%
%
%  Get Image from Imaris
%
%  Copyright Bitplane AG 2006
%
%
%  Description:
%   
%   Get and returns the Imaris DataSet.
%   This function can be used as utility for other functions; It is not
%       called directly by Imaris.
%
%

function [aImage, aVoxelSize] = BPGetImarisImage(aImarisApplication, aTimeIndex, aChannelIndex)

vImarisDataSet = aImarisApplication.mDataSet;

vExtendMin = [vImarisDataSet.mExtendMinX, vImarisDataSet.mExtendMinY, ...
  vImarisDataSet.mExtendMinZ];
vExtendMax = [vImarisDataSet.mExtendMaxX, vImarisDataSet.mExtendMaxY, ...
  vImarisDataSet.mExtendMaxZ];
vDataSize = [vImarisDataSet.mSizeX, vImarisDataSet.mSizeY, ...
  vImarisDataSet.mSizeZ, vImarisDataSet.mSizeC, vImarisDataSet.mSizeT];

aVoxelSize = (vExtendMax - vExtendMin) ./ vDataSize(1:3);

vMinT = 0;
vMinC = 0;

if nargin == 3 && aChannelIndex<=vDataSize(4) && aTimeIndex<=vDataSize(5)

  vMinT = aTimeIndex-1;
  vDataSize(5) = 1;
  vMinC = aChannelIndex-1;
  vDataSize(4) = 1;
  
elseif nargin == 2 && aTimeIndex<=vDataSize(5)

  vMinT = aTimeIndex-1;
  vDataSize(5) = 1;

end

vSize = [1, prod(vDataSize(1:3)), vDataSize(4:5)];

if strcmp(vImarisDataSet.mType,'eTypeUInt8')
  aImage = zeros(vSize, 'uint8');
elseif strcmp(vImarisDataSet.mType,'eTypeUInt16')
  aImage = zeros(vSize, 'uint16');
else
  aImage = zeros(vSize, 'single');
end

for vTimeIndex = vMinT + (1:vDataSize(5))
  for vChannelIndex = vMinC + (1:vDataSize(4))
    aImage(1, :, vTimeIndex, vChannelIndex) = vImarisDataSet.GetDataVolumeAs1DArray( ...
      vChannelIndex-1, vTimeIndex-1);
  end
end
aImage = reshape(aImage, vDataSize);