%
%
%  Merge Spot 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>
%       <Submenu name="Spots Functions">
%        <Item name="Merge Spots" icon="Matlab" tooltip="Merge all spots that are in the same folder in a single spots object.">
%          <Command>Matlab::BPSpotsMerge(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpSpots">
%          <Item name="Merge Spots" icon="Matlab" tooltip="Merge all spots that are in the same folder in a single spots object.">
%            <Command>Matlab::BPSpotsMerge(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
% 
%
%  Description:
%   
%   Merge all the spots objects that are in the same folder in a single 
%       spots object.
%   
%

function BPSpotsMerge(aImarisApplicationID)

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

% the user has to create a scene with some spots
vSurpassScene = vImarisApplication.mSurpassScene;
if isequal(vSurpassScene, [])
    msgbox('Please create some Spots in the Surpass scene!');
    return;
end

% get the spots
vSpots = vImarisApplication.mFactory.ToSpots(vImarisApplication.mSurpassSelection);

if ~vImarisApplication.mFactory.IsSpots(vSpots)  
    msgbox('Please select some Spots!');
    return;
end

vMergedSpotsXYZ = [];
vMergedSpotsT = [];
vMergedSpotsR = [];

vNumberOfSpots = 0;

vProgressDisplay = waitbar(0,'Merging spots');

vParentGroup = vSpots.GetParent;

vNumberOfChildren = vParentGroup.GetNumberOfChildren;
for vChildIndex = 1:vNumberOfChildren
    vDataItem = vParentGroup.GetChild(vChildIndex - 1);
    if vImarisApplication.mFactory.IsSpots(vDataItem)
        [vSpotsXYZ,vSpotsTime,vSpotsRadius] = vDataItem.Get;
        vMergedSpotsXYZ = [vMergedSpotsXYZ; vSpotsXYZ];
        vMergedSpotsT = [vMergedSpotsT, vSpotsTime];
        vMergedSpotsR = [vMergedSpotsR, vSpotsRadius];
        
        vDataItem.mVisible = false;
        vNumberOfSpots = vNumberOfSpots+1;
    end
    waitbar(vChildIndex/vNumberOfChildren)
end

close(vProgressDisplay);

vMergedSpots = vImarisApplication.mFactory.CreateSpots;
vMergedSpots.Set(vMergedSpotsXYZ, vMergedSpotsT, vMergedSpotsR);
vMergedSpots.mName = sprintf('Spots Merged [%i items]', vNumberOfSpots);
vMergedSpots.SetColor(0.0, 1.0, 0.0, 0.0);
vParentGroup.AddChild(vMergedSpots);