%
%
%  RGB to Gray 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="RGB to Gray" icon="Matlab" tooltip="Add new channel which intensity is given by a weighted sum of the intensity of the other channels.">
%          <Command>Matlab::BPRGB2Gray(%i,'%c')</Command>
%        </Item>
%      </Menu>
%    </CustomTools>
%  
%
%  Description:
%
%   Add a gray channel to the dataset. 
%   Its intensity is given by a weighted sum of the intensity of the other
%       channels.
%   The coefficients of the sum are given by the user.
%
%


function BPRGB2Gray(aImarisApplicationID,aChannelSelection)

% convert channel selection string into array
vChannelSelection = str2num(aChannelSelection);

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

%Get the dataset
vImarisDataSet = vImarisApplication.mDataSet.Clone;

% Draw the initial dialog with values such as their sum is equal to 1
vNumberOfChannelsSelected = sum(vChannelSelection);
if vNumberOfChannelsSelected >= 1    
    % Compute the initial weight values
    vDefaultWeigth = (1/vNumberOfChannelsSelected);

    vPrompt = cell(vNumberOfChannelsSelected-1, 1);
    vDefaultPromptAnswer = cell(vNumberOfChannelsSelected-1, 1);
    for i = 1:(vNumberOfChannelsSelected-1)
        vPrompt{i} = ['Channel ' int2str(i)];
        vDefaultPromptAnswer{i} = num2str(vDefaultWeigth);
    end
    
    vPrompt(vNumberOfChannelsSelected) = {['Channel ' int2str(vNumberOfChannelsSelected)]};
    vDefaultPromptAnswer(vNumberOfChannelsSelected) = {num2str(1 - (vNumberOfChannelsSelected-1)*vDefaultWeigth)};
    
    % Draw the dialog
    vAnswer = inputdlg(vPrompt,'RGB2Gray',1,vDefaultPromptAnswer);
    
    % Do something only if values exist
    if length(vAnswer) > 0
        vDefineWeight = str2num(char(vAnswer));
        % the sum of the defined weigths must be equal to 1
        if sum(vDefineWeight) >= 0.9 && sum(vDefineWeight) <= 1.1
            % Dataset properties
            vNumberOfTimePoints = vImarisDataSet.mSizeT;

            vNumberOfChannels = vImarisDataSet.mSizeC;

            vNumberOfSlices = vImarisDataSet.mSizeZ;
            
            vTotalCount = vNumberOfSlices*vNumberOfChannelsSelected*vNumberOfTimePoints;

            vProgressDisplay = waitbar(0,'BPRGB2Gray:Processing Volume...');

            vCount = 0;
            % Create a new channel
            vImarisDataSet.mSizeC = vNumberOfChannels + 1;            
            vImarisDataSet.SetChannelName(vNumberOfChannels, 'Gray Channel');
                        
            % Loop through the dataset...
            for vTime = 1:vNumberOfTimePoints
                for vSlice = 1:vNumberOfSlices
                    vImageSliceSum = zeros(vImarisDataSet.mSizeX,vImarisDataSet.mSizeY);
                    for vChannel = 1:vNumberOfChannels
                        if vChannelSelection(vChannel) == 1
                            % Add each channel of one slice and one
                            % timepoint with the defined weights. The
                            % resulting image is the gray image.
                            vImageSlice = double(vImarisDataSet.GetDataSlice(vSlice-1, vChannel-1, vTime-1))*vDefineWeight(vChannel);                                       
                            vImageSliceSum = vImageSliceSum + vImageSlice;
                            vCount = vCount + 1; 
                        end                        
                    end
                    
                    % The image is given back to Imaris
                    if strcmp(vImarisDataSet.mType,'eTypeUInt8')

                        vImarisDataSet.SetDataSlice(uint8(vImageSliceSum), vSlice-1, vNumberOfChannels,vTime-1);

                    elseif strcmp(vImarisDataSet.mType,'eTypeUInt16')
                                    
                        vImarisDataSet.SetDataSlice(uint16(vImageSliceSum), vSlice-1, vNumberOfChannels,vTime-1);

                    elseif strcmp(vImarisDataSet.mType,'eTypeFloat')

                        vImarisDataSet.SetDataSlice(single(vImageSliceSum), vSlice-1, vNumberOfChannels,vTime-1);
                        
                    end
                    
                    waitbar(vCount/vTotalCount)
                end
            end             
            close(vProgressDisplay)
            vImarisApplication.mDataSet = vImarisDataSet;
        end
    end
end