%
%
%  Find Spots Close to Filament 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="Find Spots Close to Filament" icon="Matlab" tooltip="Find spots close to filament.">
%          <Command>Matlab::BPSpotsCloseToFilament(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpSpots">
%          <Item name="Find Spots Close to Filament" icon="Matlab" tooltip="Find spots close to filament.">
%            <Command>Matlab::BPSpotsCloseToFilament(%i)</Command>
%          </Item>
%        </SurpassComponent>
%        <SurpassComponent name="bpFilament">
%          <Item name="Find Spots Close to Filament" icon="Matlab" tooltip="Find spots close to filament.">
%            <Command>Matlab::BPSpotsCloseToFilament(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
%
%  
%  Description:
%
%   The user has to create a Spots and a Filament component. 
%   This XTension segments the spots into two groups: Spots which are 
%       close to the filamentous structure will be colored red, the others 
%       blue. 
%   This might help to count spines.
%
%   Usage Example:
%       - Load "C2CZOSmall.ims".
%       - Create Spots (ch1, 0.5um, on, 0.5um, thresh.10)
%       - Create Filament (default values, ratio branch / trunk = 3)
%       - Select tools tab from spots component
%       - Start "Find Spots close to a Filament"
%       - Ratio = 0.7
%
%

function BPSpotsCloseToFilament(aImarisApplicationID)

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

%
% GUI - user interactions
%

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

% THE filament and THE spot object
vFilament = vImarisApplication.mFactory.ToFilament(vImarisApplication.mSurpassSelection);
vSpots = vImarisApplication.mFactory.ToSpots(vImarisApplication.mSurpassSelection);

% find a filament and some spots from the surpass scene
vSurpassScene = vImarisApplication.mSurpassScene;
for vChildIndex = 1:vSurpassScene.GetNumberOfChildren
    vDataItem = vSurpassScene.GetChild(vChildIndex - 1);
    if isequal(vSpots, [])
        if vImarisApplication.mFactory.IsSpots(vDataItem)
            vSpots = vDataItem;
        end
    end
    if isequal(vFilament, [])
        if vImarisApplication.mFactory.IsFilament(vDataItem)
            vFilament = vDataItem;
        end
    end
end

% did we find the filament?
if isequal(vFilament, [])
    msgbox('Please create a Filament!');
    return;
end

% did we find the spots?
if isequal(vSpots, [])
    msgbox('Please create some Spots!');
    return;
end

% ask user for a distance
vAnswer = inputdlg({sprintf('"%s" - "%s"\nRatio of distance (Spot - FilamentCenter) to Filament diameter', vFilament.mName, vSpots.mName)}, 'Find Spots close to Filament', 1, {'0.9'});
if isempty(vAnswer)
    return;
end
vDistanceLimit = str2double(vAnswer);

%
% ALGORITHM - get spot coordinates and filament vertex coordinates from
% imaris and compute the distance between each pair. if the shortest
% distance of a spot to a filament vertex is shorter than our limit, the
% spot is close.
%

% get the spot coordinates
vSpotsPosXYZ = vSpots.GetPositionsXYZ;
vSpotsRadius = vSpots.GetRadii';
vSpotsPosT = vSpots.GetIndicesT';

% get the filament vertices
vFilamantPosXYZ = vFilament.GetPositionsXYZ;
vFilamantRadius = vFilament.GetRadii';

% empty matrices for resulting spots (A is close, B is far)
vSpotsAPosXYZ = [];
vSpotsAPosT = [];
vSpotsARadius = [];
vSpotsBPosXYZ = [];
vSpotsBPosT = [];
vSpotsBRadius = [];

% find close and far spots
vProgressDisplay = waitbar(0, 'Finding close Spots ...');
for vSpotsIndex = 1:size(vSpotsPosXYZ,1)
    vDistanceMin = inf;
    vFilamantRadiusMin = inf;
    for vFilamantIndex = 1:length(vFilamantPosXYZ)
        vDistance = sqrt(sum((vSpotsPosXYZ(vSpotsIndex,:) - vFilamantPosXYZ(vFilamantIndex,:)).^2));
        if vDistance < vDistanceMin
            vDistanceMin = vDistance;
            vFilamantRadiusMin = vFilamantRadius(vFilamantIndex);
        end
    end
    if (vDistanceMin / vFilamantRadiusMin) < vDistanceLimit
        % close spot
        vSpotsAPosXYZ(size(vSpotsAPosXYZ,1)+1,:) = vSpotsPosXYZ(vSpotsIndex,:);
        vSpotsAPosT(size(vSpotsAPosT,1)+1,:)     = vSpotsPosT(vSpotsIndex,:);
        vSpotsARadius(size(vSpotsARadius,1)+1,:) = vSpotsRadius(vSpotsIndex,:);
    else
        % far spot
        vSpotsBPosXYZ(size(vSpotsBPosXYZ,1)+1,:) = vSpotsPosXYZ(vSpotsIndex,:);
        vSpotsBPosT(size(vSpotsBPosT,1)+1,:)     = vSpotsPosT(vSpotsIndex,:);
        vSpotsBRadius(size(vSpotsBRadius,1)+1,:) = vSpotsRadius(vSpotsIndex,:);
    end
    waitbar(vSpotsIndex / size(vSpotsPosXYZ,1));
end
close(vProgressDisplay);

% hide original spots
vSpots.mVisible = false;

% add new spots (close)
vSpotsA = vImarisApplication.mFactory.CreateSpots;
vSpotsA.Set(vSpotsAPosXYZ, vSpotsAPosT, vSpotsARadius);
vSpotsA.mName = sprintf('%s closer than %0.3f', vSpots.mName, vDistanceLimit);
vSpotsA.SetColor(1.0, 0.0, 0.0, 0.0);
vImarisApplication.mSurpassScene.AddChild(vSpotsA);

% add new spots (far)
vSpotsB = vImarisApplication.mFactory.CreateSpots;
vSpotsB.Set(vSpotsBPosXYZ, vSpotsBPosT, vSpotsBRadius);
vSpotsB.mName = sprintf('%s farer than %0.3f', vSpots.mName, vDistanceLimit);
vSpotsB.SetColor(0.0, 0.0, 1.0, 0.0);
vImarisApplication.mSurpassScene.AddChild(vSpotsB);