%
%
%  3D to 2D Projection 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="Project to 2D" icon="Matlab" tooltip="Resize the dataset to 2 dimensions.">
%          <Command>Matlab::BP3Dto2DProjection(%i)</Command>
%        </Item>
%      </Menu>
%    </CustomTools>
%
%
%  Description:
%
%   Resize the dataset to 2 dimensions.
%   2 dialog boxes ask the projection plane XY, XZ or YZ) and the 
%       projection mode (MIP or Mean) if their values are not specified 
%       as input parameters.
%
%

function BP3Dto2DProjection(aImarisApplicationID, aProjectionPlane, aProjectionMode)

% vImarisApplication = actxserver('Imaris.Application'); vImarisApplication.mVisible = true;

if isa(aImarisApplicationID, 'COM.Imaris_Application')
    vImarisApplication = aImarisApplicationID;
else
    % connect to Imaris Com interface
    vImarisServer = actxserver('ImarisServer.Server');
    vImarisApplication = vImarisServer.GetObject(aImarisApplicationID);
end
vImarisApplication.DataSetPushUndo('Projection to 2D');

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

vNumberOfTimePoints = vDataSet.mSizeT;
vNumberOfChannels = vDataSet.mSizeC;

% projection plane
vPlaneNames = ['XY'; 'XZ'; 'YZ'];

if nargin<2
    [vAnswer, vOk] = listdlg('ListString',{vPlaneNames},...
                           'SelectionMode','single',...
                           'ListSize',[200 50],...
                           'Name','3D to 2D Projection',...
                           'PromptString',{'Please select  the projection plane:'});
    if vOk<1
        return;
    end

    vProjectionPlane = vAnswer;
else
    vProjectionPlane = aProjectionPlane;
end
vProjectionAxis = 4-vProjectionPlane;

% MIP or Mean projection
if nargin<3
    vAnswer = questdlg('Please select the projection mode:', '3D to 2D Projection', ...
        'MIP', 'Mean','Cancel', 'MIP');
    if strcmp(vAnswer, 'Cancel')
        return;
    else
        vProjectionMode = vAnswer;
    end
else
    vProjectionMode = aProjectionMode;
end

vTotalCount = vNumberOfChannels*vNumberOfTimePoints;
vProgressDisplay = waitbar(0,['Projecting to ',vPlaneNames(vProjectionPlane,:),'-plane']);
vProgressCount = 0;

vImage = zeros(vDataSet.mSizeX,vDataSet.mSizeY,vDataSet.mSizeZ);
if strcmp(vDataSet.mType,'eTypeUInt8')
    vImage = uint8(vImage);
elseif strcmp(vDataSet.mType, 'eTypeUInt16')
    vImage = uint16(vImage);
elseif strcmp(vDataSet.mType, 'eTypeFloat')
    vImage = single(vImage);
end

for vChannelIndex = 1:vNumberOfChannels
    for vTimeIndex = 1:vNumberOfTimePoints
        for vSlice = 1:vDataSet.mSizeZ
            vImage(:,:,vSlice) = vDataSet.GetDataSlice( ...
                vSlice-1,vChannelIndex-1,vTimeIndex-1);
        end
        
        if strcmp(vProjectionMode, 'MIP')
            % MIP
            vImageSlice = max(vImage, [], vProjectionAxis); 
        else
            % Mean 
            vImageSlice = mean(vImage, vProjectionAxis);     
        end

        % original size must be preserved because resizing the first layer
        % would resize every layer (losing data)
        switch vProjectionPlane
            case 1,
                vImage(:,:,1) = vImageSlice;
            case 2,
                vImage(:,1,:) = vImageSlice;
            case 3,
                vImage(1,:,:) = vImageSlice;
        end

        vProgressCount = vProgressCount + 1;
        waitbar(vProgressCount/vTotalCount)

        vDataSet.SetDataVolume(vImage,vChannelIndex-1,vTimeIndex-1);
    end
end

% resize layers
switch vProjectionPlane
    case 1,
        vDataSet.mSizeZ = 1;
    case 2,
        vDataSet.mSizeY = 1;
    case 3,
        vDataSet.mSizeX = 1;
end 

vImarisApplication.mDataSet = vDataSet;

close(vProgressDisplay);