add mmwrite, mmread, and test
jan
8 years ago
parent
e4eb232b1d
commit
dcc0a1214a
@ -0,0 +1,181 @@
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function [A,rows,cols,entries,rep,field,symm] = mmread(filename)
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%
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% function [A] = mmread(filename)
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%
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% function [A,rows,cols,entries,rep,field,symm] = mmread(filename)
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%
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% Reads the contents of the Matrix Market file 'filename'
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% into the matrix 'A'. 'A' will be either sparse or full,
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% depending on the Matrix Market format indicated by
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% 'coordinate' (coordinate sparse storage), or
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% 'array' (dense array storage). The data will be duplicated
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% as appropriate if symmetry is indicated in the header.
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%
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% Optionally, size information about the matrix can be
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% obtained by using the return values rows, cols, and
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% entries, where entries is the number of nonzero entries
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% in the final matrix. Type information can also be retrieved
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% using the optional return values rep (representation), field,
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% and symm (symmetry).
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%
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mmfile = fopen(filename,'r');
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if ( mmfile == -1 )
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disp(filename);
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error('File not found');
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end;
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header = fgets(mmfile);
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if (header == -1 )
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error('Empty file.')
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end
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% NOTE: If using a version of Matlab for which strtok is not
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% defined, substitute 'gettok' for 'strtok' in the
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% following lines, and download gettok.m from the
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% Matrix Market site.
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[head0, header] = strtok(header); % see note above
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[head1, header] = strtok(header);
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[rep, header] = strtok(header);
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[field, header] = strtok(header);
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[symm, header] = strtok(header);
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head1 = lower(head1);
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rep = lower(rep);
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field = lower(field);
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symm = lower(symm);
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if isempty(symm)
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disp(['Not enough words in header line of file ',filename])
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disp('Recognized format: ')
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disp('%%MatrixMarket matrix representation field symmetry')
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error('Check header line.')
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end
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if ~strcmp(head0,'%%MatrixMarket')
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error('Not a valid MatrixMarket header.')
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end
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if ~strcmp(head1,'matrix')
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disp(['This seems to be a MatrixMarket ',head1,' file.']);
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disp('This function only knows how to read MatrixMarket matrix files.');
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disp(' ');
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error(' ');
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end
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% Read through comments, ignoring them
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commentline = fgets(mmfile);
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while ~isempty(commentline) && commentline(1) == '%',
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commentline = fgets(mmfile);
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end
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% Read size information, then branch according to
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% sparse or dense format
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switch rep,
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case 'coordinate', % read matrix given in sparse coordinate format
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[sizeinfo,count] = sscanf(commentline, '%d%d%d');
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while count == 0,
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commentline = fgets(mmfile);
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if commentline == -1,
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error('End-of-file reached before size information was found.')
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end
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[sizeinfo,count] = sscanf(commentline, '%d%d%d');
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if count > 0 && count ~= 3,
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error('Invalid size specification line.')
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end
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end
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rows = sizeinfo(1);
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cols = sizeinfo(2);
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entries = sizeinfo(3);
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T = fscanf(mmfile, '%f');
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switch field,
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case 'real', % real valued entries:
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check_size(T, 3 * entries);
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T = reshape(T(:), 3, entries)';
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A = sparse(T(:,1), T(:,2), T(:,3), rows , cols);
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case 'complex', % complex valued entries:
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check_size(T, 4 * entries);
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T = reshape(T(:), 4, entries)';
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A = sparse(T(:,1), T(:,2), T(:,3) + T(:,4)*1i, rows , cols);
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case 'pattern', % pattern matrix (no values given):
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check_size(T, 2 * entries);
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T = reshape(T(:), 2, entries)';
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A = sparse(T(:,1), T(:,2), ones(entries, 1), rows , cols);
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end
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case 'array', % read matrix given in dense array (column major) format
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[sizeinfo, count] = sscanf(commentline, '%d%d');
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while count == 0
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commentline = fgets(mmfile);
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if commentline == -1
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error('End-of-file reached before size information was found.')
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end
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[sizeinfo, count] = sscanf(commentline, '%d%d');
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if count > 0 && count ~= 2
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error('Invalid size specification line.')
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end
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end
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rows = sizeinfo(1);
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cols = sizeinfo(2);
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entries = rows*cols;
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A = fscanf(mmfile, '%f');
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switch field,
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case 'real', % real valued entries:
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% do nothing
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case 'complex', % complex valued entries:
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A = A(1:2:end-1) + 1i * A(2:2:end);
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case 'pattern', % pattern (makes no sense for dense)
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disp('Matrix type:',field)
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error('Pattern matrix type invalid for array storage format.');
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otherwise,
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disp('Matrix type:',field)
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error('Invalid matrix type specification. Check header against MM documentation.');
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end
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if any(strcmp(symm,{'symmetric','hermitian','skew-symmetric'}))
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for j=1:cols-1,
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currenti = j*rows;
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A = [A(1:currenti);
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zeros(j,1);
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A(currenti+1:length(A))];
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end
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elseif ~strcmp(symm,'general'),
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disp('Unrecognized symmetry')
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disp(symm)
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disp('Recognized choices:')
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disp(' symmetric')
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disp(' hermitian')
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disp(' skew-symmetric')
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disp(' general')
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error('Check symmetry specification in header.');
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end
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A = reshape(A,rows,cols);
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end
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fclose(mmfile);
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%
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% If symmetric, skew-symmetric or Hermitian, duplicate lower
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% triangular part and modify entries as appropriate:
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%
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switch symm,
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case 'symmetric',
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A = A + A.' - diag(diag(A));
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entries = nnz(A);
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case 'hermitian',
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A = A + A' - diag(diag(A));
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entries = nnz(A);
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case 'skew-symmetric',
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A = A - A.';
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entries = nnz(A);
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end
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% Done.
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end
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function check_size(T, n)
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if size(T) ~= n
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disp('Data file does not contain expected amount of data.');
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disp('Check that number of data lines matches nonzero count.');
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error('Invalid data.');
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end
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end
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@ -0,0 +1,60 @@
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function mmtest()
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tmpfile = [num2str(now()) '.mtx'];
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fp_err = 1e-15;
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function works = rwtest(m)
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mmwrite(tmpfile, m);
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m2 = mmread(tmpfile);
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works = all(abs(m(:) - m2(:)) < fp_err*mean(abs(m(:))));
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delete(tmpfile);
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end
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dense_r = rand(100) + 1i * rand(100);
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sparse_r = sparse(dense_r * (abs(dense_r) > mean(abs(dense_r(:)))));
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% full
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assert(rwtest(dense_r));
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assert(rwtest(sparse_r));
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% symmetric
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assert(rwtest( tril(dense_r) + tril(dense_r).' ));
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assert(rwtest( tril(sparse_r) + tril(sparse_r).' ));
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% skew-symmetric
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assert(rwtest( tril(dense_r) - tril(dense_r).' ));
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assert(rwtest( tril(sparse_r) - tril(sparse_r).' ));
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% hermitian
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assert(rwtest( tril(dense_r) + tril(dense_r)' ));
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assert(rwtest( tril(sparse_r) + tril(sparse_r)' ));
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dense_r = real(dense_r);
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sparse_r = real(sparse_r);
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% full
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assert(rwtest(dense_r));
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assert(rwtest(sparse_r));
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% symmetric
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assert(rwtest( tril(dense_r) + tril(dense_r).' ));
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assert(rwtest( tril(sparse_r) + tril(sparse_r).' ));
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% skew-symmetric
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assert(rwtest( tril(dense_r) - tril(dense_r).' ));
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assert(rwtest( tril(sparse_r) - tril(sparse_r).' ));
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% hermitian
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assert(rwtest( tril(dense_r) + tril(dense_r)' ));
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assert(rwtest( tril(sparse_r) + tril(sparse_r)' ));
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end
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@ -0,0 +1,170 @@
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function [ err ] = mmwrite(filename, A, comment, mattype, precision)
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%
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% Function: mmwrite(filename,A,comment,mattype,precision)
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%
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% Writes the sparse or dense matrix A to a Matrix Market (MM)
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% formatted file.
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%
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% Required arguments:
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%
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% filename - destination file
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%
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% A - sparse or full matrix
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%
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% Optional arguments:
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%
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% comment - matrix of comments to prepend to
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% the MM file. To build a comment matrix,
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% use str2mat. For example:
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%
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% comment = str2mat(' Comment 1' ,...
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% ' Comment 2',...
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% ' and so on.',...
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% ' to attach a date:',...
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% [' ',date]);
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% If ommitted, a single line date stamp comment
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% will be included.
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%
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% mattype - 'real'
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% 'complex'
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% 'integer'
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% 'pattern'
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% If ommitted, data will determine type.
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%
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% precision - number of digits to display for real
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% or complex values
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% If ommitted, full working precision is used.
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%
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if ( nargin == 5)
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precision = 16;
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elseif ( nargin == 4)
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precision = 16;
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elseif ( nargin == 3)
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mattype = 'real'; % placeholder
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precision = 16;
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elseif ( nargin == 2)
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comment = '';
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% Check whether there is an imaginary part:
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mattype = 'real'; % placeholder
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precision = 16;
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end
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mmfile = fopen(filename,'w');
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if ( mmfile == -1 )
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error('Cannot open file for output');
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end;
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[M, N] = size(A);
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if ~strcmp(mattype,'pattern')
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if any(imag(A(:)))
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mattype = 'complex';
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else
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mattype = 'real';
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end
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end
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%
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% Determine symmetry:
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%
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if issymmetric(A),
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symm = 'symmetric';
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elseif issymmetric(A, 'skew'),
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symm = 'skew-symmetric';
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elseif strcmp(mattype, 'complex') && ishermitian(A),
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symm = 'hermitian';
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else
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symm = 'general';
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end
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%%%%%%%%%%%%% This part for sparse matrices %%%%%%%%%%%%%%%%
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if issparse(A),
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if strcmp(symm, 'general')
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[I, J, V] = find(A);
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NZ = length(V);
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else
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ATEMP = tril(A);
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[I, J, V] = find(ATEMP);
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NZ = nnz(ATEMP);
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end
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% Sparse coordinate format:
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rep = 'coordinate';
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fprintf(mmfile,'%%%%MatrixMarket matrix %s %s %s\n', rep, mattype, symm);
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[MC, ~] = size(comment);
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if ( MC == 0 )
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fprintf(mmfile,'%% Generated %s\n',[date]);
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else
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for i=1:MC,
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fprintf(mmfile,'%%%s\n',comment(i,:));
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end
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end
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fprintf(mmfile,'%d %d %d\n',M,N,NZ);
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switch mattype,
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case 'real',
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realformat = sprintf('%%d %%d %% .%dg\n',precision);
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fprintf(mmfile, realformat, [I, J, V].');
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case 'complex',
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cplxformat = sprintf('%%d %%d %% .%dg %% .%dg\n', precision, precision);
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fprintf(mmfile, cplxformat, [I, J, real(V), imag(V)].');
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case 'pattern',
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fprintf(mmfile, '%d %d\n', [I, J].');
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otherwise,
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err = -1;
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disp('Unsupported mattype:');
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disp(mattype);
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end
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%%%%%%%%%%%%% This part for dense matrices %%%%%%%%%%%%%%%%
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else
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% Dense array format:
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rep = 'array';
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[MC, ~] = size(comment);
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fprintf(mmfile,'%%%%MatrixMarket matrix %s %s %s\n', rep, mattype, symm);
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for i=1:MC,
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fprintf(mmfile,'%%%s\n', comment(i,:));
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end;
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fprintf(mmfile,'%d %d\n',M,N);
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if ( ~ strcmp(symm,'general') )
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j_bool = 1;
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else
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j_bool = 0;
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end
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rowloop = @(j) j_bool * j + (1-j_bool);
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switch mattype,
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case 'real',
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realformat = sprintf('%% .%dg\n', precision);
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for j=1:N
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for i=rowloop(j):M
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fprintf(mmfile,realformat,A(i,j));
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end
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end
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case 'complex',
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cplxformat = sprintf('%% .%dg %% .%dg\n', precision, precision);
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for j=1:N
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for i=rowloop(j):M
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fprintf(mmfile,cplxformat,real(A(i,j)),imag(A(i,j)));
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end
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end
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case 'pattern',
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err = -2;
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disp('Pattern type inconsistant with dense matrix')
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otherwise,
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err = -2;
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disp('Unknown matrix type:')
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disp(mattype);
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end
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end
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fclose(mmfile);
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