open System
open System.Linq
-open System.Drawing
open FSharp.Collections.ParallelSeq
open Config
open Types
+let warningRatioDifferenceRBCDiameter = 1.2
+
/// <summary>
/// Analyze the given image and detect reb blood cell (RBC) in it.
/// </summary>
/// The first call returning 'false' will cancel the analysis.
/// The 'int' parameter correspond to the progression from 0 to 100</param>
/// <returns>A list of detected cells or nothing if the process has been cancelled</returns>
-let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option =
+let doAnalysis (img : Image<Bgr, byte>) (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 "№ %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 {
logWithName "Starting analysis ..."
- use img_float = img.Convert<Bgr, float32>()
+ use img_float = img.Convert<Bgr, float32> ()
use img_RBC = img_float.[1] // Green.
use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC
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)
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
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! 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"
do
// 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")
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<Bgr, byte>()
- Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
+ let imgEllipses = img_RBC_filtered.Convert<Bgr, byte> ()
+ 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")
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
+ }
/// <summary>
-/// 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.
/// </summary>
/// <param name="imgs">The images: (name * configuration * image)</param>
/// <param name="reportProgress">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</param>
-/// <returns>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name<returns>
-let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option =
- let report (percent: int) : bool =
+/// <return>'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name</return>
+let doMultipleAnalysis (imgs : (string * Config * Image<Bgr, byte>) 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<string, int>()
+ let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int> ()
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
| None -> None
with
| ex ->
- Log.Error("Analysis {0} failed: {1}", id, ex)
- None)
+ 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
projects / master-thesis.git / blobdiff