ENH: ICA support

README.md

@@ -11,8 +11,7 @@ The backend is based on [pyqtgraph](https://github.com/pyqtgraph/pyqtgraph)
 which uses Qt's [Graphics View Framework](https://doc.qt.io/qt-5/graphicsview.html)
 for the plotting.
 Development started as a [2021's Google Summer of Code Project](https://github.com/marsipu/gsoc2021).
-Currently, only `Raw.plot()` is supported. For the future support for Epochs
-and ICA-Sources is planned.
+For supported features look [here](https://mne.tools/stable/generated/mne.viz.set_browser_backend.html)
 
 ## Installation
 Install **full MNE-Python** with the instructions provided [here](https://mne.tools/stable/install/mne_python.html#d-plotting-and-source-analysis) or install **minimal MNE-Python** with

mne_qt_browser/_pg_figure.py

@@ -754,7 +754,7 @@ def update_value(self, value):
 
     def update_nchan(self):
         """Update bar size."""
-        if self.mne.group_by in ['position', 'selection']:
+        if getattr(self.mne, 'group_by', None) in ['position', 'selection']:
             self.setPageStep(1)
             self.setMaximum(len(self.mne.ch_selections) - 1)
         else:
@@ -876,7 +876,8 @@ def update_bad_epochs(self):
 
     def update_events(self):
         """Update representation of events."""
-        if self.mne.event_nums is not None and self.mne.events_visible:
+        if getattr(self.mne, 'event_nums', None) is not None \
+                and self.mne.events_visible:
             for ev_t, ev_id in zip(self.mne.event_times, self.mne.event_nums):
                 color_name = self.mne.event_color_dict[ev_id]
                 color = _get_color(color_name)
@@ -1384,6 +1385,9 @@ def _get_ypos(self):
                         ch_name not in self.mne.whitened_ch_names:
                     self.ypos = self.mne.ch_start + idx + 1
                     break
+            # Consider all indices bad
+            if self.ypos is None:
+                self.ypos = self.mne.ch_start + ch_type_idxs[0] + 1
 
     def update_x_position(self):
         """Update x-position of Scalebar."""
@@ -2552,8 +2556,6 @@ def __init__(self, **kwargs):
         # Initialize attributes which are only used by pyqtgraph, not by
         # matplotlib and add them to MNEBrowseParams.
 
-        # Blocks concurrent scolling to avoid segmentation faults
-        self.is_scrolling = False
         # Exactly one MessageBox for messages to facilitate testing/debugging
         self.msg_box = QMessageBox(self)
         # MessageBox modality needs to be adapted for tests
@@ -2705,7 +2707,7 @@ def __init__(self, **kwargs):
                 plt.addItem(grid_line)
 
         # Add events
-        if self.mne.event_nums is not None:
+        if getattr(self.mne, 'event_nums', None) is not None:
             self.mne.events_visible = True
             for ev_time, ev_id in zip(self.mne.event_times,
                                       self.mne.event_nums):
@@ -2749,7 +2751,10 @@ def __init__(self, **kwargs):
         # Initialize BrowserView (inherits QGraphicsView)
         view = BrowserView(plt, useOpenGL=self.mne.use_opengl)
         if hasattr(self.mne, 'bgcolor'):
-            view.setBackground(_get_color(self.mne.bgcolor))
+            bgcolor = self.mne.bgcolor
+        else:
+            bgcolor = 'w'
+        view.setBackground(_get_color(bgcolor))
         layout.addWidget(view, 0, 0)
 
         # Initialize Scroll-Bars
@@ -2812,6 +2817,10 @@ def __init__(self, **kwargs):
         widget.setLayout(layout)
         self.setCentralWidget(widget)
 
+        # Initialize Selection-Dialog
+        if getattr(self.mne, 'group_by', None) in ['position', 'selection']:
+            self._create_selection_fig()
+
         # Initialize Toolbar
         toolbar = self.addToolBar('Tools')
         toolbar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
@@ -2905,31 +2914,31 @@ def __init__(self, **kwargs):
                 'modifier': [None, 'Shift'],
                 'slot': [self.hscroll],
                 'parameter': [-40, '-full'],
-                'description': [f'Move left ({hscroll_type})',
-                                'Move left (full page)']
+                'description': [f'Scroll left ({hscroll_type})',
+                                'Scroll left (full page)']
             },
             'right': {
                 'alias': '→',
                 'qt_key': Qt.Key_Right,
                 'modifier': [None, 'Shift'],
                 'slot': [self.hscroll],
                 'parameter': [40, '+full'],
-                'description': [f'Move right ({hscroll_type})',
-                                'Move right (full page)']
+                'description': [f'Scroll right ({hscroll_type})',
+                                'Scroll right (full page)']
             },
             'up': {
                 'alias': '↑',
                 'qt_key': Qt.Key_Up,
                 'slot': [self.vscroll],
                 'parameter': ['-full'],
-                'description': ['Move up (full page)']
+                'description': ['Scroll up (full page)']
             },
             'down': {
                 'alias': '↓',
                 'qt_key': Qt.Key_Down,
                 'slot': [self.vscroll],
                 'parameter': ['+full'],
-                'description': ['Move down (full page)']
+                'description': ['Scroll down (full page)']
             },
             'home': {
                 'alias': dur_keys[0],
@@ -3104,6 +3113,8 @@ def _add_scalebars(self):
             self.mne.scalebar_texts[ch_type] = scale_bar_text
             self.mne.plt.addItem(scale_bar_text)
 
+        self._set_scalebars_visible(self.mne.scalebars_visible)
+
     def _update_scalebar_x_positions(self):
         if self.mne.scalebars_visible:
             for scalebar in self.mne.scalebars.values():
@@ -3161,11 +3172,6 @@ def scale_all(self, step):
 
     def hscroll(self, step):
         """Scroll horizontally by step."""
-        if self.is_scrolling:
-            return
-
-        self.is_scrolling = True
-
         if step == '+full':
             rel_step = self.mne.duration
         elif step == '-full':
@@ -3189,11 +3195,6 @@ def hscroll(self, step):
 
     def vscroll(self, step):
         """Scroll vertically by step."""
-        if self.is_scrolling:
-            return
-
-        self.is_scrolling = True
-
         if self.mne.fig_selection is not None:
             if step == '+full':
                 step = 1
@@ -3353,12 +3354,20 @@ def _mouse_moved(self, pos):
                              tr.ypos - 0.5 < y < tr.ypos + 0.5]
                     if len(trace) == 1:
                         trace = trace[0]
-                        idx = np.argmin(np.abs(trace.xData - x))
-                        yshown = trace.get_ydata()[idx]
-
+                        idx = np.searchsorted(self.mne.times, x)
+                        if self.mne.data_precomputed:
+                            data = self.mne.data[trace.order_idx]
+                        else:
+                            data = self.mne.data[trace.range_idx]
+                        yvalue = data[idx]
+                        yshown = yvalue + trace.ypos
                         self.mne.crosshair.set_data(x, yshown)
 
-                        yvalue = yshown - trace.ypos
+                        # relative x for epochs
+                        if self.mne.is_epochs:
+                            rel_idx = idx % len(self.mne.inst.times)
+                            x = self.mne.inst.times[rel_idx]
+
                         # negative because plot is inverted for Y
                         scaler = -1 if self.mne.butterfly else -2
                         inv_norm = (scaler *
@@ -3424,9 +3433,6 @@ def _xrange_changed(self, _, xrange):
         # Update Scalebars
         self._update_scalebar_x_positions()
 
-        # Relieve Scrolling-Block
-        self.is_scrolling = False
-
     def _update_events_xrange(self, xrange):
         """Add or remove event-lines depending on view-range.
 
@@ -3521,9 +3527,6 @@ def _yrange_changed(self, _, yrange):
             trace.update_color()
             trace.update_data()
 
-        # Relieve Scrolling-Block
-        self.is_scrolling = False
-
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     # DATA HANDLING
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
@@ -4029,7 +4032,8 @@ def _set_butterfly(self, butterfly):
         self._draw_traces()
 
     def _toggle_butterfly(self):
-        self._set_butterfly(not self.mne.butterfly)
+        if self.mne.instance_type != 'ica':
+            self._set_butterfly(not self.mne.butterfly)
 
     def _toggle_dc(self):
         self.mne.remove_dc = not self.mne.remove_dc
@@ -4135,11 +4139,10 @@ def _toggle_epoch_histogramm(self):
             if fig is not None:
                 self._get_dlg_from_mpl(fig)
 
-    def _update_trace_offsets(self):
-        pass
-
     def _create_selection_fig(self):
-        SelectionDialog(self)
+        if not any([isinstance(fig, SelectionDialog) for
+                    fig in self.mne.child_figs]):
+            SelectionDialog(self)
 
     def message_box(self, text, info_text=None, buttons=None,
                     default_button=None, icon=None, modal=True):
@@ -4329,6 +4332,10 @@ def _click_ch_name(self, ch_index, button):
             self._fake_click((x, y), fig=self.mne.view, button=button,
                              xform='none')
 
+    def _update_trace_offsets(self):
+        """legacy method for mne<1.0"""
+        pass
+
     def _resize_by_factor(self, factor):
         pass
 

mne_qt_browser/conftest.py

@@ -10,7 +10,8 @@
 from mne.conftest import (raw_orig, pg_backend, garbage_collect)  # noqa: F401
 
 _store = {'Raw': {},
-          'Epochs': {}}
+          'Epochs_unicolor': {},
+          'Epochs_multicolor': {}}
 
 
 def pytest_configure(config):

mne_qt_browser/tests/test_speed.py

@@ -102,7 +102,13 @@ def _initiate_hscroll(pg_fig, store, request, timer):
 
         h_mean_fps = 1 / np.median(hscroll_diffs)
         v_mean_fps = 1 / np.median(vscroll_diffs)
-        type_key = 'Epochs' if pg_fig.mne.is_epochs else 'Raw'
+        if pg_fig.mne.is_epochs:
+            if pg_fig.mne.epoch_colors is None:
+                type_key = 'Epochs_unicolor'
+            else:
+                type_key = 'Epochs_multicolor'
+        else:
+            type_key = 'Raw'
         store[type_key][request.node.callspec.id] = dict(h=h_mean_fps,
                                                          v=v_mean_fps)
         pg_fig.close()
@@ -147,6 +153,13 @@ def test_scroll_speed_raw(raw_orig, benchmark_param, store,
         sys.exit(app.exec())
 
 
+def _check_epochs_version():
+    import mne
+    from packaging.version import parse
+    if parse(mne.__version__) < parse('1.0'):
+        pytest.skip('Epochs-Test were skipped because of mne < 1.0!')
+
+
 @pytest.mark.benchmark
 @pytest.mark.parametrize('benchmark_param', [
     pytest.param({'use_opengl': False, 'precompute': False},
@@ -159,11 +172,57 @@ def test_scroll_speed_raw(raw_orig, benchmark_param, store,
                  id='precompute=True'),
     pytest.param({}, id='defaults'),
 ])
-def test_scroll_speed_epochs(raw_orig, benchmark_param, store,
-                             pg_backend, request):
+def test_scroll_speed_epochs_unicolor(raw_orig, benchmark_param, store,
+                                      pg_backend, request):
     from PyQt5.QtCore import QTimer
     from PyQt5.QtWidgets import QApplication
+    _check_epochs_version()
+    _reinit_bm_values()
+
+    app = QApplication.instance()
+    if app is None:
+        app = QApplication(sys.argv)
 
+    events = np.full((50, 3), [0, 0, 1])
+    events[:, 0] = np.arange(0, len(raw_orig), len(raw_orig) / 50) \
+        + raw_orig.first_samp
+    epochs = mne.Epochs(raw_orig, events, preload=True)
+    # Prevent problems with info's locked-stated
+    epochs.info._unlocked = True
+
+    fig = epochs.plot(show=False, block=False, **benchmark_param)
+
+    # # Wait max. 10 s for precomputed data to load
+    if fig.load_thread.isRunning():
+        fig.load_thread.wait(10000)
+
+    timer = QTimer()
+    timer.timeout.connect(partial(_initiate_hscroll, fig, store,
+                                  request, timer))
+    timer.start(0)
+
+    fig.show()
+    with pytest.raises(SystemExit):
+        sys.exit(app.exec())
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize('benchmark_param', [
+    pytest.param({'use_opengl': False, 'precompute': False},
+                 id='use_opengl=False'),
+    pytest.param({'use_opengl': True, 'precompute': False},
+                 id='use_opengl=True', marks=gl_mark),
+    pytest.param({'precompute': False, 'use_opengl': False},
+                 id='precompute=False'),
+    pytest.param({'precompute': True, 'use_opengl': False},
+                 id='precompute=True'),
+    pytest.param({}, id='defaults'),
+])
+def test_scroll_speed_epochs_multicolor(raw_orig, benchmark_param, store,
+                                        pg_backend, request):
+    from PyQt5.QtCore import QTimer
+    from PyQt5.QtWidgets import QApplication
+    _check_epochs_version()
     _reinit_bm_values()
 
     app = QApplication.instance()
@@ -191,6 +250,7 @@ def test_scroll_speed_epochs(raw_orig, benchmark_param, store,
     epoch_colors[2::3] = epoch_col3
     epoch_colors = epoch_colors.tolist()
 
+    # Multicolored Epochs might be unstable without OpenGL on macOS
     if sys.platform == 'darwin':
         benchmark_param['use_opengl'] = True
 

requirements_testing.txt

@@ -5,3 +5,4 @@ pytest-timeout
 pooch
 pyvista  # for mne sys_info to tell us about OpenGL
 tqdm
+sklearn  # for testing ICA