#!/usr/bin/env python from tempfile import mktemp from numpy import array,transpose from numpy.testing import TestCase, run_module_suite, assert_array_almost_equal, \ assert_equal, rand import scipy.sparse from scipy.io.mmio import mminfo,mmread,mmwrite class TestMMIOArray(TestCase): def test_simple(self): a = [[1,2],[3,4]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','integer','general')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_rectangular(self): a = [[1,2,3],[4,5,6]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,3,6,'array','integer','general')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_rectangular_real(self): a = [[1,2],[3.5,4],[5,6]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(3,2,6,'array','real','general')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_real(self): a = [[1,2],[3,4.0]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','real','general')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_complex(self): a = [[1,2],[3,4j]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','complex','general')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_symmetric(self): a = [[1,2],[2,4]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','integer','symmetric')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_skew_symmetric(self): a = [[1,2],[-2,4]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','integer','skew-symmetric')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_skew_symmetric_float(self): a = array([[1,2],[-2.0,4]],'f') fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','real','skew-symmetric')) b = mmread(fn) assert_array_almost_equal(a,b) def test_simple_hermitian(self): a = [[1,2+3j],[2-3j,4]] fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(2,2,4,'array','complex','hermitian')) b = mmread(fn) assert_array_almost_equal(a,b) def test_random_symmetric_real(self): sz = (20,20) a = rand(*sz) a = a + transpose(a) fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(20,20,400,'array','real','symmetric')) b = mmread(fn) assert_array_almost_equal(a,b) def test_random_rect_real(self): sz = (20,15) a = rand(*sz) fn = mktemp() mmwrite(fn,a) assert_equal(mminfo(fn),(20,15,300,'array','real','general')) b = mmread(fn) assert_array_almost_equal(a,b) _general_example = '''\ %%MatrixMarket matrix coordinate real general %================================================================================= % % This ASCII file represents a sparse MxN matrix with L % nonzeros in the following Matrix Market format: % % +----------------------------------------------+ % |%%MatrixMarket matrix coordinate real general | <--- header line % |% | <--+ % |% comments | |-- 0 or more comment lines % |% | <--+ % | M N L | <--- rows, columns, entries % | I1 J1 A(I1, J1) | <--+ % | I2 J2 A(I2, J2) | | % | I3 J3 A(I3, J3) | |-- L lines % | . . . | | % | IL JL A(IL, JL) | <--+ % +----------------------------------------------+ % % Indices are 1-based, i.e. A(1,1) is the first element. % %================================================================================= 5 5 8 1 1 1.000e+00 2 2 1.050e+01 3 3 1.500e-02 1 4 6.000e+00 4 2 2.505e+02 4 4 -2.800e+02 4 5 3.332e+01 5 5 1.200e+01 ''' _hermitian_example = '''\ %%MatrixMarket matrix coordinate complex hermitian 5 5 7 1 1 1.0 0 2 2 10.5 0 4 2 250.5 22.22 3 3 1.5e-2 0 4 4 -2.8e2 0 5 5 12. 0 5 4 0 33.32 ''' _skew_example = '''\ %%MatrixMarket matrix coordinate real skew-symmetric 5 5 7 1 1 1.0 2 2 10.5 4 2 250.5 3 3 1.5e-2 4 4 -2.8e2 5 5 12. 5 4 0 ''' _symmetric_example = '''\ %%MatrixMarket matrix coordinate real symmetric 5 5 7 1 1 1.0 2 2 10.5 4 2 250.5 3 3 1.5e-2 4 4 -2.8e2 5 5 12. 5 4 8 ''' _symmetric_pattern_example = '''\ %%MatrixMarket matrix coordinate pattern symmetric 5 5 7 1 1 2 2 4 2 3 3 4 4 5 5 5 4 ''' class TestMMIOCoordinate(TestCase): def test_read_general(self): """read a general matrix""" fn = mktemp() f = open(fn,'w') f.write(_general_example) f.close() assert_equal(mminfo(fn),(5,5,8,'coordinate','real','general')) a = [[1, 0, 0, 6, 0], [0, 10.5, 0, 0, 0], [0, 0, .015, 0, 0], [0, 250.5, 0, -280, 33.32], [0, 0, 0, 0, 12]] b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_read_hermitian(self): """read a hermitian matrix""" fn = mktemp() f = open(fn,'w') f.write(_hermitian_example) f.close() assert_equal(mminfo(fn),(5,5,7,'coordinate','complex','hermitian')) a = [[1, 0, 0, 0, 0], [0, 10.5, 0, 250.5 - 22.22j, 0], [0, 0, .015, 0, 0], [0, 250.5 + 22.22j, 0, -280, -33.32j], [0, 0, 0, 33.32j, 12]] b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_read_skew(self): """read a skew-symmetric matrix""" fn = mktemp() f = open(fn,'w') f.write(_skew_example) f.close() assert_equal(mminfo(fn),(5,5,7,'coordinate','real','skew-symmetric')) a = [[1, 0, 0, 0, 0], [0, 10.5, 0, -250.5, 0], [0, 0, .015, 0, 0], [0, 250.5, 0, -280, 0], [0, 0, 0, 0, 12]] b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_read_symmetric(self): """read a symmetric matrix""" fn = mktemp() f = open(fn,'w') f.write(_symmetric_example) f.close() assert_equal(mminfo(fn),(5,5,7,'coordinate','real','symmetric')) a = [[1, 0, 0, 0, 0], [0, 10.5, 0, 250.5, 0], [0, 0, .015, 0, 0], [0, 250.5, 0, -280, 8], [0, 0, 0, 8, 12]] b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_read_symmetric_pattern(self): """read a symmetric pattern matrix""" fn = mktemp() f = open(fn,'w') f.write(_symmetric_pattern_example) f.close() assert_equal(mminfo(fn),(5,5,7,'coordinate','pattern','symmetric')) a = [[1, 0, 0, 0, 0], [0, 1, 0, 1, 0], [0, 0, 1, 0, 0], [0, 1, 0, 1, 1], [0, 0, 0, 1, 1]] b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_empty_write_read(self): #http://projects.scipy.org/scipy/ticket/883 b = scipy.sparse.coo_matrix((10,10)) fn = mktemp() mmwrite(fn,b) assert_equal(mminfo(fn),(10,10,0,'coordinate','real','general')) a = b.todense() b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_real_write_read(self): I = array([0, 0, 1, 2, 3, 3, 3, 4]) J = array([0, 3, 1, 2, 1, 3, 4, 4]) V = array([ 1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0 ]) b = scipy.sparse.coo_matrix((V,(I,J)),shape=(5,5)) fn = mktemp() mmwrite(fn,b) assert_equal(mminfo(fn),(5,5,8,'coordinate','real','general')) a = b.todense() b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_complex_write_read(self): I = array([0, 0, 1, 2, 3, 3, 3, 4]) J = array([0, 3, 1, 2, 1, 3, 4, 4]) V = array([ 1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j, 250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j]) b = scipy.sparse.coo_matrix((V,(I,J)),shape=(5,5)) fn = mktemp() mmwrite(fn,b) assert_equal(mminfo(fn),(5,5,8,'coordinate','complex','general')) a = b.todense() b = mmread(fn).todense() assert_array_almost_equal(a,b) def test_sparse_formats(self): mats = [] I = array([0, 0, 1, 2, 3, 3, 3, 4]) J = array([0, 3, 1, 2, 1, 3, 4, 4]) V = array([ 1.0, 6.0, 10.5, 0.015, 250.5, -280.0, 33.32, 12.0 ]) mats.append( scipy.sparse.coo_matrix((V,(I,J)),shape=(5,5)) ) V = array([ 1.0 + 3j, 6.0 + 2j, 10.50 + 0.9j, 0.015 + -4.4j, 250.5 + 0j, -280.0 + 5j, 33.32 + 6.4j, 12.00 + 0.8j]) mats.append( scipy.sparse.coo_matrix((V,(I,J)),shape=(5,5)) ) for mat in mats: expected = mat.todense() for fmt in ['csr','csc','coo']: fn = mktemp() mmwrite(fn, mat.asformat(fmt)) result = mmread(fn).todense() assert_array_almost_equal(result, expected) if __name__ == "__main__": run_module_suite()