Demo widget integration, add notebook

{{ cookiecutter.namespace }}/NEXTSTEPS.md

@@ -41,6 +41,12 @@ replaced or removed.
      the file, and confirm the read data types are equal to the written data types) is
      highly encouraged.
 
+7. Define custom visualization widgets for your new extension data types in
+`src/pynwb/widgets` so that the visualizations can be displayed with
+[nwbwidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets). Register your widget
+with your extension Python class in `src/pynwb/__init__.py` or wherever your extension
+Python class is defined.
+
 8. You may need to modify `pyproject.toml` and re-run `python -m pip install -e .` if you
 use any dependencies.
 

{{ cookiecutter.namespace }}/notebooks/example.ipynb

@@ -0,0 +1,165 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "174c5018-1c0a-4f55-899d-049bb87f63d5",
+   "metadata": {},
+   "source": [
+    "# Example demonstration of the example TetrodeSeries extension neurodata type\n",
+    "\n",
+    "TODO: Update this notebook with an example usage of your extension"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "02798a80-faea-4b75-aa97-70afad90fe27",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from pynwb import NWBHDF5IO, NWBFile\n",
+    "from pynwb.testing.mock.device import mock_Device\n",
+    "from pynwb.testing.mock.ecephys import mock_ElectrodeGroup, mock_ElectrodeTable\n",
+    "from pynwb.testing.mock.file import mock_NWBFile\n",
+    "\n",
+    "from {{ cookiecutter.py_pkg_name }} import TetrodeSeries\n",
+    "\n",
+    "\n",
+    "def set_up_nwbfile(nwbfile: NWBFile = None):\n",
+    "    \"\"\"Create an NWBFile with a Device, ElectrodeGroup, and 10 electrodes in the ElectrodeTable.\"\"\"\n",
+    "    nwbfile = nwbfile or mock_NWBFile()\n",
+    "    device = mock_Device(nwbfile=nwbfile)\n",
+    "    electrode_group = mock_ElectrodeGroup(device=device, nwbfile=nwbfile)\n",
+    "    _ = mock_ElectrodeTable(n_rows=10, group=electrode_group, nwbfile=nwbfile)\n",
+    "\n",
+    "    return nwbfile"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "32be75e4-8fe9-401d-a613-8080f357d5f0",
+   "metadata": {},
+   "source": [
+    "Create an `NWBFile` object and a `TetrodeSeries` object and add the `TetrodeSeries` object to the `NWBFile`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dcd2c070-f2c9-4ffc-8637-25ec3e6f7b37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "nwbfile = set_up_nwbfile()\n",
+    "\n",
+    "all_electrodes = nwbfile.create_electrode_table_region(\n",
+    "    region=list(range(0, 10)),\n",
+    "    description=\"all the electrodes\",\n",
+    ")\n",
+    "\n",
+    "data = np.random.rand(100, 10)\n",
+    "tetrode_series = TetrodeSeries(\n",
+    "    name=\"TetrodeSeries\",\n",
+    "    description=\"description\",\n",
+    "    data=data,\n",
+    "    rate=1000.0,\n",
+    "    electrodes=all_electrodes,\n",
+    "    trode_id=1,\n",
+    ")\n",
+    "\n",
+    "nwbfile.add_acquisition(tetrode_series)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "077a8d86-9d03-40e3-b60a-c837ecb643a7",
+   "metadata": {},
+   "source": [
+    "Visualize the TetrodeSeries object with the `nwbwidgets` package using the custom widget defined in the extension"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1363282d-1a32-447d-9ca3-fc2360785cc2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from nwbwidgets import nwb2widget, default_neurodata_vis_spec\n",
+    "vis_spec = default_neurodata_vis_spec\n",
+    "vis_spec[TetrodeSeries] = TetrodeSeries.widget\n",
+    "nwb2widget(nwbfile, vis_spec)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ac894fae-6c5e-4a3d-be1e-d158aef084a4",
+   "metadata": {},
+   "source": [
+    "Write the file with the extension neurodata type to disk"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2fdaf978-6f95-4871-b26c-dad4bb62da42",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with NWBHDF5IO(\"test.nwb\", \"w\") as io:\n",
+    "    io.write(nwbfile)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a30660a3-8e64-4c5e-963d-6ecd7e31897e",
+   "metadata": {},
+   "source": [
+    "Read the NWB file from disk and print the `TetrodeSeries` object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "00e38084-b55e-4c7a-ac89-8b10e43f41c1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with NWBHDF5IO(\"test.nwb\", \"r\") as io:\n",
+    "    read_nwbfile = io.read()\n",
+    "    print(read_nwbfile.acquisition[\"TetrodeSeries\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b36569b2-09d1-4281-bf4c-fb602e53636c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{{ cookiecutter.namespace }}/requirements-dev.txt

@@ -4,6 +4,7 @@ black==23.9.1
 codespell==2.2.6
 coverage==7.3.2
 hdmf-docutils==0.4.5
+nwbwidgets==0.11.3
 pre-commit==3.4.0
 pytest==7.4.2
 pytest-cov==4.1.0

{{ cookiecutter.namespace }}/src/pynwb/{{ cookiecutter.py_pkg_name }}/__init__.py

@@ -24,5 +24,22 @@
 # `@register_class("TetrodeSeries", "{{ cookiecutter.namespace }}")`
 TetrodeSeries = get_class("TetrodeSeries", "{{ cookiecutter.namespace }}")
 
+# If NWBWidgets is installed, create a custom widget for the TetrodeSeries
+# neurodata type that displays the trode_id field
+# Usage:
+#   from nwbwidgets import nwb2widget, default_neurodata_vis_spec
+#   vis_spec = default_neurodata_vis_spec
+#   vis_spec[TetrodeSeries] = TetrodeSeries.widget
+#   nwb2widget(nwbfile, vis_spec)
+try:
+    from .widgets import TetrodeSeriesWidget
+
+    # add the widget class to the TetrodeSeries class
+    TetrodeSeries.widget = TetrodeSeriesWidget
+
+except ImportError:
+    # NWBWidgets is not installed, so we cannot create a new widget
+    pass
+
 # Remove these functions from the package
 del load_namespaces, get_class

{{ cookiecutter.namespace }}/src/pynwb/{{ cookiecutter.py_pkg_name }}/widgets/README.md

@@ -0,0 +1,3 @@
+Add widgets that define custom visualizations for your extension, so that
+the visualizations can be displayed with
+[nwbwidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets).

{{ cookiecutter.namespace }}/src/pynwb/{{ cookiecutter.py_pkg_name }}/widgets/__init__.py

@@ -0,0 +1 @@
+from .tetrode_series_widget import TetrodeSeriesWidget  # noqa: F401

{{ cookiecutter.namespace }}/src/pynwb/{{ cookiecutter.py_pkg_name }}/widgets/tetrode_series_widget.py

@@ -0,0 +1,27 @@
+from nwbwidgets.ecephys import ElectricalSeriesWidget
+from ipywidgets import widgets
+
+from .. import TetrodeSeries
+
+
+class TetrodeSeriesWidget(ElectricalSeriesWidget):  # this is an HBox
+    def __init__(self, tetrode_series: TetrodeSeries, **kwargs):
+        super().__init__(electrical_series=tetrode_series, **kwargs)
+        vbox = widgets.VBox(
+            children=[
+                self._create_trode_id_box(tetrode_series),
+                widgets.HBox(children=list(self.children)),
+            ]
+        )
+        self.children = [vbox]
+
+    def _create_trode_id_box(self, tetrode_series: TetrodeSeries):
+        field_lay = widgets.Layout(
+            max_height="40px",
+            max_width="600px",
+            min_height="30px",
+            min_width="130px",
+        )
+        key = widgets.Label("trode_id:", layout=field_lay)
+        val = widgets.Label(str(tetrode_series.trode_id), layout=field_lay)
+        return widgets.HBox(children=[key, val])