Merge pull request #72 from SpikeInterface/activity_update

Modified plot_activity_map with new spiketoolkit changes

spikewidgets/tests/test_widgets.py

@@ -25,6 +25,10 @@ def test_spectrogram(self):
     def test_geometry(self):
         sw.plot_electrode_geometry(self._RX)
 
+    def test_activitymap(self):
+        sw.plot_activity_map(self._RX, activity='rate')
+        sw.plot_activity_map(self._RX, activity='amplitude')
+
     def test_unitwaveforms(self):
         sw.plot_unit_waveforms(self._RX, self._SX)
         fig, axes = plt.subplots(self.num_units, 1)

spikewidgets/widgets/mapswidget/activitymapwidget.py

@@ -2,13 +2,13 @@
 import spiketoolkit as st
 import matplotlib.pylab as plt
 import matplotlib as mpl
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 from ..utils import LabeledRectangle
 from spikewidgets.widgets.basewidget import BaseWidget
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 
 
-def plot_activity_map(recording, channel_ids=None, trange=None, cmap='viridis', background='on', label_color='r',
+def plot_activity_map(recording, channel_ids=None, trange=None, activity='rate', log=False,
+                      cmap='viridis', background='on', label_color='r',
                       transpose=False, frame=False, colorbar=False, colorbar_bbox=None,
                       colorbar_orientation='vertical', colorbar_width=0.02, recompute_info=False,
                       ax=None, figure=None):
@@ -20,17 +20,21 @@ def plot_activity_map(recording, channel_ids=None, trange=None, cmap='viridis',
     recording: RecordingExtractor
         The recordng extractor object
     channel_ids: list
-        The channel ids to display.
+        The channel ids to display
     trange: list
         List with start time and end time
+    activity: str
+        'rate' or 'amplitude'. If 'rate' the channel spike rate is used. If 'amplitude' the spike amplitude is used
+    log: bool
+        If True, log scale is used
     cmap: matplotlib colormap
         The colormap to be used (default 'viridis')
     background: bool
         If True, a background is added in between electrodes
     transpose: bool, optional, default: False
-        Swap x and y channel coordinates if True.
+        Swap x and y channel coordinates if True
     frame: bool, optional, default: False
-        Draw a frame around the array if True.
+        Draw a frame around the array if True
     colorbar: bool
         If True, a colorbar is displayed
     colorbar_bbox: bbox
@@ -55,6 +59,8 @@ def plot_activity_map(recording, channel_ids=None, trange=None, cmap='viridis',
         recording=recording,
         channel_ids=channel_ids,
         trange=trange,
+        activity=activity,
+        log=log,
         background=background,
         cmap=cmap,
         label_color=label_color,
@@ -73,13 +79,15 @@ def plot_activity_map(recording, channel_ids=None, trange=None, cmap='viridis',
 
 
 class ActivityMapWidget(BaseWidget):
-    def __init__(self, recording, channel_ids, trange, cmap, background, label_color='r', transpose=False, frame=False,
-                 colorbar=False, colorbar_bbox=None, colorbar_orientation='vertical', colorbar_width=0.02,
-                 recompute_info=False, figure=None, ax=None):
+    def __init__(self, recording, channel_ids, activity, log, trange, cmap, background, label_color='r',
+                 transpose=False, frame=False, colorbar=False, colorbar_bbox=None, colorbar_orientation='vertical',
+                 colorbar_width=0.02, recompute_info=False, figure=None, ax=None):
         BaseWidget.__init__(self, figure, ax)
         self._recording = recording
         self._channel_ids = channel_ids
+        self._activity = activity
         self._trange = trange
+        self._log = log
         self._transpose = transpose
         self._cmap = cmap
         self._frame = frame
@@ -92,6 +100,7 @@ def __init__(self, recording, channel_ids, trange, cmap, background, label_color
         self._recompute_info = recompute_info
         self.colorbar = None
         self.name = 'ActivityMap'
+        assert activity in ['rate', 'amplitude'], "'activity' can be either 'rate' or 'amplitude'"
         assert 'location' in self._recording.get_shared_channel_property_names(), "Activity map requires 'location'" \
                                                                                   "property"
 
@@ -106,13 +115,14 @@ def _do_plot(self):
             self._trange = [int(t * self._recording.get_sampling_frequency()) for t in self._trange]
 
         locations = self._recording.get_channel_locations(channel_ids=self._channel_ids)
-        activity = st.postprocessing.compute_channel_spiking_activity(self._recording,
-                                                                      start_frame=self._trange[0],
-                                                                      end_frame=self._trange[1],
-                                                                      method='detection',
-                                                                      align=False,
-                                                                      recompute_info=self._recompute_info,
-                                                                      verbose=False)
+        spike_rates, spike_amplitudes = st.postprocessing.compute_channel_spiking_activity(self._recording,
+                                                                                           start_frame=self._trange[0],
+                                                                                           end_frame=self._trange[1],
+                                                                                           method='detection',
+                                                                                           align=False,
+                                                                                           recompute_info=
+                                                                                           self._recompute_info,
+                                                                                           verbose=False)
         if self._transpose:
             locations = np.roll(locations, 1, axis=1)
 
@@ -143,10 +153,21 @@ def _do_plot(self):
         elec_x = 0.9 * pitch_x
         elec_y = 0.9 * pitch_y
 
+        if self._activity == 'rate':
+            activity = spike_rates
+        else:  # amplitude
+            activity = np.abs(spike_amplitudes)
+
         max_activity = np.round(np.max(activity), 2)
+        min_activity = np.round(np.min(activity), 2)
+
+        if self._log:
+            if np.any(activity < 1):
+                activity += (1 - np.min(activity))
+            activity = np.log(activity)
 
         # normalize
-        activity -= np.min(activity)
+        activity -= (np.min(activity) + 1e-5)
         activity /= np.ptp(activity)
 
         for (loc, act, ch) in zip(locations, activity, self._recording.get_channel_ids()):
@@ -198,17 +219,22 @@ def _do_plot(self):
 
             cax = inset_axes(self.ax, width="100%", height="100%", bbox_to_anchor=bbox,
                              bbox_transform=self.ax.transData)
-            scalable = mpl.cm.ScalarMappable(norm=mpl.colors.Normalize(vmin=0, vmax=1), cmap=self._cmap)
+            if self._log:
+                norm = mpl.colors.LogNorm(vmin=1e-5, vmax=1)
+            else:
+                norm = mpl.colors.Normalize(vmin=0, vmax=1)
+            scalable = mpl.cm.ScalarMappable(norm=norm, cmap=self._cmap)
             self.colorbar = self.figure.colorbar(scalable, cax=cax,
                                                  orientation=self._colorbar_orient)#, shrink=0.5)
             cax.yaxis.set_ticks_position('left')
             cax.yaxis.set_label_position('left')
             self.colorbar.set_ticks((0, 1))
-            self.colorbar.set_ticklabels((0, max_activity))
+            self.colorbar.set_ticklabels((min_activity, max_activity))
             if self._colorbar_orient == 'vertical':
                 rotation = 90
             else:
                 rotation = 0
-            self.colorbar.set_label('Sp/s', rotation=rotation)
-
-
+            if self._activity == 'rate':
+                self.colorbar.set_label('Sp/s', rotation=rotation)
+            else:
+                self.colorbar.set_label('Amp.', rotation=rotation)

spikewidgets/widgets/mapswidget/templatemapswidget.py

@@ -150,7 +150,10 @@ def _do_plot(self):
         for i, (template, unit) in enumerate(zip(templates, unit_ids)):
             ax = self.get_tiled_ax(i, nrows, ncols)
             temp_map = np.abs(fun(template, axis=1))
+
             if self._log:
+                if np.any(temp_map < 1):
+                    temp_map += (1 - np.min(temp_map))
                 temp_map = np.log(temp_map)
 
             # normalize