Merge pull request #198 from alejoe91/performance-panel

Improve web mode "snappiness"

Author: chrishalcrow

spikeinterface_gui/basescatterview.py

@@ -9,10 +9,10 @@ class BaseScatterView(ViewBase):
     _depend_on = None
     _settings = [
             {'name': "auto_decimate", 'type': 'bool', 'value' : True },
-            {'name': 'max_spikes_per_unit', 'type': 'int', 'value' : 10_000 },
+            {'name': 'max_spikes_per_unit', 'type': 'int', 'value' : 5_000 },
             {'name': 'alpha', 'type': 'float', 'value' : 0.7, 'limits':(0, 1.), 'step':0.05 },
             {'name': 'scatter_size', 'type': 'float', 'value' : 2., 'step':0.5 },
-            {'name': 'num_bins', 'type': 'int', 'value' : 400, 'step': 1 },
+            {'name': 'num_bins', 'type': 'int', 'value' : 100, 'step': 1 },
         ]
     _need_compute = False
 
@@ -407,6 +407,8 @@ def _panel_make_layout(self):
         # Add SelectionGeometry event handler to capture lasso vertices
         self.scatter_fig.on_event('selectiongeometry', self._on_panel_selection_geometry)
 
+        self.hist_source = ColumnDataSource(data={"x": [], "y": []})
+        self.hist_data_source = ColumnDataSource(data=dict(x=[], y=[], color=[]))
         self.hist_fig = bpl.figure(
             tools="reset,wheel_zoom",
             sizing_mode="stretch_both",
@@ -416,6 +418,8 @@ def _panel_make_layout(self):
             y_range=self.y_range,
             styles={"flex": "1"}  # Make histogram narrower than scatter plot
         )
+        self.lines_hist = self.hist_fig.multi_line('x', 'y', source=self.hist_data_source,
+                                                   line_color='color', line_width=2)
         self.hist_fig.toolbar.logo = None
         self.hist_fig.yaxis.axis_label = self.y_label
         self.hist_fig.xaxis.axis_label = "Count"
@@ -447,24 +451,23 @@ def _panel_make_layout(self):
                 ),
             )
         )
-        self.hist_lines = []
+        # self.hist_lines = []
         self.noise_harea = []
         self.plotted_inds = []
 
     def _panel_refresh(self):
         from bokeh.models import ColumnDataSource, Range1d
 
-        # clear figures
-        for renderer in self.hist_lines:
-            self.hist_fig.renderers.remove(renderer)
-        self.hist_lines = []
         self.plotted_inds = []
 
         max_count = 1
         xs = []
         ys = []
         colors = []
 
+        xh = []
+        yh = []
+        colors_h = []
         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)
@@ -484,33 +487,33 @@ def _panel_refresh(self):
             max_count = max(max_count, np.max(hist_count))
             self.plotted_inds.extend(inds)
 
-            hist_lines = self.hist_fig.line(
-                "x",
-                "y",
-                source=ColumnDataSource(
-                    {"x":hist_count,
-                     "y":hist_bins[:-1],
-                     }
-                ),
-                line_color=color,
-                line_width=2,
-            )
-            self.hist_lines.append(hist_lines)
+            # Prepare data for multi_line
+            xh.append(hist_count)
+            yh.append(hist_bins[:-1])
+            colors_h.append(color)
+
         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
 
         # Add scatter plot with correct alpha parameter
-        self.scatter_source.data = {
-            "x": xs,
-            "y": ys,
-            "color": colors
-        }
+        self.scatter_source.data = dict(
+            x=xs,
+            y=ys,
+            color=colors
+        )
         self.scatter.glyph.size = self.settings['scatter_size']
         self.scatter.glyph.fill_alpha = self.settings['alpha']
 
+        # Update histogram multi_line data
+        self.hist_data_source.data = dict(
+            x=xh,
+            y=yh,
+            color=colors_h
+        )
+
         # handle selected spikes
         self._panel_update_selected_spikes()
 
@@ -529,7 +532,6 @@ def _panel_on_select_button(self, event):
             self.scatter_fig.toolbar.active_drag = None
             self.scatter_source.selected.indices = []
 
-
     def _panel_change_segment(self, event):
         self._current_selected = 0
         segment_index = int(self.segment_selector.value.split()[-1])

spikeinterface_gui/crosscorrelogramview.py

@@ -18,6 +18,8 @@ def __init__(self, controller=None, parent=None, backend="qt"):
         ViewBase.__init__(self, controller=controller, parent=parent,  backend=backend)
 
         self.ccg, self.bins = self.controller.get_correlograms()
+        self.figure_cache = {}
+        self.max_cache_size = 20
 
 
     def _on_settings_changed(self):
@@ -64,24 +66,33 @@ def _qt_refresh(self):
 
         for r in range(n):
             for c in range(r, n):
-                
-                i = unit_ids.index(visible_unit_ids[r])
-                j = unit_ids.index(visible_unit_ids[c])
-                count = ccg[i, j, :]
-                
-                plot = pg.PlotItem()
-                if not self.settings['display_axis']:
-                    plot.hideAxis('bottom')
-                    plot.hideAxis('left')
-                
-                if r==c:
-                    unit_id = visible_unit_ids[r]
-                    color = colors[unit_id]
+                unit_id1 = visible_unit_ids[r]
+                unit_id2 = visible_unit_ids[c]
+                if (unit_id1, unit_id2) in self.figure_cache:
+                    plot = self.figure_cache[(unit_id1, unit_id2)]
                 else:
-                    color = (120,120,120,120)
-                
-                curve = pg.PlotCurveItem(bins, count, stepMode='center', fillLevel=0, brush=color, pen=color)
-                plot.addItem(curve)
+                    # create new plot
+                    i = unit_ids.index(visible_unit_ids[r])
+                    j = unit_ids.index(visible_unit_ids[c])
+                    count = ccg[i, j, :]
+
+                    plot = pg.PlotItem()
+                    if not self.settings['display_axis']:
+                        plot.hideAxis('bottom')
+                        plot.hideAxis('left')
+
+                    if r == c:
+                        unit_id = visible_unit_ids[r]
+                        color = colors[unit_id]
+                    else:
+                        color = (120, 120, 120, 120)
+
+                    curve = pg.PlotCurveItem(bins, count, stepMode='center', fillLevel=0, brush=color, pen=color)
+                    plot.addItem(curve)
+                    # cache plot
+                    if len(self.figure_cache) >= self.max_cache_size:
+                        self.figure_cache.pop(next(iter(self.figure_cache)))
+                    self.figure_cache[(unit_id1, unit_id2)] = plot
                 self.grid.addItem(plot, row=r, col=c)
 
     ## panel ##
@@ -102,18 +113,12 @@ def _panel_make_layout(self):
             self.empty_plot_pane,
             sizing_mode="stretch_both",
         )
-        self.is_warning_active = False
-
-        self.plots = []
 
     def _panel_refresh(self):
         import panel as pn
         import bokeh.plotting as bpl
         from bokeh.layouts import gridplot
-        from .utils_panel import _bg_color, insert_warning, clear_warning
-
-        # clear previous plot
-        self.plots = []
+        from .utils_panel import _bg_color
 
         if self.ccg is None:
             return
@@ -127,67 +132,75 @@ def _panel_refresh(self):
         }
         ccg = self.ccg
         bins = self.bins
-
+        figures = []
         first_fig = None
         for r in range(n):
             row_plots = []
             for c in range(r, n):
-                i = unit_ids.index(visible_unit_ids[r])
-                j = unit_ids.index(visible_unit_ids[c])
-                count = ccg[i, j, :]
+                unit1 = visible_unit_ids[r]
+                unit2 = visible_unit_ids[c]
 
-                # Create Bokeh figure
-                if first_fig is not None:
-                    extra_kwargs = dict(x_range=first_fig.x_range)
+                if (unit1, unit2) in self.figure_cache:
+                    fig = self.figure_cache[(unit1, unit2)]
                 else:
-                    extra_kwargs = dict()
-                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",
-                    **extra_kwargs,
-                )
-                fig.toolbar.logo = None
-
-                # Get color from controller
-                if r == c:
-                    unit_id = visible_unit_ids[r]
-                    color = colors[unit_id]
-                    fill_alpha = 0.7
-                else:
-                    color = "lightgray"
-                    fill_alpha = 0.4
-
-                fig.quad(
-                    top=count,
-                    bottom=0,
-                    left=bins[:-1],
-                    right=bins[1:],
-                    fill_color=color,
-                    line_color=color,
-                    alpha=fill_alpha,
-                )
-                if first_fig is None:
-                    first_fig = fig
-
+                    # create new figure
+                    i = unit_ids.index(unit1)
+                    j = unit_ids.index(unit2)
+                    count = ccg[i, j, :]
+
+                    # Create Bokeh figure
+                    if first_fig is not None:
+                        extra_kwargs = dict(x_range=first_fig.x_range)
+                    else:
+                        extra_kwargs = dict()
+                    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",
+                        **extra_kwargs,
+                    )
+                    fig.toolbar.logo = None
+
+                    # Get color from controller
+                    if r == c:
+                        unit_id = visible_unit_ids[r]
+                        color = colors[unit_id]
+                        fill_alpha = 0.7
+                    else:
+                        color = "lightgray"
+                        fill_alpha = 0.4
+
+                    fig.quad(
+                        top=count,
+                        bottom=0,
+                        left=bins[:-1],
+                        right=bins[1:],
+                        fill_color=color,
+                        line_color=color,
+                        alpha=fill_alpha,
+                    )
+                    if first_fig is None:
+                        first_fig = fig
+                    # Cache figure
+                    if len(self.figure_cache) >= self.max_cache_size:
+                        self.figure_cache.pop(next(iter(self.figure_cache)))
+                    self.figure_cache[(unit1, unit2)] = fig
                 row_plots.append(fig)
             # Fill row with None for proper spacing
             full_row = [None] * r + row_plots + [None] * (n - len(row_plots))
-            self.plots.append(full_row)
-
-        if len(self.plots) > 0:
-            grid = gridplot(self.plots, toolbar_location="right", sizing_mode="stretch_both")
-            self.layout[0] = pn.Column(
-                grid,
-                styles={'background-color': f'{_bg_color}'}
-            )
-        else:
-            self.layout[0] = self.empty_plot_pane
+            figures.append(full_row)
+
+        grid = gridplot(figures, toolbar_location="right", sizing_mode="stretch_both")
+        grid.toolbar.logo = None
+        self.layout[0] = pn.Column(
+            grid,
+            styles={'background-color': f'{_bg_color}'}
+        )
 
 
 

spikeinterface_gui/curationview.py

@@ -82,7 +82,6 @@ def _qt_make_layout(self):
 
         v = QT.QVBoxLayout()
         h.addLayout(v)
-        v.addWidget(QT.QLabel("<b>Deleted</b>"))
         self.table_delete = QT.QTableWidget(selectionMode=QT.QAbstractItemView.SingleSelection,
                                      selectionBehavior=QT.QAbstractItemView.SelectRows)
         v.addWidget(self.table_delete)
@@ -99,7 +98,6 @@ def _qt_make_layout(self):
 
         v = QT.QVBoxLayout()
         h.addLayout(v)
-        v.addWidget(QT.QLabel("<b>Merges</b>"))
         self.table_merge = QT.QTableWidget(selectionMode=QT.QAbstractItemView.SingleSelection,
                                      selectionBehavior=QT.QAbstractItemView.SelectRows)
         # self.table_merge.setContextMenuPolicy(QT.Qt.CustomContextMenu)
@@ -118,7 +116,6 @@ def _qt_make_layout(self):
 
         v = QT.QVBoxLayout()
         h.addLayout(v)
-        v.addWidget(QT.QLabel("<b>Splits</b>"))
         self.table_split = QT.QTableWidget(selectionMode=QT.QAbstractItemView.SingleSelection,
                                      selectionBehavior=QT.QAbstractItemView.SelectRows)
         v.addWidget(self.table_split)
@@ -139,7 +136,7 @@ def _qt_refresh(self):
         self.table_merge.clear()
         self.table_merge.setRowCount(len(merged_units))
         self.table_merge.setColumnCount(1)
-        self.table_merge.setHorizontalHeaderLabels(["Merges"])
+        self.table_merge.setHorizontalHeaderLabels(["merges"])
         self.table_merge.setSortingEnabled(False)
         for ix, group in enumerate(merged_units):
             item = QT.QTableWidgetItem(str(group))
@@ -153,7 +150,7 @@ def _qt_refresh(self):
         self.table_delete.clear()
         self.table_delete.setRowCount(len(removed_units))
         self.table_delete.setColumnCount(1)
-        self.table_delete.setHorizontalHeaderLabels(["unit_id"])
+        self.table_delete.setHorizontalHeaderLabels(["removed"])
         self.table_delete.setSortingEnabled(False)
         for i, unit_id in enumerate(removed_units):
             color = self.get_unit_color(unit_id)
@@ -172,7 +169,7 @@ def _qt_refresh(self):
         self.table_split.clear()
         self.table_split.setRowCount(len(splits))
         self.table_split.setColumnCount(1)
-        self.table_split.setHorizontalHeaderLabels(["Split units"])
+        self.table_split.setHorizontalHeaderLabels(["splits"])
         self.table_split.setSortingEnabled(False)
         for i, split in enumerate(splits):
             unit_id = split["unit_id"]