#!/usr/bin/env python from __future__ import division, print_function, absolute_import from tempfile import mkdtemp, mktemp import os import shutil import numpy as np from numpy import array,transpose, pi from numpy.testing import (TestCase, run_module_suite, assert_equal, assert_array_equal, assert_array_almost_equal) import scipy.sparse from scipy.io.mmio import mminfo, mmread, mmwrite class TestMMIOArray(TestCase): def setUp(self): self.tmpdir = mkdtemp() self.fn = os.path.join(self.tmpdir, 'testfile.mtx') def tearDown(self): shutil.rmtree(self.tmpdir) def check(self, a, info): mmwrite(self.fn, a) assert_equal(mminfo(self.fn), info) b = mmread(self.fn) assert_array_almost_equal(a, b) def test_simple_integer(self): self.check([[1, 2], [3, 4]], (2, 2, 4, 'array', 'integer', 'general')) def test_simple_upper_triangle_integer(self): self.check([[0, 1], [0, 0]], (2, 2, 4, 'array', 'integer', 'general')) def test_simple_lower_triangle_integer(self): self.check([[0, 0], [1, 0]], (2, 2, 4, 'array', 'integer', 'general')) def test_simple_rectangular_integer(self): self.check([[1, 2, 3], [4, 5, 6]], (2, 3, 6, 'array', 'integer', 'general')) def test_simple_rectangular_float(self): self.check([[1, 2], [3.5, 4], [5, 6]], (3, 2, 6, 'array', 'real', 'general')) def test_simple_float(self): self.check([[1, 2], [3, 4.0]], (2, 2, 4, 'array', 'real', 'general')) def test_simple_complex(self): self.check([[1, 2], [3, 4j]], (2, 2, 4, 'array', 'complex', 'general')) def test_simple_symmetric_integer(self): self.check([[1, 2], [2, 4]], (2, 2, 4, 'array', 'integer', 'symmetric')) def test_simple_skew_symmetric_integer(self): self.check([[1, 2], [-2, 4]], (2, 2, 4, 'array', 'integer', 'skew-symmetric')) def test_simple_skew_symmetric_float(self): self.check(array([[1, 2], [-2.0, 4]], 'f'), (2, 2, 4, 'array', 'real', 'skew-symmetric')) def test_simple_hermitian_complex(self): self.check([[1, 2+3j], [2-3j, 4]], (2, 2, 4, 'array', 'complex', 'hermitian')) def test_random_symmetric_float(self): sz = (20, 20) a = np.random.random(sz) a = a + transpose(a) self.check(a, (20, 20, 400, 'array', 'real', 'symmetric')) def test_random_rectangular_float(self): sz = (20, 15) a = np.random.random(sz) self.check(a, (20, 15, 300, 'array', 'real', 'general')) class TestMMIOSparseCSR(TestMMIOArray): def setUp(self): self.tmpdir = mkdtemp() self.fn = os.path.join(self.tmpdir, 'testfile.mtx') def tearDown(self): shutil.rmtree(self.tmpdir) def check(self, a, info): mmwrite(self.fn, a) assert_equal(mminfo(self.fn), info) b = mmread(self.fn) assert_array_almost_equal(a.todense(), b.todense()) def test_simple_integer(self): self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4]]), (2, 2, 4, 'coordinate', 'integer', 'general')) def test_simple_upper_triangle_integer(self): self.check(scipy.sparse.csr_matrix([[0, 1], [0, 0]]), (2, 2, 1, 'coordinate', 'integer', 'general')) def test_simple_lower_triangle_integer(self): self.check(scipy.sparse.csr_matrix([[0, 0], [1, 0]]), (2, 2, 1, 'coordinate', 'integer', 'general')) def test_simple_rectangular_integer(self): self.check(scipy.sparse.csr_matrix([[1, 2, 3], [4, 5, 6]]), (2, 3, 6, 'coordinate', 'integer', 'general')) def test_simple_rectangular_float(self): self.check(scipy.sparse.csr_matrix([[1, 2], [3.5, 4], [5, 6]]), (3, 2, 6, 'coordinate', 'real', 'general')) def test_simple_float(self): self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4.0]]), (2, 2, 4, 'coordinate', 'real', 'general')) def test_simple_complex(self): self.check(scipy.sparse.csr_matrix([[1, 2], [3, 4j]]), (2, 2, 4, 'coordinate', 'complex', 'general')) def test_simple_symmetric_integer(self): self.check(scipy.sparse.csr_matrix([[1, 2], [2, 4]]), (2, 2, 3, 'coordinate', 'integer', 'symmetric')) def test_simple_skew_symmetric_integer(self): self.check(scipy.sparse.csr_matrix([[1, 2], [-2, 4]]), (2, 2, 3, 'coordinate', 'integer', 'skew-symmetric')) def test_simple_skew_symmetric_float(self): self.check(scipy.sparse.csr_matrix(array([[1, 2], [-2.0, 4]], 'f')), (2, 2, 3, 'coordinate', 'real', 'skew-symmetric')) def test_simple_hermitian_complex(self): self.check(scipy.sparse.csr_matrix([[1, 2+3j], [2-3j, 4]]), (2, 2, 3, 'coordinate', 'complex', 'hermitian')) def test_random_symmetric_float(self): sz = (20, 20) a = np.random.random(sz) a = a + transpose(a) a = scipy.sparse.csr_matrix(a) self.check(a, (20, 20, 210, 'coordinate', 'real', 'symmetric')) def test_random_rectangular_float(self): sz = (20, 15) a = np.random.random(sz) a = scipy.sparse.csr_matrix(a) self.check(a, (20, 15, 300, 'coordinate', 'real', 'general')) _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 setUp(self): self.tmpdir = mkdtemp() self.fn = os.path.join(self.tmpdir, 'testfile.mtx') def tearDown(self): shutil.rmtree(self.tmpdir) def check_read(self, example, a, info): f = open(self.fn, 'w') f.write(example) f.close() assert_equal(mminfo(self.fn), info) b = mmread(self.fn).todense() assert_array_almost_equal(a, b) def test_read_general(self): 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]] self.check_read(_general_example, a, (5, 5, 8, 'coordinate', 'real', 'general')) def test_read_hermitian(self): 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]] self.check_read(_hermitian_example, a, (5, 5, 7, 'coordinate', 'complex', 'hermitian')) def test_read_skew(self): 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]] self.check_read(_skew_example, a, (5, 5, 7, 'coordinate', 'real', 'skew-symmetric')) def test_read_symmetric(self): 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]] self.check_read(_symmetric_example, a, (5, 5, 7, 'coordinate', 'real', 'symmetric')) def test_read_symmetric_pattern(self): 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]] self.check_read(_symmetric_pattern_example, a, (5, 5, 7, 'coordinate', 'pattern', 'symmetric')) def test_empty_write_read(self): # http://projects.scipy.org/scipy/ticket/883 b = scipy.sparse.coo_matrix((10, 10)) mmwrite(self.fn, b) assert_equal(mminfo(self.fn), (10, 10, 0, 'coordinate', 'real', 'symmetric')) a = b.todense() b = mmread(self.fn).todense() assert_array_almost_equal(a, b) def test_bzip2_py3(self): # test if fix for #2152 works try: # bz2 module isn't always built when building Python. import bz2 except: return 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)) mmwrite(self.fn, b) fn_bzip2 = "%s.bz2" % self.fn with open(self.fn, 'rb') as f_in: f_out = bz2.BZ2File(fn_bzip2, 'wb') f_out.write(f_in.read()) f_out.close() a = mmread(fn_bzip2).todense() assert_array_almost_equal(a, b.todense()) def test_gzip_py3(self): # test if fix for #2152 works try: # gzip module can be missing from Python installation import gzip except: return 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)) mmwrite(self.fn, b) fn_gzip = "%s.gz" % self.fn with open(self.fn, 'rb') as f_in: f_out = gzip.open(fn_gzip, 'wb') f_out.write(f_in.read()) f_out.close() a = mmread(fn_gzip).todense() assert_array_almost_equal(a, b.todense()) 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)) mmwrite(self.fn, b) assert_equal(mminfo(self.fn), (5, 5, 8, 'coordinate', 'real', 'general')) a = b.todense() b = mmread(self.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)) mmwrite(self.fn, b) assert_equal(mminfo(self.fn), (5, 5, 8, 'coordinate', 'complex', 'general')) a = b.todense() b = mmread(self.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(dir=self.tmpdir) # safe, we own tmpdir mmwrite(fn, mat.asformat(fmt)) result = mmread(fn).todense() assert_array_almost_equal(result, expected) def test_precision(self): test_values = [pi] + [10**(i) for i in range(0, -10, -1)] test_precisions = range(1, 10) for value in test_values: for precision in test_precisions: # construct sparse matrix with test value at last main diagonal n = 10**precision + 1 A = scipy.sparse.dok_matrix((n, n)) A[n-1, n-1] = value # write matrix with test precision and read again mmwrite(self.fn, A, precision=precision) A = scipy.io.mmread(self.fn) # check for right entries in matrix assert_array_equal(A.row, [n-1]) assert_array_equal(A.col, [n-1]) assert_array_almost_equal(A.data, [float('%%.%dg' % precision % value)]) if __name__ == "__main__": run_module_suite()