fDefStructure.m

function Object=fDefStructure(Object,Mode)
nObj=length(Object);
n=nObj;
if nObj==0
    nObj=1;
end
if isfield(Object,'Name')==0
    for i=1:nObj    
        Object(i).Name='';
    end
end
if isfield(Object,'File')==0
    for i=1:nObj    
        Object(i).File='';
    end
end
if isfield(Object,'Directory')==0
    for i=1:nObj    
        Object(i).Directory='';
    end
end

if isfield(Object,'Results')==0
    for i=1:nObj    
        Object(i).Results = single([]);
    end
else
    for i=1:nObj
        Object(i).Results = single(Object(i).Results);
    end
end

if strcmp(Mode,'Molecule')
    if isfield(Object,'Type')==0
        if isfield(Object,'data')==0
            Object(i).Type = '';  
        else
            for i=1:nObj    
                if length(Object(i).data{1}.w)==3 && length(Object(i).data{1}.h)==1
                    Object(i).Type = 'stretched';
                    for n = 1:length(Object(i).data)
                        Object(i).Results(n,9:11) = single(Object(i).data{n}.w);
                    end
                elseif length(Object(i).data{1}.w)==2
                    Object(i).Type = 'ring1';
                    for n = 1:length(Object(i).data)
                        Object(i).Results(n,9) = single(Object(i).data{n}.r(2));
                        Object(i).Results(n,10) = single(Object(i).data{n}.w(2));
                        Object(i).Results(n,11) = single(Object(i).data{n}.h(2));
                    end
                elseif length(Object(i).data{1}.w)==3
                    Object(i).Type = 'ring2';
                    for n = 1:length(Object(i).data)
                        Object(i).Results(n,9) = single(Object(i).data{n}.r(2));
                        Object(i).Results(n,10) = single(Object(i).data{n}.w(2));
                        Object(i).Results(n,11) = single(Object(i).data{n}.h(2));
                        Object(i).Results(n,12) = single(Object(i).data{n}.r(3));
                        Object(i).Results(n,13) = single(Object(i).data{n}.w(3));
                        Object(i).Results(n,14) = single(Object(i).data{n}.h(3));
                    end
                else
                    Object(i).Type = 'symmetric';                
                end
            end
        end
    end
end    

if isfield(Object,'Selected')==0
    for i=1:nObj
        Object(i).Selected=0;
    end
end
if isfield(Object,'Visible')==0
    for i=1:nObj
        Object(i).Visible=1;
    end
end
if isfield(Object,'Drift')==0
    for i=1:nObj    
        Object(i).Drift=0;
    end
end
if isfield(Object,'PixelSize')==0
    for i=1:nObj    
        Object(i).PixelSize=1;
    end
end
if isfield(Object,'Color')==0
    for i=1:nObj 
        Object(i).Color=[0 0 1];
    end
else
    for i=1:nObj    
        if ischar(Object(i).Color)
            Object(i).Color=ColorCode(Object(i).Color);
        end
    end
end

if strcmp(Mode,'Filament')
    if isfield(Object,'ResultsCenter') == 1
        for i=1:nObj     
            Object(i).Results = single(Object(i).ResultsCenter);
        end
    end
    if isfield(Object,'Orientation') == 1
        for i=1:nObj     
            if size(Object(i).Results,1) == length(Object(i).Orientation)
                Object(i).Results(:,8) = single(Object(i).Orientation');
            else
                Object(i).Results(:,8) = single(Object(i).Orientation(1:size(Object(i).Results,1))');
            end
        end
    end
    if isfield(Object,'PosStart') == 0
        if isfield(Object,'ResultsCenter') == 0
            for i=1:nObj                
                Object(i).PosStart = single([]);
                Object(i).PosCenter = single([]);
                Object(i).PosEnd = single([]);
            end
        else
            for i=1:nObj    
                Object(i).PosStart = single(Object(i).ResultsStart(:,3:4));
                Object(i).PosCenter = single(Object(i).ResultsCenter(:,3:4));
                Object(i).PosEnd = single(Object(i).ResultsEnd(:,3:4));
            end
        end
    end
    
    if isfield(Object,'Data')==0
        if isfield(Object,'data')==1
            for i=1:nObj    
                for n = 1:length(Object(i).data)
                    Data = Object(i).data{n};
                    Object(i).Data{n} = single([[Data.x]' [Data.y]' [Data.l]' [Data.w]' [Data.h]' [Data.b]']);
                end
            end
        else
            for i=1:nObj    
                Object(i).Data={};
            end
        end
    end
    
end

if isfield(Object,'PathData')==0
    if isfield(Object,'NewResults')==0
        for i=1:nObj    
            Object(i).PathData = single([]);
        end
    else
        if isempty(Object(i).NewResults)
            for i=1:nObj    
                Object(i).PathData = single([]);
            end    
        else
            for i=1:nObj    
                Object(i).PathData = single(zeros(size(Object(i).NewResults,1),4));
                Object(i).PathData(:,3:4) = single(Object(i).NewResults(:,5:6));
            end
        end
    end
end

for i=1:nObj    
    Object(i).PlotHandles = [];
end      

if isfield(Object,'p')==1
    Object=rmfield(Object,'p');
end
if isfield(Object,'Config')==1
    Object=rmfield(Object,'Config');
end
if isfield(Object,'DriftControl')==1
    Object=rmfield(Object,'DriftControl');
end
if isfield(Object,'plot1')==1
    Object=rmfield(Object,'plot1');
end
if isfield(Object,'plot2')==1
    Object=rmfield(Object,'plot2');
end
if isfield(Object,'Check')==1
    Object=rmfield(Object,'Check');
end
if isfield(Object,'data')==1
    Object=rmfield(Object,'data');
end
if isfield(Object,'ResultsCenter')==1
    Object=rmfield(Object,'ResultsCenter');
end
if isfield(Object,'ResultsStart')==1
    Object=rmfield(Object,'ResultsStart');
end
if isfield(Object,'ResultsEnd')==1
    Object=rmfield(Object,'ResultsEnd');
end
if isfield(Object,'pTrack')==1
    Object=rmfield(Object,'pTrack');
end
if isfield(Object,'pTrackSelectW')==1
    Object=rmfield(Object,'pTrackSelectW');
end
if isfield(Object,'pTrackSelectB')==1
    Object=rmfield(Object,'pTrackSelectB');
end
if isfield(Object,'NewResults')==1
    Object=rmfield(Object,'NewResults');
end
if isfield(Object,'Path')==1
    Object=rmfield(Object,'Path');
end
if isfield(Object,'Orientation')==1
    Object=rmfield(Object,'Orientation');
end
if n==0
    Object(1)=[];
end

function color=ColorCode(char)
switch(char)
    case 'b'
        color=[0 0 1];
    case 'r'
        color=[1 0 0];
    case 'g'
        color=[1 0 0];
    case 'p'
        color=[1 0.5 0.5];        
    case 'o'
        color=[1 0.5 0];                
    case 'y' 
        color=[1 1 0];
end