Merge pull request #226 from pynapple-org/dev

Adding Event trigger average for all dimensions

docs/HISTORY.md

@@ -9,6 +9,13 @@ In 2018, Francesco started neuroseries, a Python package built on Pandas. It was
 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.
 
 
+0.5.1 (2024-01-29)
+------------------
+
+- Implementing `event_trigger_average` for all dimensions.
+- Hiding jitted functions from users.
+
+
 0.5.0 (2023-12-12)
 ------------------
 

docs/gen_ref_pages.py

@@ -12,56 +12,68 @@
 
 io_orders = ['interface_nwb', 'interface_npz', 'folder', 'misc'] + deprecated
 
+ignored = ['_jitted_functions']
 
 for path in sorted(Path("pynapple").rglob("*.py")):
-    print(path)
     module_path = path.relative_to("pynapple").with_suffix("")
-    doc_path = path.relative_to("pynapple").with_suffix(".md")
-    full_doc_path = Path("reference", doc_path)
-
-    parts = tuple(module_path.parts)
-
-    if parts[-1] == "__init__":
-        parts = parts[:-1]
-        doc_path = doc_path.with_name("index.md")
-        full_doc_path = full_doc_path.with_name("index.md")
-    elif parts[-1] == "__main__":
-        continue
-
-    if len(parts):
-        nav[parts] = doc_path.as_posix()
-    # if the md file name is `module.md`, generate documentation from docstrings
-    if full_doc_path.name != 'index.md':
-        # sys.exit()
-        with mkdocs_gen_files.open(full_doc_path, "w") as fd:
-            ident = "pynapple."+".".join(parts)
-            fd.write(f"::: {ident}")
-    # if the md file name is `index.md`, add the list of modules with hyperlinks
-    else:
-        this_module_path = Path("pynapple") / path.parent.name
-        module_index = ""
-
-        module_order = sorted(this_module_path.rglob("*.py"))
-        module_order = [m.name.replace('.py', '') for m in module_order]
+
+    if module_path.name not in ignored:
+
+        doc_path = path.relative_to("pynapple").with_suffix(".md")
+        full_doc_path = Path("reference", doc_path)
+
+        # print(module_path, "\t", doc_path, "\t", full_doc_path)
+
+        parts = tuple(module_path.parts)
+
+        if parts[-1] == "__init__":
+            parts = parts[:-1]
+            doc_path = doc_path.with_name("index.md")
+            full_doc_path = full_doc_path.with_name("index.md")
+        elif parts[-1] == "__main__":
+            continue
+
+        # print(parts, doc_path)
+        # if str(doc_path) == "core/_jitted_functions.md":
+        #     sys.exit()
+
+        if len(parts):
+            nav[parts] = doc_path.as_posix()
+
+        # if the md file name is `module.md`, generate documentation from docstrings
+        if full_doc_path.name != 'index.md':
+
+            with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+                ident = "pynapple."+".".join(parts)
+                fd.write(f"::: {ident}")
 
-        if "io" in this_module_path.name:
-            module_order = io_orders
+        else:
+            this_module_path = Path("pynapple") / path.parent.name
+            module_index = ""
+
+            module_order = sorted(this_module_path.rglob("*.py"))
+            module_order = [m.name.replace('.py', '') for m in module_order]
+
+            if "io" in this_module_path.name:
+                module_order = io_orders
 
-        for m in module_order:
-            if "__init__" in m:
-                continue
+            for m in module_order:
+                if "__init__" in m:
+                    continue
+                if m[0] == "_":
+                    continue
 
-            module_name = m
-            if m in deprecated:
-                module_name += " (deprecated)"
-            module_index += f"* [{module_name}]" \
-                            "("+m+".md)\n"
+                module_name = m
+                if m in deprecated:
+                    module_name += " (deprecated)"
+                module_index += f"* [{module_name}]" \
+                                "("+m+".md)\n"
 
-        with mkdocs_gen_files.open(full_doc_path, "w") as fd:
-            fd.write(module_index)
+            with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+                fd.write(module_index)
 
 
-    mkdocs_gen_files.set_edit_path(full_doc_path, path)
+        mkdocs_gen_files.set_edit_path(full_doc_path, path)
 
 with mkdocs_gen_files.open("reference/index.md", "w") as nav_file:
     nav_file.writelines(nav.build_literate_nav())

pynapple/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 from .core import *
 from .io import *
 from .process import *

pynapple/core/__init__.py

@@ -1,3 +1,4 @@
-from .interval_set import *
-from .time_series import *
-from .ts_group import *
+from .interval_set import IntervalSet
+from .time_index import TsIndex
+from .time_series import Ts, Tsd, TsdFrame, TsdTensor
+from .ts_group import TsGroup

pynapple/core/interval_set.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # @Date:   2022-01-25 21:50:48
-# @Last Modified by:   gviejo
-# @Last Modified time: 2023-10-15 16:18:42
+# @Last Modified by:   Guillaume Viejo
+# @Last Modified time: 2024-01-29 12:16:38
 
 """
 """
@@ -14,7 +14,7 @@
 import pandas as pd
 from numba import jit
 
-from .jitted_functions import jitdiff, jitin_interval, jitintersect, jitunion
+from ._jitted_functions import jitdiff, jitin_interval, jitintersect, jitunion
 from .time_index import TsIndex
 
 all_warnings = np.array(

pynapple/core/time_series.py

@@ -2,7 +2,7 @@
 # @Author: gviejo
 # @Date:   2022-01-27 18:33:31
 # @Last Modified by:   Guillaume Viejo
-# @Last Modified time: 2024-01-08 16:09:01
+# @Last Modified time: 2024-01-29 14:36:05
 
 """
 
@@ -35,8 +35,7 @@
 from scipy import signal
 from tabulate import tabulate
 
-from .interval_set import IntervalSet
-from .jitted_functions import (
+from ._jitted_functions import (
     jitbin,
     jitbin_array,
     jitcount,
@@ -49,6 +48,7 @@
     jitvaluefromtensor,
     pjitconvolve,
 )
+from .interval_set import IntervalSet
 from .time_index import TsIndex
 
 

pynapple/core/ts_group.py

@@ -2,7 +2,7 @@
 # @Author: gviejo
 # @Date:   2022-01-28 15:10:48
 # @Last Modified by:   Guillaume Viejo
-# @Last Modified time: 2023-09-21 15:57:41
+# @Last Modified time: 2024-01-29 12:16:24
 
 
 import os
@@ -13,13 +13,13 @@
 import pandas as pd
 from tabulate import tabulate
 
-from .interval_set import IntervalSet
-from .jitted_functions import (
+from ._jitted_functions import (
     jitcount,
     jittsrestrict_with_count,
     jitunion,
     jitunion_isets,
 )
+from .interval_set import IntervalSet
 
 # from .time_units import format_timestamps
 from .time_index import TsIndex
@@ -254,7 +254,7 @@ def set_info(self, *args, **kwargs):
         *args
             pandas.Dataframe or list of pandas.DataFrame
         **kwargs
-            Can be either pandas.Series or numpy.ndarray
+            Can be either pandas.Series, numpy.ndarray, list or tuple
 
         Raises
         ------
@@ -286,7 +286,7 @@ def set_info(self, *args, **kwargs):
               1             2  pfc
               2             4  ca1
 
-        To add metadata with a pd.Series or numpy.ndarray:
+        To add metadata with a pd.Series, numpy.ndarray, list or tuple:
 
         >>> hd = pd.Series(index = [0,1,2], data = [0,1,1])
         >>> tsgroup.set_info(hd=hd)
@@ -314,9 +314,9 @@ def set_info(self, *args, **kwargs):
                         self._metadata[k] = v
                     else:
                         raise RuntimeError("Index are not equals")
-                elif isinstance(v, np.ndarray):
+                elif isinstance(v, (np.ndarray, list, tuple)):
                     if len(self._metadata) == len(v):
-                        self._metadata[k] = v
+                        self._metadata[k] = np.asarray(v)
                     else:
                         raise RuntimeError("Array is not the same length.")
         return

pynapple/process/__init__.py

@@ -1,5 +1,26 @@
-from .correlograms import *
-from .decoding import *
-from .perievent import *
-from .randomize import *
-from .tuning_curves import *
+from .correlograms import (
+    compute_autocorrelogram,
+    compute_crosscorrelogram,
+    compute_eventcorrelogram,
+)
+from .decoding import decode_1d, decode_2d
+from .perievent import (
+    compute_event_trigger_average,
+    compute_perievent,
+    compute_perievent_continuous,
+)
+from .randomize import (
+    jitter_timestamps,
+    resample_timestamps,
+    shift_timestamps,
+    shuffle_ts_intervals,
+)
+from .tuning_curves import (
+    compute_1d_mutual_info,
+    compute_1d_tuning_curves,
+    compute_1d_tuning_curves_continuous,
+    compute_2d_mutual_info,
+    compute_2d_tuning_curves,
+    compute_2d_tuning_curves_continuous,
+    compute_discrete_tuning_curves,
+)

pynapple/process/perievent.py

@@ -2,7 +2,7 @@
 # @Author: gviejo
 # @Date:   2022-01-30 22:59:00
 # @Last Modified by:   Guillaume Viejo
-# @Last Modified time: 2024-01-26 15:52:19
+# @Last Modified time: 2024-01-29 12:47:56
 
 import numpy as np
 
@@ -179,7 +179,7 @@ def compute_perievent_continuous(data, tref, minmax, ep=None, time_unit="s"):
     time_idx = np.hstack((idx1, np.zeros(1), idx2))
     windowsize = np.array([idx1.shape[0], idx2.shape[0]])
 
-    new_data_array = nap.jitted_functions.jitcontinuous_perievent(
+    new_data_array = nap._jitted_functions.jitcontinuous_perievent(
         time_array, data_array, time_target_array, starts, ends, windowsize
     )
 
@@ -289,7 +289,7 @@ def compute_event_trigger_average(
     data_target_array = feature.values
 
     if data_target_array.ndim == 1:
-        eta = nap.jitted_functions.jitperievent_trigger_average(
+        eta = nap._jitted_functions.jitperievent_trigger_average(
             time_array,
             count_array,
             time_target_array,
@@ -301,7 +301,7 @@ def compute_event_trigger_average(
         )
         eta = np.squeeze(eta, -1)
     else:
-        eta = nap.jitted_functions.jitperievent_trigger_average(
+        eta = nap._jitted_functions.jitperievent_trigger_average(
             time_array,
             count_array,
             time_target_array,