%
%
%  Filament Split Branch Levels 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 On Branch Levels" icon="Matlab" tooltip="Split filament on branch levels.">
%          <Command>Matlab::BPFilamentSplitBranchLevels(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpFilament">
%          <Item name="Split Branch Levels" icon="Matlab" tooltip="Split filament on branch levels.">
%            <Command>Matlab::BPFilamentSplitBranchLevels(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
% 
%
%  Description:
%
%   Split one filament object in different filaments. 
%   The branches directly connected to the root are first-level branches; 
%       The branches directly connected to the first-level branches are 
%       second-level branches; and so on. 
%   For each level, a new filament object, which collects the branches of
%       the level, is created. 
%   The number of filaments created is equal to the maximal level of the
%       branches of the original filament.
%
%

function BPFilamentSplitBranchLevels(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 filament coordinates
[vFilamentXYZ,vFilamentRadius,vFilamentEdges] = vFilament.Get;

% new spots indices
vSpotsIndex = 1;
% level of each spot
vSpotsLevel = 1;
% index of the spots in the new subgroup
vNewLabel = 1;
% number of spots in each group
vLabelHeight = 1;
% total number of spots
vNumberOfSpots = 1;

vProgressDisplay = waitbar(0,'Splitting the filament');

vNumberOfEdges = size(vFilamentEdges,1);
for vEdgeIndex = 1:vNumberOfEdges
    vEdge = vFilamentEdges(vEdgeIndex,:)+1;

    vRootFirst = find(vSpotsIndex==vEdge(1));
    vRootSecond = find(vSpotsIndex==vEdge(2));
    
    vFound = false;
    if isempty(vRootFirst) && length(vRootSecond)==1
        vSpot = vEdge(1);
        vLevel = vSpotsLevel(vRootSecond);
        vFound = true;
    elseif length(vRootFirst)==1 && isempty(vRootSecond)
        vSpot = vEdge(2);
        vLevel = vSpotsLevel(vRootFirst);
        vFound = true;
    end
    
    if vFound
        vNumberOfSpots = vNumberOfSpots+1;
        vSpotsIndex(vNumberOfSpots) = vSpot;
        [vEdge, vSide] = find(vFilamentEdges==vSpot-1);
        if length(vEdge)>2 % is branch?
            vLevel = vLevel+1;
        end
        vSpotsLevel(vNumberOfSpots) = vLevel;
        if vLevel>numel(vLabelHeight)
            vLabelHeight(vLevel) = 1;
        else
            vLabelHeight(vLevel) = vLabelHeight(vLevel)+1;
        end
        vNewLabel(vNumberOfSpots) = vLabelHeight(vLevel);
    end
    
    waitbar(vEdgeIndex/vNumberOfEdges)
end

vEdgesLevel = 1:vNumberOfEdges;
vNewEdges = vFilamentEdges;
for vEdgeIndex = 1:vNumberOfEdges
    vEdge = vFilamentEdges(vEdgeIndex,:)+1;
    if vSpotsLevel(vEdge(1))==vSpotsLevel(vEdge(2))
        vEdgesLevel(vEdgeIndex) = vSpotsLevel(vEdge(1));
        %vNewEdges = [vNewEdges; vNewLabel(vEdge)-1];
        vNewEdges(vEdgeIndex,:) = vNewLabel(vEdge)-1;
    else
        vEdgesLevel(vEdgeIndex) = -1;
    end
end

close(vProgressDisplay);

vParent = vImarisApplication.mFactory.CreateDataContainer;
vParent.mName = sprintf('%s Branch Levels', vFilament.mName);
vFilament.GetParent.AddChild(vParent);

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

vNumberOfBranches = max(vSpotsLevel);
for vBranchLevel = 1:vNumberOfBranches
    vNewFilament = vImarisApplication.mFactory.CreateFilament;
    vNewFilament.mIndexT = vImarisApplication.mVisibleIndexT;
    
    vThisSpots = vSpotsIndex(vSpotsLevel==vBranchLevel);
    
    vNewFilament.Set(vFilamentXYZ(vThisSpots,:),vFilamentRadius(vThisSpots), ...
        vNewEdges(vEdgesLevel==vBranchLevel,:));
    
    vNewFilament.mName = sprintf('%s [level %i]', vFilament.mName, vBranchLevel);

    % computes the color
    vPercent = (vBranchLevel-1)/max(vNumberOfBranches-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);
    
end