From 57efb6003254b234fdad2837e5ee666933a4355f Mon Sep 17 00:00:00 2001 From: bvenn Date: Fri, 20 Sep 2019 12:51:55 +0200 Subject: [PATCH] add getCorrelationAtCoor clean up Trace module fix fittingFunction --- src/BioFSharp.ImgP/Trace.fs | 89 ++++++++++++++++++++++++++++--------- 1 file changed, 69 insertions(+), 20 deletions(-) diff --git a/src/BioFSharp.ImgP/Trace.fs b/src/BioFSharp.ImgP/Trace.fs index 4385dc98..e4c28fa7 100644 --- a/src/BioFSharp.ImgP/Trace.fs +++ b/src/BioFSharp.ImgP/Trace.fs @@ -80,6 +80,8 @@ module Ricker = module Trace = + + [] let inline cwtDataOfCoor (marr: Marr.MarrWavelet) y x (paddedData:seq<'a[,]>)= ///calculates the wavelet transformation at position 'x,y' with MarrWavelet 'marr' let C3DWTatPositionAndFrame (marr: Marr.MarrWavelet) (paddedframe:'a[,]) y x = @@ -89,13 +91,33 @@ module Trace = for a = 0 to 2*offset do for b = 0 to 2*offset do acc <- ((marr.Values).[a,b] * ((paddedframe).[((x+offsetpadding)+(a-offset)),((y+offsetpadding)+(b-offset))] |> float) )::acc - acc |> List.fold (fun acc x -> acc + x) 0. //CONSTANT ENERGY times 1/(sqrt |scale|) + acc + |> List.sum + |> fun x -> x / (sqrt (Math.Abs marr.Scale)) //CONSTANT ENERGY times 1/(sqrt |scale|) let result = [|0..(Seq.length paddedData) - 1|] |> Array.map (fun fr -> C3DWTatPositionAndFrame marr (paddedData |> Seq.item fr) y x) result + + ///calculates the correlations value at a specified coordinate + let inline getCorrelationAtCoor borderpadding (marr: Marr.MarrWavelet) y x (paddedData:seq<'a[,]>)= + ///calculates the wavelet transformation at position 'x,y' with MarrWavelet 'marr' + let C3DWTatPositionAndFrame (paddedframe:'a[,]) y x = + let offset = marr.PadAreaRadius + Array2D.init (2*offset) (2*offset) (fun a b -> + let waveletvalue = (marr.Values).[a,b] + let datavalue = float paddedframe.[((x+borderpadding)+(a-offset)),((y+borderpadding)+(b-offset))] + waveletvalue * datavalue) + |> Array2D.toLongColumnArray + |> Array.sum + |> fun x -> x / (sqrt (Math.Abs marr.Scale)) + + let result = + Array.init (Seq.length paddedData) (fun fr -> C3DWTatPositionAndFrame (paddedData |> Seq.item fr) y x) + result + [] let inline findTraceOfBestCoor marrList (paddedData:seq<'a[,]>) (coor:float*float) = let yCoor = (fst coor) |> Core.Operators.round |> int let xCoor = (snd coor) |> Core.Operators.round |> int @@ -105,7 +127,6 @@ module Trace = |> List.map (fun x -> let corrcoeff = cwtDataOfCoor x yCoor xCoor paddedData corrcoeff) - //searches for the index of the wavelet in marrList with the highest score (representing the best matching waveletfunction). let indexOfBestScale = let foldedIntensities= @@ -123,16 +144,40 @@ module Trace = let radius = (marrList.[indexOfBestScale]).Zero (radius,trace) + ///calculates the correlation values of a specified coordinate with given wavelets and returns the trace of highest correlation + let inline getTraceOfBestCorrelation borderpadding marrList (paddedData:seq<'a[,]>) (coor:float*float) = + let yCoor = (fst coor) |> round 0 |> int + let xCoor = (snd coor) |> round 0 |> int + //calculates the summed correlation values of each wavelet transformed trace + let intensityList = + marrList + |> List.map (fun x -> + getCorrelationAtCoor borderpadding x yCoor xCoor paddedData + |> Array.sum) + //gives the index of the best matching waveletfunction based on summed correlation values for each wavelet + let indexOfBestScale = + intensityList + |> List.indexed + |> List.maxBy snd + |> fst + //trace of highest correlation (best matching waveletfunction at this position) + let trace = intensityList.[indexOfBestScale] + //radius of the best matching waveletfunction at this position + let radius = (marrList.[indexOfBestScale]).Zero + (radius,trace) + + [] + ///padds the trace with 20k data points randomly selected for let paddTrace (cwtTrace:float[])= let rnd = System.Random() let padding = 20000 //number of zeros the data is padded with - let listRnd = Array.map (fun x -> cwtTrace.[rnd.Next(0,cwtTrace.Length-1)]|> float ) [|0..padding-1|] + let listRnd = Array.init padding (fun _ -> cwtTrace.[rnd.Next(0,cwtTrace.Length-1)]|> float ) let paddedCWT3Dtrace = Array.append (Array.append listRnd cwtTrace) listRnd paddedCWT3Dtrace - ///computes the continious wavelet transform of the padded trace with wavelet type Ricker. - let cWT1D (paddedTrace: float []) (myRicker: Ricker.myRicker)= - let padding = 20000 + ///computes the continuous wavelet transform of the padded trace with wavelet type myRicker. + let transform2D borderpadding (myRicker: Ricker.myRicker) (paddedTrace: float []) = + let padding = borderpadding let myRickerOffsetRise = (6. * myRicker.ScaleRise) |> ceil |> int let myRickerOffset = myRicker.PadArea let arr = Array.zeroCreate (paddedTrace.Length - (2 * padding)) @@ -144,12 +189,14 @@ module Trace = else (arr.[i-padding] <- (acc2 / Math.Sqrt(myRicker.ScaleDecay))) //corrects for admissibility (see Polikar wavelet tutorial) loop 0. (- myRickerOffsetRise) arr - - - let findLocalMaxima2D paddedTrace ricker neighbourPoints = + [] + let cWT1D (paddedTrace: float []) (myRicker: Ricker.myRicker) = transform2D 20000 myRicker paddedTrace + + ///calculates the positions of maxima with given neighbourPoints and returns a maximaArray and the wavelet transformed trace + let isolateLocalMaxima borderpadding paddedTrace ricker neighbourPoints = let (cWTArray: float []) = - cWT1D paddedTrace ricker + transform2D borderpadding ricker paddedTrace let arrayOfMaxima = Array.zeroCreate (Array.length cWTArray) ///gets coordinates of pixel and number of pixel in surrounding and gives bool, if coor has highest value let checkListsForContinuousDecline pointindex = @@ -171,8 +218,7 @@ module Trace = //checks order of each direction (left/right) let boolList = surroundingList |> List.map (fun x -> isSortedAsc x) //if any list is not sorted -> false - not (boolList |> List.contains false) - + not (List.exists (fun x -> x = false) boolList) //calculates decline for every point for i=neighbourPoints to (cWTArray.Length)-(neighbourPoints+1) do if checkListsForContinuousDecline i = true @@ -180,19 +226,22 @@ module Trace = else arrayOfMaxima.[i] <- 0. arrayOfMaxima,cWTArray - ///gives maximaarray (checked with x neigbours) * CWT trace of maximal correlation - let collectMaxima rickerarray neighbourPoints (paddedTrace:float[]) = - let numberOfFrames = paddedTrace.Length - (2 * 3000) + [] + let findLocalMaxima2D = isolateLocalMaxima + + ///takes a collection of wavelets and a padded trace and computes a merged trace, where maxima of each trace are merged + let collectMaxima rickerarray neighbourPoints borderpadding (paddedTrace:float[]) = + let numberOfFrames = paddedTrace.Length - (2 * borderpadding) let arr = Array.zeroCreate numberOfFrames let arrCurve = Array.zeroCreate numberOfFrames let maximaArray = rickerarray - |> Array.map (fun x -> fst (findLocalMaxima2D paddedTrace x neighbourPoints)) + |> Array.map (fun x -> fst (isolateLocalMaxima borderpadding paddedTrace x neighbourPoints)) |> fun x -> x |> JaggedArray.transpose |> Array.map (fun x -> x |> Array.max) let curveArray = rickerarray - |> Array.map (fun x -> snd (findLocalMaxima2D paddedTrace x neighbourPoints)) + |> Array.map (fun x -> snd (isolateLocalMaxima borderpadding paddedTrace x neighbourPoints)) |> fun x -> x |> JaggedArray.transpose |> Array.map (fun x -> x |> Array.max) @@ -239,9 +288,9 @@ module Trace = /// gets finalcentroidlist and cellnumber and fits the fitting with threshold to trace. With numberOfSurroundingIntensities you can set the area in which a maxima has to be the highest point - let fittingCaSignalToMaxima rickerarray threshold numberOfSurroundingIntensities rise (paddedTrace:float[]) = - let numberOfFrames = paddedTrace.Length - (2 * 3000) - let (maximaarray,cWTCurve) = collectMaxima rickerarray numberOfSurroundingIntensities paddedTrace + let fittingCaSignalToMaxima rickerarray threshold borderpadding numberOfSurroundingIntensities rise (paddedTrace:float[]) = + let numberOfFrames = paddedTrace.Length - (2 * borderpadding) + let (maximaarray,cWTCurve) = collectMaxima rickerarray numberOfSurroundingIntensities borderpadding paddedTrace let fittedList = [|(int rise)..numberOfFrames-1|]