function [vertices, label, colortable] = Read_Brain_Annotation(filename)
% [vertices, label, colortable] = Read_Brain_Annotation(annotfilename.annot)
%
% vertices expected to be simply from 0 to number of vertices - 1;
% label is the vector of annotation
%
% colortable is empty struct if not embedded in .annot. Else, it will be
% a struct.
% colortable.numEntries = number of Entries
% colortable.orig_tab = name of original colortable
% colortable.struct_names = list of structure names (e.g. central sulcus and so on)
% colortable.table = n x 5 matrix. 1st column is r, 2nd column is g, 3rd column
% is b, 4th column is flag, 5th column is resultant integer values
% calculated from r + g*2^8 + b*2^16 + flag*2^24. flag expected to be all 0.


%
% read_annotation.m
%
% Original Author: Bruce Fischl
% CVS Revision Info:
%    $Author: nicks $
%    $Date: 2007/01/10 22:55:09 $
%    $Revision: 1.4 $
%
% Copyright (C) 2002-2007,
% The General Hospital Corporation (Boston, MA). 
% All rights reserved.
%
% Distribution, usage and copying of this software is covered under the
% terms found in the License Agreement file named 'COPYING' found in the
% FreeSurfer source code root directory, and duplicated here:
% https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
%
% General inquiries: freesurfer@nmr.mgh.harvard.edu
% Bug reports: analysis-bugs@nmr.mgh.harvard.edu
%

fp = fopen(filename, 'r', 'b');

if(fp < 0)
   disp('Annotation file cannot be opened');
   return;
end

A = fread(fp, 1, 'int');

tmp = fread(fp, 2*A, 'int');
vertices = tmp(1:2:end);
label = tmp(2:2:end);

bool = fread(fp, 1, 'int');
if(isempty(bool)) %means no colortable
   disp('No Colortable found.');
   colortable = struct([]);
   fclose(fp);
   return; 
end

if(bool)
    
    %Read colortable
    numEntries = fread(fp, 1, 'int');

    if(numEntries > 0)
        
        disp(['Reading from Original Version']);
        colortable.numEntries = numEntries;
        len = fread(fp, 1, 'int');
        colortable.orig_tab = fread(fp, len, '*char')';
        colortable.orig_tab = colortable.orig_tab(1:end-1);

        colortable.struct_names = cell(numEntries,1);
        colortable.table = zeros(numEntries,5);
        for i = 1:numEntries
            len = fread(fp, 1, 'int');
            colortable.struct_names{i} = fread(fp, len, '*char')';
            colortable.struct_names{i} = colortable.struct_names{i}(1:end-1);
            colortable.table(i,1) = fread(fp, 1, 'int');
            colortable.table(i,2) = fread(fp, 1, 'int');
            colortable.table(i,3) = fread(fp, 1, 'int');
            colortable.table(i,4) = fread(fp, 1, 'int');
            colortable.table(i,5) = colortable.table(i,1) + colortable.table(i,2)*2^8 + colortable.table(i,3)*2^16 + colortable.table(i,4)*2^24;
        end
        disp(['colortable with ' num2str(colortable.numEntries) ' entries read (originally ' colortable.orig_tab ')']);

    else
        version = -numEntries;
        if(version~=2)    
            disp(['Error! Does not handle version ' num2str(version)]);
        else
            disp(['Reading from version ' num2str(version)]);
        end
        numEntries = fread(fp, 1, 'int');
        colortable.numEntries = numEntries;
        len = fread(fp, 1, 'int');
        colortable.orig_tab = fread(fp, len, '*char')';
        colortable.orig_tab = colortable.orig_tab(1:end-1);
        
        colortable.struct_names = cell(numEntries,1);
        colortable.table = zeros(numEntries,5);
        
        numEntriesToRead = fread(fp, 1, 'int');
        for i = 1:numEntriesToRead
            structure = fread(fp, 1, 'int')+1;
            if (structure < 0)
                disp(['Error! Read entry, index ' num2str(structure)]);
            end
            if(~isempty(colortable.struct_names{structure}))
                disp(['Error! Duplicate Structure ' num2str(structure)]);
            end
            len = fread(fp, 1, 'int');
            colortable.struct_names{structure} = fread(fp, len, '*char')';
            colortable.struct_names{structure} = colortable.struct_names{structure}(1:end-1);
            colortable.table(structure,1) = fread(fp, 1, 'int');
            colortable.table(structure,2) = fread(fp, 1, 'int');
            colortable.table(structure,3) = fread(fp, 1, 'int');
            colortable.table(structure,4) = fread(fp, 1, 'int');
            colortable.table(structure,5) = colortable.table(structure,1) + colortable.table(structure,2)*2^8 + colortable.table(structure,3)*2^16 + colortable.table(structure,4)*2^24;       
        end
        disp(['colortable with ' num2str(colortable.numEntries) ' entries read (originally ' colortable.orig_tab ')']);
    end    
else
    disp('Error! Should not be expecting bool = 0');    
end

fclose(fp);