Add functions to apply an area opening and to compute granulometry.
[master-thesis.git] / Parasitemia / Parasitemia / ImgTools.fs
index 7253390..e9cbbe9 100644 (file)
@@ -3,11 +3,13 @@
 open System
 open System.Drawing
 open System.Collections.Generic
+open System.Linq
 
 open Emgu.CV
 open Emgu.CV.Structure
 
 open Utils
+open Heap
 
 // Normalize image values between 0uy and 255uy.
 let normalizeAndConvert (img: Image<Gray, float32>) : Image<Gray, byte> =
@@ -18,10 +20,266 @@ let normalizeAndConvert (img: Image<Gray, float32>) : Image<Gray, byte> =
     img.MinMax(min, max, minLocation, maxLocation)
     ((img - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert<Gray, byte>()
 
+
 let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
     let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
     img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
 
+
+let findMaxima (img: Image<Gray, byte>) : IEnumerable<HashSet<Point>> =
+    use suppress = new Image<Gray, byte>(img.Size)
+    let w = img.Width
+    let h = img.Height
+
+    let imgData = img.Data
+    let suppressData = suppress.Data
+
+    let result = List<List<Point>>()
+
+    let flood (start: Point) : List<List<Point>> =
+        let sameLevelToCheck = Stack<Point>()
+        let betterLevelToCheck = Stack<Point>()
+        betterLevelToCheck.Push(start)
+
+        let result' = List<List<Point>>()
+
+        while betterLevelToCheck.Count > 0 do
+            let p = betterLevelToCheck.Pop()
+            if suppressData.[p.Y, p.X, 0] = 0uy
+            then
+                suppressData.[p.Y, p.X, 0] <- 1uy
+                sameLevelToCheck.Push(p)
+                let current = List<Point>()
+
+                let mutable betterExists = false
+
+                while sameLevelToCheck.Count > 0 do
+                    let p' = sameLevelToCheck.Pop()
+                    let currentLevel = imgData.[p'.Y, p'.X, 0]
+                    current.Add(p') |> ignore
+                    for i in -1 .. 1 do
+                        for j in -1 .. 1 do
+                            if i <> 0 || j <> 0
+                            then
+                                let ni = i + p'.Y
+                                let nj = j + p'.X
+                                if ni >= 0 && ni < h && nj >= 0 && nj < w
+                                then
+                                    let level = imgData.[ni, nj, 0]
+                                    let notSuppressed = suppressData.[ni, nj, 0] = 0uy
+
+                                    if level = currentLevel && notSuppressed
+                                    then
+                                        suppressData.[ni, nj, 0] <- 1uy
+                                        sameLevelToCheck.Push(Point(nj, ni))
+                                    elif level > currentLevel
+                                    then
+                                        betterExists <- true
+                                        if notSuppressed
+                                        then
+                                            betterLevelToCheck.Push(Point(nj, ni))
+
+                if not betterExists
+                then
+                    result'.Add(current)
+        result'
+
+    for i in 0 .. h - 1 do
+        for j in 0 .. w - 1 do
+            let maxima = flood (Point(j, i))
+            if maxima.Count > 0
+            then result.AddRange(maxima)
+
+    result.Select(fun l -> HashSet<Point>(l))
+
+
+type PriorityQueue () =
+    let q = List<HashSet<Point>>() // TODO: Check performance with an HasSet
+    let mutable highest = -1 // Value of the first elements of 'q'.
+
+    member this.Next () : byte * Point =
+        if this.IsEmpty
+        then
+            invalidOp "Queue is empty"
+        else
+            let l = q.[0]
+            let next = l.First()
+            l.Remove(next) |> ignore
+            let value = byte highest
+            if l.Count = 0
+            then
+                q.RemoveAt(0)
+                highest <- highest - 1
+                while q.Count > 0 && q.[0] = null do
+                    q.RemoveAt(0)
+                    highest <- highest - 1
+            value, next
+
+    member this.Max =
+        highest |> byte
+
+    (*member this.UnionWith (other: PriorityQueue) =
+        while not other.IsEmpty do
+            let p, v = other.Next
+            this.Add p v*)
+
+    member this.Add (value: byte) (p: Point) =
+        let vi = int value
+
+        if this.IsEmpty
+        then
+            highest <- int value
+            q.Insert(0, null)
+        elif vi > highest
+        then
+            for i in highest .. vi - 1  do
+                q.Insert(0, null)
+            highest <- vi
+        elif highest - vi >= q.Count
+        then
+            for i in 0 .. highest - vi - q.Count do
+                q.Add(null)
+
+        let pos = highest - vi
+        if q.[pos] = null
+        then
+            q.[pos] <- HashSet<Point>([p])
+        else
+            q.[pos].Add(p) |> ignore
+
+
+    member this.IsEmpty =
+        q.Count = 0
+
+    member this.Clear () =
+        while highest >= 0 do
+            q.[highest] <- null
+            highest <- highest - 1
+
+
+
+type MaximaState =  Uncertain | Validated | TooBig
+type Maxima = {
+    elements : HashSet<Point>
+    mutable intensity: byte option
+    mutable state: MaximaState }
+
+
+let areaOpen (img: Image<Gray, byte>) (area: int) =
+    let w = img.Width
+    let h = img.Height
+
+    let maxima = findMaxima img |> Seq.map (fun m -> { elements = m; intensity = None; state = Uncertain }) |> List.ofSeq
+    let toValidated = Stack<Maxima>(maxima)
+
+    while toValidated.Count > 0 do
+        let m = toValidated.Pop()
+        if m.elements.Count <= area
+        then
+            let queue =
+                let q = PriorityQueue()
+                let firstElements = HashSet<Point>()
+                for p in m.elements do
+                    for i in -1 .. 1 do
+                        for j in -1 .. 1 do
+                            if i <> 0 || j <> 0
+                            then
+                                let ni = i + p.Y
+                                let nj = j + p.X
+                                let p' = Point(nj, ni)
+                                if ni >= 0 && ni < h && nj >= 0 && nj < w && not (m.elements.Contains(p')) && not (firstElements.Contains(p'))
+                                then
+                                    firstElements.Add(p') |> ignore
+                                    q.Add (img.Data.[ni, nj, 0]) p'
+                q
+
+            let mutable intensity = queue.Max
+            let nextElements = HashSet<Point>()
+
+            let mutable stop = false
+            while not stop do
+                let intensity', p = queue.Next ()
+
+                if intensity' = intensity // The intensity doesn't change.
+                then
+                    if m.elements.Count + nextElements.Count + 1 > area
+                    then
+                        m.state <- Validated
+                        m.intensity <- Some intensity
+                        stop <- true
+                    else
+                        nextElements.Add(p) |> ignore
+                elif intensity' < intensity
+                then
+                    m.elements.UnionWith(nextElements)
+                    if m.elements.Count = area
+                    then
+                        m.state <- Validated
+                        m.intensity <- Some (intensity')
+                        stop <- true
+                    else
+                        intensity <- intensity'
+                        nextElements.Clear()
+                        nextElements.Add(p) |> ignore
+                else // i' > i
+                    seq {
+                        for m' in maxima do
+                            if m' <> m && m'.elements.Contains(p) then
+                                if m'.elements.Count + m.elements.Count <= area
+                                then
+                                    m'.state <- Uncertain
+                                    m'.elements.UnionWith(m.elements)
+                                    if not <| toValidated.Contains m' // FIXME: Maybe use state instead of scanning the whole list.
+                                    then
+                                        toValidated.Push(m')
+                                    stop <- true
+                                yield false
+                    } |> Seq.forall id |> ignore
+
+                    if not stop
+                    then
+                        m.state <- Validated
+                        m.intensity <- Some (intensity)
+                        stop <- true
+
+                if not stop
+                then
+                    for i in -1 .. 1 do
+                        for j in -1 .. 1 do
+                            if i <> 0 || j <> 0
+                            then
+                                let ni = i + p.Y
+                                let nj = j + p.X
+                                let p' = Point(nj, ni)
+                                if ni < 0 || ni >= h || nj < 0 || nj >= w
+                                then
+                                    m.state <- Validated
+                                    m.intensity <- Some (intensity)
+                                    stop <- true
+                                elif not (m.elements.Contains(p')) && not (nextElements.Contains(p'))
+                                then
+                                    queue.Add (img.Data.[ni, nj, 0]) p'
+
+                if queue.IsEmpty
+                then
+                    if m.elements.Count + nextElements.Count <= area
+                    then
+                        m.state <- Validated
+                        m.intensity <- Some intensity'
+                        m.elements.UnionWith(nextElements)
+                    stop <- true
+
+    for m in maxima do
+        if m.state = Validated
+        then
+            match m.intensity with
+            | Some i ->
+                for p in m.elements do
+                    img.Data.[p.Y, p.X, 0] <- i
+            | _ -> ()
+    ()
+
+
 // Zhang and Suen algorithm.
 // Modify 'mat' in place.
 let thin (mat: Matrix<byte>) =
@@ -73,6 +331,7 @@ let thin (mat: Matrix<byte>) =
         data2 <- tmp
 
 
+// FIXME: replace by a queue or stack.
 let pop (l: List<'a>) : 'a =
     let n = l.[l.Count - 1]
     l.RemoveAt(l.Count - 1)