Merge pull request #194 from pynapple-org/dev

Dev

docs/HISTORY.md

@@ -8,6 +8,19 @@ Around 2016-2017, Luke Sjulson started *TSToolbox2*, still in Matlab and which i
 In 2018, Francesco started neuroseries, a Python package built on Pandas. It was quickly adopted in Adrien's lab, especially by Guillaume Viejo, a postdoc in the lab. Gradually, the majority of the lab was using it and new functions were constantly added.
 In 2021, Guillaume and other trainees in Adrien's lab decided to fork from neuroseries and started *pynapple*. The core of pynapple is largely built upon neuroseries. Some of the original changes to TSToolbox made by Luke were included in this package, especially the *time_support* property of all ts/tsd objects.
 
+0.4.1 (2023-10-30)
+------------------
+
+- Implementing `get` method that return both an interval or the closest timepoint
+
+
+0.4.0 (2023-10-11)
+------------------
+
+- Implementing the numpy array container approach within pynapple
+- TsdTensor for objects larger than 2 dimensions is now available
+
+
 0.3.6 (2023-09-11)
 ------------------
 

pynapple/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 from .core import *
 from .io import *
 from .process import *

pynapple/core/time_series.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 # @Author: gviejo
 # @Date:   2022-01-27 18:33:31
-# @Last Modified by:   gviejo
-# @Last Modified time: 2023-10-27 14:26:55
+# @Last Modified by:   Guillaume Viejo
+# @Last Modified time: 2023-10-30 16:43:22
 
 """
 
@@ -754,10 +754,11 @@ def find_support(self, min_gap, time_units="s"):
 
         return IntervalSet(start=starts, end=ends)
 
-    def get(self, start, end, time_units="s"):
+    def get(self, start, end=None, time_units="s"):
         """Slice the time series from start to end such that all the timestamps satisfy start<=t<=end.
+        If end is None, only the timepoint closest to start is returned.
 
-        By default, the time support doesn't change. If you want to change the
+        By default, the time support doesn't change. If you want to change the time support, use the restrict function.
 
         Parameters
         ----------
@@ -767,13 +768,27 @@ def get(self, start, end, time_units="s"):
             The end
         """
         assert isinstance(start, Number), "start should be a float or int"
-        assert isinstance(end, Number), "end should be a float or int"
-        assert start < end, "Start should not precede end"
-        start, end = TsIndex.format_timestamps(np.array([start, end]), time_units)
         time_array = self.index.values
-        idx_start = np.searchsorted(time_array, start)
-        idx_end = np.searchsorted(time_array, end, side="right")
-        return self[idx_start:idx_end]
+
+        if end is None:
+            start = TsIndex.format_timestamps(np.array([start]), time_units)[0]
+            idx = np.searchsorted(time_array, start)
+            if idx == 0:
+                return self[idx]
+            elif idx >= self.shape[0]:
+                return self[-1]
+            else:
+                if start - time_array[idx - 1] < time_array[idx] - start:
+                    return self[idx - 1]
+                else:
+                    return self[idx]
+        else:
+            assert isinstance(end, Number), "end should be a float or int"
+            assert start < end, "Start should not precede end"
+            start, end = TsIndex.format_timestamps(np.array([start, end]), time_units)
+            idx_start = np.searchsorted(time_array, start)
+            idx_end = np.searchsorted(time_array, end, side="right")
+            return self[idx_start:idx_end]
 
 
 class TsdTensor(NDArrayOperatorsMixin, _AbstractTsd):

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pynapple"
-version = "0.4.0"
+version = "0.4.1"
 description = "PYthon Neural Analysis Package Pour Laboratoires d’Excellence"
 readme = "README.md"
 authors = [{ name = "Guillaume Viejo", email = "[email protected]" }]

setup.py

@@ -61,8 +61,8 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/pynapple-org/pynapple',
-    version='v0.4.0',
+    version='v0.4.1',
     zip_safe=False,
     long_description_content_type='text/markdown',
-    download_url='https://github.com/pynapple-org/pynapple/archive/refs/tags/v0.4.0.tar.gz'
+    download_url='https://github.com/pynapple-org/pynapple/archive/refs/tags/v0.4.1.tar.gz'
 )

tests/test_time_series.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 # @Author: gviejo
 # @Date:   2022-04-01 09:57:55
-# @Last Modified by:   gviejo
-# @Last Modified time: 2023-10-29 16:19:01
+# @Last Modified by:   Guillaume Viejo
+# @Last Modified time: 2023-10-30 16:39:56
 #!/usr/bin/env python
 
 """Tests of time series for `pynapple` package."""
@@ -367,7 +367,7 @@ def test_restrict_inherit_time_support(self, tsd):
         np.testing.assert_approx_equal(tsd2.time_support.start[0], ep.start[0])
         np.testing.assert_approx_equal(tsd2.time_support.end[0], ep.end[0])
 
-    def test_get(self, tsd):
+    def test_get_interval(self, tsd):
         tsd2 = tsd.get(10, 20)
         assert len(tsd2) == 11
         np.testing.assert_array_equal(tsd2.index.values, tsd.index.values[10:21])
@@ -383,6 +383,15 @@ def test_get(self, tsd):
         with pytest.raises(Exception):
             tsd.get([10], 20)
 
+    def test_get_timepoint(self, tsd):
+        if not isinstance(tsd, nap.Ts):
+            np.testing.assert_array_equal(tsd.get(-1), tsd[0])
+            np.testing.assert_array_equal(tsd.get(0), tsd[0])
+            np.testing.assert_array_equal(tsd.get(0.1), tsd[0])
+            np.testing.assert_array_equal(tsd.get(0.5), tsd[1])
+            np.testing.assert_array_equal(tsd.get(0.6), tsd[1])
+            np.testing.assert_array_equal(tsd.get(1), tsd[1])
+            np.testing.assert_array_equal(tsd.get(1000), tsd[-1])
 
 ####################################################
 # Test for tsd