Merge branch 'main' into metrics-view

Author: samuelgarcia

spikeinterface_gui/controller.py

@@ -268,6 +268,7 @@ def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save
         self.segment_slices = {seg_index: slice(seg_limits[seg_index], seg_limits[seg_index + 1]) for seg_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]
         # this is dict of list because per segment spike_indices[segment_index][unit_id]
         spike_indices = spike_vector_to_indices(spike_vector2, unit_ids)
         # this is flatten

spikeinterface_gui/layout_presets.py

@@ -42,7 +42,7 @@ def get_layout_description(preset_name, layout=None):
 default_layout = dict(
     zone1=['curation', 'spikelist'],
     zone2=['unitlist', 'mergelist'],
-    zone3=['trace', 'tracemap',  'spikeamplitude', 'spikedepth'],
+    zone3=['trace', 'tracemap',  'spikeamplitude', 'spikedepth', 'spikerate'],
     zone4=[],
     zone5=['probe'],
     zone6=['ndscatter', 'similarity'],

spikeinterface_gui/rateview.py

@@ -0,0 +1,157 @@
+from .view_base import ViewBase
+import numpy as np
+
+
+class SpikeRateView(ViewBase):
+    _supported_backend = ['qt', 'panel']
+    _settings = [
+            {'name': 'bin_s', 'type': 'int', 'value' : 60 },
+        ]
+    _need_compute = False
+
+    def __init__(self, controller=None, parent=None, backend="qt"):
+        ViewBase.__init__(self, controller=controller, parent=parent,  backend=backend)
+    
+    def _on_settings_changed(self):
+        self.refresh()
+
+    ## Qt ##
+
+    def _qt_make_layout(self):
+        from .myqt import QT
+        import pyqtgraph as pg
+
+        self.layout = QT.QVBoxLayout()
+
+        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)
+
+        h = QT.QHBoxLayout()
+        self.layout.addLayout(h)
+
+        self.plot = pg.PlotItem(viewBox=None)
+        self.graphicsview = pg.GraphicsView()
+        self.graphicsview.setCentralItem(self.plot)
+        self.layout.addWidget(self.graphicsview)
+
+    def _qt_refresh(self):
+        import pyqtgraph as pg
+
+        self.plot.clear()
+
+        seg_index =  self.combo_seg.currentIndex()
+
+        visible_unit_ids = self.controller.get_visible_unit_ids()
+        
+        sampling_frequency = self.controller.sampling_frequency
+
+        total_frames = self.controller.final_spike_samples
+        bins_s = self.settings['bin_s']
+        num_bins = total_frames[seg_index] // int(sampling_frequency) // bins_s
+        
+        for r, unit_id in enumerate(visible_unit_ids):
+
+            spike_inds = self.controller.get_spike_indices(unit_id, seg_index=seg_index)
+            spikes = self.controller.spikes[spike_inds]['sample_index']
+
+            count, bins = np.histogram(spikes, bins=num_bins)
+            
+            color = self.get_unit_color(unit_id)
+            curve = pg.PlotCurveItem(
+                (bins[1:]+bins[:-1])/(2*sampling_frequency), 
+                count/bins_s, 
+                pen=pg.mkPen(color, width=2)
+            )
+            self.plot.addItem(curve)
+
+        # Make lower y-lim 0
+        self.plot.getViewBox().autoRange()
+        current_max_y_range = self.plot.getViewBox().viewRange()[1][1]
+        self.plot.getViewBox().setYRange(0, current_max_y_range)
+        
+    ## panel ##
+
+    def _panel_make_layout(self):
+        import panel as pn
+        import bokeh.plotting as bpl
+        from .utils_panel import _bg_color
+
+        self.segment_index = 0
+        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}",
+        )
+        self.segment_selector.param.watch(self._panel_change_segment, 'value')
+
+        self.rate_fig = bpl.figure(
+            width=250,
+            height=250,
+            tools="pan,wheel_zoom,reset",
+            active_drag="pan",
+            active_scroll="wheel_zoom",
+            background_fill_color=_bg_color,
+            border_fill_color=_bg_color,
+            outline_line_color="white",
+        )
+        self.rate_fig.toolbar.logo = None
+        self.rate_fig.grid.visible = False
+
+        self.layout = pn.Column(
+            pn.Row(self.segment_selector, sizing_mode="stretch_width"),
+            pn.Row(self.rate_fig,sizing_mode="stretch_both"),
+        )
+        self.is_warning_active = False
+
+    def _panel_refresh(self):
+        import panel as pn
+        import bokeh.plotting as bpl
+        from bokeh.layouts import gridplot
+        from .utils_panel import _bg_color
+
+        seg_index =  self.segment_index
+
+        visible_unit_ids = self.controller.get_visible_unit_ids()
+
+        sampling_frequency = self.controller.sampling_frequency
+
+        total_frames = self.controller.final_spike_samples
+        bins_s = self.settings['bin_s']
+        num_bins = total_frames[seg_index] // int(sampling_frequency) // bins_s
+
+        # clear fig
+        self.rate_fig.renderers = []
+        
+        for unit_id in visible_unit_ids:
+
+            spike_inds = self.controller.get_spike_indices(unit_id, seg_index=seg_index)
+            spikes = self.controller.spikes[spike_inds]['sample_index']
+
+            count, bins = np.histogram(spikes, bins=num_bins)
+            
+            # Get color from controller
+            color = self.get_unit_color(unit_id)
+
+            line = self.rate_fig.line(
+                x=(bins[1:]+bins[:-1])/(2*sampling_frequency),
+                y=count/bins_s,
+                color=color,
+                line_width=2,
+            )
+
+        self.rate_fig.y_range.start = 0
+
+    def _panel_change_segment(self, event):
+        self.segment_index = int(self.segment_selector.value.split()[-1])
+        self.refresh()
+
+
+
+SpikeRateView._gui_help_txt = """
+# SpikeRateView View
+
+This view shows firing rate for spikes per `bin_s`.
+"""

spikeinterface_gui/tests/test_mainwindow_panel.py

@@ -100,9 +100,9 @@ def test_launcher(verbose=True):
     if not test_folder.is_dir():
         setup_module()
 
-    # win = test_mainwindow(start_app=True, verbose=True, curation=True)
+    win = test_mainwindow(start_app=True, verbose=True, curation=True)
 
-    test_launcher(verbose=True)
+    # test_launcher(verbose=True)
 
 # TO RUN with panel serve:
 # win = test_mainwindow(start_app=False, verbose=True, curation=True)

spikeinterface_gui/viewlist.py

@@ -15,6 +15,7 @@
 from .curationview import CurationView
 from .mainsettingsview import MainSettingsView
 from .metricsview import MetricsView
+from .rateview import SpikeRateView
 
 possible_class_views = dict(
     probe = ProbeView, # probe view is first, since it updates channels upon unit changes
@@ -34,4 +35,5 @@
     curation = CurationView,
     mainsettings=MainSettingsView,
     metrics = MetricsView,
+    spikerate=SpikeRateView,
 )