Add main_setting to use recorting times (and other time-related fixes)

Author: alejoe91

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

spikeinterface_gui/basescatterview.py

@@ -36,9 +36,10 @@ def __init__(self, spike_data, y_label, controller=None, parent=None, backend="q
         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]
@@ -53,8 +54,8 @@ 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:
@@ -85,7 +86,7 @@ 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_inds = self.controller.get_spike_indices(visible_unit_id, segment_index=segment_index)
             spike_times = self.controller.spikes["sample_index"][spike_inds] / fs
             spike_data = self.spike_data[spike_inds]
 
@@ -119,7 +120,7 @@ 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 +164,12 @@ def on_unit_visibility_changed(self):
                 self._current_selected = self.controller.get_indices_spike_selected().size
         self.refresh()
 
+    def on_time_info_updated(self):
+        return self.refresh()
+
+    def on_use_times_updated(self):
+        return self.refresh()
+
     ## QT zone ##
     def _qt_make_layout(self):
         from .myqt import QT
@@ -174,8 +181,8 @@ 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)
@@ -235,6 +242,12 @@ 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)
+        self.refresh()
+        self.notify_time_info_updated()
+
     def _qt_refresh(self):
         from .myqt import QT
         import pyqtgraph as pg
@@ -246,13 +259,18 @@ 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 +294,7 @@ 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 +314,8 @@ 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 +333,16 @@ 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)
@@ -445,11 +463,13 @@ def _panel_refresh(self):
         ys = []
         colors = []
 
+        segment_index = self.controller.get_time()[1]
+
         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)
@@ -504,9 +524,12 @@ 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
+        self.controller.set_time(segment_index=self.segment_index)
+        t_start, t_end = self.controller.get_t_start_t_end()
+        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 +547,16 @@ 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.segment_index
+            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)

spikeinterface_gui/controller.py

@@ -25,6 +25,7 @@
 _default_main_settings = dict(
     max_visible_units=10,
     color_mode='color_by_unit',
+    use_times=False
 )
 
 from spikeinterface.widgets.sorting_summary import _default_displayed_unit_properties
@@ -264,7 +265,7 @@ def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save
 
         # self.num_spikes = self.analyzer.sorting.count_num_spikes_per_unit(outputs="dict")
         seg_limits = np.searchsorted(self.spikes["segment_index"], np.arange(num_seg + 1))
-        self.segment_slices = {seg_index: slice(seg_limits[seg_index], seg_limits[seg_index + 1]) for seg_index in range(num_seg)}
+        self.segment_slices = {segment_index: slice(seg_limits[segment_index], seg_limits[segment_index + 1]) for segment_index in range(num_seg)}
 
         spike_vector2 = self.analyzer.sorting.to_spike_vector(concatenated=False)
         self.final_spike_samples = [segment_spike_vector[-1][0] for segment_spike_vector in spike_vector2]
@@ -275,7 +276,7 @@ def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save
         spike_per_seg = [s.size for s in spike_vector2]
         # dict[unit_id] -> all indices for this unit across segments
         self._spike_index_by_units = {}
-        # dict[seg_index][unit_id] -> all indices for this unit for one segment
+        # dict[segment_index][unit_id] -> all indices for this unit for one segment
         self._spike_index_by_segment_and_units = spike_indices_abs
         for unit_id in unit_ids:
             inds = []
@@ -302,10 +303,7 @@ def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save
         self.displayed_unit_properties = displayed_unit_properties
 
         # set default time info
-        self.time_info = dict(
-            time_by_seg=np.array([0] * self.num_segments, dtype="float64"),
-            segment_index=0
-        )
+        self.update_time_info()
 
         self.curation = curation
         # TODO: Reload the dictionary if it already exists
@@ -401,10 +399,10 @@ def get_time(self):
         """
         Returns selected time and segment index
         """
-        seg_index = self.time_info['segment_index']
+        segment_index = self.time_info['segment_index']
         time_by_seg = self.time_info['time_by_seg']
-        time = time_by_seg[seg_index]
-        return time, seg_index
+        time = time_by_seg[segment_index]
+        return time, segment_index
 
     def set_time(self, time=None, segment_index=None):
         """
@@ -418,7 +416,49 @@ def set_time(self, time=None, segment_index=None):
             segment_index = self.time_info['segment_index']
         if time is not None:
             self.time_info['time_by_seg'][segment_index] = time
-    
+
+    def update_time_info(self):
+        # set default time info
+        if self.main_settings["use_times"] and self.analyzer.has_recording():
+            self.time_info = dict(
+                time_by_seg=np.array(
+                    [
+                        self.analyzer.recording.get_start_time(segment_index) for segment_index in range(self.num_segments)
+                    ],
+                    dtype="float64"),
+                segment_index=0
+            )
+        else:
+            self.time_info = dict(
+                time_by_seg=np.array([0] * self.num_segments, dtype="float64"),
+                segment_index=0
+            )
+
+    def get_t_start_t_stop(self):
+        segment_index = self.time_info["segment_index"]
+        if self.main_settings["use_times"] and self.analyzer.has_recording():
+            t_start = self.analyzer.recording.get_start_time(segment_index=segment_index)
+            t_stop = self.analyzer.recording.get_end_time(segment_index=segment_index)
+            return t_start, t_stop
+        else:
+            return 0, self.get_num_samples(segment_index) / self.sampling_frequency
+
+    def sample_index_to_time(self, sample_index):
+        segment_index = self.time_info["segment_index"]
+        if self.main_settings["use_times"] and self.analyzer.has_recording():
+            time = self.analyzer.recording.sample_index_to_time(sample_index, segment_index=segment_index)
+            return time
+        else:
+            return sample_index / self.sampling_frequency
+
+    def time_to_sample_index(self, time):
+        segment_index = self.time_info["segment_index"]
+        if self.main_settings["use_times"] and self.analyzer.has_recording():
+            time = self.analyzer.recording.time_to_sample_index(time, segment_index=segment_index)
+            return time
+        else:
+            return int(time * self.sampling_frequency)
+
     def get_information_txt(self):
         nseg = self.analyzer.get_num_segments()
         nchan = self.analyzer.get_num_channels()
@@ -552,13 +592,13 @@ def set_indices_spike_selected(self, inds):
             sample_index = self.spikes['sample_index'][self._spike_selected_indices[0]]
             self.set_time(time=sample_index / self.sampling_frequency, segment_index=segment_index)
 
-    def get_spike_indices(self, unit_id, seg_index=None):
-        if seg_index is None:
+    def get_spike_indices(self, unit_id, segment_index=None):
+        if segment_index is None:
             # dict[unit_id] -> all indices for this unit across segments
             return self._spike_index_by_units[unit_id]
         else:
-            # dict[seg_index][unit_id] -> all indices for this unit for one segment
-            return self._spike_index_by_segment_and_units[seg_index][unit_id]
+            # dict[segment_index][unit_id] -> all indices for this unit for one segment
+            return self._spike_index_by_segment_and_units[segment_index][unit_id]
 
     def get_num_samples(self, segment_index):
         return self.analyzer.get_num_samples(segment_index=segment_index)
@@ -838,7 +878,7 @@ def make_manual_split_if_possible(self, unit_id):
         indices = self.get_indices_spike_selected()
         if len(indices) == 0:
             return False
-        spike_inds = self.get_spike_indices(unit_id, seg_index=None)
+        spike_inds = self.get_spike_indices(unit_id, segment_index=None)
         if not np.all(np.isin(indices, spike_inds)):
             return False
 

spikeinterface_gui/curationview.py

@@ -53,7 +53,7 @@ def unsplit(self):
     def select_and_notify_split(self, split_unit_id):
         self.controller.set_visible_unit_ids([split_unit_id])
         self.notify_unit_visibility_changed()
-        spike_inds = self.controller.get_spike_indices(split_unit_id, seg_index=None)
+        spike_inds = self.controller.get_spike_indices(split_unit_id, segment_index=None)
         active_split = [s for s in self.controller.curation_data['splits'] if s['unit_id'] == split_unit_id][0]
         split_indices = active_split['indices'][0]
         self.controller.set_indices_spike_selected(spike_inds[split_indices])