%
%
%  Spots Split Into Surface Objects 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="Spots Split Into Surface Objects" icon="Matlab" tooltip="Spots split into surface objects.">
%          <Command>Matlab::BPSpotsSplitIntoSurfaceObjects(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpSpots">
%          <Item name="Split Into Surface Objects" icon="Matlab" tooltip="Spots split into surface objects.">
%            <Command>Matlab::BPSpotsSplitIntoSurfaceObjects(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
% 
%
%  Description:
%   
%   For each surface object in the same folder of the spots, create a new 
%       spots object containing the spots that lies inside the surface.
%   Works on surface objects: To obtain them, Split Isosurface or 
%       Create Surface Object from Contour Surface.
%
%

function BPSpotsSplitIntoSurfaceObjects(aImarisApplicationID)

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


% 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

% get the spots coordinates
[vSpotsXYZ,vSpotsTime,vSpotsRadius] = vSpots.Get;
vNumberOfSpots = length(vSpotsRadius);
vSpotsName = vSpots.mName;

vSpots.mVisible = false;

% get the parent group
vParentGroup = vSpots.GetParent;

% mask volume
vMin = min(vSpotsXYZ);
vMax = max(vSpotsXYZ);

% add 4% border to be sure to include all spots (avoid edge effects)
vDelta = vMax-vMin;
vMin = vMin-vDelta*0.02;
vMax = vMax+vDelta*0.02;

vMaskSize = 350; 

vMaxMaskSize = vMaskSize/max(vMax-vMin);

% spots coordinates on the mask
vSpotsOnMaskXYZ(:,1) = ceil((vSpotsXYZ(:,1)-vMin(1))*vMaxMaskSize);
vSpotsOnMaskXYZ(:,2) = ceil((vSpotsXYZ(:,2)-vMin(2))*vMaxMaskSize);
vSpotsOnMaskXYZ(:,3) = ceil((vSpotsXYZ(:,3)-vMin(3))*vMaxMaskSize);

% the zeros belongs to the first interval
vSpotsOnMaskXYZ = max(vSpotsOnMaskXYZ,1); 

vMaskSize = max(vSpotsOnMaskXYZ);

vProgressDisplay = waitbar(0,'Splitting spots into isosurfaces');

% loop over the children of the parent looking for the isosurfaces
vNumberOfChildren = vParentGroup.GetNumberOfChildren;
for vChildIndex = 1:vNumberOfChildren
    vDataItem = vParentGroup.GetChild(vChildIndex - 1);

    if vImarisApplication.mFactory.IsSurface(vDataItem)
        vSurface = vDataItem;

        vMask = vSurface.GetMask(vMin(1), vMin(2), vMin(3), vMax(1), vMax(2), vMax(3),...
            vMaskSize(1), vMaskSize(2), vMaskSize(3));

        % search the element of the spot that lies inside the surface
        vIndexSpotsInside = [];
        vNumberOfSpotsInside = 0;
        for vSpotsIndex = 1:vNumberOfSpots

            vSlice = vMask.GetDataSlice(vSpotsOnMaskXYZ(vSpotsIndex,3)-1, 0, 0);

            if vSlice(vSpotsOnMaskXYZ(vSpotsIndex,1),...
                    vSpotsOnMaskXYZ(vSpotsIndex,2))==1
                vNumberOfSpotsInside = vNumberOfSpotsInside+1;
                vIndexSpotsInside(vNumberOfSpotsInside) = vSpotsIndex;
            end 
        end
        
        vSpotsInside = vImarisApplication.mFactory.CreateSpots;
        if vNumberOfSpotsInside>0
            vSpotsInside.Set(vSpotsXYZ(vIndexSpotsInside,:),vSpotsTime(vIndexSpotsInside),...
                vSpotsRadius(vIndexSpotsInside));
        end
        vSpotsInside.mName = sprintf('%s inside %s', vSpotsName, vSurface.mName);
        vSpotsInside.SetColor(0.0, 1.0, 0.0, 0.0);
        vParentGroup.AddChild(vSpotsInside);
    end
    waitbar(vChildIndex/vNumberOfChildren);
end

close(vProgressDisplay);