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_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_csvreader(self):
data = np.random.random((101, 3))
fn = tempfile.mktemp()
try:
np.savetxt(fn, data)
# calc offsets
offsets = [0]
with open(fn, PyCSVReader.DEFAULT_OPEN_MODE) as new_fh:
while new_fh.readline():
offsets.append(new_fh.tell())
reader = PyCSVReader(fn)
assert reader.dimension() == 3
trajinfo = reader._get_traj_info(fn)
np.testing.assert_equal(offsets, trajinfo.offsets)
finally:
os.unlink(fn)
def test_compare_readline(self):
data = np.arange(99*3).reshape(-1, 3)
fn = tempfile.mktemp()
try:
np.savetxt(fn, data)
# calc offsets
reader = CSVReader(fn)
assert reader.dimension() == 3
trajinfo = reader._get_traj_info(fn)
offset = [0]
with open(fn, CSVReader.DEFAULT_OPEN_MODE) as fh2:
while fh2.readline():
offset.append(fh2.tell())
fh2.seek(0)
for ii, off in enumerate(trajinfo.offsets):
fh2.seek(off)
line = fh2.readline()
fh2.seek(offset[ii])
line2 = fh2.readline()
self.assertEqual(line, line2, "differs at offset %i (%s != %s)" % (ii, off, offset[ii]))
finally:
os.unlink(fn)
def test_compare_readline(self):
data = np.arange(99*3).reshape(-1, 3)
with tempfile.NamedTemporaryFile(delete=False) as f:
fn = f.name
np.savetxt(fn, data)
# calc offsets
reader = CSVReader(fn)
assert reader.dimension() == 3
trajinfo = reader._get_traj_info(fn)
offset = [0]
with open(fn, CSVReader.DEFAULT_OPEN_MODE) as fh2:
while fh2.readline():
offset.append(fh2.tell())
fh2.seek(0)
np.testing.assert_equal(trajinfo.offsets, offset)
for ii, off in enumerate(trajinfo.offsets):
fh2.seek(off)
line = fh2.readline()
fh2.seek(offset[ii])
line2 = fh2.readline()
self.assertEqual(line, line2, "differs at offset %i (%s != %s)" % (ii, off, offset[ii]))
