def setUp(self):
testpath = abspath(join(abspath(__file__), pardir)) + '/../../util/tests/data/'
import pyemma.util.discrete_trajectories as dt
self.dtraj = dt.read_discrete_trajectory(testpath + '2well_traj_100K.dat')
self.tau = 10
self.msm = markov_state_model(self.dtraj, self.tau)
def read_dtrajs_from_pattern(patterns, logger=getLogger()):
"""
Parameters
----------
patterns : single pattern or list of patterns
eg. '*.txt' or ['/foo/*/bar/*.txt', '*.txt']
Returns
-------
list of discrete trajectories : list of numpy arrays, dtype=int
"""
dtrajs = []
filenames = paths_from_patterns(patterns)
if filenames == []:
raise ValueError('no match to given pattern')
for dt in filenames:
# skip directories
if os.path.isdir(dt):
continue
logger.info('reading discrete trajectory: %s' % dt)
try:
dtrajs.append(read_discrete_trajectory(dt))
except Exception as e:
logger.error('Exception occurred during reading of %s:\n%s' %
(dt, e))
raise
return dtrajs
def read_dtrajs_from_pattern(patterns, logger=getLogger()):
"""
Parameters
----------
patterns : single pattern or list of patterns
eg. '*.txt' or ['/foo/*/bar/*.txt', '*.txt']
Returns
-------
list of discrete trajectories : list of numpy arrays, dtype=int
"""
dtrajs = []
filenames = paths_from_patterns(patterns)
if filenames == []:
raise ValueError('no match to given pattern')
for dt in filenames:
# skip directories
if os.path.isdir(dt):
continue
logger.info('reading discrete trajectory: %s' % dt)
try:
dtrajs.append(read_discrete_trajectory(dt))
except Exception as e:
logger.error(
'Exception occurred during reading of %s:\n%s' % (dt, e))
raise
return dtrajs
def setUp(self):
testpath = abspath(join(abspath(__file__),
pardir)) + '/../../util/tests/data/'
import pyemma.util.discrete_trajectories as dt
self.dtraj = dt.read_discrete_trajectory(testpath +
'2well_traj_100K.dat')
self.tau = 10
self.msm = markov_state_model(self.dtraj, self.tau)
def read_discrete_trajectory(filename):
r"""Read discrete trajectory from ascii file.
Parameters
----------
filename : str
The filename of the discretized trajectory file.
The filename can either contain the full or the
relative path to the file.
Returns
-------
dtraj : (M, ) ndarray of int
Discrete state trajectory.
See also
--------
write_discrete_trajectory
Notes
-----
The discrete trajectory file contains a single column with
integer entries.
Examples
--------
>>> from tempfile import NamedTemporaryFile
>>> from pyemma.msm.io import write_discrete_trajectory, load_discrete_trajectory
Use temporary file
>>> tmpfile = NamedTemporaryFile()
Discrete trajectory
>>> dtraj = np.array([0, 1, 0, 0, 1, 1, 0])
Write to disk (as ascii file)
>>> write_discrete_trajectory(tmpfile.name, dtraj)
Read from disk
>>> X = read_discrete_trajectory(tmpfile.name)
>>> X
array([0, 1, 0, 0, 1, 1, 0])
"""
return trajectory.read_discrete_trajectory(filename)
def read_discrete_trajectory(filename):
r"""Read discrete trajectory from ascii file.
Parameters
----------
filename : str
The filename of the discretized trajectory file.
The filename can either contain the full or the
relative path to the file.
Returns
-------
dtraj : (M, ) ndarray of int
Discrete state trajectory.
See also
--------
write_discrete_trajectory
Notes
-----
The discrete trajectory file contains a single column with
integer entries.
Examples
--------
>>> from tempfile import NamedTemporaryFile
>>> from pyemma.msm.io import write_discrete_trajectory, load_discrete_trajectory
Use temporary file
>>> tmpfile = NamedTemporaryFile()
Discrete trajectory
>>> dtraj = np.array([0, 1, 0, 0, 1, 1, 0])
Write to disk (as ascii file)
>>> write_discrete_trajectory(tmpfile.name, dtraj)
Read from disk
>>> X = read_discrete_trajectory(tmpfile.name)
>>> X
array([0, 1, 0, 0, 1, 1, 0])
"""
return trajectory.read_discrete_trajectory(filename)
def test_read_discrete_trajectory(self):
dtraj_np = np.loadtxt(self.filename, dtype=int)
dtraj = dt.read_discrete_trajectory(self.filename)
self.assertTrue(np.all(dtraj_np == dtraj))
def test_read_discrete_trajectory(self):
dtraj_np=np.loadtxt(self.filename, dtype=int)
dtraj=dt.read_discrete_trajectory(self.filename)
self.assertTrue(np.all(dtraj_np==dtraj))
def test_big(self):
dtraj = dt.read_discrete_trajectory(testpath+'2well_traj_100K.dat')
# just run these to see if there's any exception
dt.index_states(dtraj)