Adds Reader.timeseries

package/CHANGELOG

@@ -17,6 +17,9 @@ mm/dd/yy
 
   * 0.16.2
 
+Deprecations
+  * deprecated core.Timeseries module (Issue #1383)
+
 Enhancements
 
 Fixes

package/MDAnalysis/coordinates/DCD.py

@@ -81,6 +81,7 @@
 import os
 import errno
 import numpy as np
+from numpy.lib.utils import deprecate
 import struct
 import types
 import warnings
@@ -578,6 +579,7 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
         # XXX needs to be implemented
         return self._read_timeseries(atom_numbers, start, stop, step, format)
 
+    @deprecate(message="This method will be removed in 0.17")
     def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
         """Populate a :class:`~MDAnalysis.core.Timeseries.TimeseriesCollection` object
         with time series computed from the trajectory.

package/MDAnalysis/coordinates/__init__.py

@@ -538,10 +538,6 @@ class can choose an appropriate reader automatically.
  ``timeseries(atomGroup, [start[,stop[,skip[,format]]]])``
      returns a subset of coordinate data
 
- ``correl(timeseriesCollection[,start[,stop[,skip]]])``
-     populate a :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` object
-     with observable timeseries computed from the trajectory
-
 
 Attributes
 ..........

package/MDAnalysis/coordinates/base.py

@@ -1461,6 +1461,60 @@ def __repr__(self):
             natoms=self.n_atoms
         ))
 
+    def timeseries(self, asel=None, start=None, stop=None, step=None,
+                   format='fac'):
+        """Return a subset of coordinate data for an AtomGroup
+
+        Parameters
+        ----------
+        asel : :class:`~MDAnalysis.core.groups.AtomGroup` (optional)
+            The :class:`~MDAnalysis.core.groups.AtomGroup` to read the
+            coordinates from. Defaults to None, in which case the full set of
+            coordinate data is returned.
+        start :  int (optional)
+             Begin reading the trajectory at frame index `start` (where 0 is the index
+             of the first frame in the trajectory); the default ``None`` starts
+             at the beginning.
+        stop : int (optional)
+             End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded.
+             The trajectory is read to the end with the default ``None``.
+        step : int (optional)
+             Step size for reading; the default ``None`` is equivalent to 1 and means to
+             read every frame.
+        format : str (optional)
+            the order/shape of the return data array, corresponding
+            to (a)tom, (f)rame, (c)oordinates all six combinations
+            of 'a', 'f', 'c' are allowed ie "fac" - return array
+            where the shape is (frame, number of atoms,
+            coordinates)
+
+        """
+        start, stop, step = self.check_slice_indices(start, stop, step)
+        nframes = len(range(start, stop, step))
+
+        if asel is not None:
+            if len(asel) == 0:
+                raise NoDataError(
+                    "Timeseries requires at least one atom to analyze")
+            atom_numbers = asel.indices
+            natoms = len(atom_numbers)
+        else:
+            atom_numbers = None
+            natoms = self.n_atoms
+
+        if not format in ('fac', None):
+            # need to add swapping around axes etc
+            raise NotImplementedError
+
+        # allocate output array
+        coordinates = np.empty((nframes, natoms, 3), dtype=np.float32)
+        for i, ts in enumerate(self[start:stop:step]):
+            # if atom_number == None, this will cause view of array
+            # do we need copy in this case?
+            coordinates[i] = ts.positions[atom_numbers].copy()
+
+        return coordinates
+
     def add_auxiliary(self, auxname, auxdata, format=None, **kwargs):
         """Add auxiliary data to be read alongside trajectory.
 

package/MDAnalysis/core/Timeseries.py

@@ -61,9 +61,12 @@
 from __future__ import division, absolute_import
 import warnings
 
+from numpy.lib.utils import deprecate
+
 from . import groups
 
 
+@deprecate(message="This class will be removed in 0.17")
 class TimeseriesCollection(object):
     '''A collection of timeseries objects.
 
@@ -185,6 +188,7 @@ def _getAuxData(self):
         return auxData
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Timeseries(object):
     '''Base timeseries class - define subclasses for specific timeseries computations
     '''
@@ -240,6 +244,7 @@ def getAuxData(self):
         return [0.] * self.n_atoms
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Atom(Timeseries):
     '''Create a timeseries that returns coordinate data for an atom or group of atoms ::
 
@@ -276,6 +281,7 @@ def getAtomCounts(self):
         return [1, ] * self.n_atoms
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Bond(Timeseries):
     '''Create a timeseries that returns a timeseries for a bond
 
@@ -291,6 +297,7 @@ def __init__(self, atoms):
         Timeseries.__init__(self, 'r', atoms, 1)
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Angle(Timeseries):
     '''Create a timeseries that returns a timeseries for an angle
 
@@ -306,6 +313,7 @@ def __init__(self, atoms):
         Timeseries.__init__(self, 'a', atoms, 1)
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Dihedral(Timeseries):
     '''Create a timeseries that returns a timeseries for a dihedral angle
 
@@ -321,6 +329,7 @@ def __init__(self, atoms):
         Timeseries.__init__(self, 'h', atoms, 1)
 
 
+@deprecate(message="This class will be removed in 0.17")
 class Distance(Timeseries):
     '''Create a timeseries that returns distances between 2 atoms
 
@@ -343,6 +352,7 @@ def __init__(self, code, atoms):
         Timeseries.__init__(self, code, atoms, size)
 
 
+@deprecate(message="This class will be removed in 0.17")
 class CenterOfGeometry(Timeseries):
     '''Create a timeseries that returns the center of geometry of a group of atoms
 
@@ -359,6 +369,7 @@ def getAuxData(self):
         return [1.] * self.n_atoms
 
 
+@deprecate(message="This class will be removed in 0.17")
 class CenterOfMass(Timeseries):
     '''Create a timeseries that returns the center of mass of a group of atoms
 
@@ -375,6 +386,7 @@ def getAuxData(self):
         return [a.mass for a in self.atoms]
 
 
+@deprecate(message="This class will be removed in 0.17")
 class WaterDipole(Timeseries):
     r'''Create a Timeseries that returns a timeseries for the bisector vector of a 3-site water
 

package/MDAnalysis/core/universe.py

@@ -467,26 +467,8 @@ def transfer_to_memory(self, start=None, stop=None, step=None,
         verbose = _set_verbose(verbose, quiet, default=False)
 
         if not isinstance(self.trajectory, MemoryReader):
-            # Try to extract coordinates using Timeseries object
-            # This is significantly faster, but only implemented for certain
-            # trajectory file formats
-            try:
-                coordinates = self.trajectory.timeseries(
-                    self.atoms, start=start, stop=stop, step=step, format='fac')
-            # if the Timeseries extraction fails,
-            # fall back to a slower approach
-            except AttributeError:
-                n_frames = len(range(
-                    *self.trajectory.check_slice_indices(start, stop, step)
-                ))
-                pm_format = '{step}/{numsteps} frames copied to memory (frame {frame})'
-                pm = ProgressMeter(n_frames, interval=1,
-                                   verbose=verbose, format=pm_format)
-                coordinates = []  # TODO: use pre-allocated array
-                for i, ts in enumerate(self.trajectory[start:stop:step]):
-                    coordinates.append(np.copy(ts.positions))
-                    pm.echo(i, frame=ts.frame)
-                coordinates = np.array(coordinates)
+            coordinates = self.trajectory.timeseries(
+                self.atoms, start=start, stop=stop, step=step, format='fac')
 
             # Overwrite trajectory in universe with an MemoryReader
             # object, to provide fast access and allow coordinates