Slicing fixes

package/MDAnalysis/coordinates/dcdtimeseries.pyx

@@ -59,7 +59,7 @@ cdef extern from "correl.h":
 
 import numpy as np
 
-def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int skip):
+def __read_timecorrel(object self, object atoms, object atomcounts, object format, object auxdata, int sizedata, int lowerb, int upperb, int start, int stop, int step):
     cdef dcdhandle* dcd
     cdef numpy.ndarray atomlist, atomcountslist, auxlist
     cdef numpy.ndarray data, temp
@@ -69,8 +69,10 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
 
     dcd = <dcdhandle*>PyCObject_AsVoidPtr(self._dcd_C_ptr)
     cdef int n_frames
-    if (stop == -1): stop = dcd.nsets
-    n_frames = (stop-start+1) / skip
+
+    if stop == dcd.nsets: stop -= 1;
+    n_frames = ((stop-start) / step) + 1;
+    if (stop-start) % step == 0: n_frames -= 1;
     cdef int numdata
     numdata = len(format)
     if numdata==0:
@@ -109,18 +111,25 @@ def __read_timecorrel(object self, object atoms, object atomcounts, object forma
     cdef int index, numskip
     cdef int i, j
     cdef float unitcell[6]
+    cdef int remaining_frames = stop-start
+    numskip = 0
+    print n_frames
     for i from 0 <= i < n_frames:
-        if (skip > 1):
+        if (step > 1 and i > 0):
             # Check if we have fixed atoms
             # XXX not done
-            numskip = skip - (dcd.setsread % skip) - 1
+            numskip = step - 1
+            if(remaining_frames < numskip):
+               numskip = 1
+
             rc = skip_dcdstep(dcd.fd, dcd.natoms, dcd.nfixed, dcd.charmm, numskip)
             if (rc < 0):
                 raise IOError("Error skipping frame from DCD file")
-            dcd.setsread = dcd.setsread + numskip
+        dcd.setsread = dcd.setsread + numskip
         rc = read_dcdsubset(dcd.fd, dcd.natoms, lowerb, upperb, tempX, tempY, tempZ, unitcell, dcd.nfixed, dcd.first, dcd.freeind, dcd.fixedcoords, dcd.reverse, dcd.charmm)
-        dcd.first=0
-        dcd.setsread = dcd.setsread + 1
+        dcd.first = 0
+        dcd.setsread += 1
+        remaining_frames = stop - dcd.setsread
         if (rc < 0):
             raise IOError("Error reading frame from DCD file")
         # Copy into data array based on format

package/MDAnalysis/coordinates/src/dcd.c

@@ -467,8 +467,8 @@ __read_timeseries(PyObject *self, PyObject *args)
    Py_DECREF(temp);
 
 
-   if (stop == dcd->nsets) { stop = dcd->nsets -1; }
-   n_frames = ((stop-start) / step)+ 1;
+   if (stop == dcd->nsets) { stop = dcd->nsets - 1; }
+   n_frames = ((stop-start) / step) + 1;
    if ((stop-start) % step == 0) { n_frames--;}
    //n_frames = dcd->nsets / skip;
    n_atoms = PyList_Size((PyObject*)atoms);

package/MDAnalysis/core/Timeseries.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- http://www.MDAnalysis.org
 # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
@@ -52,6 +52,7 @@
 .. autoclass:: WaterDipole
 
 """
+import warnings
 
 from . import AtomGroup
 
@@ -104,16 +105,30 @@ def clear(self):
         '''clear the timeseries collection'''
         self.timeseries = []
 
-    def compute(self, trj, start=0, stop=-1, skip=1):
+    def compute(self, trj, start=None, stop=None, skip=None, step=None):
         '''Iterate through the trajectory *trj* and compute the time series.
 
          *trj*
             dcd trajectory object (i.e. :attr:`Universe.trajectory`)
+         *start*
+            First frame of trajectory to analyse, Default: None becomes 0.
+         *stop*
+            Frame index to stop analysis. Default: None becomes
+            n_frames. Iteration stops *before* this frame number,
+            which means that the trajectory would be read until the end.
+         *step*
+            Step between frames to analyse, Default: None becomes 1.
+         *Deprecated*
+            Skip is deprecated in favor of step.
 
-         *start, stop, skip*
-            Frames to calculate parts of the trajectory. It is important to
-            note that *start* and *stop* are inclusive
         '''
+        if skip is not None:
+            step = skip
+            warnings.warn("Skip is deprecated and will be removed in"
+                          "in 1.0. Use step instead.",
+                          category=DeprecationWarning)
+
+        start, stop, step = trj.check_slice_indices(start, stop, skip)
         self.data = trj.correl(self, start, stop, skip)
         # Now remap the timeseries data to each timeseries
         typestr = "|f8"

testsuite/MDAnalysisTests/coordinates/test_dcd.py

@@ -432,9 +432,10 @@ def test_coordinates(self):
 class TestDCDCorrel(TestCase):
     def setUp(self):
         # Note: setUp is executed for *every* test !
-        super(TestDCDCorrel, self).setUp()
         import MDAnalysis.core.Timeseries as TS
-
+        self.universe = mda.Universe(PSF, DCD)
+        self.dcd = self.universe.trajectory
+        self.ts = self.universe.coord
         self.collection = TS.TimeseriesCollection()
         C = self.collection
         all = self.universe.atoms
@@ -458,7 +459,9 @@ def setUp(self):
 
     def tearDown(self):
         del self.collection
-        super(TestDCDCorrel, self).tearDown()
+        del self.universe
+        del self.dcd
+        del self.ts
 
     def test_correl(self):
         assert_equal(len(self.collection), 10, "Correl: len(collection)")