Add check for time series ordering

stingray/base.py

@@ -1127,6 +1127,10 @@ class StingrayTimeseries(StingrayObject):
     ephem : str
         The JPL ephemeris used to barycenter the data, if any (e.g. DE430)
 
+    skip_checks : bool
+        Skip checks on the time array. Useful when the user is reasonably sure that the
+        input data are valid.
+
     **other_kw :
         Used internally. Any other keyword arguments will be set as attributes of the object.
 
@@ -1176,6 +1180,7 @@ def __init__(
         ephem: str = None,
         timeref: str = None,
         timesys: str = None,
+        skip_checks: bool = False,
         **other_kw,
     ):
         StingrayObject.__init__(self)
@@ -1198,6 +1203,12 @@ def __init__(
             if self.time.shape[0] != new_arr.shape[0]:
                 raise ValueError(f"Lengths of time and {kw} must be equal.")
             setattr(self, kw, new_arr)
+        from .utils import is_sorted
+
+        if not skip_checks:
+            if self.time is not None and not is_sorted(self.time):
+                warnings.warn("The time array is not sorted. Sorting it now.")
+                self.sort(inplace=True)
 
     @property
     def time(self):
@@ -2151,7 +2162,7 @@ def sort(self, reverse=False, inplace=False):
         --------
         >>> time = [2, 1, 3]
         >>> count = [200, 100, 300]
-        >>> ts = StingrayTimeseries(time, array_attrs={"counts": count}, dt=1)
+        >>> ts = StingrayTimeseries(time, array_attrs={"counts": count}, dt=1, skip_checks=True)
         >>> ts_new = ts.sort()
         >>> ts_new.time
         array([1, 2, 3])

stingray/events.py

@@ -145,6 +145,9 @@ class EventList(StingrayTimeseries):
     rmf_file : str, default None
         The file name of the RMF file to use for calibration.
 
+    skip_checks : bool, default False
+        Skip checks for the validity of the event list. Use with caution.
+
     **other_kw :
         Used internally. Any other keyword arguments will be ignored
 
@@ -211,6 +214,7 @@ def __init__(
         timeref=None,
         timesys=None,
         rmf_file=None,
+        skip_checks=False,
         **other_kw,
     ):
         if ncounts is not None:
@@ -243,6 +247,7 @@ def __init__(
             timeref=timeref,
             timesys=timesys,
             rmf_file=rmf_file,
+            skip_checks=skip_checks,
             **other_kw,
         )
 
@@ -502,7 +507,8 @@ def sort(self, inplace=False):
 
         Examples
         --------
-        >>> events = EventList(time=[0, 2, 1], energy=[0.3, 2, 0.5], pi=[3, 20, 5])
+        >>> events = EventList(time=[0, 2, 1], energy=[0.3, 2, 0.5], pi=[3, 20, 5],
+        ...                    skip_checks=True)
         >>> e1 = events.sort()
         >>> assert np.allclose(e1.time, [0, 1, 2])
         >>> assert np.allclose(e1.energy, [0.3, 0.5, 2])

stingray/lightcurve.py

@@ -4,6 +4,7 @@
 :class::class:`Lightcurve` is used to create light curves out of photon counting data
 or to save existing light curves in a class that's easy to use.
 """
+
 import os
 import logging
 import warnings

stingray/tests/test_base.py

@@ -850,9 +850,10 @@ def test_sort(self):
         bleh = [4, 1, 2, 0.5]
         mjdref = 57000
 
-        lc = StingrayTimeseries(
-            times, array_attrs={"blah": blah, "_bleh": bleh}, dt=1, mjdref=mjdref
-        )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            lc = StingrayTimeseries(
+                times, array_attrs={"blah": blah, "_bleh": bleh}, dt=1, mjdref=mjdref
+            )
 
         lc_new = lc.sort()
 
@@ -1223,12 +1224,14 @@ def test_non_overlapping_join_infer(self):
 
     def test_overlapping_join_infer(self):
         """Join two non-overlapping event lists."""
-        ts = StingrayTimeseries(
-            time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]]
-        )
-        ts_other = StingrayTimeseries(
-            time=[5.1, 7, 6.1, 6.11, 10.1], energy=[2, 3, 8, 1, 2], gti=[[5, 7], [8, 10]]
-        )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ts = StingrayTimeseries(
+                time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]]
+            )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ts_other = StingrayTimeseries(
+                time=[5.1, 7, 6.1, 6.11, 10.1], energy=[2, 3, 8, 1, 2], gti=[[5, 7], [8, 10]]
+            )
         ts_new = ts.join(ts_other, strategy="infer")
 
         assert (ts_new.time == np.array([1, 1.1, 5, 5.1, 6, 6.1, 6.11, 7, 10, 10.1])).all()
@@ -1237,15 +1240,20 @@ def test_overlapping_join_infer(self):
 
     def test_overlapping_join_change_mjdref(self):
         """Join two non-overlapping event lists."""
-        ts = StingrayTimeseries(
-            time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]], mjdref=57001
-        )
-        ts_other = StingrayTimeseries(
-            time=np.asarray([5.1, 7, 6.1, 6.11, 10.1]) + 86400,
-            energy=[2, 3, 8, 1, 2],
-            gti=np.asarray([[5, 7], [8, 10]]) + 86400,
-            mjdref=57000,
-        )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ts = StingrayTimeseries(
+                time=[1, 1.1, 10, 6, 5],
+                energy=[10, 6, 3, 11, 2],
+                gti=[[1, 3], [5, 6]],
+                mjdref=57001,
+            )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ts_other = StingrayTimeseries(
+                time=np.asarray([5.1, 7, 6.1, 6.11, 10.1]) + 86400,
+                energy=[2, 3, 8, 1, 2],
+                gti=np.asarray([[5, 7], [8, 10]]) + 86400,
+                mjdref=57000,
+            )
         with pytest.warns(UserWarning, match="Attribute mjdref is different"):
             ts_new = ts.join(ts_other, strategy="intersection")
 

stingray/tests/test_events.py

@@ -488,10 +488,12 @@ def test_non_overlapping_join_infer(self):
 
     def test_overlapping_join_infer(self):
         """Join two non-overlapping event lists."""
-        ev = EventList(time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]])
-        ev_other = EventList(
-            time=[5.1, 7, 6.1, 6.11, 10.1], energy=[2, 3, 8, 1, 2], gti=[[5, 7], [8, 10]]
-        )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ev = EventList(time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]])
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ev_other = EventList(
+                time=[5.1, 7, 6.1, 6.11, 10.1], energy=[2, 3, 8, 1, 2], gti=[[5, 7], [8, 10]]
+            )
         ev_new = ev.join(ev_other, strategy="infer")
 
         assert (ev_new.time == np.array([1, 1.1, 5, 5.1, 6, 6.1, 6.11, 7, 10, 10.1])).all()
@@ -500,15 +502,20 @@ def test_overlapping_join_infer(self):
 
     def test_overlapping_join_change_mjdref(self):
         """Join two non-overlapping event lists."""
-        ev = EventList(
-            time=[1, 1.1, 10, 6, 5], energy=[10, 6, 3, 11, 2], gti=[[1, 3], [5, 6]], mjdref=57001
-        )
-        ev_other = EventList(
-            time=np.asarray([5.1, 7, 6.1, 6.11, 10.1]) + 86400,
-            energy=[2, 3, 8, 1, 2],
-            gti=np.asarray([[5, 7], [8, 10]]) + 86400,
-            mjdref=57000,
-        )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ev = EventList(
+                time=[1, 1.1, 10, 6, 5],
+                energy=[10, 6, 3, 11, 2],
+                gti=[[1, 3], [5, 6]],
+                mjdref=57001,
+            )
+        with pytest.warns(UserWarning, match="The time array is not sorted."):
+            ev_other = EventList(
+                time=np.asarray([5.1, 7, 6.1, 6.11, 10.1]) + 86400,
+                energy=[2, 3, 8, 1, 2],
+                gti=np.asarray([[5, 7], [8, 10]]) + 86400,
+                mjdref=57000,
+            )
         with pytest.warns(UserWarning, match="Attribute mjdref is different"):
             ev_new = ev.join(ev_other, strategy="intersection")
 

stingray/tests/test_lombscargle.py

@@ -213,8 +213,8 @@ def test_raise_on_invalid_function(self, func_name):
             func()
 
     def test_no_dt(self):
-        el1 = EventList(self.lc1.counts, self.lc1.time, dt=None)
-        el2 = EventList(self.lc2.counts, self.lc2.time, dt=None)
+        el1 = EventList(self.lc1.time, self.lc1.counts, dt=None)
+        el2 = EventList(self.lc2.time, self.lc2.counts, dt=None)
         with pytest.raises(ValueError):
             lscs = LombScargleCrossspectrum(el1, el2)