Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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326 lines
9.8 KiB
326 lines
9.8 KiB
import sys
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import os
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import gc
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import threading
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import numpy as np
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from numpy.testing import assert_equal, assert_, assert_allclose
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from scipy.sparse import (_sparsetools, coo_matrix, csr_matrix, csc_matrix,
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bsr_matrix, dia_matrix)
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from scipy.sparse.sputils import supported_dtypes, matrix
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from scipy._lib._testutils import check_free_memory
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import pytest
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from pytest import raises as assert_raises
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def test_exception():
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assert_raises(MemoryError, _sparsetools.test_throw_error)
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def test_threads():
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# Smoke test for parallel threaded execution; doesn't actually
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# check that code runs in parallel, but just that it produces
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# expected results.
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nthreads = 10
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niter = 100
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n = 20
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a = csr_matrix(np.ones([n, n]))
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bres = []
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class Worker(threading.Thread):
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def run(self):
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b = a.copy()
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for j in range(niter):
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_sparsetools.csr_plus_csr(n, n,
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a.indptr, a.indices, a.data,
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a.indptr, a.indices, a.data,
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b.indptr, b.indices, b.data)
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bres.append(b)
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threads = [Worker() for _ in range(nthreads)]
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for thread in threads:
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thread.start()
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for thread in threads:
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thread.join()
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for b in bres:
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assert_(np.all(b.toarray() == 2))
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def test_regression_std_vector_dtypes():
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# Regression test for gh-3780, checking the std::vector typemaps
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# in sparsetools.cxx are complete.
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for dtype in supported_dtypes:
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ad = matrix([[1, 2], [3, 4]]).astype(dtype)
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a = csr_matrix(ad, dtype=dtype)
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# getcol is one function using std::vector typemaps, and should not fail
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assert_equal(a.getcol(0).todense(), ad[:,0])
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@pytest.mark.slow
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def test_nnz_overflow():
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# Regression test for gh-7230 / gh-7871, checking that coo_todense
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# with nnz > int32max doesn't overflow.
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nnz = np.iinfo(np.int32).max + 1
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# Ensure ~20 GB of RAM is free to run this test.
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check_free_memory((4 + 4 + 1) * nnz / 1e6 + 0.5)
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# Use nnz duplicate entries to keep the dense version small.
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row = np.zeros(nnz, dtype=np.int32)
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col = np.zeros(nnz, dtype=np.int32)
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data = np.zeros(nnz, dtype=np.int8)
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data[-1] = 4
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s = coo_matrix((data, (row, col)), shape=(1, 1), copy=False)
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# Sums nnz duplicates to produce a 1x1 array containing 4.
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d = s.toarray()
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assert_allclose(d, [[4]])
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@pytest.mark.skipif(not (sys.platform.startswith('linux') and np.dtype(np.intp).itemsize >= 8),
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reason="test requires 64-bit Linux")
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class TestInt32Overflow(object):
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"""
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Some of the sparsetools routines use dense 2D matrices whose
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total size is not bounded by the nnz of the sparse matrix. These
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routines used to suffer from int32 wraparounds; here, we try to
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check that the wraparounds don't occur any more.
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"""
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# choose n large enough
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n = 50000
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def setup_method(self):
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assert self.n**2 > np.iinfo(np.int32).max
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# check there's enough memory even if everything is run at the
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# same time
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try:
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parallel_count = int(os.environ.get('PYTEST_XDIST_WORKER_COUNT', '1'))
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except ValueError:
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parallel_count = np.inf
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check_free_memory(3000 * parallel_count)
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def teardown_method(self):
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gc.collect()
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def test_coo_todense(self):
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# Check *_todense routines (cf. gh-2179)
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#
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# All of them in the end call coo_matrix.todense
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n = self.n
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i = np.array([0, n-1])
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j = np.array([0, n-1])
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data = np.array([1, 2], dtype=np.int8)
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m = coo_matrix((data, (i, j)))
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r = m.todense()
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assert_equal(r[0,0], 1)
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assert_equal(r[-1,-1], 2)
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del r
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gc.collect()
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@pytest.mark.slow
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def test_matvecs(self):
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# Check *_matvecs routines
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n = self.n
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i = np.array([0, n-1])
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j = np.array([0, n-1])
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data = np.array([1, 2], dtype=np.int8)
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m = coo_matrix((data, (i, j)))
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b = np.ones((n, n), dtype=np.int8)
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for sptype in (csr_matrix, csc_matrix, bsr_matrix):
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m2 = sptype(m)
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r = m2.dot(b)
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assert_equal(r[0,0], 1)
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assert_equal(r[-1,-1], 2)
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del r
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gc.collect()
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del b
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gc.collect()
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@pytest.mark.slow
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def test_dia_matvec(self):
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# Check: huge dia_matrix _matvec
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n = self.n
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data = np.ones((n, n), dtype=np.int8)
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offsets = np.arange(n)
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m = dia_matrix((data, offsets), shape=(n, n))
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v = np.ones(m.shape[1], dtype=np.int8)
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r = m.dot(v)
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assert_equal(r[0], np.int8(n))
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del data, offsets, m, v, r
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gc.collect()
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_bsr_ops = [pytest.param("matmat", marks=pytest.mark.xslow),
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pytest.param("matvecs", marks=pytest.mark.xslow),
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"matvec",
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"diagonal",
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"sort_indices",
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pytest.param("transpose", marks=pytest.mark.xslow)]
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@pytest.mark.slow
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@pytest.mark.parametrize("op", _bsr_ops)
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def test_bsr_1_block(self, op):
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# Check: huge bsr_matrix (1-block)
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#
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# The point here is that indices inside a block may overflow.
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def get_matrix():
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n = self.n
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data = np.ones((1, n, n), dtype=np.int8)
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indptr = np.array([0, 1], dtype=np.int32)
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indices = np.array([0], dtype=np.int32)
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m = bsr_matrix((data, indices, indptr), blocksize=(n, n), copy=False)
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del data, indptr, indices
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return m
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gc.collect()
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try:
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getattr(self, "_check_bsr_" + op)(get_matrix)
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finally:
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gc.collect()
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@pytest.mark.slow
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@pytest.mark.parametrize("op", _bsr_ops)
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def test_bsr_n_block(self, op):
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# Check: huge bsr_matrix (n-block)
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#
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# The point here is that while indices within a block don't
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# overflow, accumulators across many block may.
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def get_matrix():
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n = self.n
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data = np.ones((n, n, 1), dtype=np.int8)
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indptr = np.array([0, n], dtype=np.int32)
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indices = np.arange(n, dtype=np.int32)
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m = bsr_matrix((data, indices, indptr), blocksize=(n, 1), copy=False)
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del data, indptr, indices
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return m
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gc.collect()
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try:
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getattr(self, "_check_bsr_" + op)(get_matrix)
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finally:
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gc.collect()
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def _check_bsr_matvecs(self, m):
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m = m()
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n = self.n
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# _matvecs
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r = m.dot(np.ones((n, 2), dtype=np.int8))
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assert_equal(r[0,0], np.int8(n))
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def _check_bsr_matvec(self, m):
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m = m()
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n = self.n
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# _matvec
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r = m.dot(np.ones((n,), dtype=np.int8))
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assert_equal(r[0], np.int8(n))
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def _check_bsr_diagonal(self, m):
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m = m()
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n = self.n
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# _diagonal
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r = m.diagonal()
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assert_equal(r, np.ones(n))
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def _check_bsr_sort_indices(self, m):
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# _sort_indices
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m = m()
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m.sort_indices()
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def _check_bsr_transpose(self, m):
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# _transpose
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m = m()
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m.transpose()
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def _check_bsr_matmat(self, m):
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m = m()
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n = self.n
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# _bsr_matmat
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m2 = bsr_matrix(np.ones((n, 2), dtype=np.int8), blocksize=(m.blocksize[1], 2))
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m.dot(m2) # shouldn't SIGSEGV
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del m2
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# _bsr_matmat
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m2 = bsr_matrix(np.ones((2, n), dtype=np.int8), blocksize=(2, m.blocksize[0]))
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m2.dot(m) # shouldn't SIGSEGV
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@pytest.mark.skip(reason="64-bit indices in sparse matrices not available")
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def test_csr_matmat_int64_overflow():
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n = 3037000500
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assert n**2 > np.iinfo(np.int64).max
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# the test would take crazy amounts of memory
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check_free_memory(n * (8*2 + 1) * 3 / 1e6)
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# int64 overflow
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data = np.ones((n,), dtype=np.int8)
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indptr = np.arange(n+1, dtype=np.int64)
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indices = np.zeros(n, dtype=np.int64)
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a = csr_matrix((data, indices, indptr))
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b = a.T
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assert_raises(RuntimeError, a.dot, b)
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def test_upcast():
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a0 = csr_matrix([[np.pi, np.pi*1j], [3, 4]], dtype=complex)
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b0 = np.array([256+1j, 2**32], dtype=complex)
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for a_dtype in supported_dtypes:
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for b_dtype in supported_dtypes:
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msg = "(%r, %r)" % (a_dtype, b_dtype)
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if np.issubdtype(a_dtype, np.complexfloating):
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a = a0.copy().astype(a_dtype)
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else:
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a = a0.real.copy().astype(a_dtype)
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if np.issubdtype(b_dtype, np.complexfloating):
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b = b0.copy().astype(b_dtype)
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else:
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b = b0.real.copy().astype(b_dtype)
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if not (a_dtype == np.bool_ and b_dtype == np.bool_):
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c = np.zeros((2,), dtype=np.bool_)
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assert_raises(ValueError, _sparsetools.csr_matvec,
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2, 2, a.indptr, a.indices, a.data, b, c)
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if ((np.issubdtype(a_dtype, np.complexfloating) and
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not np.issubdtype(b_dtype, np.complexfloating)) or
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(not np.issubdtype(a_dtype, np.complexfloating) and
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np.issubdtype(b_dtype, np.complexfloating))):
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c = np.zeros((2,), dtype=np.float64)
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assert_raises(ValueError, _sparsetools.csr_matvec,
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2, 2, a.indptr, a.indices, a.data, b, c)
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c = np.zeros((2,), dtype=np.result_type(a_dtype, b_dtype))
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_sparsetools.csr_matvec(2, 2, a.indptr, a.indices, a.data, b, c)
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assert_allclose(c, np.dot(a.toarray(), b), err_msg=msg)
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def test_endianness():
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d = np.ones((3,4))
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offsets = [-1,0,1]
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a = dia_matrix((d.astype('<f8'), offsets), (4, 4))
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b = dia_matrix((d.astype('>f8'), offsets), (4, 4))
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v = np.arange(4)
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assert_allclose(a.dot(v), [1, 3, 6, 5])
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assert_allclose(b.dot(v), [1, 3, 6, 5])
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