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_rectangular_real(self):
a = [[1, 2], [3.5, 4], [5, 6]]
fn = self.fn
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_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 matrixFactorization_graphlab(self,rows,cols,r,c,algo):
if platform.system() == 'Windows':
base_dir = 'D:'
elif platform.system() == 'Linux':
base_dir = '/workspace'
# Pull out the sparse sub-matrix for current co-cluster
#print r,c
Y_sparse = self.coo_submatrix_pull(rows,cols)
# Convert Data into Matrix Market format and write the Training data to file
Y_mm_file_name = base_dir + '/sdap/data/temp/mf'
# Remove the current files in .../data/temp/
#cmd = "rm -f" + base_dir + "/sdap/data/temp/*"
#os.system(cmd)
if os.path.isdir(base_dir + "/sdap/data/temp/"):
shutil.rmtree(base_dir + "/sdap/data/temp/")
os.mkdir(base_dir + "/sdap/data/temp/")
Y_mm_file = open(Y_mm_file_name,'w')
mm.mmwrite(Y_mm_file,Y_sparse,comment="")
# Call Matrix Factorization code
cmd = "~/graphlabapi/release/demoapps/pmf/pmf "+ Y_mm_file_name +" --matrixmarket=true --D="+str(self.D)+" --lambda="+str(self.lambda_reg)+" --minval=0.5 --maxval=5.0 --ncpus=16 --max_iter=50 --threshold=1e-6"
subprocess.call(cmd,shell=True)#,stdout=subprocess.PIPE,stderr=subprocess.STDOUT) #TO DO replace
#os.system(cmd)
# Read all the files for the output Latent Factors and return Us and Vs
U,V = self.readLatentFactors(base_dir)
#print U.shape, len(rows)
#print V.shape, len(cols)
#import sys
#sys.exit()
return U,V
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_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_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_rectangular(self):
a = [[1, 2, 3], [4, 5, 6]]
fn = self.fn
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_complex(self):
a = [[1, 2], [3, 4j]]
fn = self.fn
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_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_simple_real(self):
a = [[1, 2], [3, 4.0]]
fn = self.fn
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_real(self):
a = [[1,2],[3,4.0]]
fn = self.fn
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_hermitian(self):
a = [[1, 2 + 3j], [2 - 3j, 4]]
fn = self.fn
mmwrite(fn, a)
assert_equal(mminfo(fn), (2, 2, 4, "array", "complex", "hermitian"))
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 = self.fn
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_skew_symmetric(self):
a = [[1, 2], [-2, 4]]
fn = self.fn
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_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_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_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)
def test_random_rect_real(self):
sz = (20, 15)
a = rand(*sz)
fn = self.fn
mmwrite(fn, a)
assert_equal(mminfo(fn), (20, 15, 300, "array", "real", "general"))
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)
def test_random_symmetric_real(self):
sz = (20, 20)
a = rand(*sz)
a = a + transpose(a)
fn = self.fn
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_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_simple_pattern(self):
a = scipy.sparse.csr_matrix([[0, 1.5], [3.0, 2.5]])
p = np.zeros_like(a.todense())
p[a.todense() > 0] = 1
info = (2, 2, 3, 'coordinate', 'pattern', 'general')
mmwrite(self.fn, a, field='pattern')
assert_equal(mminfo(self.fn), info)
b = mmread(self.fn)
assert_array_almost_equal(p, b.todense())
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_simple_pattern(self):
a = scipy.sparse.csr_matrix([[0, 1.5], [3.0, 2.5]])
p = np.zeros_like(a.todense())
p[a.todense() > 0] = 1
info = (2, 2, 3, 'coordinate', 'pattern', 'general')
mmwrite(self.fn, a, field='pattern')
assert_equal(mminfo(self.fn), info)
b = mmread(self.fn)
assert_array_almost_equal(p, b.todense())
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_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_empty_write_read(self):
# https://github.com/scipy/scipy/issues/1410 (Trac #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_empty_write_read(self):
# https://github.com/scipy/scipy/issues/1410 (Trac #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_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_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_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 _mmio_example(m=100, n=100, k=10):
print ('\nTesting mmio read and write ...\n')
import scipy.io.mmio as mmio
W_org = random.rand(m, k)
H_org = random.rand(n, k)
X = W_org.dot(H_org.T)
X[random.rand(m, n) < 0.5] = 0
X_sparse = sps.csr_matrix(X)
filename = '_temp_mmio.mtx'
mmio.mmwrite(filename, X_sparse)
A = mmio.mmread(filename)
alg = NMF_ANLS_BLOCKPIVOT()
rslt = alg.run(X_sparse, k, max_iter=50)
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)])
def _mmio_example(m=100, n=100, k=10):
print '\nTesting mmio read and write ...\n'
import scipy.io.mmio as mmio
W_org = random.rand(m, k)
H_org = random.rand(n, k)
X = W_org.dot(H_org.T)
X[random.rand(n, k) < 0.5] = 0
X_sparse = sps.csr_matrix(X)
filename = '_temp_mmio.mtx'
mmio.mmwrite(filename, X_sparse)
A = mmio.mmread(filename)
alg = NMF_ANLS_BLOCKPIVOT()
rslt = alg.run(X_sparse, k, max_iter=50)
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_allclose(A.data, [float('%%.%dg' % precision % value)])
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_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_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_gzip_py3(self):
# test if fix for #2152 works
try:
# gzip module can be missing from Python installation
import gzip
except ImportError:
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_bzip2_py3(self):
# test if fix for #2152 works
try:
# bz2 module isn't always built when building Python.
import bz2
except ImportError:
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 check_exact(self, a, info):
mmwrite(self.fn, a)
assert_equal(mminfo(self.fn), info)
b = mmread(self.fn)
assert_equal(a, b)
def exportMmf(self, filename):
"""Exports the matrix to a Matrix Market file of the given `filename`.
"""
from scipy.io import mmio
mmio.mmwrite(filename, self.matrix)
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 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 check_exact(self, a, info):
mmwrite(self.fn, a)
assert_equal(mminfo(self.fn), info)
b = mmread(self.fn)
assert_equal(a, b)