def test_read_with_skipping_first_few_couple_lines_multiple_trajectoryfiles(self):
for skip in [0, 3, 13]:
r1 = CSVReader([self.filename1, self.filename2])
out_with_skip = r1.get_output(skip=skip)
r2 = CSVReader([self.filename1, self.filename2])
out = r2.get_output()
np.testing.assert_almost_equal(out_with_skip[0], out[0][skip::],
err_msg="The first %s rows of the first file were skipped, but that did not "
"match the rows with skip=0 and sliced by [%s::]" % (skip, skip))
np.testing.assert_almost_equal(out_with_skip[1], out[1][skip::],
err_msg="The first %s rows of the second file were skipped, but that did not"
" match the rows with skip=0 and sliced by [%s::]" % (skip, skip))
def test_read_with_skipping_first_few_couple_lines(self):
for skip in [0, 3, 13]:
# FIXME: opening the same file twice is not being liked by py27
r1 = CSVReader(self.filename1, chunksize=30)
out_with_skip = r1.get_output(skip=skip)[0]
assert len(out_with_skip) == len(self.data[skip:])
r2 = CSVReader(self.filename1, chunksize=30)
self.maxDiff=None
#self.assertDictEqual(r1.__dict__, r2.__dict__)
out = r2.get_output()[0]
np.testing.assert_almost_equal(out_with_skip, out[skip::],
err_msg="The first %s rows were skipped, but that did not "
"match the rows with skip=0 and sliced by [%s::]" % (skip, skip))
def test_read_1file_oneline(self):
tiny = np.array([1, 2, 3])
with tempfile.NamedTemporaryFile(mode='wb', suffix='.dat', delete=False) as f:
np.savetxt(f, tiny)
f.close()
reader = CSVReader(f.name, delimiters=" ")
np.testing.assert_equal(reader.get_output()[0], np.atleast_2d(tiny).T)
def test_with_kwargs(self):
args = {'header': 27}
reader = CSVReader(self.filename1, **args)
output = reader.get_output()
np.testing.assert_almost_equal(output[0], self.data)
def test_newline_at_eof_with_header(self):
with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
f.write("#x y z\n1 2 3\n4 5 6\n\n")
f.close()
desired = np.genfromtxt(f.name, dtype=np.float32).reshape(-1, 3)
reader = CSVReader(f.name)
result = reader.get_output()[0]
np.testing.assert_allclose(result, desired)
def test_read_1file_with_header(self):
reader = CSVReader(self.file_with_header)
self.assertEqual(reader.number_of_trajectories(), 1)
self.assertEqual(reader.dimension(), self.nd)
self.assertEqual(reader.n_frames_total(), self.nt)
output = reader.get_output()
np.testing.assert_almost_equal(output[0], self.data)
def test_holes_in_file(self):
x = "1 2 3\n4 5 6\n7 8 9"
desired = np.fromstring(x, sep=" ", dtype=np.float32).reshape(-1, 3)
with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
f.write(x)
f.close()
reader = CSVReader(f.name)
result = reader.get_output()[0]
np.testing.assert_allclose(result, desired)
def test_newline_at_eof_carriage_return(self):
x = "1 2 3\r\n4 5 6\r\n"
desired = np.fromstring(x, sep=" ", dtype=np.float32).reshape(-1, 3)
with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
f.write(x)
f.close()
reader = CSVReader(f.name)
result = reader.get_output()[0]
np.testing.assert_allclose(result, desired)
def test_with_stride(self):
reader = CSVReader(self.filename1)
for s in [2, 3, 7, 10]:
output = reader.get_output(stride=s)[0]
np.testing.assert_almost_equal(output, self.data[::s], err_msg="stride=%s"%s)