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#!/usr/bin/env python
#
# Authors: Travis Oliphant, Ed Schofield, Robert Cimrman, and others
""" Test functions for sparse matrices
"""
__usage__ = """
Build sparse:
python setup.py build
Run tests if scipy is installed:
python -c 'import scipy;scipy.sparse.test(<level>)'
Run tests if sparse is not installed:
python tests/test_sparse.py [<level>]
"""
import numpy
from numpy import arange, zeros, array, dot, ones, matrix, asmatrix, asarray, \
float32, float64, complex64, complex128
import random
from numpy.testing import *
set_package_path()
from scipy.sparse import csc_matrix, csr_matrix, dok_matrix, coo_matrix, \
spidentity, speye, lil_matrix
from scipy.linsolve import splu
restore_path()
class _test_cs:
def setUp(self):
self.dat = matrix([[1,0,0,2],[3,0,1,0],[0,2,0,0]],'d')
self.datsp = self.spmatrix(self.dat)
def check_getelement(self):
assert_equal(self.datsp[0,0],1)
assert_equal(self.datsp[0,1],0)
assert_equal(self.datsp[1,0],3)
assert_equal(self.datsp[2,1],2)
def check_sum(self):
"""Does the matrix's sum(,axis=0) method work?
"""
assert_array_equal(self.dat.sum(), self.datsp.sum())
assert_array_equal(self.dat.sum(axis=None), self.datsp.sum(axis=None))
assert_array_equal(self.dat.sum(axis=0), self.datsp.sum(axis=0))
assert_array_equal(self.dat.sum(axis=1), self.datsp.sum(axis=1))
def check_mean(self):
"""Does the matrix's mean(,axis=0) method work?
"""
assert_array_equal(self.dat.mean(), self.datsp.mean())
assert_array_equal(self.dat.mean(axis=None), self.datsp.mean(axis=None))
assert_array_equal(self.dat.mean(axis=0), self.datsp.mean(axis=0))
assert_array_equal(self.dat.mean(axis=1), self.datsp.mean(axis=1))
def check_todense(self):
chk = self.datsp.todense()
assert_array_equal(chk,self.dat)
a = matrix([1.,2.,3.])
dense_dot_dense = a * self.dat
check = a * self.datsp.todense()
assert_array_equal(dense_dot_dense, check)
b = matrix([1.,2.,3.,4.]).T
dense_dot_dense = self.dat * b
check2 = self.datsp.todense() * b
assert_array_equal(dense_dot_dense, check2)
def check_toarray(self):
dat = asarray(self.dat)
chk = self.datsp.toarray()
assert_array_equal(chk, dat)
a = array([1.,2.,3.])
dense_dot_dense = dot(a, dat)
check = dot(a, self.datsp.toarray())
assert_array_equal(dense_dot_dense, check)
b = array([1.,2.,3.,4.])
dense_dot_dense = dot(dat, b)
check2 = dot(self.datsp.toarray(), b)
assert_array_equal(dense_dot_dense, check2)
def check_setelement(self):
a = self.datsp - self.datsp
a[1,2] = 4.0
a[0,1] = 3
a[2,0] = 2.0
assert_array_equal(a.todense(),[[0,3,0,0],[0,0,4,0],[2,0,0,0]])
def check_add(self):
a = self.datsp
b = self.datsp.copy()
b[0,2] = 2.0
c = a + b
assert_array_equal(c.todense(),[[2,0,2,4],[6,0,2,0],[0,4,0,0]])
def check_elmul(self):
a = self.datsp
b = self.datsp.copy()
b[0,2] = 2.0
c = a ** b
assert_array_equal(c.todense(),[[1,0,0,4],[9,0,1,0],[0,4,0,0]])
def check_rmatvec(self):
M = self.spmatrix(matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
assert_array_almost_equal([1,2,3,4]*M, dot([1,2,3,4], M.toarray()))
row = matrix([[1,2,3,4]])
assert_array_almost_equal(row*M, row*M.todense())
def check_matvec(self):
M = self.spmatrix(matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]]))
col = matrix([1,2,3]).T
assert_array_almost_equal(M * col, M.todense() * col)
# Should this be supported or not?!
#flat = array([1,2,3])
#assert_array_almost_equal(M*flat, M.todense()*flat)
# Currently numpy dense matrices promote the result to a 1x3 matrix,
# whereas sparse matrices leave the result as a rank-1 array. Which
# is preferable?
# Note: the following command does not work. Both NumPy matrices
# and spmatrices should raise exceptions!
# assert_array_almost_equal(M*[1,2,3], M.todense()*[1,2,3])
# The current relationship between sparse matrix products and array
# products is as follows:
assert_array_almost_equal(M*array([1,2,3]), dot(M.A,[1,2,3]))
assert_array_almost_equal(M*[[1],[2],[3]], asmatrix(dot(M.A,[1,2,3])).T)
# Note that the result of M * x is dense if x has a singleton dimension.
# Currently M.matvec(asarray(col)) is rank-1, whereas M.matvec(col)
# is rank-2. Is this desirable?
def check_matmat(self):
a = matrix([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]])
a2 = array([[3,0,0],[0,1,0],[2,0,3.0],[2,3,0]])
b = matrix([[0,1],[1,0],[0,2]],'d')
asp = self.spmatrix(a)
bsp = self.spmatrix(b)
assert_array_almost_equal((asp*bsp).todense(), a*b)
assert_array_almost_equal((asp*b).todense(), a*b)
assert_array_almost_equal((a*bsp).todense(), a*b)
assert_array_almost_equal((a2*bsp).todense(), a*b)
# Now try performing cross-type multplication:
csp = bsp.tocsc()
c = b
assert_array_almost_equal((asp*csp).todense(), a*c)
assert_array_almost_equal((asp.matmat(csp)).todense(), a*c)
assert_array_almost_equal((asp*c).todense(), a*c)
assert_array_almost_equal((a*csp).todense(), a*c)
assert_array_almost_equal((a2*csp).todense(), a*c)
csp = bsp.tocsr()
assert_array_almost_equal((asp*csp).todense(), a*c)
assert_array_almost_equal((asp.matmat(csp)).todense(), a*c)
assert_array_almost_equal((asp*c).todense(), a*c)
assert_array_almost_equal((a*csp).todense(), a*c)
assert_array_almost_equal((a2*csp).todense(), a*c)
csp = bsp.tocoo()
assert_array_almost_equal((asp*csp).todense(), a*c)
assert_array_almost_equal((asp.matmat(csp)).todense(), a*c)
assert_array_almost_equal((asp*c).todense(), a*c)
assert_array_almost_equal((a*csp).todense(), a*c)
assert_array_almost_equal((a2*csp).todense(), a*c)
# Test provided by Andy Fraser, 2006-03-26
L = 30
frac = .3
random.seed(0) # make runs repeatable
A = self.spmatrix((L,2))
for i in xrange(L):
for j in xrange(2):
r = random.random()
if r < frac:
A[i,j] = r/frac
B = A*A.T
assert_array_almost_equal(B.todense(), A.todense() * A.T.todense())
assert_array_almost_equal(B.todense(), A.todense() * A.todense().T)
def check_tocoo(self):
a = self.datsp.tocoo()
assert_array_almost_equal(a.todense(), self.dat)
def check_tocsc(self):
a = self.datsp.tocsc()
assert_array_almost_equal(a.todense(), self.dat)
b = complexsp = self.spmatrix(self.dat+3j)
c = b.tocsc()
assert_array_almost_equal(c.todense(), self.dat+3j)
def check_tocsr(self):
a = self.datsp.tocsr()
assert_array_almost_equal(a.todense(), self.dat)
def check_transpose(self):
a = self.datsp.transpose()
b = self.dat.transpose()
assert_array_equal(a.todense(), b)
assert_array_equal(a.transpose().todense(), self.dat)
assert_array_equal(a.transpose().todense(), self.datsp.todense())
def check_large(self):
# Create a 100x100 matrix with 100 non-zero elements
# and play around with it
A = dok_matrix((100,100))
for k in range(100):
i = random.randrange(100)
j = random.randrange(100)
A[i,j] = 1.
csr = A.tocsr()
csc = A.tocsc()
csc2 = csr.tocsc()
coo = A.tocoo()
csr2 = coo.tocsr()
assert_array_equal(A.transpose().todense(), csr.transpose().todense())
assert_array_equal(csc.todense(), csr.todense())
assert_array_equal(csr.todense(), csr2.todense())
assert_array_equal(csr2.todense().transpose(), coo.transpose().todense())
assert_array_equal(csr2.todense(), csc2.todense())
csr_plus_csc = csr + csc
csc_plus_csr = csc + csr
assert_array_equal(csr_plus_csc.todense(), (2*A).todense())
assert_array_equal(csr_plus_csc.todense(), csc_plus_csr.todense())
def check_add_dense(self):
""" Check whether adding a dense matrix to a sparse matrix works
"""
sum1 = self.dat + self.datsp
assert_array_equal(sum1, 2*self.dat)
sum2 = self.datsp + self.dat
assert_array_equal(sum2, 2*self.dat)
def check_copy(self):
""" Check whether the copy=True and copy=False keywords work
"""
pass
# Eventually we'd like to allow matrix products between dense
# and sparse matrices using the normal dot() function:
#def check_dense_dot_sparse(self):
# a = array([1.,2.,3.])
# dense_dot_dense = dot(a, self.dat)
# dense_dot_sparse = dot(a, self.datsp)
# assert_array_equal(dense_dot_dense, dense_dot_sparse)
#def check_sparse_dot_dense(self):
# b = array([1.,2.,3.,4.])
# dense_dot_dense = dot(self.dat, b)
# dense_dot_sparse = dot(self.datsp, b)
# assert_array_equal(dense_dot_dense, dense_dot_sparse)
def check_solve(self):
""" Test whether the lu_solve command segfaults, as reported by Nils
Wagner for a 64-bit machine, 02 March 2005 (EJS)
"""
n = 20
A = self.spmatrix((n,n), dtype=complex)
x = numpy.random.rand(n)
y = numpy.random.rand(n-1)+1j*numpy.random.rand(n-1)
r = numpy.random.rand(n)
for i in range(len(x)):
A[i,i] = x[i]
for i in range(len(y)):
A[i,i+1] = y[i]
A[i+1,i] = numpy.conjugate(y[i])
B = A.tocsc()
xx = splu(B).solve(r)
# Don't actually test the output until we know what it should be ...
class _test_horiz_slicing:
"""Tests vertical slicing (e.g. [:, 0]). Tests for individual sparse
matrix types that implement this should derive from this class.
"""
def check_get_horiz_slice(self):
"""Test for new slice functionality (EJS)"""
B = asmatrix(arange(50.).reshape(5,10))
A = self.spmatrix(B)
assert_array_equal(B[1,:], A[1,:].todense())
assert_array_equal(B[1,2:5], A[1,2:5].todense())
C = matrix([[1, 2, 1], [4, 0, 6], [0, 0, 0], [0, 0, 1]])
D = self.spmatrix(C)
assert_array_equal(C[1, 1:3], D[1, 1:3].todense())
# Now test slicing when a row contains only zeros
E = matrix([[1, 2, 1], [4, 0, 0], [0, 0, 0], [0, 0, 1]])
F = self.spmatrix(E)
assert_array_equal(E[1, 1:3], F[1, 1:3].todense())
assert_array_equal(E[2, -2:], F[2, -2:].A)
# The following should raise exceptions:
caught = 0
try:
a = A[:,11]
except IndexError:
caught += 1
try:
a = A[6,3:7]
except IndexError:
caught += 1
assert caught == 2
class _test_vert_slicing:
"""Tests vertical slicing (e.g. [:, 0]). Tests for individual sparse
matrix types that implement this should derive from this class.
"""
def check_get_vert_slice(self):
"""Test for new slice functionality (EJS)"""
B = asmatrix(arange(50.).reshape(5,10))
A = self.spmatrix(B)
assert_array_equal(B[2:5,0], A[2:5,0].todense())
assert_array_equal(B[:,1], A[:,1].todense())
C = matrix([[1, 2, 1], [4, 0, 6], [0, 0, 0], [0, 0, 1]])
D = self.spmatrix(C)
assert_array_equal(C[1:3, 1], D[1:3, 1].todense())
assert_array_equal(C[:, 2], D[:, 2].todense())
# Now test slicing when a column contains only zeros
E = matrix([[1, 0, 1], [4, 0, 0], [0, 0, 0], [0, 0, 1]])
F = self.spmatrix(E)
assert_array_equal(E[:, 1], F[:, 1].todense())
assert_array_equal(E[-2:, 2], F[-2:, 2].todense())
# The following should raise exceptions:
caught = 0
try:
a = A[:,11]
except IndexError:
caught += 1
try:
a = A[6,3:7]
except IndexError:
caught += 1
assert caught == 2
class _test_fancy_indexing:
"""Tests fancy indexing features. The tests for any matrix formats
that implement these features should derive from this class.
"""
# This isn't supported by any matrix objects yet:
def check_sequence_indexing(self):
B = asmatrix(arange(50.).reshape(5,10))
A = self.spmatrix(B)
assert_array_equal(B[(1,2),(3,4)], A[(1,2),(3,4)].todense())
assert_array_equal(B[(1,2,3),(3,4,5)], A[(1,2,3),(3,4,5)].todense())
def check_fancy_indexing(self):
"""Test for new indexing functionality"""
B = ones((5,10), float)
A = dok_matrix(B)
# Write me!
# Both slicing and fancy indexing: not yet supported
# assert_array_equal(B[(1,2),:], A[(1,2),:].todense())
# assert_array_equal(B[(1,2,3),:], A[(1,2,3),:].todense())
class test_csr(_test_cs, _test_horiz_slicing, ScipyTestCase):
spmatrix = csr_matrix
def check_constructor1(self):
b = matrix([[0,4,0],
[3,0,1],
[0,2,0]],'d')
bsp = csr_matrix(b)
assert_array_almost_equal(bsp.data,[4,3,1,2])
assert_array_equal(bsp.colind,[1,0,2,1])
assert_array_equal(bsp.indptr,[0,1,3,4])
assert_equal(bsp.getnnz(),4)
assert_equal(bsp.getformat(),'csr')
assert_array_almost_equal(bsp.todense(),b)
def check_constructor2(self):
b = zeros((6,6),'d')
b[3,4] = 5
bsp = csr_matrix(b)
assert_array_almost_equal(bsp.data,[5])
assert_array_equal(bsp.colind,[4])
assert_array_equal(bsp.indptr,[0,0,0,0,1,1,1])
assert_array_almost_equal(bsp.todense(),b)
def check_constructor3(self):
b = matrix([[1,0],
[0,2],
[3,0]],'d')
bsp = csr_matrix(b)
assert_array_almost_equal(bsp.data,[1,2,3])
assert_array_equal(bsp.colind,[0,1,0])
assert_array_equal(bsp.indptr,[0,1,2,3])
assert_array_almost_equal(bsp.todense(),b)
def check_empty(self):
"""Test manipulating empty matrices. Fails in SciPy SVN <= r1768
"""
# This test should be made global (in _test_cs), but first we
# need a uniform argument order / syntax for constructing an
# empty sparse matrix. (coo_matrix is currently different).
shape = (5, 5)
for mytype in [float32, float64, complex64, complex128]:
a = self.spmatrix(shape, dtype=mytype)
b = a + a
c = 2 * a
d = a + a.tocsc()
e = a * a.tocoo()
assert_equal(e.A, a.A*a.A)
# These fail in all revisions <= r1768:
assert(e.dtype.type == mytype)
assert(e.A.dtype.type == mytype)
class test_csc(_test_cs, _test_vert_slicing, ScipyTestCase):
spmatrix = csc_matrix
def check_constructor1(self):
b = matrix([[1,0,0],[3,0,1],[0,2,0]],'d')
bsp = csc_matrix(b)
assert_array_almost_equal(bsp.data,[1,3,2,1])
assert_array_equal(bsp.rowind,[0,1,2,1])
assert_array_equal(bsp.indptr,[0,2,3,4])
assert_equal(bsp.getnnz(),4)
assert_equal(bsp.getformat(),'csc')
def check_constructor2(self):
b = zeros((6,6),'d')
b[2,4] = 5
bsp = csc_matrix(b)
assert_array_almost_equal(bsp.data,[5])
assert_array_equal(bsp.rowind,[2])
assert_array_equal(bsp.indptr,[0,0,0,0,0,1,1])
def check_constructor3(self):
b = matrix([[1,0],[0,2],[3,0]],'d')
bsp = csc_matrix(b)
assert_array_almost_equal(bsp.data,[1,3,2])
assert_array_equal(bsp.rowind,[0,2,1])
assert_array_equal(bsp.indptr,[0,2,3])
def check_empty(self):
"""Test manipulating empty matrices. Fails in SciPy SVN <= r1768
"""
# This test should be made global (in _test_cs), but first we
# need a uniform argument order / syntax for constructing an
# empty sparse matrix. (coo_matrix is currently different).
shape = (5, 5)
for mytype in [float32, float64, complex64, complex128]:
a = self.spmatrix(shape, dtype=mytype)
b = a + a
c = 2 * a
d = a + a.tocsc()
e = a * a.tocoo()
assert_equal(e.A, a.A*a.A)
assert(e.dtype.type == mytype)
assert(e.A.dtype.type == mytype)
class test_dok(_test_cs, ScipyTestCase):
spmatrix = dok_matrix
def check_mult(self):
A = dok_matrix((10,10))
A[0,3] = 10
A[5,6] = 20
D = A*A.T
E = A*A.H
assert_array_equal(D.A, E.A)
def check_add(self):
A = dok_matrix((3,2))
A[0,1] = -10
A[2,0] = 20
A += 10
B = matrix([[10, 0], [10, 10], [30, 10]])
assert_array_equal(A.todense(), B)
def check_convert(self):
"""Test provided by Andrew Straw. Fails in SciPy <= r1477.
"""
(m, n) = (6, 7)
a=dok_matrix((m, n))
# set a few elements, but none in the last column
a[2,1]=1
a[0,2]=2
a[3,1]=3
a[1,5]=4
a[4,3]=5
a[4,2]=6
# assert that the last column is all zeros
assert_array_equal( a.toarray()[:,n-1], zeros(m,) )
# make sure it still works for CSC format
csc=a.tocsc()
assert_array_equal( csc.toarray()[:,n-1], zeros(m,) )
# now test CSR
(m, n) = (n, m)
b = a.transpose()
assert b.shape == (m, n)
# assert that the last row is all zeros
assert_array_equal( b.toarray()[m-1,:], zeros(n,) )
# make sure it still works for CSR format
csr=b.tocsr()
assert_array_equal( csr.toarray()[m-1,:], zeros(n,))
def check_set_slice(self):
"""Test for slice functionality (EJS)"""
A = dok_matrix((5,10))
B = zeros((5,10), float)
A[:,0] = 1
B[:,0] = 1
assert_array_equal(A.todense(), B)
A[1,:] = 2
B[1,:] = 2
assert_array_equal(A.todense(), B)
A[:,:] = 3
B[:,:] = 3
assert_array_equal(A.todense(), B)
A[1:5, 3] = 4
B[1:5, 3] = 4
assert_array_equal(A.todense(), B)
A[1, 3:6] = 5
B[1, 3:6] = 5
assert_array_equal(A.todense(), B)
A[1:4, 3:6] = 6
B[1:4, 3:6] = 6
assert_array_equal(A.todense(), B)
A[1, 3:10:3] = 7
B[1, 3:10:3] = 7
assert_array_equal(A.todense(), B)
A[1:5, 0] = range(1,5)
B[1:5, 0] = range(1,5)
assert_array_equal(A.todense(), B)
A[0, 1:10:2] = xrange(1,10,2)
B[0, 1:10:2] = xrange(1,10,2)
assert_array_equal(A.todense(), B)
caught = 0
# The next 6 commands should raise exceptions
try:
A[0,0] = range(100)
except TypeError:
caught += 1
try:
A[0,0] = arange(100)
except TypeError:
caught += 1
try:
A[0,:] = range(100)
except ValueError:
caught += 1
try:
A[:,1] = range(100)
except ValueError:
caught += 1
try:
A[:,1] = A.copy()
except:
caught += 1
try:
A[:,-1] = range(5)
except IndexError:
caught += 1
assert caught == 6
class test_lil(_test_cs, _test_horiz_slicing, ScipyTestCase):
spmatrix = lil_matrix
def check_mult(self):
A = matrix(zeros((10,10)))
A[0,3] = 10
A[5,6] = 20
B = lil_matrix((10,10))
B[0,3] = 10
B[5,6] = 20
assert_array_equal(A * A.T, (B * B.T).todense())
assert_array_equal(A * A.H, (B * B.H).todense())
def check_lil_lil_assignment(self):
""" Tests whether a row of one lil_matrix can be assigned to
another.
"""
B = lil_matrix((10,10))
B[0,3] = 10
B[5,6] = 20
B[8,3] = 30
B[3,8] = 40
B[8,9] = 50
A = B / 10
B[0, :] = A[0, :]
assert_array_equal(A[0, :].A, B[0, :].A)
assert_array_equal(A[0, :].A, array([[0, 0, 0, 1, 0, 0, 0, 0, 0, 0]]))
def check_lil_from_csr(self):
""" Tests whether a lil_matrix can be constructed from a
csr_matrix.
"""
B = lil_matrix((10,10))
B[0,3] = 10
B[5,6] = 20
B[8,3] = 30
B[3,8] = 40
B[8,9] = 50
C = B.tocsr()
D = lil_matrix(C)
assert_array_equal(C.A, D.A)
class test_construct_utils(ScipyTestCase):
def check_identity(self):
a = spidentity(3)
b = array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='d')
assert_array_equal(a.toarray(), b)
def check_eye(self):
a = speye(2, 3 )
# print a, a.__repr__
b = array([[1, 0, 0], [0, 1, 0]], dtype='d')
assert_array_equal(a.toarray(), b)
a = speye(3, 2)
# print a, a.__repr__
b = array([[1, 0], [0, 1], [0, 0]], dtype='d')
assert_array_equal( a.toarray(), b)
a = speye(3, 3)
# print a, a.__repr__
b = array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='d')
assert_array_equal(a.toarray(), b)
class test_coo(ScipyTestCase):
def check_normalize( self ):
row = numpy.array([2, 3, 1, 3, 0, 1, 3, 0, 2, 1, 2])
col = numpy.array([0, 1, 0, 0, 1, 1, 2, 2, 2, 2, 1])
data = numpy.array([ 6., 10., 3., 9., 1., 4.,
11., 2., 8., 5., 7.])
# coo.todense()
# matrix([[ 0., 1., 2.],
# [ 3., 4., 5.],
# [ 6., 7., 8.],
# [ 9., 10., 11.]])
coo = coo_matrix((data,(row,col)),(4,3))
ndata,nrow,ncol = coo._normalize(rowfirst=True)
assert(zip(nrow,ncol,ndata) == sorted(zip(row,col,data))) #should sort by rows, then cols
assert_array_equal(coo.data, data) #coo.data has not changed
assert_array_equal(coo.row, row) #coo.row has not changed
assert_array_equal(coo.col, col) #coo.col has not changed
ndata,nrow,ncol = coo._normalize(rowfirst=False)
assert(zip(ncol,nrow,ndata) == sorted(zip(col,row,data))) #should sort by cols, then rows
assert_array_equal(coo.data, ndata) #coo.data has changed
assert_array_equal(coo.row, nrow) #coo.row has changed
assert_array_equal(coo.col, ncol) #coo.col has changed
assert_array_equal(coo.tocsr().todense(), coo.todense())
assert_array_equal(coo.tocsc().todense(), coo.todense())
if __name__ == "__main__":
ScipyTest().run()
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