Merge branch 'MouseLand:main' into main

docs/tutorials/plotting_example.ipynb

@@ -7,6 +7,13 @@
     "# Example plots using kilosort.data_tools"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Note that `kilosort.data_tools` was added in `v4.0.21`, so you will need to update Kilosort4 to at least that version to use these examples. This can be done using `pip install kilosort --upgrade`."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -42,7 +49,7 @@
     "from kilosort.io import load_ops\n",
     "from kilosort.data_tools import (\n",
     "    mean_waveform, cluster_templates, get_good_cluster, get_cluster_spikes,\n",
-    "    get_spike_waveforms, get_best_channel\n",
+    "    get_spike_waveforms, get_best_channels\n",
     "    )\n",
     "\n",
     "\n",
@@ -101,7 +108,7 @@
     "# Time in s for spike time axis\n",
     "t2 = spike_times / ops['fs']\n",
     "# Get single-channel waveform for each spike\n",
-    "chan = get_best_channel(cluster_id, results_dir)\n",
+    "chan = get_best_channels(results_dir)[cluster_id]\n",
     "waves = get_spike_waveforms(spike_times, results_dir, chan=chan)\n",
     "\n",
     "# Plot each waveform, using spike time as 3rd dimension\n",

kilosort/data_tools.py

@@ -34,7 +34,7 @@ def mean_waveform(cluster_id, results_dir, n_spikes=np.inf, bfile=None, best=Tru
     """
     results_dir = Path(results_dir)
     if best:
-        chan = get_best_channel(cluster_id, results_dir)
+        chan = get_best_channels(results_dir)[cluster_id]
     else:
         chan = None
 
@@ -45,12 +45,14 @@ def mean_waveform(cluster_id, results_dir, n_spikes=np.inf, bfile=None, best=Tru
     return mean_wave
 
 
-def get_best_channel(cluster_id, results_dir):
-    """Get channel number with largest template norm for this cluster."""
+def get_best_channels(results_dir):
+    """Get channel numbers with largest template norm for each cluster."""
     templates = np.load(results_dir / 'templates.npy')
-    chan = (templates**2).sum(axis=1).argmax(axis=-1)[cluster_id]
-    return chan
+    best_chans = (templates**2).sum(axis=1).argmax(axis=-1)
+    return best_chans
 
+def get_best_channel(results_dir, cluster_id):
+    return get_best_channels(results_dir)[cluster_id]
 
 def get_cluster_spikes(cluster_id, results_dir, n_spikes=np.inf):
     """Get `n_spikes` random spike times assigned to `cluster_id`."""

kilosort/gui/probe_view_box.py

@@ -59,17 +59,23 @@ def setup(self):
         layout = QtWidgets.QVBoxLayout()
         layout.addWidget(QtWidgets.QLabel('Left click to toggle excluded channels'))
         layout.addWidget(self.probe_view, 95)
+
         chan_box = QtWidgets.QHBoxLayout()
         chan_box.addWidget(self.aspect_toggle)
         chan_box.addWidget(self.channel_toggle)
         layout.addLayout(chan_box)
-        layout.addWidget(self.template_toggle)
-        layout.addWidget(self.center_toggle)
-        op_box = QtWidgets.QHBoxLayout()
-        op_box.addWidget(self.color_toggle)
-        op_box.addWidget(self.number_toggle)
-        layout.addLayout(op_box)
+
+        temp_box = QtWidgets.QHBoxLayout()
+        temp_box.addWidget(self.template_toggle)
+        temp_box.addWidget(self.color_toggle)
+        layout.addLayout(temp_box)
+
+        center_box = QtWidgets.QHBoxLayout()
+        center_box.addWidget(self.center_toggle)
+        center_box.addWidget(self.number_toggle)
+        layout.addLayout(center_box)
         layout.addWidget(self.spot_scale)
+
         self.setLayout(layout)
 
     def reset_spots_variables(self):
@@ -116,7 +122,7 @@ def update_spots_variables(self, probe, template_args):
         for ind, (xc, yc) in enumerate(zip(self.xc, self.yc)):
             self.channel_map_dict[(xc, yc)] = ind
 
-    def get_template_spots(self, nC, dmin, dminx, max_dist, x_centers, device):
+    def get_template_spots(self, nC, dmin, dminx, max_dist, x_centers):
         ops = {
             'yc': self.yc, 'xc': self.xc, 'max_channel_distance': max_dist,
             'x_centers': x_centers, 'settings': {'dmin': dmin, 'dminx': dminx},
@@ -125,7 +131,9 @@ def get_template_spots(self, nC, dmin, dminx, max_dist, x_centers, device):
         ops = template_centers(ops)
         [ys, xs] = np.meshgrid(ops['yup'], ops['xup'])
         ys, xs = ys.flatten(), xs.flatten()
-        iC, ds = nearest_chans(ys, self.yc, xs, self.xc, nC, device=device)
+        iC, ds = nearest_chans(
+            ys, self.yc, xs, self.xc, nC, device=self.gui.device
+            )
 
         igood = ds[0,:] <= max_dist**2
         iC = iC[:,igood]

kilosort/gui/settings_box.py

@@ -19,6 +19,9 @@
 
 _DEFAULT_DTYPE = 'int16'
 _ALLOWED_FILE_TYPES = ['.bin', '.dat', '.bat', '.raw']  # For binary data
+_PROBE_SETTINGS = [
+    'nearest_chans', 'dmin', 'dminx', 'max_channel_distance', 'x_centers'
+    ]
 
 class SettingsBox(QtWidgets.QGroupBox):
     settingsUpdated = QtCore.Signal()
@@ -247,6 +250,8 @@ def setup(self):
                 )
             inp = getattr(self, f'{k}_input')
             inp.editingFinished.connect(self.update_parameter)
+            if k in _PROBE_SETTINGS:
+                inp.editingFinished.connect(self.show_probe_layout())
 
         row_count += rspan
         layout.addWidget(
@@ -550,10 +555,7 @@ def update_settings(self):
 
     def get_probe_template_args(self):
         epw = self.extra_parameters_window
-        template_args = [
-            epw.nearest_chans, epw.dmin, epw.dminx, 
-            epw.max_channel_distance, epw.x_centers, self.gui.device
-            ]
+        template_args = [getattr(epw, k) for k in _PROBE_SETTINGS]
         return template_args
 
     @QtCore.Slot()
@@ -862,6 +864,8 @@ def __init__(self, parent):
             layout.addWidget(getattr(self, f'{k}_input'), row_count, col+3, 1, 2)
             inp = getattr(self, f'{k}_input')
             inp.editingFinished.connect(self.update_parameter)
+            if k in _PROBE_SETTINGS:
+                inp.editingFinished.connect(self.main_settings.show_probe_layout)
 
         self.setLayout(layout)