Merge pull request #181 from alejoe91/handle-times

Add main_setting to use recording times

Author: samuelgarcia

spikeinterface_gui/backend_panel.py

@@ -13,6 +13,7 @@ class SignalNotifier(param.Parameterized):
     channel_visibility_changed = param.Event()
     manual_curation_updated = param.Event()
     time_info_updated = param.Event()
+    use_times_updated = param.Event()
     active_view_updated = param.Event()
     unit_color_changed = param.Event()
 
@@ -35,6 +36,9 @@ def notify_manual_curation_updated(self):
     def notify_time_info_updated(self):
         self.param.trigger("time_info_updated")
 
+    def notify_use_times_updated(self):
+        self.param.trigger("use_times_updated")
+
     def notify_active_view_updated(self):
         # this is used to keep an "active view" in the main window
         # when a view triggers this event, it self-declares it as active
@@ -65,6 +69,7 @@ def connect_view(self, view):
         view.notifier.param.watch(self.on_channel_visibility_changed, "channel_visibility_changed")
         view.notifier.param.watch(self.on_manual_curation_updated, "manual_curation_updated")
         view.notifier.param.watch(self.on_time_info_updated, "time_info_updated")
+        view.notifier.param.watch(self.on_use_times_updated, "use_times_updated")
         view.notifier.param.watch(self.on_active_view_updated, "active_view_updated")
         view.notifier.param.watch(self.on_unit_color_changed, "unit_color_changed")
 
@@ -110,6 +115,15 @@ def on_time_info_updated(self, param):
                 continue
             view.on_time_info_updated()
 
+    def on_use_times_updated(self, param):
+        # use times is updated also when a view is not active
+        if not self._active:
+            return
+        for view in self.controller.views:
+            if param.obj.view == view:
+                continue
+            view.on_use_times_updated()
+
     def on_active_view_updated(self, param):
         if not self._active:
             return

spikeinterface_gui/backend_qt.py

@@ -19,6 +19,7 @@ class SignalNotifier(QT.QObject):
     channel_visibility_changed = QT.pyqtSignal()
     manual_curation_updated = QT.pyqtSignal()
     time_info_updated = QT.pyqtSignal()
+    use_times_updated = QT.pyqtSignal()
     unit_color_changed = QT.pyqtSignal()
 
     def __init__(self, parent=None, view=None):
@@ -40,6 +41,9 @@ def notify_manual_curation_updated(self):
     def notify_time_info_updated(self):
         self.time_info_updated.emit()
 
+    def notify_use_times_updated(self):
+        self.use_times_updated.emit()
+
     def notify_unit_color_changed(self):
         self.unit_color_changed.emit()
 
@@ -63,6 +67,7 @@ def connect_view(self, view):
         view.notifier.channel_visibility_changed.connect(self.on_channel_visibility_changed)
         view.notifier.manual_curation_updated.connect(self.on_manual_curation_updated)
         view.notifier.time_info_updated.connect(self.on_time_info_updated)
+        view.notifier.use_times_updated.connect(self.on_use_times_updated)
         view.notifier.unit_color_changed.connect(self.on_unit_color_changed)
 
     def on_spike_selection_changed(self):
@@ -110,7 +115,16 @@ def on_time_info_updated(self):
                 # do not refresh it self
                 continue
             view.on_time_info_updated()
-    
+
+    def on_use_times_updated(self):
+        if not self._active:
+            return
+        for view in self.controller.views:
+            if view.qt_widget == self.sender().parent():
+                # do not refresh it self
+                continue
+            view.on_use_times_updated()
+
     def on_unit_color_changed(self):
         if not self._active:
             return
@@ -383,7 +397,6 @@ def open_help(self):
     def refresh(self):
         view = self._view()
         view.refresh()
-        
 
 areas = {
     'right' : QT.Qt.RightDockWidgetArea,

spikeinterface_gui/basescatterview.py

@@ -32,13 +32,15 @@ def __init__(self, spike_data, y_label, controller=None, parent=None, backend="q
         self._lasso_vertices = {segment_index: None for segment_index in range(controller.num_segments)}
         # this is used in panel
         self._current_selected = 0
+        self._block_auto_refresh_and_notify = False
 
         ViewBase.__init__(self, controller=controller, parent=parent,  backend=backend)
 
 
-    def get_unit_data(self, unit_id, seg_index=0):
-        inds = self.controller.get_spike_indices(unit_id, seg_index=seg_index)
-        spike_times = self.controller.spikes["sample_index"][inds] / self.controller.sampling_frequency
+    def get_unit_data(self, unit_id, segment_index=0):
+        inds = self.controller.get_spike_indices(unit_id, segment_index=segment_index)
+        spike_indices = self.controller.spikes["sample_index"][inds]
+        spike_times = self.controller.sample_index_to_time(spike_indices)
         spike_data = self.spike_data[inds]
         ptp = np.ptp(spike_data)
         hist_min, hist_max = [np.min(spike_data) - 0.2 * ptp, np.max(spike_data) + 0.2 * ptp]
@@ -53,15 +55,15 @@ def get_unit_data(self, unit_id, seg_index=0):
 
         return spike_times, spike_data, hist_count, hist_bins, inds
 
-    def get_selected_spikes_data(self, seg_index=0, visible_inds=None):
-        sl = self.controller.segment_slices[seg_index]
+    def get_selected_spikes_data(self, segment_index=0, visible_inds=None):
+        sl = self.controller.segment_slices[segment_index]
         spikes_in_seg = self.controller.spikes[sl]
         selected_indices = self.controller.get_indices_spike_selected()
         if visible_inds is not None:
             selected_indices = np.intersect1d(selected_indices, visible_inds)
         mask = np.isin(sl.start + np.arange(len(spikes_in_seg)), selected_indices)
         selected_spikes = spikes_in_seg[mask]
-        spike_times = selected_spikes['sample_index'] / self.controller.sampling_frequency
+        spike_times = self.controller.sample_index_to_time(selected_spikes['sample_index'])
         spike_data = self.spike_data[sl][mask]
         return (spike_times, spike_data)
 
@@ -85,8 +87,8 @@ def select_all_spikes_from_lasso(self, keep_already_selected=False):
         for segment_index, vertices in self._lasso_vertices.items():
             if vertices is None:
                 continue
-            spike_inds = self.controller.get_spike_indices(visible_unit_id, seg_index=segment_index)
-            spike_times = self.controller.spikes["sample_index"][spike_inds] / fs
+            spike_inds = self.controller.get_spike_indices(visible_unit_id, segment_index=segment_index)
+            spike_times = self.controller.sample_index_to_time(self.controller.spikes["sample_index"][spike_inds])
             spike_data = self.spike_data[spike_inds]
 
             points = np.column_stack((spike_times, spike_data))
@@ -119,7 +121,7 @@ def split(self):
 
         if self.controller.num_segments > 1:
             # check that lasso vertices are defined for all segments
-            if not all(self._lasso_vertices[seg_index] is not None for seg_index in range(self.controller.num_segments)):
+            if not all(self._lasso_vertices[segment_index] is not None for segment_index in range(self.controller.num_segments)):
                 # Use the new continue_from_user pattern
                 self.continue_from_user(
                     "Not all segments have lasso selection. "
@@ -163,6 +165,15 @@ def on_unit_visibility_changed(self):
                 self._current_selected = self.controller.get_indices_spike_selected().size
         self.refresh()
 
+    def _qt_on_time_info_updated(self):
+        if self.combo_seg.currentIndex() != self.controller.get_time()[1]:
+            self._block_auto_refresh_and_notify = True
+            self.refresh()
+            self._block_auto_refresh_and_notify = False
+
+    def on_use_times_updated(self):
+        self.refresh()
+
     ## QT zone ##
     def _qt_make_layout(self):
         from .myqt import QT
@@ -174,8 +185,8 @@ def _qt_make_layout(self):
         tb = self.qt_widget.view_toolbar
         self.combo_seg = QT.QComboBox()
         tb.addWidget(self.combo_seg)
-        self.combo_seg.addItems([ f'Segment {seg_index}' for seg_index in range(self.controller.num_segments) ])
-        self.combo_seg.currentIndexChanged.connect(self.refresh)
+        self.combo_seg.addItems([ f'Segment {segment_index}' for segment_index in range(self.controller.num_segments) ])
+        self.combo_seg.currentIndexChanged.connect(self._qt_change_segment)
         add_stretch_to_qtoolbar(tb)
         self.lasso_but = QT.QPushButton("select", checkable = True)
         tb.addWidget(self.lasso_but)
@@ -184,9 +195,6 @@ def _qt_make_layout(self):
             self.split_but = QT.QPushButton("split")
             tb.addWidget(self.split_but)
             self.split_but.clicked.connect(self.split)
-            shortcut_split = QT.QShortcut(self.qt_widget)
-            shortcut_split.setKey(QT.QKeySequence("ctrl+s"))
-            shortcut_split.activated.connect(self.split)
         h = QT.QHBoxLayout()
         self.layout.addLayout(h)
 
@@ -235,6 +243,13 @@ def _qt_initialize_plot(self):
     def _qt_on_spike_selection_changed(self):
         self.refresh()
 
+    def _qt_change_segment(self):
+        segment_index = self.combo_seg.currentIndex()
+        self.controller.set_time(segment_index=segment_index)
+        if not self._block_auto_refresh_and_notify:
+            self.refresh()
+            self.notify_time_info_updated()
+
     def _qt_refresh(self):
         from .myqt import QT
         import pyqtgraph as pg
@@ -246,13 +261,18 @@ def _qt_refresh(self):
         if self.spike_data is None:
             return
 
+        segment_index = self.controller.get_time()[1]
+        # Update combo_seg if it doesn't match the current segment index
+        if self.combo_seg.currentIndex() != segment_index:
+            self.combo_seg.setCurrentIndex(segment_index)
+
         max_count = 1
         all_inds = []
         for unit_id in self.controller.get_visible_unit_ids():
 
             spike_times, spike_data, hist_count, hist_bins, inds = self.get_unit_data(
                 unit_id, 
-                seg_index=self.combo_seg.currentIndex()
+                segment_index=segment_index
             )
 
             # make a copy of the color
@@ -276,7 +296,7 @@ def _qt_refresh(self):
         y_range_plot_1 = self.plot.getViewBox().viewRange()
         self.viewBox2.setYRange(y_range_plot_1[1][0], y_range_plot_1[1][1], padding = 0.0)
 
-        spike_times, spike_data = self.get_selected_spikes_data(seg_index=self.combo_seg.currentIndex(), visible_inds=all_inds)
+        spike_times, spike_data = self.get_selected_spikes_data(segment_index=self.combo_seg.currentIndex(), visible_inds=all_inds)
 
         self.scatter_select.setData(spike_times, spike_data)
 
@@ -296,8 +316,8 @@ def _qt_on_lasso_finished(self, points, shift_held=False):
         self.lasso.setData([], [])
         vertices = np.array(points)
 
-        seg_index = self.combo_seg.currentIndex()
-        sl = self.controller.segment_slices[seg_index]
+        segment_index = self.combo_seg.currentIndex()
+        sl = self.controller.segment_slices[segment_index]
         spikes_in_seg = self.controller.spikes[sl]
 
         # Create mask for visible units
@@ -315,16 +335,16 @@ def _qt_on_lasso_finished(self, points, shift_held=False):
                 self.notify_spike_selection_changed()
             return
 
-        if self._lasso_vertices[seg_index] is None:
-            self._lasso_vertices[seg_index] = []
+        if self._lasso_vertices[segment_index] is None:
+            self._lasso_vertices[segment_index] = []
 
         if shift_held:
             # If shift is held, append the vertices to the current lasso vertices
-            self._lasso_vertices[seg_index].append(vertices)
+            self._lasso_vertices[segment_index].append(vertices)
             keep_already_selected = True
         else:
             # If shift is not held, clear the existing lasso vertices for this segment
-            self._lasso_vertices[seg_index] = [vertices]
+            self._lasso_vertices[segment_index] = [vertices]
             keep_already_selected = False
 
         self.select_all_spikes_from_lasso(keep_already_selected=keep_already_selected)
@@ -341,11 +361,11 @@ def _panel_make_layout(self):
 
         self.lasso_tool = LassoSelectTool()
 
-        self.segment_index = 0
+        segment_index = self.controller.get_time()[1]
         self.segment_selector = pn.widgets.Select(
             name="",
             options=[f"Segment {i}" for i in range(self.controller.num_segments)],
-            value=f"Segment {self.segment_index}",
+            value=f"Segment {segment_index}",
         )
         self.segment_selector.param.watch(self._panel_change_segment, 'value')
 
@@ -381,8 +401,8 @@ def _panel_make_layout(self):
         self.scatter_fig.toolbar.active_drag = None
         self.scatter_fig.xaxis.axis_label = "Time (s)"
         self.scatter_fig.yaxis.axis_label = self.y_label
-        time_max = self.controller.get_num_samples(self.segment_index) / self.controller.sampling_frequency
-        self.scatter_fig.x_range = Range1d(0., time_max)
+        t_start, t_stop = self.controller.get_t_start_t_stop()
+        self.scatter_fig.x_range = Range1d(t_start, t_stop)
 
         # Add SelectionGeometry event handler to capture lasso vertices
         self.scatter_fig.on_event('selectiongeometry', self._on_panel_selection_geometry)
@@ -445,11 +465,17 @@ def _panel_refresh(self):
         ys = []
         colors = []
 
+        segment_index = self.controller.get_time()[1]
+        # get view segment index from segment selector
+        segment_index_from_selector = self.segment_selector.options.index(self.segment_selector.value)
+        if segment_index != segment_index_from_selector:
+            self.segment_selector.value = f"Segment {segment_index}"
+
         visible_unit_ids = self.controller.get_visible_unit_ids()
         for unit_id in visible_unit_ids:
             spike_times, spike_data, hist_count, hist_bins, inds = self.get_unit_data(
                 unit_id,
-                seg_index=self.segment_index
+                segment_index=segment_index
             )
             color = self.get_unit_color(unit_id)
             xs.extend(spike_times)
@@ -470,6 +496,9 @@ def _panel_refresh(self):
                 line_width=2,
             )
             self.hist_lines.append(hist_lines)
+        t_start, t_end = self.controller.get_t_start_t_stop()
+        self.scatter_fig.x_range.start = t_start
+        self.scatter_fig.x_range.end = t_end
 
         self._max_count = max_count
 
@@ -503,10 +532,13 @@ def _panel_on_select_button(self, event):
 
     def _panel_change_segment(self, event):
         self._current_selected = 0
-        self.segment_index = int(self.segment_selector.value.split()[-1])
-        time_max = self.controller.get_num_samples(self.segment_index) / self.controller.sampling_frequency
-        self.scatter_fig.x_range.end = time_max
+        segment_index = int(self.segment_selector.value.split()[-1])
+        self.controller.set_time(segment_index=segment_index)
+        t_start, t_end = self.controller.get_t_start_t_stop()
+        self.scatter_fig.x_range.start = t_start
+        self.scatter_fig.x_range.end = t_end
         self.refresh()
+        self.notify_time_info_updated()
 
     def _on_panel_selection_geometry(self, event):
         """
@@ -524,16 +556,16 @@ def _on_panel_selection_geometry(self, event):
                 return
 
             # Append the current polygon to the lasso vertices if shift is held
-            seg_index = self.segment_index
-            if self._lasso_vertices[seg_index] is None:
-                self._lasso_vertices[seg_index] = []
+            segment_index = self.controller.get_time()[1]
+            if self._lasso_vertices[segment_index] is None:
+                self._lasso_vertices[segment_index] = []
             if len(selected) > self._current_selected:
                 self._current_selected = len(selected)
                 # Store the current polygon for the current segment
-                self._lasso_vertices[seg_index].append(polygon)
+                self._lasso_vertices[segment_index].append(polygon)
                 keep_already_selected = True
             else:
-                self._lasso_vertices[seg_index] = [polygon]
+                self._lasso_vertices[segment_index] = [polygon]
                 keep_already_selected = False
 
             self.select_all_spikes_from_lasso(keep_already_selected)
@@ -551,7 +583,8 @@ def _panel_update_selected_spikes(self):
         selected_spike_indices = np.intersect1d(selected_spike_indices, self.plotted_inds)
         if len(selected_spike_indices) > 0:
             # map absolute indices to visible spikes
-            sl = self.controller.segment_slices[self.segment_index]
+            segment_index = self.controller.get_time()[1]
+            sl = self.controller.segment_slices[segment_index]
             spikes_in_seg = self.controller.spikes[sl]
             visible_mask = np.zeros(len(spikes_in_seg), dtype=bool)
             for unit_index, unit_id in self.controller.iter_visible_units():
@@ -573,7 +606,8 @@ def _panel_on_spike_selection_changed(self):
             return
         elif len(selected_indices) == 1:
             selected_segment = self.controller.spikes[selected_indices[0]]['segment_index']
-            if selected_segment != self.segment_index:
+            segment_index = self.controller.get_time()[1]
+            if selected_segment != segment_index:
                 self.segment_selector.value = f"Segment {selected_segment}"
                 self._panel_change_segment(None)
         # update selected spikes