Merge pull request #232 from pynapple-org/dev

Dev

pynapple/core/config.py

@@ -45,10 +45,27 @@ class PynappleConfig:
         array-like objects to NumPy arrays. This is useful for users who frequently work with array-like objects from other
         libraries (e.g., JAX, TensorFlow) and prefer not to receive warnings for automatic
         conversions. Defaults to False, which means warnings will be shown.
+    suppress_time_index_sorting_warnings : boolean
+        Control the warning raised when passing a non-sorted array for time index.
+        It can be useful to catch data where timestamps are not properly sorted before using pynapple.
+    time_index_precision : int
+        Precision for the time index is set to nanoseconds. It's a fixed parameter in pynapple and cannot be changed.
     """
 
     def __init__(self):
         self.suppress_conversion_warnings = False
+        self.suppress_time_index_sorting_warnings = False
+
+    @property
+    def time_index_precision(self):
+        """Precision for the time index
+
+        Returns
+        -------
+        Int
+            Parameter for the `numpy.around` function when rounding time index
+        """
+        return 9
 
     @property
     def suppress_conversion_warnings(self):
@@ -65,6 +82,22 @@ def suppress_conversion_warnings(self, value):
             raise ValueError("suppress_conversion_warnings must be a boolean value.")
         self._suppress_conversion_warnings = value
 
+    @property
+    def suppress_time_index_sorting_warnings(self):
+        """
+        Gets or sets the suppression state for sorting time index. When set to True,
+        warnings for sorting are suppressed. Ensures that only boolean values are assigned.
+        """
+        return self._suppress_time_index_sorting_warnings
+
+    @suppress_time_index_sorting_warnings.setter
+    def suppress_time_index_sorting_warnings(self, value):
+        if not isinstance(value, bool):
+            raise ValueError(
+                "suppress_time_index_sorting_warnings must be a boolean value."
+            )
+        self._suppress_time_index_sorting_warnings = value
+
     def restore_defaults(self):
         """
         Set all configuration settings to their default values.
@@ -73,6 +106,7 @@ def restore_defaults(self):
         to its initial, default configuration.
         """
         self.suppress_conversion_warnings = False
+        self.suppress_time_index_sorting_warnings = False
 
 
 # Initialize a config instance

pynapple/core/time_index.py

@@ -1,12 +1,6 @@
-# -*- coding: utf-8 -*-
-# @Author: Guillaume Viejo
-# @Date:   2023-09-21 13:32:03
-# @Last Modified by:   Guillaume Viejo
-# @Last Modified time: 2024-02-13 16:55:44
-
 """
 
-    Similar to pandas.Index, TsIndex holds the timestamps associated with the data of a time series.
+    Similar to pandas.Index, `TsIndex` holds the timestamps associated with the data of a time series.
     This class deals with conversion between different time units for all pynapple objects as well
     as making sure that timestamps are property sorted before initializing any objects.    
         - `us`: microseconds
@@ -18,6 +12,8 @@
 
 import numpy as np
 
+from .config import nap_config
+
 
 class TsIndex(np.ndarray):
     """
@@ -47,11 +43,11 @@ def format_timestamps(t, units="s"):
             Description
         """
         if units == "s":
-            t = np.around(t, 9)
+            t = np.around(t, nap_config.time_index_precision)
         elif units == "ms":
-            t = np.around(t / 1.0e3, 9)
+            t = np.around(t / 1.0e3, nap_config.time_index_precision)
         elif units == "us":
-            t = np.around(t / 1.0e6, 9)
+            t = np.around(t / 1.0e6, nap_config.time_index_precision)
         else:
             raise ValueError("unrecognized time units type")
 
@@ -80,11 +76,11 @@ def return_timestamps(t, units="s"):
             IF units is not in ['s', 'ms', 'us']
         """
         if units == "s":
-            t = np.around(t, 9)
+            t = np.around(t, nap_config.time_index_precision)
         elif units == "ms":
-            t = np.around(t * 1.0e3, 9)
+            t = np.around(t * 1.0e3, nap_config.time_index_precision)
         elif units == "us":
-            t = np.around(t * 1.0e6, 9)
+            t = np.around(t * 1.0e6, nap_config.time_index_precision)
         else:
             raise ValueError("unrecognized time units type")
 
@@ -108,7 +104,7 @@ def sort_timestamps(t, give_warning=True):
             Description
         """
         if not (np.diff(t) >= 0).all():
-            if give_warning:
+            if give_warning and not nap_config.suppress_time_index_sorting_warnings:
                 warn("timestamps are not sorted", UserWarning)
             t = np.sort(t)
         return t

tests/test_abstract_tsd.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 # @Author: Guillaume Viejo
 # @Date:   2023-09-25 11:53:30
-# @Last Modified by:   Guillaume Viejo
-# @Last Modified time: 2024-02-13 17:33:25
+# @Last Modified by:   gviejo
+# @Last Modified time: 2024-02-26 13:06:55
 
 import pynapple as nap
 import numpy as np

tests/test_config.py

@@ -130,3 +130,7 @@ def test_config_supress_warning_d(cls, t, d, conf, expectation):
             cls(t=t, d=MockArray(d))
     finally:
         nap.config.nap_config.restore_defaults()
+
+
+def test_get_time_index_precision():
+    assert nap.config.nap_config.time_index_precision == 9

tests/test_time_index.py

@@ -2,7 +2,7 @@
 # @Author: gviejo
 # @Date:   2022-11-30 09:29:21
 # @Last Modified by:   gviejo
-# @Last Modified time: 2023-11-08 17:16:26
+# @Last Modified time: 2024-02-26 13:14:41
 """Tests of time units for `pynapple` package."""
 
 import pynapple as nap
@@ -27,13 +27,13 @@ def test_return_timestamps():
     t = np.random.rand(100)
 
     np.testing.assert_array_almost_equal(t, nap.TsIndex.return_timestamps(t))
-    np.testing.assert_array_almost_equal(t/1e3, nap.TsIndex.return_timestamps(t, 'ms'))
-    np.testing.assert_array_almost_equal(t/1e6, nap.TsIndex.return_timestamps(t, 'us'))
+    np.testing.assert_array_almost_equal(t*1e3, nap.TsIndex.return_timestamps(t, 'ms'))
+    np.testing.assert_array_almost_equal(t*1e6, nap.TsIndex.return_timestamps(t, 'us'))
 
     with pytest.raises(ValueError, match="unrecognized time units type"):
         nap.TsIndex.return_timestamps(t, units='aaaa')
 
-def test_return_timestamps():
+def test_sort_timestamps():
     t = np.random.rand(100)
 
     np.testing.assert_array_almost_equal(np.sort(t), nap.TsIndex.sort_timestamps(t, False))