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_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_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 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_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_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_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_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_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 main():
if (len(sys.argv) != 2):
print "Usage: " + sys.argv[0] + " matrix-name"
sys.exit(0)
# end if
matrixName = sys.argv[1] + ".mtx"
mm = open(sys.argv[1] + '.mm', 'w')
outputName = sys.argv[1] + ".png"
#outputName=sys.argv[1]+ ".pdf"
(n, n, nz, void, fld, symm) = mminfo(matrixName)
A = mmread(matrixName).tocsr().tocoo()
# creating a file in coo format
#print n, n, A.size
mm.write(str(n) + ' ' + str(n) + ' ' + str(A.size) + '\n')
for i in range(A.size):
mm.write(
str(A.row[i]) + ' ' + str(A.col[i]) + ' ' + str(A.data[i]) + '\n')
#print A.row[i]+1, A.col[i]+1 , A.data[i]
# end for
#print repr(A)
#print A.col
#print A.size
# end of creating a file in coo format
#pylab.title("Matrix :" + matrixName, fontsize=22)
pylab.title("Matrix: " + sys.argv[1] + ", n:" + str(n) + ", nz:" +
str(A.size) + '\n',
fontsize=10)
pylab.spy(A, marker='.', markersize=1)
pylab.savefig(outputName, format=None)
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_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_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_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_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_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 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_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_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_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 = 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_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_read_symmetric(self):
fn = self.fn
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, 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_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_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_read_symmetric_pattern(self):
fn = self.fn
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_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_read_general(self):
fn = self.fn
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, 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_symmetric(self):
fn = self.fn
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_general(self):
fn = self.fn
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_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):
#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):
# 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_read_symmetric_pattern(self):
fn = self.fn
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):
# 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 check_read(self, example, a, info, dense, over32, over64):
with open(self.fn, 'w') as f:
f.write(example)
assert_equal(mminfo(self.fn), info)
if (over32 and (np.intp(0).itemsize < 8)) or over64:
assert_raises(OverflowError, mmread, self.fn)
else:
b = mmread(self.fn)
if not dense:
b = b.todense()
assert_equal(a, b)
def check_read(self, example, a, info, dense, over32, over64):
with open(self.fn, 'w') as f:
f.write(example)
assert_equal(mminfo(self.fn), info)
if (over32 and (np.intp(0).itemsize < 8)) or over64:
assert_raises(OverflowError, mmread, self.fn)
else:
b = mmread(self.fn)
if not dense:
b = b.todense()
assert_equal(a, b)
def test_read_hermitian(self):
fn = self.fn
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_general(self):
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_symmetric_pattern(self):
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_read_hermitian(self):
fn = self.fn
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):
fn = self.fn
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_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 multiply(fname):
mat = mmread(fname)
rows, cols, nnzs = mminfo(fname)[0:3]
vec = np.ones((rows, 1), dtype=np.int)
matcoo = mat.tocoo()
start1 = timeit.default_timer()
matcoo.dot(vec)
stop1 = timeit.default_timer()
t1 = (stop1 - start1) * math.pow(10, 6)
matcsr = mat.tocsr()
start2 = timeit.default_timer()
matcsr.dot(vec)
stop2 = timeit.default_timer()
t2 = (stop2 - start2) * math.pow(10, 6)
matcsc = mat.tocsc()
start3 = timeit.default_timer()
matcsc.dot(vec)
stop3 = timeit.default_timer()
t3 = (stop3 - start3) * math.pow(10, 6)
matlil = mat.tolil()
start4 = timeit.default_timer()
matlil.dot(vec)
stop4 = timeit.default_timer()
t4 = (stop4 - start4) * math.pow(10, 6)
matdia = mat.todia()
start5 = timeit.default_timer()
matdia.dot(vec)
stop5 = timeit.default_timer()
t5 = (stop5 - start5) * math.pow(10, 6)
matdok = mat.todok()
start6 = timeit.default_timer()
matdok.dot(vec)
stop6 = timeit.default_timer()
t6 = (stop6 - start6) * math.pow(10, 6)
return rows, cols, nnzs, t1, t2, t3, t4, t5, t6
def generate_mm_and_plot(matrixname):
matrixName=matrixname+ ".mtx"
mm = open(matrixname +'.mm', 'w')
outputName=matrixname + ".png"
#outputName=matrixname + ".pdf"
(n,n,nz,void,fld,symm) = mminfo(matrixName)
A = mmread(matrixName).tocsr().tocoo()
# creating a file in coo format
#print n, n, A.size
mm.write( str(n) + ' ' + str(n) + ' ' + str(A.size) + '\n')
for i in range(A.size):
mm.write( str(A.row[i])+ ' ' + str(A.col[i])+ ' ' + str(A.data[i])+ '\n')
#print A.row[i]+1, A.col[i]+1 , A.data[i]
# end for
#print repr(A)
#print A.col
#print A.size
# end of creating a file in coo format
#pylab.title("Matrix :" + matrixname, fontsize=22)
pylab.title("Matrix: " + matrixname + ", n:" + str(n) + ", nz:" + str(A.size) + '\n' ,fontsize=10 )
pylab.spy(A,marker='.',markersize=1)
pylab.savefig(outputName,format=None)
conf = SparkConf().setAppName("SparseMultiplication").setMaster("local[4]")
sc = SparkContext(conf=conf)
sqlContext = SQLContext(sc)
print("Successfully imported Spark")
except ImportError as e:
print("Can not import Spark", e)
sys.exit(1)
"""if __name__ == "__main__":
def myFunc(s):
words = s.split("\n")
return len(words)"""
fname = '/Users/nehapulipati/Downloads/bcsstk01.mtx'
mat = mmread(fname)
sp_rows, sp_cols, nnzs = mminfo(fname)[0:3]
newmat = mat.tocsc()
sm3 = scipy.sparse.rand(3, 2, density=0.2, format='csc')
rand_mat = scipy.sparse.rand(sp_cols, sp_cols, density=0.2, format='csc')
value1 = newmat.data
col_index1 = newmat.indices
row_pointers1 = newmat.indptr
value2 = rand_mat.data
col_index2 = rand_mat.indices
row_pointers2 = rand_mat.indptr
start2 = timeit.default_timer()
just = newmat * rand_mat
stop2 = timeit.default_timer()
t2 = (stop2 - start2)
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 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())