From 2eeeee6302c58e0b7c37cec6dfce423154178e64 Mon Sep 17 00:00:00 2001
From: Ben Dichter <ben.dichter@gmail.com>
Date: Wed, 20 Nov 2024 14:17:30 +0100
Subject: [PATCH] add EventDetection code to ecephys tutorial

---
 docs/gallery/domain/ecephys.py | 41 ++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 14 deletions(-)

diff --git a/docs/gallery/domain/ecephys.py b/docs/gallery/domain/ecephys.py
index 7abcff550..ee2d69a16 100644
--- a/docs/gallery/domain/ecephys.py
+++ b/docs/gallery/domain/ecephys.py
@@ -324,18 +324,38 @@
     description="shank0",
 )
 
-
-spike_events = SpikeEventSeries(name='SpikeEvents_Shank0',
-                                description="events detected with 100uV threshold",
-                                data=spike_snippets,
-                                timestamps=np.arange(20),
-                                electrodes=shank0)
+spike_events = SpikeEventSeries(
+    name='SpikeEvents_Shank0',
+    description="events detected with 100uV threshold",
+    data=spike_snippets,
+    timestamps=np.arange(20),
+    electrodes=shank0,
+)
 nwbfile.add_acquisition(spike_events)
 
+############################################
+# If you need to store the complete, continuous raw voltage traces, along with unsorted spike times, you should store
+# the traces with :py:class:`~pynwb.ecephys.ElectricalSeries` objects as :ref:`acquisition <basic_timeseries>` data,
+# and use the :py:class:`~pynwb.ecephys.EventDetection` class to identify the spike events in your raw traces.
+
+from pynwb.ecephys import EventDetection
+
+event_detection = EventDetection(
+    name="threshold_events",
+    detection_method="thresholding, 1.5 * std",
+    source_electricalseries=raw_electrical_series,
+    source_idx=[1000, 2000, 3000],
+    times=[.033, .066, .099],
+)
+
+ecephys_module.add(event_detection)
+
 #######################
+# # If you do not want to store the raw voltage traces and only the waveform 'snippets' surrounding spike events,
+# # you should use :py:class:`~pynwb.ecephys.SpikeEventSeries` objects.
+#
 # Designating electrophysiology data
 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-#
 # As mentioned above, :py:class:`~pynwb.ecephys.ElectricalSeries` objects
 # are meant for storing specific types of extracellular recordings. In addition to this
 # :py:class:`~pynwb.base.TimeSeries` class, NWB provides some :ref:`modules_overview`
@@ -343,13 +363,6 @@
 # :py:mod:`API documentation <pynwb.ecephys>` and :ref:`basics` for more details on
 # using these objects.
 #
-# For storing unsorted spiking data, there are two options. Which one you choose depends on what data you 
-# have available. If you need to store the complete, continuous raw voltage traces, you should store the traces with
-# :py:class:`~pynwb.ecephys.ElectricalSeries` objects as :ref:`acquisition <basic_timeseries>` data, and use
-# the :py:class:`~pynwb.ecephys.EventDetection` class for identifying the spike events in your raw traces.
-# If you do not want to store the raw voltage traces and only the waveform 'snippets' surrounding spike events,
-# you should use :py:class:`~pynwb.ecephys.SpikeEventSeries` objects.
-#
 # The results of spike sorting (or clustering) should be stored in the top-level :py:class:`~pynwb.misc.Units` table.
 # The :py:class:`~pynwb.misc.Units` table can contain simply the spike times of sorted units, or you can also include 
 # individual and mean waveform information in some of the optional, predefined :py:class:`~pynwb.misc.Units` table