%
%
%  Filament Split Into Branches 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="Filament Functions">
%        <Item name="Split Filament Into Branches" icon="Matlab" tooltip="Split filament into branches.">
%          <Command>Matlab::BPFilamentSplitIntoBranches(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpFilament">
%          <Item name="Split Into Branches" icon="Matlab" tooltip="Split filament into branches.">
%            <Command>Matlab::BPFilamentSplitIntoBranches(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
% 
%
%  Description:
%
%   Split one filament object in different filaments. 
%   The new filaments go from the root to a terminal of the original
%       filament and they do not have branches. 
%   The number of filaments created is equal to the number of terminals
%       of the original filament.
%

function BPFilamentSplitIntoBranches(aImarisApplicationID)

% 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 filament
vFilament = vImarisApplication.mFactory.ToFilament(vImarisApplication.mSurpassSelection);

% search the filament if not previously selected
vSurpassScene = vImarisApplication.mSurpassScene;
if ~vImarisApplication.mFactory.IsFilament(vFilament)        
    for vChildIndex = 1:vSurpassScene.GetNumberOfChildren
        vDataItem = vSurpassScene.GetChild(vChildIndex - 1);
        if vImarisApplication.mFactory.IsFilament(vDataItem)
            vFilament = vDataItem;
            break;
        end
    end
    % did we find the filament?
    if isequal(vFilament, [])
        msgbox('Please create some filament!');
        return;
    end
end

% get the spots coordinates
[vFilamentXYZ, vFilamentRadius, vFilamentEdges] = vFilament.Get;

vNumberOfSpots = length(vFilamentRadius);

% find the terminals
vNumberOfTerminals = 0;
vTerminals = [];

vProgressDisplay = waitbar(0, 'Splitting filament into branches');

for vSpots = 1:vNumberOfSpots
    vEdge = find(vFilamentEdges==vSpots-1);
    if length(vEdge)==1
        vNumberOfTerminals = vNumberOfTerminals + 1;
        vTerminals(vNumberOfTerminals) = vSpots;
    end
end

waitbar(0.3);

vParent = vImarisApplication.mFactory.CreateDataContainer;
vParent.mName = sprintf('%s Branches', vFilament.mName);
vFilament.GetParent.AddChild(vParent);
vFilament.mVisible = 0;

% get the jet colormap
vColorMap = jet;
vColorMapSize = size(vColorMap,1);
% close the figure opened by jet
close;

for vTerminalIndex = 1:vNumberOfTerminals
    vLength = 1;
    vTerminal = vTerminals(vTerminalIndex);
    vPath = vTerminal;
    
    vFound = true;
    while vFound
        [vEdge, vSide] = find(vFilamentEdges==vTerminal-1);
        
        vFound = false;
        for vNeighborIndex = 1:length(vEdge)
            vNeighbor = vFilamentEdges(vEdge(vNeighborIndex), 3-vSide(vNeighborIndex))+1;
            if vNeighbor<vTerminal
                vNewTerminal = vNeighbor;
                vFound = true;
           end
        end

        if vFound
            vLength = vLength + 1;
            vTerminal = vNewTerminal;
            vPath(vLength) = vTerminal;
        end
    end
    
    % terminal-root -> root-terminal
    vPath = fliplr(vPath);
    
    vNewFilament = vImarisApplication.mFactory.CreateFilament;
    vNewFilament.mIndexT = vImarisApplication.mVisibleIndexT;
    
    vNewFilament.Set(vFilamentXYZ(vPath,:),vFilamentRadius(vPath), ...
        [0:vLength-2;1:vLength-1]');
    
    vNewFilament.mName = sprintf('%s [branch %i]', vFilament.mName, vTerminalIndex);
    
    % computes the color
    vPercent = (vTerminalIndex-1)/max(vNumberOfTerminals-1,1)*(vColorMapSize-1)+1;
    vFloor = floor(vPercent);
    vColor = vColorMap(vFloor,:);
    if vFloor<vPercent
        vPercent = vPercent - vFloor;
        vColor = vPercent*vColor+(1-vPercent)*vColorMap(vFloor+1,:);
    end
    
    vNewFilament.SetColor(vColor(1),vColor(2),vColor(3), 0.0);
    vParent.AddChild(vNewFilament);
    
    waitbar(0.3+0.7*vTerminalIndex/vNumberOfTerminals);
end

close(vProgressDisplay);