Refactor raster plot and remove GUI docs from conf.py

doc/conf.py

@@ -115,7 +115,6 @@
     'navbar_sidebarrel': False,
     'navbar_links': [
         ("Examples", "auto_examples/index"),
-        ("GUI", "gui/index"),
         ("API", "api"),
         ("Glossary", "glossary"),
         ("What's new", "whats_new"),

doc/whats_new.rst

@@ -61,6 +61,9 @@ Changelog
 - Added :class:`~hnn_core/viz/NetworkPlotter` to visualize and animate network simulations,
   by `Nick Tolley`_ in :gh:`649`.
 
+- Updated :func:`~hnn_core/viz/plot_spikes_raster` logic to always include all 
+  cell types in raster plots, by `Abdul Samad Siddiqui`_ in :gh:`754`.
+
 Bug
 ~~~
 - Fix inconsistent connection mapping from drive gids to cell gids, by

hnn_core/tests/test_viz.py

@@ -198,7 +198,8 @@ def test_dipole_visualization(setup_net):
     with pytest.raises(TypeError, match="trial_idx must be an instance of"):
         net.cell_response.plot_spikes_raster(trial_idx='blah', show=False)
     net.cell_response.plot_spikes_raster(trial_idx=0, show=False)
-    net.cell_response.plot_spikes_raster(trial_idx=[0, 1], show=False)
+    fig = net.cell_response.plot_spikes_raster(trial_idx=[0, 1], show=False)
+    assert len(fig.axes[0].collections) > 0, "No data plotted in raster plot"
 
     with pytest.raises(TypeError, match="trial_idx must be an instance of"):
         net.cell_response.plot_spikes_hist(trial_idx='blah')

hnn_core/viz.py

@@ -514,17 +514,12 @@ def plot_spikes_raster(cell_response, trial_idx=None, ax=None, show=True):
     _validate_type(trial_idx, list, 'trial_idx', 'int, list of int')
 
     # Extract desired trials
-    if len(cell_response._spike_times[0]) > 0:
-        spike_times = np.concatenate(
-            np.array(cell_response._spike_times, dtype=object)[trial_idx])
-        spike_types = np.concatenate(
-            np.array(cell_response._spike_types, dtype=object)[trial_idx])
-        spike_gids = np.concatenate(
-            np.array(cell_response._spike_gids, dtype=object)[trial_idx])
-    else:
-        spike_times = np.array([])
-        spike_types = np.array([])
-        spike_gids = np.array([])
+    spike_times = np.concatenate(
+        np.array(cell_response._spike_times, dtype=object)[trial_idx])
+    spike_types = np.concatenate(
+        np.array(cell_response._spike_types, dtype=object)[trial_idx])
+    spike_gids = np.concatenate(
+        np.array(cell_response._spike_gids, dtype=object)[trial_idx])
 
     cell_types = ['L2_basket', 'L2_pyramidal', 'L5_basket', 'L5_pyramidal']
     cell_type_colors = {'L5_pyramidal': 'r', 'L5_basket': 'b',
@@ -533,22 +528,25 @@ def plot_spikes_raster(cell_response, trial_idx=None, ax=None, show=True):
     if ax is None:
         _, ax = plt.subplots(1, 1, constrained_layout=True)
 
-    ypos = 0
     events = []
     for cell_type in cell_types:
         cell_type_gids = np.unique(spike_gids[spike_types == cell_type])
         cell_type_times, cell_type_ypos = [], []
         for gid in cell_type_gids:
             gid_time = spike_times[spike_gids == gid]
             cell_type_times.append(gid_time)
-            cell_type_ypos.append(ypos)
-            ypos = ypos - 1
+            cell_type_ypos.append(-gid)
 
         if cell_type_times:
             events.append(
                 ax.eventplot(cell_type_times, lineoffsets=cell_type_ypos,
                              color=cell_type_colors[cell_type],
                              label=cell_type, linelengths=5))
+        else:
+            events.append(
+                ax.eventplot([-1], lineoffsets=[-1],
+                             color=cell_type_colors[cell_type],
+                             label=cell_type, linelengths=5))
 
     ax.legend(handles=[e[0] for e in events], loc=1)
     ax.set_facecolor('k')