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mmread_binary.m
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mmread_binary.m
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function [A,rows,cols,entries,rep,field,symm] = mmread(filename)
% By Evan Bollig (2012)
% Based on matrix market mmread, but adds support for BINARY content for
% Coordinate matrices as (int,int,double).
%
% function [A] = mmread(filename)
%
% function [A,rows,cols,entries,rep,field,symm] = mmread(filename)
%
% Reads the contents of the Matrix Market file 'filename'
% into the matrix 'A'. 'A' will be either sparse or full,
% depending on the Matrix Market format indicated by
% 'coordinate' (coordinate sparse storage), or
% 'array' (dense array storage). The data will be duplicated
% as appropriate if symmetry is indicated in the header.
%
% Optionally, size information about the matrix can be
% obtained by using the return values rows, cols, and
% entries, where entries is the number of nonzero entries
% in the final matrix. Type information can also be retrieved
% using the optional return values rep (representation), field,
% and symm (symmetry).
%
mmfile = fopen(filename,'r');
if ( mmfile == -1 )
disp(filename);
error('File not found');
end;
header = fgets(mmfile);
if (header == -1 )
error('Empty file.')
end
% NOTE: If using a version of Matlab for which strtok is not
% defined, substitute 'gettok' for 'strtok' in the
% following lines, and download gettok.m from the
% Matrix Market site.
[head0,header] = strtok(header); % see note above
[head1,header] = strtok(header);
[rep,header] = strtok(header);
[field,header] = strtok(header);
[symm,header] = strtok(header);
head1 = lower(head1);
rep = lower(rep);
field = lower(field);
symm = lower(symm);
if ( length(symm) == 0 )
disp(['Not enough words in header line of file ',filename])
disp('Recognized format: ')
disp('%%MatrixMarket matrix representation field symmetry')
error('Check header line.')
end
if ( ~ strcmp(head0,'%%MatrixMarket') )
error('Not a valid MatrixMarket header.')
end
if ( ~ strcmp(head1,'matrix') )
disp(['This seems to be a MatrixMarket ',head1,' file.']);
disp('This function only knows how to read MatrixMarket matrix files.');
disp(' ');
error(' ');
end
% Read through comments, ignoring them
commentline = fgets(mmfile);
while length(commentline) > 0 & commentline(1) == '%',
commentline = fgets(mmfile);
end
% Read size information, then branch according to
% sparse or dense format
if ( strcmp(rep,'coordinate')) % read matrix given in sparse
% coordinate matrix format
[sizeinfo,count] = sscanf(commentline,'%d%d%d');
while ( count == 0 )
commentline = fgets(mmfile);
if (commentline == -1 )
error('End-of-file reached before size information was found.')
end
[sizeinfo,count] = sscanf(commentline,'%d%d%d');
if ( count > 0 & count ~= 3 )
error('Invalid size specification line.')
end
end
rows = sizeinfo(1);
cols = sizeinfo(2);
entries = sizeinfo(3);
if ( strcmp(field,'real') ) % real valued entries:
% [T,count] = fscanf(mmfile,'%f',3);
T=[];
for inefficient = 1:entries
ineff_row = fread(mmfile,1,'int');
ineff_col = fread(mmfile,1,'int');
ineff_val = fread(mmfile,1,'double');
T = [T; ineff_row, ineff_col, ineff_val];
end
%T = [T; fscanf(mmfile,'%f')];
if ( size(T,2) ~= 3 ) & ( size(T,1) ~= entries )
message = ...
str2mat('Data file does not contain expected amount of data.',...
'Check that number of data lines matches nonzero count.');
disp(message);
error('Invalid data.');
end
% T = reshape(T,3,entries)';
A = sparse(T(:,1), T(:,2), T(:,3), rows , cols);
elseif ( strcmp(field,'complex')) % complex valued entries:
%
% T = fscanf(mmfile,'%f',4);
% T = [T; fscanf(mmfile,'%f')];
% if ( size(T) ~= 4*entries )
% message = ...
% str2mat('Data file does not contain expected amount of data.',...
% 'Check that number of data lines matches nonzero count.');
% disp(message);
% error('Invalid data.');
% end
% T = reshape(T,4,entries)';
% A = sparse(T(:,1), T(:,2), T(:,3) + T(:,4)*sqrt(-1), rows , cols);
%
error('No support for complex/pattern')
elseif ( strcmp(field,'pattern')) % pattern matrix (no values given):
%
% T = fscanf(mmfile,'%f',2);
% T = [T; fscanf(mmfile,'%f')];
% if ( size(T) ~= 2*entries )
% message = ...
% str2mat('Data file does not contain expected amount of data.',...
% 'Check that number of data lines matches nonzero count.');
% disp(message);
% error('Invalid data.');
% end
% T = reshape(T,2,entries)';
% A = sparse(T(:,1), T(:,2), ones(entries,1) , rows , cols);
error('No support for complex/pattern')
end
%
% elseif ( strcmp(rep,'array') ) % read matrix given in dense
% % array (column major) format
%
% [sizeinfo,count] = sscanf(commentline,'%d%d');
% while ( count == 0 )
% commentline = fgets(mmfile);
% if (commentline == -1 )
% error('End-of-file reached before size information was found.')
% end
% [sizeinfo,count] = sscanf(commentline,'%d%d');
% if ( count > 0 & count ~= 2 )
% error('Invalid size specification line.')
% end
% end
% rows = sizeinfo(1);
% cols = sizeinfo(2);
% entries = rows*cols;
% if ( strcmp(field,'real') ) % real valued entries:
% A = fscanf(mmfile,'%f',1);
% A = [A; fscanf(mmfile,'%f')];
% if ( strcmp(symm,'symmetric') | strcmp(symm,'hermitian') | strcmp(symm,'skew-symmetric') )
% for j=1:cols-1,
% currenti = j*rows;
% A = [A(1:currenti); zeros(j,1);A(currenti+1:length(A))];
% end
% elseif ( ~ strcmp(symm,'general') )
% disp('Unrecognized symmetry')
% disp(symm)
% disp('Recognized choices:')
% disp(' symmetric')
% disp(' hermitian')
% disp(' skew-symmetric')
% disp(' general')
% error('Check symmetry specification in header.');
% end
% A = reshape(A,rows,cols);
% elseif ( strcmp(field,'complex')) % complx valued entries:
% tmpr = fscanf(mmfile,'%f',1);
% tmpi = fscanf(mmfile,'%f',1);
% A = tmpr+tmpi*i;
% for j=1:entries-1
% tmpr = fscanf(mmfile,'%f',1);
% tmpi = fscanf(mmfile,'%f',1);
% A = [A; tmpr + tmpi*i];
% end
% if ( strcmp(symm,'symmetric') | strcmp(symm,'hermitian') | strcmp(symm,'skew-symmetric') )
% for j=1:cols-1,
% currenti = j*rows;
% A = [A(1:currenti); zeros(j,1);A(currenti+1:length(A))];
% end
% elseif ( ~ strcmp(symm,'general') )
% disp('Unrecognized symmetry')
% disp(symm)
% disp('Recognized choices:')
% disp(' symmetric')
% disp(' hermitian')
% disp(' skew-symmetric')
% disp(' general')
% error('Check symmetry specification in header.');
% end
% A = reshape(A,rows,cols);
% elseif ( strcmp(field,'pattern')) % pattern (makes no sense for dense)
% disp('Matrix type:',field)
% error('Pattern matrix type invalid for array storage format.');
% else % Unknown matrix type
% disp('Matrix type:',field)
% error('Invalid matrix type specification. Check header against MM documentation.');
% end
end
%
% If symmetric, skew-symmetric or Hermitian, duplicate lower
% triangular part and modify entries as appropriate:
%
if ( strcmp(symm,'symmetric') )
A = A + A.' - diag(diag(A));
entries = nnz(A);
elseif ( strcmp(symm,'hermitian') )
A = A + A' - diag(diag(A));
entries = nnz(A);
elseif ( strcmp(symm,'skew-symmetric') )
A = A - A';
entries = nnz(A);
end
fclose(mmfile);
% Done.