doAnalysis (img: Image) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
+let doAnalysis (img : Image) (name : string) (config : Config) (reportProgress : (int -> bool) option) : AnalysisResult option =
// To report the progress of this function from 0 to 100.
// Return 'None' if the process must be aborted.
- let reportWithVal (percent: int) (value: 'a) : 'a option =
+ let reportWithVal (percent : int) (value : 'a) : 'a option =
match reportProgress with
- | Some f ->
- if f percent
- then Some value
- else None
+ | Some f -> if f percent then Some value else None
| _ -> Some value
- let report (percent: int) : unit option =
+ let report (percent : int) : unit option =
reportWithVal percent ()
- let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
- 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)
+ let inline buildLogWithName (text : string) = sprintf "â %s: %s" name text
+ let logWithName mess = Log.Info "%s" (buildLogWithName mess)
+ let inline logTimeWithName (text : string) (f : unit -> 'a option) : 'a option = Log.LogWithTime Severity.INFO f "%s" (buildLogWithName text)
+ // Monadic construction to be able to abort the progress when running.
maybe {
do! report 0
logWithName "Starting analysis ..."
- use img_float = img.Convert()
+ use img_float = img.Convert ()
- 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)
+ logWithName (sprintf "Nominal erythrocyte diameter: %O" 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)
@@ -68,18 +67,17 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr
let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
- let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
- //let! radius = logTimeWithName "Granulometry (morpho)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
+ let! radius = logTimeWithName "Granulometry (area)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32))
+ //let! radius = logTimeWithName "Granulometry (morpho)" (fun () -> reportWithVal 10 (Granulometry.findRadiusByClosing img_RBC_filtered range 1. true |> float32))
config.SetRBCRadius <| radius
- logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius)
+ logWithName (sprintf "Found erythrocyte diameter: %O" config.RBCRadius)
do! report 20
do!
let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
- if secondAreaOpening > initialAreaOpening
- then
+ if secondAreaOpening > initialAreaOpening then
logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
else
report 30
@@ -93,16 +91,25 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr
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 = Edges.find img_RBC_filtered
- removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
- reportWithVal 50 (edges, xGradient, yGradient))
+ let! edges, xGradient, yGradient =
+ logTimeWithName "Finding edges" (
+ fun () ->
+ let edges, xGradient, yGradient = Edges.find img_RBC_filtered
+ removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
+ reportWithVal 50 (edges, xGradient, yGradient)
+ )
let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config))
let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses))
- let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config))
+ let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img.Width img.Height config))
+
+ do
+ if config.RBCRadiusByResolution.μm / config.RBCRadius.μm > warningRatioDifferenceRBCDiameter then
+ logWithName (sprintf "Warning: erythrocyte diameter found is too low compared to the nominal erythrocyte diameter, maybe the PPI image resolution is lesser than %.0f ppi" config.Parameters.resolution)
+ elif config.RBCRadius.μm / config.RBCRadiusByResolution.μm > warningRatioDifferenceRBCDiameter then
+ logWithName (sprintf "Warning: erythrocyte diameter found is too high compared to the nominal erythrocyte diameter, maybe the PPI image resolution is higher than %.0f" config.Parameters.resolution)
logWithName "Analysis finished"
@@ -110,10 +117,10 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr
// Output pictures if debug flag is set.
match config.Debug with
| DebugOn output ->
- let dirPath = System.IO.Path.Combine(output, name)
+ let dirPath = System.IO.Path.Combine (output, name)
System.IO.Directory.CreateDirectory dirPath |> ignore
- let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+ let buildFileName postfix = System.IO.Path.Combine (dirPath, name + postfix)
IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
@@ -121,26 +128,26 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr
IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
- let imgAllEllipses = img_RBC_filtered.Copy()
- Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray(200.0)) 0.04
+ let imgAllEllipses = img_RBC_filtered.Copy ()
+ Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Gray 200.0) 0.04
IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
- let imgEllipses = img_RBC_filtered.Convert()
- Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ let imgEllipses = img_RBC_filtered.Convert ()
+ Drawing.drawEllipses imgEllipses prunedEllipses (Bgr (0.0, 240.0, 240.0)) 1.0
IO.saveImg imgEllipses (buildFileName " - ellipses.png")
- let imgCells = img.Copy()
+ let imgCells = img.Copy ()
Drawing.drawCells imgCells false cells
IO.saveImg imgCells (buildFileName " - cells.png")
- let imgCells' = img.Copy()
+ let imgCells' = img.Copy ()
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")
@@ -148,33 +155,41 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr
IO.saveImg img_RBC_filtered (buildFileName " - source - RBC.png")
IO.saveImg img_parasites_filtered (buildFileName " - source - parasites.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")
+ IO.saveImg img_float.[2] (buildFileName " - source - red.png")
+ IO.saveImg img_float.[1] (buildFileName " - source - green.png")
+ IO.saveImg img_float.[0] (buildFileName " - source - blue.png")
| _ -> ()
- return cells }
+ return
+ {
+ Cells = cells
+ RBCSize_μm = config.RBCRadius.μm
+ RBCSize_px = config.RBCRadius.Pixel
+ }
+
+ //return cells
+ }
///
-/// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core.
+/// Do multiple analyses on the same time. The number of concurrent process depends on the number of the core.
///
/// The images: (name * configuration * image)
/// An optional function to report progress and/or cancel the process.
/// The first call returning 'false' will cancel the analysis.
/// The 'int' parameter correspond to the progression from 0 to 100
-/// 'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name
-let doMultipleAnalysis (imgs: (string * Config * Image) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
- let report (percent: int) : bool =
+/// 'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name
+let doMultipleAnalysis (imgs : (string * Config * Image) list) (reportProgress : (int -> bool) option) : (string * AnalysisResult) list option =
+ let report (percent : int) : bool =
match reportProgress with
| Some f -> f percent
| _ -> true
- let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary()
+ let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary ()
let nbImgs = List.length imgs
- let reportProgressImg (id: string) (progress: int) =
- progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
- report (progressPerAnalysis.Values.Sum() / nbImgs)
+ let reportProgressImg (id : string) (progress : int) =
+ progressPerAnalysis.AddOrUpdate (id, progress, (fun _ _ -> progress)) |> ignore
+ report (progressPerAnalysis.Values.Sum () / nbImgs)
let n = Environment.ProcessorCount
@@ -182,14 +197,21 @@ let doMultipleAnalysis (imgs: (string * Config * Image) 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 %s failed: %O" id ex
+ None
+ )
|> PSeq.withDegreeOfParallelism n
|> PSeq.toList
// If one of the analyses has been aborted we return 'None'.
- if List.length results <> List.length imgs
- then None
- else Some results
+ if List.length results <> List.length imgs then
+ None
+ else
+ Some results