%
%
%  Smooth time Function for Imaris
%
%  Copyright Bitplane AG 2006
%
%
%  Installation:
%
%  - Copy this file into the XTensions folder in the Imaris installation directory.
%  - You will find this function in the Image Processing menu
%
%    <CustomTools>
%      <Menu>
%        <Item name="SmoothTime" icon="Matlab" tooltip="Smooth the intensity of each voxel along the time dimension using a gaussian filter.">
%          <Command>Matlab::BPSmoothTime(%i)</Command>
%        </Item>
%      </Menu>
%    </CustomTools>
%  
%
%  Description:
%   
%   Smooth the intensity of each voxel along the time dimension using a 
%       gaussian filter. 
%
%

function BPSmoothTime(aImarisApplicationID, aSigma, aChannelIndex)

% connect to Imaris Com interface
if ~isa(aImarisApplicationID, 'COM.Imaris_Application')
    vImarisServer = actxserver('ImarisServer.Server');
    vImarisApplication = vImarisServer.GetObject(aImarisApplicationID);
else
    vImarisApplication = aImarisApplicationID;
end
vImarisApplication.DataSetPushUndo('Smooth Time');

% get the data set 
vImarisDataSet = vImarisApplication.mDataSet.Clone;

vChannelIndex = 1;
for vChannelId = 1:vImarisDataSet.mSizeC
  if vImarisApplication.GetChannelVisibility(vChannelId-1) == true
    vChannelIndex = vChannelId;
    break;
  end
end

if nargin<3
    vSigma = 1;
    vAnswer = inputdlg({'Channel','Filter Width'}, 'Smooth Time', ...
        1, {num2str(vChannelIndex),num2str(vSigma)});
    if isempty(vAnswer)
        return;
    else
        vChannelIndex = str2double(char(vAnswer(1)));
        vSigma = str2double(char(vAnswer(2)));
    end
else
    vChannelIndex = aChannelIndex;
    vSigma = aSigma;
end

vImageProcessing = vImarisApplication.mImageProcessing;

vNumberOfTimePoints = vImarisDataSet.mSizeT;
vNumberOfSlices = vImarisDataSet.mSizeZ;

vProgressDisplay = waitbar(0,'Smoothing Time');

% prepare the dataset 
vDataSet = vImarisApplication.mFactory.CreateDataSet;
vDataSet.Create(vImarisDataSet.mType, vImarisDataSet.mSizeX, vImarisDataSet.mSizeY, ...
    vNumberOfTimePoints, 1, 1);

vDataSet.mExtendMinX = 0;
vDataSet.mExtendMinY = 0;
vDataSet.mExtendMinZ = 0;
% gaussian filter does not operate along X and Y axis
vDataSet.mExtendMaxX = 5000*vImarisDataSet.mSizeX;
vDataSet.mExtendMaxY = 5000*vImarisDataSet.mSizeY;
vDataSet.mExtendMaxZ = vNumberOfTimePoints;

for vSlice = 1:vNumberOfSlices
    % sets the time slices in the Z dimension
    for vTime = 1:vNumberOfTimePoints
        vDataSet.SetDataSlice(vImarisDataSet.GetDataSlice(vSlice-1, vChannelIndex-1, vTime-1), ...
            vTime-1, 0, 0);
    end

    %vImageSlice = GaussFilter1D(vImageSlice,3,vSigma,0);
    vDataSet = vImageProcessing.GaussFilterDataSet(vDataSet, vSigma);
    
    % filtered image is returned and saved at the different time
    % coordinates
    for vTime = 1:vNumberOfTimePoints
        vImarisDataSet.SetDataSlice(vDataSet.GetDataSlice(vTime-1, 0, 0), ...
            vSlice-1, vChannelIndex-1, vTime-1);
    end

    waitbar(vSlice/vNumberOfSlices)
end
close(vProgressDisplay);

vImarisApplication.mDataSet = vImarisDataSet;