module ParasitemiaCore.Analysis
open System
open System.Linq
open System.Drawing
open FSharp.Collections.ParallelSeq
open Emgu.CV
open Emgu.CV.Structure
open Logger
open Utils
open Morpho
open ImgTools
open Config
open Types
///
/// Analyze the given image and detect reb blood cell (RBC) in it.
///
/// The image
/// The name, used during logging
/// The configuration, must not be shared with another analysis
/// 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
/// 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 =
// 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 =
match reportProgress with
| Some f ->
if f percent
then Some value
else None
| _ -> Some value
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)
maybe {
do! report 0
logWithName "Starting analysis ..."
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_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_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite
logWithName (sprintf "Nominal erytrocyte diameter: %A" 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 range =
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))
config.SetRBCRadius <| radius
logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
do! report 20
do!
let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
if secondAreaOpening > initialAreaOpening
then
logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30)
else
report 30
// Removing parasites.
areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f)
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! 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))
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)
System.IO.Directory.CreateDirectory dirPath |> ignore
let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
IO.saveMat (edges * 255.0) (buildFileName " - edges.png")
IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png")
IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png")
let imgAllEllipses = img.Copy()
Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 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
IO.saveImg imgEllipses (buildFileName " - ellipses.png")
let imgCells = img.Copy()
Drawing.drawCells imgCells false cells
IO.saveImg imgCells (buildFileName " - cells.png")
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")
IO.saveImg img_RBC_filtered (buildFileName " - filtered.png")
IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png")
IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png")
IO.saveImg img_RBC (buildFileName " - source - RBC.png")
IO.saveImg img_parasites (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")
| _ -> ()
return cells }
///
/// Do multiple analyses on the same time. The number of concurrent process depends if 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 =
match reportProgress with
| Some f -> f percent
| _ -> true
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 n = Environment.ProcessorCount
let results =
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)
|> 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