fc_sanitise(original_cell_array, brainArea)

function [sanitised_cell_array] = fc_sanitise(original_cell_array, brainArea)

%======= FUNCTION SANITISE: Sanitise a cell array
% Author: James Allen
% Date: July 2006

% A function to search through a cell array of strings, removing those
% containing certain characters, changing other characters, and
% returning the resulting cell array. Purpose is to accept a list of
% www.CoCoMac.org sourceSite fields or targetSite fields, and remove
% ambiguous entries (those containing \ or /, e.g. V1/V2), those containing
% wildcards (#), or to change 'dangerous' characters
% brainArea also supplied for log entry purposes

[noOfUnsanitisedSites, dummy] = size(original_cell_array);

if noOfUnsanitisedSites == 0
    error('Error - no source sites found in sourceSites file!')
end

sanitised_cell_array = {}; % Var for making a sanitised sourceSite list
log_sanitiseSources = {}; % For keeping a log of any changes made to original_cell_array

for sanitiseCounter = 1:noOfUnsanitisedSites
    
    % Check for / \ or # - if present, the sourcesite will be discarded.
    % Also discard if empty.
    if isempty(strfind(original_cell_array{sanitiseCounter}, '/')) == 1
        if isempty(strfind(original_cell_array{sanitiseCounter}, '\')) == 1
            if isempty(strfind(original_cell_array{sanitiseCounter}, '#')) == 1
                if isempty(original_cell_array{sanitiseCounter}) == 0       % If NOT empty

                    % If we got to here, the sourcesite must not contain a
                    % / \ or # and is not empty, so...
                    % Assign the source site to the sanitised source sites
                    % array:
                    sanitised_cell_array{end+1, 1} = original_cell_array{sanitiseCounter}; % If there were no / \ or #, then the string (with any characters changed) gets added to the new cell array
                
                end % End of condition: if not empty
            else
                log_sanitiseSources{end+1, 1} = ['Dropped brain area ' original_cell_array{sanitiseCounter} ' because it contained a #'];
            end % End of condition: if there is no '#' in the sourcesite name

        else
            log_sanitiseSources{end+1, 1} = ['Dropped brain area ' original_cell_array{sanitiseCounter} ' because it contained a \'];
        end % End of condition: if there is no '\' in the sourcesite name

    else
        log_sanitiseSources{end+1, 1} = ['Dropped brain area ' original_cell_array{sanitiseCounter} ' because it contained a /'];
    end % End of condition: if there is no '/' in the sourcesite name

end % End of sanitisation loop: going through all entries in original_cell_array, removing those with / \ or #, changing forbidden filename characters
%--------------------------------------


%==========================================================
%---- Save any changes to original_cell_array as a log file
%==========================================================

log_filename = 'sanitiseLog.txt';

try
    log_file = fopen(log_filename, 'at'); % a = append t = text
catch
    error(['Error opening sanitiseLog file :' lasterr])
end

[noOfChanges dummy] = size(log_sanitiseSources);
logMatrix = char(log_sanitiseSources); % convert to char array so it can be written to file

%--------------------------------------
%---- Save procedure if we are working on startNodes
if nargin == 1    %If only 1 argument supplied, it must be a call to go through a list of sourceSites
    fprintf(log_file, '%s \n', datestr(now));  %Add a timestamp to the log

    if noOfChanges == 0
        fprintf(log_file, '%s \n', 'No changes made to sourceSite names');
    else

        fprintf(log_file, '%s \n', 'Changes made to sourceSites: ');
        for saveCounter = 1:noOfChanges
            fprintf(log_file, '%s \n', logMatrix(saveCounter, :));
        end
    end
    %--------------------------------------
    %---- Save procedure if we are working on endNodes
elseif nargin == 2 %If 2 supplied, must have supplied an associated brain area (to put in log), so we're dealing with an endNode
    if noOfChanges > 0
        fprintf(log_file, '%s \n', ['Removed the following targetNode from sourceSite ' brainArea ':']);

        for saveCounter = 1:noOfChanges
            fprintf(log_file, '%s \n', logMatrix(saveCounter, :));
        end
    end
else
    error('Error in sanitising function, problem ascertaining nargin')
end

fclose(log_file);
%==========================================================
% End of save changes
%==========================================================

return