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PTVlab (Particle Tracking Velocimetry - lab)

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PTVlab (Particle Tracking Velocimetry - lab)

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A GUI based tool to preprocess, analyze, validate, postprocess, visualize and simulate PTV data.

smoothn(varargin)
function [z,s,exitflag] = smoothn(varargin)

%SMOOTHN Robust spline smoothing for 1-D to N-D data.
%   SMOOTHN provides a fast, automatized and robust discretized smoothing
%   spline for data of any dimension.
%
%   Z = SMOOTHN(Y) automatically smoothes the uniformly-sampled array Y. Y
%   can be any N-D noisy array (time series, images, 3D data,...). Non
%   finite data (NaN or Inf) are treated as missing values.
%
%   Z = SMOOTHN(Y,S) smoothes the array Y using the smoothing parameter S.
%   S must be a real positive scalar. The larger S is, the smoother the
%   output will be. If the smoothing parameter S is omitted (see previous
%   option) or empty (i.e. S = []), it is automatically determined using
%   the generalized cross-validation (GCV) method.
%
%   Z = SMOOTHN(Y,W) or Z = SMOOTHN(Y,W,S) specifies a weighting array W of
%   real positive values, that must have the same size as Y. Note that a
%   nil weight corresponds to a missing value.
%
%   Robust smoothing
%   ----------------
%   Z = SMOOTHN(...,'robust') carries out a robust smoothing that minimizes
%   the influence of outlying data.
%
%   [Z,S] = SMOOTHN(...) also returns the calculated value for S so that
%   you can fine-tune the smoothing subsequently if needed.
%
%   An iteration process is used in the presence of weighted and/or missing
%   values. Z = SMOOTHN(...,OPTION_NAME,OPTION_VALUE) smoothes with the
%   termination parameters specified by OPTION_NAME and OPTION_VALUE. They
%   can contain the following criteria:
%       -----------------
%       TolZ:       Termination tolerance on Z (default = 1e-3)
%                   TolZ must be in ]0,1[
%       MaxIter:    Maximum number of iterations allowed (default = 100)
%       Initial:    Initial value for the iterative process (default =
%                   initial data)
%       -----------------
%   Syntax: [Z,...] = SMOOTHN(...,'MaxIter',500,'TolZ',1e-4,'Initial',Z0);
%
%   [Z,S,EXITFLAG] = SMOOTHN(...) returns a boolean value EXITFLAG that
%   describes the exit condition of SMOOTHN:
%       1       SMOOTHN converged.
%       0       Maximum number of iterations was reached.
%
%   Class Support
%   -------------
%   Input array can be numeric or logical. The returned array is of class
%   double.
%
%   Notes
%   -----
%   The N-D (inverse) discrete cosine transform functions <a
%   href="matlab:web('http://www.biomecardio.com/matlab/dctn.html')"
%   >DCTN</a> and <a
%   href="matlab:web('http://www.biomecardio.com/matlab/idctn.html')"
%   >IDCTN</a> are required.
%
%   To be made
%   ----------
%   Estimate the confidence bands (see Wahba 1983, Nychka 1988).
%
%   Reference
%   --------- 
%   Garcia D, Robust smoothing of gridded data in one and higher dimensions
%   with missing values. Computational Statistics & Data Analysis, 2010. 
%   <a
%   href="matlab:web('http://www.biomecardio.com/pageshtm/publi/csda10.pdf')">PDF download</a>
%
%   Examples:
%   --------
%   % 1-D example
%   x = linspace(0,100,2^8);
%   y = cos(x/10)+(x/50).^2 + randn(size(x))/10;
%   y([70 75 80]) = [5.5 5 6];
%   z = smoothn(y); % Regular smoothing
%   zr = smoothn(y,'robust'); % Robust smoothing
%   subplot(121), plot(x,y,'r.',x,z,'k','LineWidth',2)
%   axis square, title('Regular smoothing')
%   subplot(122), plot(x,y,'r.',x,zr,'k','LineWidth',2)
%   axis square, title('Robust smoothing')
%
%   % 2-D example
%   xp = 0:.02:1;
%   [x,y] = meshgrid(xp);
%   f = exp(x+y) + sin((x-2*y)*3);
%   fn = f + randn(size(f))*0.5;
%   fs = smoothn(fn);
%   subplot(121), surf(xp,xp,fn), zlim([0 8]), axis square
%   subplot(122), surf(xp,xp,fs), zlim([0 8]), axis square
%
%   % 2-D example with missing data
%   n = 256;
%   y0 = peaks(n);
%   y = y0 + rand(size(y0))*2;
%   I = randperm(n^2);
%   y(I(1:n^2*0.5)) = NaN; % lose 1/2 of data
%   y(40:90,140:190) = NaN; % create a hole
%   z = smoothn(y); % smooth data
%   subplot(2,2,1:2), imagesc(y), axis equal off
%   title('Noisy corrupt data')
%   subplot(223), imagesc(z), axis equal off
%   title('Recovered data ...')
%   subplot(224), imagesc(y0), axis equal off
%   title('... compared with original data')
%
%   % 3-D example
%   [x,y,z] = meshgrid(-2:.2:2);
%   xslice = [-0.8,1]; yslice = 2; zslice = [-2,0];
%   vn = x.*exp(-x.^2-y.^2-z.^2) + randn(size(x))*0.06;
%   subplot(121), slice(x,y,z,vn,xslice,yslice,zslice,'cubic')
%   title('Noisy data')
%   v = smoothn(vn);
%   subplot(122), slice(x,y,z,v,xslice,yslice,zslice,'cubic')
%   title('Smoothed data')
%
%   % Cardioid
%   t = linspace(0,2*pi,1000);
%   x = 2*cos(t).*(1-cos(t)) + randn(size(t))*0.1;
%   y = 2*sin(t).*(1-cos(t)) + randn(size(t))*0.1;
%   z = smoothn(complex(x,y));
%   plot(x,y,'r.',real(z),imag(z),'k','linewidth',2)
%   axis equal tight
%
%   % Cellular vortical flow
%   [x,y] = meshgrid(linspace(0,1,24));
%   Vx = cos(2*pi*x+pi/2).*cos(2*pi*y);
%   Vy = sin(2*pi*x+pi/2).*sin(2*pi*y);
%   Vx = Vx + sqrt(0.05)*randn(24,24); % adding Gaussian noise
%   Vy = Vy + sqrt(0.05)*randn(24,24); % adding Gaussian noise
%   I = randperm(numel(Vx));
%   Vx(I(1:30)) = (rand(30,1)-0.5)*5; % adding outliers
%   Vy(I(1:30)) = (rand(30,1)-0.5)*5; % adding outliers
%   Vx(I(31:60)) = NaN; % missing values
%   Vy(I(31:60)) = NaN; % missing values
%   Vs = smoothn(complex(Vx,Vy),'robust'); % automatic smoothing
%   subplot(121), quiver(x,y,Vx,Vy,2.5), axis square
%   title('Noisy velocity field')
%   subplot(122), quiver(x,y,real(Vs),imag(Vs)), axis square
%   title('Smoothed velocity field')
%
%   See also SMOOTH, GSMOOTHN, DCTN, IDCTN.
%
%   -- Damien Garcia -- 2009/03, revised 2010/06
%   Visit my <a
%   href="matlab:web('http://www.biomecardio.com/matlab/smoothn.html')">website</a> for more details about SMOOTHN 

% Check input arguments
error(nargchk(1,10,nargin));

%% Test & prepare the variables
%---
k = 0;
while k<nargin && ~ischar(varargin{k+1}), k = k+1; end
%---
% y = array to be smoothed
y = double(varargin{1});
sizy = size(y);
noe = prod(sizy); % number of elements
if noe<2, z = y; return, end
%---
% Smoothness parameter and weights
W = ones(sizy);
s = [];
if k==2
    if isempty(varargin{2}) || isscalar(varargin{2}) % smoothn(y,s)
        s = varargin{2}; % smoothness parameter
    else % smoothn(y,W)
        W = varargin{2}; % weight array
    end
elseif k==3 % smoothn(y,W,s)
        W = varargin{2}; % weight array
        s = varargin{3}; % smoothness parameter
end
if ~isequal(size(W),sizy)
        error('MATLAB:smoothn:SizeMismatch',...
            'Arrays for data and weights must have same size.')
elseif ~isempty(s) && (~isscalar(s) || s<0)
    error('MATLAB:smoothn:IncorrectSmoothingParameter',...
        'The smoothing parameter must be a scalar >=0')
end
%---
% "Maximal number of iterations" criterion
I = find(strcmpi(varargin,'MaxIter'),1);
if isempty(I)
    MaxIter = 100; % default value for MaxIter
else
    try
        MaxIter = varargin{I+1};
    catch
        error('MATLAB:smoothn:IncorrectMaxIter',...
            'MaxIter must be an integer >=1')
    end
    if ~isnumeric(MaxIter) || ~isscalar(MaxIter) ||...
            MaxIter<1 || MaxIter~=round(MaxIter)
        error('MATLAB:smoothn:IncorrectMaxIter',...
            'MaxIter must be an integer >=1')        
    end    
end
%---
% "Tolerance on smoothed output" criterion
I = find(strcmpi(varargin,'TolZ'),1);
if isempty(I)
    TolZ = 1e-3; % default value for TolZ
else
    try
        TolZ = varargin{I+1};
    catch
        error('MATLAB:smoothn:IncorrectTolZ',...
            'TolZ must be in ]0,1[')
    end
    if ~isnumeric(TolZ) || ~isscalar(TolZ) || TolZ<=0 || TolZ>=1 
        error('MATLAB:smoothn:IncorrectTolZ',...
            'TolZ must be in ]0,1[')
    end    
end
%---
% "Initial Guess" criterion
I = find(strcmpi(varargin,'Initial'),1);
if isempty(I)
    isinitial = false; % default value for TolZ
else
    isinitial = true;
    try
        z0 = varargin{I+1};
    catch
        error('MATLAB:smoothn:IncorrectInitialGuess',...
            'Z0 must be a valid initial guess for Z')
    end
    if ~isnumeric(z0) || ~isequal(size(z0),sizy) 
        error('MATLAB:smoothn:IncorrectTolZ',...
            'Z0 must be a valid initial guess for Z')
    end    
end
%---
% Weights. Zero weights are assigned to not finite values (Inf or NaN),
% (Inf/NaN values = missing data).
IsFinite = isfinite(y);
nof = nnz(IsFinite); % number of finite elements
W = W.*IsFinite;
if any(W<0)
    error('MATLAB:smoothn:NegativeWeights',...
        'Weights must all be >=0')
else 
    W = W/max(W(:));
end
%---
% Weighted or missing data?
isweighted = any(W(:)<1);
%---
% Robust smoothing?
isrobust = any(strcmpi(varargin,'robust'));
%---
% Automatic smoothing?
isauto = isempty(s);
%---
% DCTN and IDCTN are required
test4DCTNandIDCTN

%% Creation of the Lambda tensor
%---
% Lambda contains the eingenvalues of the difference matrix used in this
% penalized least squares process.
d = ndims(y);
Lambda = zeros(sizy);
for i = 1:d
    siz0 = ones(1,d);
    siz0(i) = sizy(i);
    Lambda = bsxfun(@plus,Lambda,...
        cos(pi*(reshape(1:sizy(i),siz0)-1)/sizy(i)));
end
Lambda = -2*(d-Lambda);
if ~isauto, Gamma = 1./(1+s*Lambda.^2); end

%% Upper and lower bound for the smoothness parameter
% The average leverage (h) is by definition in [0 1]. Weak smoothing occurs
% if h is close to 1, while over-smoothing appears when h is near 0. Upper
% and lower bounds for h are given to avoid under- or over-smoothing. See
% equation relating h to the smoothness parameter (Equation #12 in the
% referenced CSDA paper).
N = sum(sizy~=1); % tensor rank of the y-array
hMin = 1e-6; hMax = 0.99;
sMinBnd = (((1+sqrt(1+8*hMax.^(2/N)))/4./hMax.^(2/N)).^2-1)/16;
sMaxBnd = (((1+sqrt(1+8*hMin.^(2/N)))/4./hMin.^(2/N)).^2-1)/16;

%% Initialize before iterating
%---
Wtot = W;
%--- Initial conditions for z
if isweighted
    %--- With weighted/missing data
    % An initial guess is provided to ensure faster convergence. For that
    % purpose, a nearest neighbor interpolation followed by a coarse
    % smoothing are performed.
    %---
    if isinitial % an initial guess (z0) has been provided
        z = z0;
    else
        z = InitialGuess(y,IsFinite);
    end
    
else
    z = zeros(sizy);
end
%---
z0 = z;
y(~IsFinite) = 0; % arbitrary values for missing y-data
%---
tol = 1;
RobustIterativeProcess = true;
RobustStep = 1;
nit = 0;
%--- Error on p. Smoothness parameter s = 10^p
errp = 0.1;
opt = optimset('TolX',errp);
%--- Relaxation factor RF: to speedup convergence
RF = 1 + 0.75*isweighted;

%% Main iterative process
%---
while RobustIterativeProcess
    %--- "amount" of weights (see the function GCVscore)
    aow = sum(Wtot(:))/noe; % 0 < aow <= 1
    %---
    while tol>TolZ && nit<MaxIter
        nit = nit+1;
        DCTy = dctn(Wtot.*(y-z)+z);
        if isauto && ~rem(log2(nit),1)
            %---
            % The generalized cross-validation (GCV) method is used.
            % We seek the smoothing parameter s that minimizes the GCV
            % score i.e. s = Argmin(GCVscore)^.
            % Because this process is time-consuming, it is performed from
            % time to time (when nit is a power of 2)
            %---
            fminbnd(@gcv,log10(sMinBnd),log10(sMaxBnd),opt);
        end
        z = RF*idctn(Gamma.*DCTy) + (1-RF)*z;
        
        % if no weighted/missing data => tol=0 (no iteration)
        tol = isweighted*norm(z0(:)-z(:))/norm(z(:));
       
        z0 = z; % re-initialization
    end
    exitflag = nit<MaxIter;

    if isrobust %-- Robust Smoothing: iteratively re-weighted process
        %--- average leverage
        h = sqrt(1+16*s); h = sqrt(1+h)/sqrt(2)/h; h = h^N;
        %--- take robust weights into account
        Wtot = W.*RobustWeights(y-z,IsFinite,h);
        %--- re-initialize for another iterative weighted process
        isweighted = true; tol = 1; nit = 0; 
        %---
        RobustStep = RobustStep+1;
        RobustIterativeProcess = RobustStep<4; % 3 robust steps are enough.
    else
        RobustIterativeProcess = false; % stop the whole process
    end
end

%% Warning messages
%---
if isauto
    if abs(log10(s)-log10(sMinBnd))<errp
        warning('MATLAB:smoothn:SLowerBound',...
            ['s = ' num2str(s,'%.3e') ': the lower bound for s ',...
            'has been reached. Put s as an input variable if required.'])
    elseif abs(log10(s)-log10(sMaxBnd))<errp
        warning('MATLAB:smoothn:SUpperBound',...
            ['s = ' num2str(s,'%.3e') ': the upper bound for s ',...
            'has been reached. Put s as an input variable if required.'])
    end
end
if nargout<3 && ~exitflag
    warning('MATLAB:smoothn:MaxIter',...
        ['Maximum number of iterations (' int2str(MaxIter) ') has ',...
        'been exceeded. Increase MaxIter option or decrease TolZ value.'])
end


%% GCV score
%---
function GCVscore = gcv(p)
    % Search the smoothing parameter s that minimizes the GCV score
    %---
    s = 10^p;
    Gamma = 1./(1+s*Lambda.^2);
    %--- RSS = Residual sum-of-squares
    if aow>0.9 % aow = 1 means that all of the data are equally weighted
        % very much faster: does not require any inverse DCT
        RSS = norm(DCTy(:).*(Gamma(:)-1))^2;
    else
        % take account of the weights to calculate RSS:
        yhat = idctn(Gamma.*DCTy);
        RSS = norm(sqrt(Wtot(IsFinite)).*(y(IsFinite)-yhat(IsFinite)))^2;
    end
    %---
    TrH = sum(Gamma(:));
    GCVscore = RSS/nof/(1-TrH/noe)^2;
end

end

%% Robust weights
function W = RobustWeights(r,I,h)
    % weights for robust smoothing.
    MAD = median(abs(r(I)-median(r(I)))); % median absolute deviation
    u = abs(r/(1.4826*MAD)/sqrt(1-h)); % studentized residuals
    c = 4.685; W = (1-(u/c).^2).^2.*((u/c)<1); % bisquare weights
    % c = 2.385; W = 1./(1+(u/c).^2); % Cauchy weights
    % c = 2.795; W = u<c; % Talworth weights
    W(isnan(W)) = 0; 
end

%% Test for DCTN and IDCTN
function test4DCTNandIDCTN
    if ~exist('dctn','file')
        error('MATLAB:smoothn:MissingFunction',...
            ['DCTN and IDCTN are required. Download DCTN <a href="matlab:web(''',...
            'http://www.biomecardio.com/matlab/dctn.html'')">here</a>.'])
    elseif ~exist('idctn','file')
        error('MATLAB:smoothn:MissingFunction',...
            ['DCTN and IDCTN are required. Download IDCTN <a href="matlab:web(''',...
            'http://www.biomecardio.com/matlab/idctn.html'')">here</a>.'])
    end
end

%% Initial Guess with weighted/missing data
function z = InitialGuess(y,I)
    %-- nearest neighbor interpolation (in case of missing values)
    if any(~I(:))
        if license('test','image_toolbox')
            [z,L] = bwdist(I);
            z = y;
            z(~I) = y(L(~I));
        else
        % If BWDIST does not exist, NaN values are all replaced with the
        % same scalar. The initial guess is not optimal and a warning
        % message thus appears.
            z = y;
            z(~I) = mean(y(I));
            warning('MATLAB:smoothn:InitialGuess',...
                ['BWDIST (Image Processing Toolbox) does not exist. ',...
                'The initial guess may not be optimal; additional',...
                ' iterations can thus be required to ensure complete',...
                ' convergence. Increase ''MaxIter'' criterion if necessary.'])    
        end
    else
        z = y;
    end
    %-- coarse fast smoothing using one-tenth of the DCT coefficients
    siz = size(z);
    z = dctn(z);
    for k = 1:ndims(z)
        z(ceil(siz(k)/10)+1:end,:) = 0;
        z = reshape(z,circshift(siz,[0 1-k]));
        z = shiftdim(z,1);
    end
    z = idctn(z);
end

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