Fix lasso selection and split shortcut

Author: alejoe91

spikeinterface_gui/backend_qt.py

@@ -398,7 +398,6 @@ def open_help(self):
     def refresh(self):
         view = self._view()
         view.refresh()
-        
 
 areas = {
     'right' : QT.Qt.RightDockWidgetArea,

spikeinterface_gui/basescatterview.py

@@ -62,7 +62,7 @@ def get_selected_spikes_data(self, segment_index=0, visible_inds=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)
 
@@ -87,7 +87,7 @@ def select_all_spikes_from_lasso(self, keep_already_selected=False):
             if vertices is None:
                 continue
             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_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))
@@ -191,9 +191,6 @@ 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)
 
@@ -399,8 +396,8 @@ 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_end = self.controller.get_t_start_t_end()
+        self.scatter_fig.x_range = Range1d(t_start, t_end)
 
         # Add SelectionGeometry event handler to capture lasso vertices
         self.scatter_fig.on_event('selectiongeometry', self._on_panel_selection_geometry)

spikeinterface_gui/controller.py

@@ -450,7 +450,7 @@ def get_times_chunk(self, segment_index, t1, t2):
             recording = self.analyzer.recording
             times_chunk = recording.get_times(segment_index=segment_index)[ind1:ind2]
         else:
-            times_chunk = np.arange(ind2 - ind1, dtype='float64') / self.controller.sampling_frequency + max(t1, 0)
+            times_chunk = np.arange(ind2 - ind1, dtype='float64') / self.sampling_frequency + max(t1, 0)
         return times_chunk
 
     def get_chunk_indices(self, t1, t2, segment_index):

spikeinterface_gui/curationview.py

@@ -64,11 +64,9 @@ def _qt_make_layout(self):
         from .myqt import QT
         import pyqtgraph as pg
 
-
         self.merge_info = {}
         self.layout = QT.QVBoxLayout()
 
-
         tb = self.qt_widget.view_toolbar
         if self.controller.curation_can_be_saved():
             but = QT.QPushButton("Save in analyzer")
@@ -92,8 +90,6 @@ def _qt_make_layout(self):
         self.table_delete.customContextMenuRequested.connect(self._qt_open_context_menu_delete)
         self.table_delete.itemSelectionChanged.connect(self._qt_on_item_selection_changed_delete)
 
-
-
         self.delete_menu = QT.QMenu()
         act = self.delete_menu.addAction('Restore')
         act.triggered.connect(self.restore_units)

spikeinterface_gui/myqt.py

@@ -5,7 +5,6 @@
 http://mikeboers.com/blog/2015/07/04/static-libraries-in-a-dynamic-world#the-fold
 """
 
-
 class ModuleProxy(object):
 
     def __init__(self, prefixes, modules):

spikeinterface_gui/spikeamplitudeview.py

@@ -28,10 +28,15 @@ def __init__(self, controller=None, parent=None, backend="qt"):
         )
 
     def _qt_make_layout(self):
+        from .myqt import QT
         super()._qt_make_layout()
         self.noise_harea = []
         if self.settings["noise_level"]:
             self._qt_add_noise_area()
+        # add split shortcut, so that it's not duplicated
+        shortcut_split = QT.QShortcut(self.qt_widget)
+        shortcut_split.setKey(QT.QKeySequence("ctrl+s"))
+        shortcut_split.activated.connect(self.split)
 
     def _qt_refresh(self):
         super()._qt_refresh()
@@ -95,4 +100,5 @@ def _panel_add_noise_area(self):
 
 ### Controls
 - **select** : activate lasso selection to select individual spikes
+- **split** or **ctrl+s** : split the selected spikes into a new unit (only if one unit is visible)
 """

spikeinterface_gui/spikedepthview.py

@@ -25,4 +25,5 @@ def __init__(self, controller=None, parent=None, backend="qt"):
 
 ### Controls
 - **select** : activate lasso selection to select individual spikes
+- **split** or **ctrl+s** : split the selected spikes into a new unit (only if one unit is visible)
 """

spikeinterface_gui/tests/test_mainwindow_qt.py

@@ -71,7 +71,7 @@ def test_mainwindow(start_app=False, verbose=True, curation=False, only_some_ext
     for segment_index in range(analyzer.get_num_segments()):
         shift = (segment_index + 1) * 100
         # add a gap to times
-        gap = 1
+        gap = 5
         times = analyzer.recording.get_times(segment_index)
         times = times + shift
         times[len(times)//2:] += gap  # add a gap in the middle

spikeinterface_gui/tracemapview.py

@@ -143,23 +143,16 @@ def _qt_seek(self, t):
         self.scroll_time.setPageStep(int(sr*xsize))
         self.scroll_time.valueChanged.connect(self._qt_on_scroll_time)
 
-<<<<<<< HEAD
         segment_index = self.controller.get_time()[1]
-        times_chunk, data_curves, scatter_x, scatter_y, scatter_colors, scatter_unit_ids = \
+        times_chunk, data_curves, scatter_x, scatter_y, scatter_colors = \
             self.get_data_in_chunk(t1, t2, segment_index)
+        data_curves = data_curves.T
 
         if times_chunk.size == 0:
             self.image.hide()
             self.scatter.clear()
             return
-        
-=======
-        seg_index = self.controller.get_time()[1]
-        times_chunk, data_curves, scatter_x, scatter_y, scatter_colors = \
-            self.get_data_in_chunk(t1, t2, seg_index)
-        data_curves = data_curves.T
 
->>>>>>> 4d644768f573b50e1ce051e7bc234fc21bc5ab93
         if self.color_limit is None:
             self.color_limit = np.max(np.abs(data_curves))
 
@@ -283,14 +276,9 @@ def _panel_refresh(self):
         else:
             auto_scale = False
 
-<<<<<<< HEAD
-        times_chunk, data_curves, scatter_x, scatter_y, scatter_colors, scatter_unit_ids = \
-            self.get_data_in_chunk(t1, t2, segment_index)
-=======
         times_chunk, data_curves, scatter_x, scatter_y, scatter_colors = \
             self.get_data_in_chunk(t1, t2, seg_index)
         data_curves = data_curves.T
->>>>>>> 4d644768f573b50e1ce051e7bc234fc21bc5ab93
 
         if self.color_limit is None:
             self.color_limit = np.max(np.abs(data_curves))
@@ -320,13 +308,8 @@ def _panel_refresh(self):
 
     # TODO: if from a different unit, change unit visibility
     def _panel_on_tap(self, event):
-<<<<<<< HEAD
-        segment_index = self.controller.get_time()[1]
-        ind_spike_nearest = self.find_nearest_spike(self.controller, event.x, segment_index)
-=======
         seg_index = self.controller.get_time()[1]
         ind_spike_nearest = find_nearest_spike(self.controller, event.x, seg_index)
->>>>>>> 4d644768f573b50e1ce051e7bc234fc21bc5ab93
         if ind_spike_nearest is not None:
             self.controller.set_indices_spike_selected([ind_spike_nearest])
             self._panel_seek_with_selected_spike()

spikeinterface_gui/viewlist.py

@@ -17,8 +17,10 @@
 from .metricsview import MetricsView
 from .spikerateview import SpikeRateView
 
+# probe and mainsettings view are first, since they affect other views (e.g., time info)
 possible_class_views = dict(
-    probe = ProbeView, # probe view is first, since it updates channels upon unit changes
+    probe = ProbeView,
+    mainsettings = MainSettingsView,
     unitlist = UnitListView,
     spikelist = SpikeListView,
     merge = MergeView,
@@ -35,5 +37,4 @@
     curation = CurationView,
     spikerate = SpikeRateView,
     metrics = MetricsView,    
-    mainsettings = MainSettingsView,
 )