unify unassigned frame assignment

pyemma/msm/estimators/_dtraj_stats.py

@@ -23,7 +23,7 @@
 from msmtools import estimation as msmest
 from pyemma.util.annotators import alias, aliased
 from pyemma.util.linalg import submatrix
-from pyemma.util.discrete_trajectories import visited_set, rewrite_dtrajs_to_core_sets
+from pyemma.util.discrete_trajectories import visited_set
 
 __author__ = 'noe'
 
@@ -184,15 +184,11 @@ def count_lagged(self, lag, count_mode='sliding', mincount_connectivity='1/n',
         # Compute count matrix
         count_mode = count_mode.lower()
         if core_set is not None and count_mode in ('sliding', 'sample'):
-
-            # set non-core states to -1
-            for d in self._dtrajs:
-                d[~np.in1d(d, core_set)] = -1
-
             if milestoning_method == 'last_core':
 
                 # assign -1 frames to last visited core
                 for d in self._dtrajs:
+                    assert d[0] != -1
                     while -1 in d:
                         mask = (d == -1)
                         d[mask] = d[np.roll(mask, -1)]

pyemma/util/discrete_trajectories.py

@@ -283,16 +283,12 @@ def rewrite_dtrajs_to_core_sets(dtrajs, core_set, in_place=False):
     if not in_place:
         dtrajs = copy.deepcopy(dtrajs)
 
-    # build a boolean expression to create a mask of indices within the core set.
-    expr = ['(d == {i})'.format(i=i) for i in core_set]
-    expr = '|'.join(expr)
-
     # if we have no state definition at the beginning of a trajectory, we store the offset to the first milestone.
     offsets = [0]*len(dtrajs)
 
     for i, d in enumerate(dtrajs):
-        within_core_set = eval(expr)
-        outside_core_set = np.logical_not(within_core_set)
+        # set non-core states to -1
+        outside_core_set = ~np.in1d(d, core_set)
         if not np.any(outside_core_set):
             continue
         d[outside_core_set] = -1