Merge pull request #175 from samuelgarcia/metrics-view

Metrics view

Author: samuelgarcia

spikeinterface_gui/controller.py

@@ -614,6 +614,9 @@ def has_extension(self, extension_name):
     def handle_metrics(self):
         return self.metrics is not None
 
+    def get_units_table(self):
+        return self.units_table
+
     def get_all_pcs(self):
 
         if self._pc_projections is None and self.pc_ext is not None:

spikeinterface_gui/layout_presets.py

@@ -47,7 +47,7 @@ def get_layout_description(preset_name, layout=None):
     zone5=['probe'],
     zone6=['ndscatter', 'similarity'],
     zone7=['waveform', 'waveformheatmap', ],
-    zone8=['correlogram', 'isi', 'mainsettings'],
+    zone8=['correlogram', 'isi', 'metrics', 'mainsettings'],
 )
 _presets['default'] = default_layout
 

spikeinterface_gui/metricsview.py

@@ -0,0 +1,176 @@
+import warnings
+import numpy as np
+
+
+from .view_base import ViewBase
+
+from spikeinterface.postprocessing.unit_locations import possible_localization_methods
+
+
+_default_visible_metrics = ("snr", "firing_rate")
+
+class MetricsView(ViewBase):
+    _supported_backend = ['qt', ]
+    _settings = [
+        {'name': 'num_bins', 'type': 'int', 'value' : 30 },
+    ]
+
+    def __init__(self, controller=None, parent=None, backend="qt"):
+        units_table = controller.get_units_table()
+        self.visible_metrics_dict = dict()
+        for col in units_table.columns:
+            if units_table[col].dtype.kind == "f":
+                self.visible_metrics_dict[col] = col in _default_visible_metrics
+
+        ViewBase.__init__(self, controller=controller, parent=parent,  backend=backend)
+
+
+
+    ## Qt ##
+    def _qt_make_layout(self):
+        from .myqt import QT
+        import pyqtgraph as pg
+        from .utils_qt import ViewBoxHandlingDoubleClickToPosition
+    
+        self.layout = QT.QVBoxLayout()
+
+        visible_metrics_tree = []
+        for col, visible in self.visible_metrics_dict.items():
+            visible_metrics_tree.append(
+                {'name': str(col), 'type': 'bool', 'value': visible}
+            )
+        self.qt_visible_metrics = pg.parametertree.Parameter.create( name='visible columns', type='group', children=visible_metrics_tree)
+        self.tree_visible_metrics = pg.parametertree.ParameterTree(parent=self.qt_widget)
+        self.tree_visible_metrics.header().hide()
+        self.tree_visible_metrics.setParameters(self.qt_visible_metrics, showTop=True)
+        # self.tree_visible_metrics.setWindowTitle(u'visible columns')
+        # self.tree_visible_metrics.setWindowFlags(QT.Qt.Window)
+        self.qt_visible_metrics.sigTreeStateChanged.connect(self._qt_on_visible_metrics_changed)
+        self.layout.addWidget(self.tree_visible_metrics)
+        self.tree_visible_metrics.hide()
+        
+
+        tb = self.qt_widget.view_toolbar
+        but = QT.QPushButton('metrics')
+        but.clicked.connect(self._qt_select_metrics)
+        tb.addWidget(but)
+
+        self.grid = pg.GraphicsLayoutWidget()
+        self.layout.addWidget(self.grid)
+
+        self._qt_creat_grid()
+
+        
+
+    def _qt_creat_grid(self):
+        import pyqtgraph as pg
+        from .myqt import QT
+
+        visible_metrics = [k for k, v in self.visible_metrics_dict.items() if v]
+        self.grid.clear()
+        n = len(visible_metrics)
+        if len(visible_metrics) == 0:
+            return
+        
+        
+
+        self.plots = {}
+        for r in range(n):
+            for c in range(r, n):
+                
+                plot = pg.PlotItem()
+                self.grid.addItem(plot, row=r, col=c)
+                self.plots[(r, c)] = plot
+
+                if r == c:
+                    label_style = {'color': "#7BFF00", 'font-size': '14pt'}
+                    plot.setLabel('bottom', visible_metrics[c], **label_style)
+
+    def _qt_refresh(self):
+        import pyqtgraph as pg
+        from .myqt import QT
+
+
+        visible_metrics = [k for k, v in self.visible_metrics_dict.items() if v]
+        n = len(visible_metrics)
+
+        units_table = self.controller.get_units_table()
+
+        white_brush = QT.QColor('white')
+        white_brush.setAlpha(200)
+
+
+        for r in range(n):
+            for c in range(r, n):
+                col1 = visible_metrics[r]
+                col2 = visible_metrics[c]
+
+                plot = self.plots[(r, c)]
+                plot.clear()
+                if c > r:
+                    scatter = pg.ScatterPlotItem(pen=pg.mkPen(None), brush=white_brush, size=11, pxMode = True)
+                    plot.addItem(scatter)
+                    values1 = units_table[col1].values
+                    values2 = units_table[col2].values
+
+                    scatter.setData(x=values2, y=values1)
+
+                    visible_unit_ids = self.controller.get_visible_unit_ids()
+                    visible_unit_ids = self.controller.get_visible_unit_indices()
+
+                    for unit_ind, unit_id in self.controller.iter_visible_units():
+                        color = self.get_unit_color(unit_id)
+                        scatter.addPoints(x=[values2[unit_ind]], y=[values1[unit_ind]],  pen=pg.mkPen(None), brush=color)
+
+                    # self.scatter.addPoints(x=scatter_x[unit_id], y=scatter_y[unit_id],  pen=pg.mkPen(None), brush=color)
+                    # self.scatter_select.setData(selected_scatter_x, selected_scatter_y)
+                elif c == r:
+                    values1 = units_table[visible_metrics[r]].values
+
+                    count, bins = np.histogram(values1, bins=self.settings['num_bins'])
+                    curve = pg.PlotCurveItem(bins, count, stepMode='center', fillLevel=0, brush=white_brush, pen=white_brush)
+                    plot.addItem(curve)
+
+                    for unit_ind, unit_id in self.controller.iter_visible_units():
+                        x = values1[unit_ind]
+                        color = self.get_unit_color(unit_id)
+                        line = pg.InfiniteLine(pos=x, angle=90, movable=False, pen=color)
+                        plot.addItem(line)
+
+
+                #     color = self.get_unit_color(unit_id)
+                # else:
+                #     color = (120,120,120,120)
+                
+                # curve = pg.PlotCurveItem(self.bins, count, stepMode='center', fillLevel=0, brush=color, pen=color)
+
+
+
+
+    def _qt_select_metrics(self):
+        if not self.tree_visible_metrics.isVisible():
+            self.tree_visible_metrics.show()
+        else:
+            self.tree_visible_metrics.hide()
+    
+        self.layout.addWidget(self.tree_visible_metrics)
+    
+    def _qt_on_visible_metrics_changed(self):
+        
+        for col in self.visible_metrics_dict.keys():
+            # update the internal dict with the qt tree
+            self.visible_metrics_dict[col] = self.qt_visible_metrics[col]
+        self._qt_creat_grid()
+        self.refresh()
+
+
+
+
+
+    ## panel ##
+    def _panel_make_layout(self):
+        import panel as pn
+        import bokeh.plotting as bpl
+        from bokeh.models import ColumnDataSource, HoverTool, Label, PanTool
+        from bokeh.events import Tap, PanStart, PanEnd
+        from .utils_panel import CustomCircle, _bg_color

spikeinterface_gui/tests/debug_views.py

@@ -14,8 +14,8 @@
 from pathlib import Path
 
 
-# test_folder = Path(__file__).parent / 'my_dataset_small'
-test_folder = Path(__file__).parent / 'my_dataset_big'
+test_folder = Path(__file__).parent / 'my_dataset_small'
+# test_folder = Path(__file__).parent / 'my_dataset_big'
 # test_folder = Path(__file__).parent / 'my_dataset_multiprobe'
 
 
@@ -34,8 +34,9 @@ def debug_one_view():
                             )
 
     # view_class = possible_class_views['unitlist']
-    view_class = possible_class_views['mainsettings']
+    # view_class = possible_class_views['mainsettings']
     # view_class = possible_class_views['spikeamplitude']
+    view_class = possible_class_views['metrics']
     widget = ViewWidget(view_class)
     view = view_class(controller=controller, parent=widget, backend='qt')
     widget.set_view(view)

spikeinterface_gui/tests/test_mainwindow_qt.py

@@ -14,7 +14,7 @@
 import sys
 
 
-test_folder = Path(__file__).parent / 'my_dataset_small'
+# test_folder = Path(__file__).parent / 'my_dataset_small'
 test_folder = Path(__file__).parent / 'my_dataset_big'
 # test_folder = Path(__file__).parent / 'my_dataset_multiprobe'
 

spikeinterface_gui/viewlist.py

@@ -14,6 +14,7 @@
 from .tracemapview import TraceMapView
 from .curationview import CurationView
 from .mainsettingsview import MainSettingsView
+from .metricsview import MetricsView
 from .rateview import SpikeRateView
 
 possible_class_views = dict(
@@ -33,5 +34,6 @@
     tracemap = TraceMapView,
     curation = CurationView,
     mainsettings=MainSettingsView,
+    metrics = MetricsView,
     spikerate=SpikeRateView,
 )