smooth3D.m

function smoothedImage=smooth3D(image,smoothradius, ResolutionX, ResolutionY, ResolutionZ,displaywaitbar)
%Smooth image in 3D

%Einar Heiberg

if nargin<6
  displaywaitbar = false;
end;

XSize=size(image,1);
YSize=size(image,2);
TSize=size(image,3);
ZSize=size(image,4);
timeframes=1:TSize;

%smoothing filter
n = 9;

%X direction
x = linspace(-n*ResolutionX,n*ResolutionX,2*n+1);
f = exp(-(x.^2)/(smoothradius.^2));
f = f./sum(f(:));
f = single(f);
fx = f(:);

%Y direction
x = linspace(-n*ResolutionY,n*ResolutionY,2*n+1);
f = exp(-(x.^2)/(smoothradius.^2));
f = f./sum(f(:));
f = single(f);
fy = f(:)';

%Z direction
x = linspace(-n*ResolutionZ,n*ResolutionZ,2*n+1);
f = exp(-(x.^2)/(smoothradius.^2));
f = f./sum(f(:));
f = single(f);
fz = reshape(f,[1 1 length(f)]);

%smooth
%temp=repmat(single(0),[XSize YSize TSize ZSize]);

if displaywaitbar
  h = waitbar(0,'Please wait.');
end;
  
%Create output
temp = single(0)*single(image);

if displaywaitbar
  h = waitbar(0.1,h);
end;

if ZSize>1
    
  %Smooth in x-dir
  for tloop=timeframes
    temp(:,:,tloop,:) = econv3(...
      single(squeeze(image(:,:,tloop,:))),fx);
  end;

  if displaywaitbar
    h = waitbar(0.4,h);
  end;

  %Smooth in y-dir
  for tloop=timeframes
    temp(:,:,tloop,:) = econv3(squeeze(temp(:,:,tloop,:)),fy);
  end;

  if displaywaitbar
    h = waitbar(0.7,h);
  end;
  
  %Smooth in z-dir
  for tloop=timeframes
    temp(:,:,tloop,:) = econv3(squeeze(temp(:,:,tloop,:)),fz);
  end;
  
  if displaywaitbar
    h = waitbar(1,h);
  end;
  
else
  %Smooth in x-dir
    
  temp = econv3(...
    single(squeeze(image)),fx);

  if displaywaitbar
    h = waitbar(0.55,h);
  end;
  
  %Smooth in y-dir
  temp = econv3(squeeze(temp),fy);
  
  if displaywaitbar
    h = waitbar(1,h);
  end;
  
end

%Store output
smoothedImage=temp;

if displaywaitbar
  close(h);
end;