Merge pull request #248 from alejoe91/fix-traces-multi-shank

Fix tracemapview for multishank

Author: samuelgarcia

spikeinterface_gui/controller.py

@@ -693,6 +693,12 @@ def get_traces(self, trace_source='preprocessed', **kargs):
     def get_contact_location(self):
         location = self.analyzer.get_channel_locations()
         return location
+
+    def get_channel_groups(self):
+        if self.has_extension("recording"):
+            return self.analyzer.recording.get_channel_groups()
+        else:
+            return np.zeros(self.analyzer.get_num_channels(), dtype=int)
 
     def get_waveform_sweep(self):
         return self.nbefore, self.nafter
@@ -704,7 +710,7 @@ def get_waveforms(self, unit_id):
         wfs = self.waveforms_ext.get_waveforms_one_unit(unit_id, force_dense=False)
         if self.analyzer.sparsity is None:
             # dense waveforms
-            chan_inds = np.arange(self.analyzer.recording.get_num_channels(), dtype='int64')
+            chan_inds = np.arange(self.analyzer.get_num_channels(), dtype='int64')
         else:
             # sparse waveforms
             chan_inds = self.analyzer.sparsity.unit_id_to_channel_indices[unit_id]

spikeinterface_gui/tracemapview.py

@@ -24,8 +24,14 @@ class TraceMapView(ViewBase, MixinViewTrace):
 
     def __init__(self, controller=None, parent=None, backend="qt"):
         pos = controller.get_contact_location()
-        self.channel_order = np.lexsort((-pos[:, 0], pos[:, 1], ))
+        channel_groups = controller.get_channel_groups()
+        self.channel_order = np.lexsort((-pos[:, 0], pos[:, 1], channel_groups))
         self.channel_order_reverse = np.argsort(self.channel_order, kind="stable")
+        if len(np.unique(channel_groups)) > 1:
+            self.chan_group_offsets, = np.nonzero(np.diff(np.sort(channel_groups)))
+            self.chan_group_offsets = self.chan_group_offsets + 1
+        else:
+            self.chan_group_offsets = None
         self.color_limit = None
         self.last_data_curves = None
         self.factor = None
@@ -163,6 +169,11 @@ def _qt_seek(self, t):
         self.plot.setXRange(t1, t2, padding=0.0)
         self.plot.setYRange(0, num_chans, padding=0.0)
 
+        if self.chan_group_offsets is not None:
+            for ch in self.chan_group_offsets:
+                hline = pg.InfiniteLine(pos=ch, angle=0, movable=False, pen=pg.mkPen("black"))
+                self.plot.addItem(hline)
+
     def _qt_on_time_info_updated(self):
         # Update segment and time slider range
         time, segment_index = self.controller.get_time()
@@ -224,7 +235,7 @@ def _panel_make_layout(self):
         self.figure.xaxis.major_tick_line_color = "white"
         self.figure.yaxis.visible = False
         self.figure.x_range = Range1d(start=0, end=0.5)
-        self.figure.y_range = Range1d(start=0, end=1)
+        self.figure.y_range = Range1d(start=0, end=self.controller.num_channels)
 
 
         # Add data sources
@@ -245,6 +256,9 @@ def _panel_make_layout(self):
             x="x", y="y", size=10, fill_color="color", fill_alpha=self.settings['alpha'], source=self.spike_source
         )
 
+        if self.chan_group_offsets is not None:
+            self.figure.hspan(y=list(self.chan_group_offsets), line_color="yellow")
+
         # # Add hover tool for spikes
         # hover_spikes = HoverTool(renderers=[self.spike_renderer], tooltips=[("Unit", "@unit_id")])
         # self.figure.add_tools(hover_spikes)

spikeinterface_gui/waveformview.py

@@ -945,7 +945,7 @@ def _panel_clear_scalebars(self):
         self.scalebar_lines_source.data = dict(xs=[], ys=[], colors=[])
 
     def _panel_add_scalebars(self):
-        from bokeh.models import Span, Label
+        from bokeh.models import Label
 
         if not self.settings["x_scalebar"] and not self.settings["y_scalebar"]:
             return