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 ImgTools
open Config
open Types

let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
    // To report the progress of this function from 0 to 100.
    let inline report (percent: int) =
        match reportProgress with
        | Some f -> f 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) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)

    logWithName "Starting analysis ..."

    use green = img.Item(1)
    let greenFloat = green.Convert<Gray, float32>()
    let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation

    logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)

    let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // 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.
    logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)

    report 10

    let range =
        let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
        int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
    //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
    config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)

    logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)

    report 20

    let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
    if secondAreaOpening > initialAreaOpening
    then
        logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)

    let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
    //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config

    let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
        let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
        removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
        edges, xGradient, yGradient)

    let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)

    report 60

    let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)

    report 80

    let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)

    report 100

    logWithName "Analysis finished"

    // 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)

        saveMat (edges * 255.0) (buildFileName " - edges.png")

        saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
        saveImg parasites.stain (buildFileName " - parasites - stain.png")
        saveImg parasites.infection (buildFileName " - parasites - infection.png")

        let imgAllEllipses = img.Copy()
        drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
        saveImg imgAllEllipses (buildFileName " - ellipses - all.png")

        let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
        drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
        saveImg imgEllipses (buildFileName " - ellipses.png")

        let imgCells = img.Copy()
        drawCells imgCells false cells
        saveImg imgCells (buildFileName " - cells.png")

        let imgCells' = img.Copy()
        drawCells imgCells' true cells
        saveImg imgCells' (buildFileName " - cells - full.png")

        let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
        for m in ImgTools.findMaxima filteredGreenMaxima do
            ImgTools.drawPoints filteredGreenMaxima m 255.f
        saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")

        saveImg filteredGreen (buildFileName " - filtered.png")
        saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
        //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")

        saveImg green (buildFileName " - green.png")

        use blue = img.Item(0)
        saveImg blue (buildFileName " - blue.png")

        use red = img.Item(2)
        saveImg red (buildFileName " - red.png")
    | _ -> ()

    cells

// ID * cell list.
let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
    let inline report (percent: int) =
        match reportProgress with
        | Some f -> f percent
        | _ -> ()

    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 n = Environment.ProcessorCount

    imgs
    |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
    |> PSeq.withDegreeOfParallelism n
    |> PSeq.toList