makeNet(data)

function [net netLabels] = makeNet(data)

%========================================
% Construct the empty network matrix 'net'
% and associated cell array 'netLabels'
% Rows of 'net' = STARTnodes
% Columns of 'net' = ENDnodes
% i.e. net(startNodes, endNodes)
%========================================

%----------------------------------------
% Get a list of all the startNodes and endNodes in the data set, and put
% into cell array 'netLabels', to act as a reference for matrix 'net'
% showing which rows / columns of 'net' correspond to which nodes

nodes_withDups = {data.startNode data.endNode}; %Cell array of ALL startNodes and endNodes in 'data'
nodes = unique(nodes_withDups); %As above but duplicates removed

if isempty(nodes)
    errordlg('makeNet could not find any data in variable ''data''')
    net = [];
    netLabels = {};
    return;
end

% Get how many 
noOfNodes = length(nodes);

% Initialise 'net' matrix with 0s, size = noOfNodes
net = zeros(noOfNodes);

% Initialise 'netLabels' cell array for storing node labels, size =
% noOfNodes
netLabels = cell(1,noOfNodes); 

%Enter the row / column headings in netLabels (the nodes)
for cellCounter = 1:noOfNodes
    netLabels{1,cellCounter} = nodes{cellCounter};     
end
%----------------------------------------
 

%========================================
% Fill in the net with data values
%========================================

%[sizeData dummy] = size(data);
sizeData = length(data);

for dataCounter = 1:sizeData    
   %----------------------------------------
   %---- Find index
   % Find the index for the current startNode in the netLabels cell array
   % (the 'coordinate'). 
   
   startCoord = strmatch(data(dataCounter).startNode, netLabels, 'exact');
   if isempty(startCoord)
       error(['Error - cant find the startnode ' data(dataCounter).startNode ' in netLabels!'])
   end
   
   % Find the position of the current endNode in the netLabels cell array
   endCoord = strmatch(data(dataCounter).endNode, netLabels, 'exact');
   if isempty(endCoord)
       error(['Error - cant find the endnode ' data(dataCounter).endNode ' in netLabels!'])  
   end 
   %----------------------------------------
   
   %----------------------------------------
   %---- Enter values
   % If the current value in net is 0, and the new value
   % (data.fibreDensity) is in range 1-3, enter the value
   if (net(startCoord, endCoord) == 0) & (1 <= str2num(data(dataCounter).fibreDensity) <= 3)
        net(startCoord, endCoord) = str2num(data(dataCounter).fibreDensity);  
        
   % If the new value already exists in table, warn that found duplicate
   % data
   elseif net(startCoord, endCoord) == str2num(data(dataCounter).fibreDensity)
       
       % Uncomment for more information:
       % disp(['Found duplicate data for connection ' data(dataCounter).startNode '  -->  ' data(dataCounter).endNode ' (fibre density ' data(dataCounter).fibreDensity ')'])
   
   % If the new value does not agree with already stored value, but is in range 1 - 3,
   % warn that found conflicting data. Store an averaged value.
   elseif (net(startCoord, endCoord) ~= str2num(data(dataCounter).fibreDensity) & (1 <= str2num(data(dataCounter).fibreDensity) <= 3)) 

       average_density = mean( [net(startCoord, endCoord) str2num(data(dataCounter).fibreDensity)] );
       fc_saveLog(['!! Found conflicting data values for ' data(dataCounter).startNode '  -->  ' data(dataCounter).endNode ' - already stored density of ' num2str(net(startCoord, endCoord)) ' but found a conflicting value of ' data(dataCounter).fibreDensity '! Have stored average value: ' num2str(average_density)]);
       net(startCoord, endCoord) = average_density;
       
   % Otherwise, something has gone wrong - it may be a density value outside
   % range 1-3?
   else    
       warning(['Something went wrong with a data value for ' data(dataCounter).startNode '  -->  ' data(dataCounter).endNode ' , perhaps an unexpected fibre density - value was ' data(dataCounter).fibreDensity])
   end
   %----------------------------------------
end
%========================================

%========================================
% Set main diagonal to all 0s - connections
% between a node and itself should be 0
%========================================
sizeNet = length(net);

for deleteCounter = 1:sizeNet
    if net(deleteCounter, deleteCounter) ~= 0
        net(deleteCounter, deleteCounter) = 0;
        %disp(['Deleted connection between node ' netLabels{deleteCounter} ' and itself'])
    end
end
%========================================

%========================================
% Perform CLUSTERING on the net
%========================================
[net, netLabels] = clustering(net, netLabels);

%========================================

return