Feature bipolar references

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Changed
 - PySide2 installed by default if wrapped Qt bindings (PyQt5, PySide2) are not found ([#187](https://github.com/cbrnr/mnelab/pull/187) by [Guillaume Dollé](https://github.com/gdolle))
+- Add support for bipolar reference [#173](https://github.com/cbrnr/mnelab/pull/173) by [Guillaume Dollé](https://github.com/gdolle))
 
 ## [0.6.2] - 2020-10-30
 ### Fixed

mnelab/dialogs/__init__.py

@@ -18,13 +18,16 @@
 from .metainfodialog import MetaInfoDialog
 from .montagedialog import MontageDialog
 from .pickchannelsdialog import PickChannelsDialog
+from .referencebipolardialog import ReferenceBipolarDialog
 from .referencedialog import ReferenceDialog
 from .runicadialog import RunICADialog
 from .xdfstreamsdialog import XDFStreamsDialog
 
 
-__all__ = [AnnotationsDialog, AppendDialog, CalcDialog,
-           ChannelPropertiesDialog, CropDialog, EpochDialog, ERDSDialog,
-           ErrorMessageBox, EventsDialog, FilterDialog, FindEventsDialog,
-           HistoryDialog, InterpolateBadsDialog, MetaInfoDialog, MontageDialog,
-           PickChannelsDialog, ReferenceDialog, RunICADialog, XDFStreamsDialog]
+__all__ = [AnnotationsDialog, CalcDialog, AppendDialog, ERDSDialog,
+           ChannelPropertiesDialog, CropDialog,
+           EpochDialog, ErrorMessageBox, EventsDialog, FilterDialog,
+           FindEventsDialog, HistoryDialog, InterpolateBadsDialog,
+           MetaInfoDialog, MontageDialog, PickChannelsDialog,
+           ReferenceBipolarDialog, ReferenceDialog, RunICADialog,
+           XDFStreamsDialog]

mnelab/dialogs/referencebipolardialog.py

@@ -0,0 +1,127 @@
+
+# Authors: Clemens Brunner <[email protected]>
+#
+# License: BSD (3-clause)
+
+from qtpy.QtWidgets import (QDialog, QVBoxLayout, QListWidget,
+                            QDialogButtonBox, QPushButton, QLabel,
+                            QGridLayout, QGroupBox, QFileDialog)
+from qtpy.QtCore import Slot
+import json
+
+
+class ReferenceBipolarDialog(QDialog):
+    def __init__(self, parent, channels, selected=None, title="Pick channels"):
+        super().__init__(parent)
+        self.setWindowTitle(title)
+        if(selected is None):
+            selected = []
+        self.initial_selection = selected
+        vbox = QVBoxLayout(self)
+        vbox2 = QVBoxLayout(self)
+        gbox = QGroupBox()
+        grid = QGridLayout()
+
+        grid.addWidget(QLabel("Channels (select by pair)"), 0, 0)
+        self.channels = QListWidget()
+        self.channels.insertItems(0, channels)
+        self.channels.setSelectionMode(QListWidget.ExtendedSelection)
+        grid.addWidget(self.channels, 1, 0)
+
+        grid.addWidget(QLabel("Bipolar channels: "), 0, 2)
+        self.selected = QListWidget()
+        if(len(selected)):
+            self.selected.insertItem(0, str(selected))
+        grid.addWidget(self.selected, 1, 2)
+
+        self.pushbutton_add = QPushButton("Add")
+        vbox2.addWidget(self.pushbutton_add)
+        self.pushbutton_add.pressed.connect(self.add_buttons)
+        self.pushbutton_add.pressed.connect(self.toggle_buttons)
+
+        self.pushbutton_rm = QPushButton("Remove")
+        vbox2.addWidget(self.pushbutton_rm)
+        self.pushbutton_rm.pressed.connect(self.rm_buttons)
+        self.pushbutton_rm.pressed.connect(self.toggle_buttons)
+
+        self.pushbutton_open = QPushButton("Open")
+        vbox2.addWidget(self.pushbutton_open)
+        self.pushbutton_open.pressed.connect(self.open_buttons)
+        self.pushbutton_open.pressed.connect(self.toggle_buttons)
+
+        self.pushbutton_save = QPushButton("Save")
+        vbox2.addWidget(self.pushbutton_save)
+        self.pushbutton_save.pressed.connect(self.save_buttons)
+        self.pushbutton_save.pressed.connect(self.toggle_buttons)
+
+        vbox2.addStretch(1)
+        gbox.setLayout(vbox2)
+        grid.addWidget(gbox, 1, 1)
+        vbox.addLayout(grid)
+
+        self.buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
+                                          QDialogButtonBox.Cancel)
+        vbox.addWidget(self.buttonbox)
+        self.buttonbox.accepted.connect(self.accept)
+        self.buttonbox.rejected.connect(self.reject)
+        self.selected.itemSelectionChanged.connect(self.toggle_buttons)
+        self.toggle_buttons()  # initialize OK button state
+
+    @Slot()
+    def toggle_buttons(self):
+        """slot TOGGLE buttons.
+        """
+        if(self.selected.count()):
+            self.buttonbox.button(QDialogButtonBox.Ok).setEnabled(True)
+            self.pushbutton_save.setEnabled(True)
+        else:
+            self.buttonbox.button(QDialogButtonBox.Ok).setEnabled(False)
+            self.pushbutton_save.setEnabled(False)
+
+    @Slot()
+    def add_buttons(self):
+        """slot ADD button.
+        """
+        if(len(self.channels.selectedItems()) == 2):
+            pair = [item.data(0) for item in self.channels.selectedItems()]
+            self.selected.insertItem(0, str(pair))
+
+    @Slot()
+    def rm_buttons(self):
+        """slot RM button.
+        """
+        selected = self.selected.selectedItems()
+        if(not selected):
+            return
+        for item in selected:
+            self.selected.takeItem(self.selected.row(item))
+
+    @Slot()
+    def open_buttons(self):
+        """open saved bipolar channels
+        """
+        dialog = QFileDialog()
+        dialog.setFileMode(QFileDialog.AnyFile)
+        if dialog.exec_():
+            fnames = dialog.selectedFiles()
+            fname = fnames.pop(0)
+            with open(fname) as file:
+                bichan = json.loads(file.read())
+                for i in bichan:
+                    self.selected.insertItem(0, str(i))
+
+    @Slot()
+    def save_buttons(self):
+        """saved bipolar channels
+        """
+        dialog = QFileDialog()
+        fd = dialog.getSaveFileName()
+        fname = fd[0]
+        print("Saving bipolar reference profile: ", fname)
+        with open(fname, 'w') as file:
+            sel = [self.selected.item(i).text()
+                   for i in range(self.selected.count())]
+            sell = [[i.strip("'").strip('"')
+                     for i in j[1:-1].split(", ")] for j in sel]
+            file.write(json.dumps(sell))
+            print("Profile saved!")

mnelab/dialogs/referencedialog.py

@@ -13,14 +13,17 @@ def __init__(self, parent):
         vbox = QVBoxLayout(self)
         grid = QGridLayout()
         self.average = QRadioButton("Average")
+        self.bipolar = QRadioButton("Bipolar")
         self.channels = QRadioButton("Channel(s):")
         self.average.toggled.connect(self.toggle)
+        self.bipolar.toggled.connect(self.toggle)
         self.channellist = QLineEdit()
         self.channellist.setEnabled(False)
         self.average.setChecked(True)
         grid.addWidget(self.average, 0, 0)
         grid.addWidget(self.channels, 1, 0)
         grid.addWidget(self.channellist, 1, 1)
+        grid.addWidget(self.bipolar, 2, 0)
         vbox.addLayout(grid)
         buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
                                      QDialogButtonBox.Cancel)

mnelab/mainwindow.py

@@ -22,15 +22,15 @@
                       EpochDialog, ErrorMessageBox, EventsDialog, FilterDialog,
                       FindEventsDialog, HistoryDialog, InterpolateBadsDialog,
                       MetaInfoDialog, MontageDialog, PickChannelsDialog,
-                      ReferenceDialog, RunICADialog, XDFStreamsDialog)
+                      ReferenceBipolarDialog, ReferenceDialog, RunICADialog,
+                      XDFStreamsDialog)
 from .widgets.infowidget import InfoWidget
 from .model import LabelsNotFoundError, InvalidAnnotationsError
 from .utils import have, has_locations, image_path, interface_style
 from .io import writers
 from .io.xdf import get_xml, get_streams
 from .viz import plot_erds
 
-
 __version__ = "0.7.0.dev0"
 
 MAX_RECENT = 6  # maximum number of recent files
@@ -136,15 +136,16 @@ def __init__(self, model):
         self.actions["export_bads"] = file_menu.addAction(
             "Export &bad channels...",
             lambda: self.export_file(model.export_bads, "Export bad channels",
-                                     "*.csv"))
+                                     "*.csv", "bad_channels"))
         self.actions["export_events"] = file_menu.addAction(
             "Export &events...",
             lambda: self.export_file(model.export_events, "Export events",
-                                     "*.csv"))
+                                     "*.csv", "events"))
         self.actions["export_annotations"] = file_menu.addAction(
             "Export &annotations...",
             lambda: self.export_file(model.export_annotations,
-                                     "Export annotations", "*.csv"))
+                                     "Export annotations", "*.csv",
+                                     "annotations"))
         self.actions["export_ica"] = file_menu.addAction(
             "Export ICA...",
             lambda: self.export_file(model.export_ica,
@@ -440,9 +441,22 @@ def open_file(self, f, text, ffilter="*"):
         if fname:
             f(fname)
 
-    def export_file(self, f, text, ffilter="*"):
+    def export_file(self, f, text, ffilter="*", suffix=''):
         """Export to file."""
-        fname = QFileDialog.getSaveFileName(self, text, filter=ffilter)[0]
+
+        if suffix != '':
+            suffix = "_"+suffix
+
+        curent_file_path = Path(self.model.current["data"].filenames[0]).parent
+        curent_file_name = self.model.current["name"]
+
+        Dialog = QFileDialog.getSaveFileName(self, text,
+                                             str(curent_file_path.joinpath(
+                                                 curent_file_name+suffix)),
+                                             filter=ffilter)
+
+        fname = Dialog[0]
+
         if fname:
             if ffilter != "*":
                 exts = [ext.replace("*", "") for ext in ffilter.split()]
@@ -812,6 +826,15 @@ def set_reference(self):
             self.auto_duplicate()
             if dialog.average.isChecked():
                 self.model.set_reference("average")
+            elif dialog.bipolar.isChecked():
+                channels = self.model.current["data"].info["ch_names"]
+                selected = None
+                dialog = ReferenceBipolarDialog(self, channels,
+                                                selected=selected)
+                if dialog.exec_():
+                    selected = [dialog.selected.item(i).text()
+                                for i in range(dialog.selected.count())]
+                    self.model.set_reference("bipolar", selected)
             else:
                 ref = [c.strip() for c in dialog.channellist.text().split(",")]
                 self.model.set_reference(ref)

mnelab/model.py

@@ -170,6 +170,7 @@ def export_bads(self, fname):
         fname = join(split(fname)[0], name + ext)
         with open(fname, "w") as f:
             f.write(",".join(self.current["data"].info["bads"]))
+        print("Bad channels exported: ", fname)
 
     def export_events(self, fname):
         """Export events to a CSV file."""
@@ -178,6 +179,7 @@ def export_events(self, fname):
         fname = join(split(fname)[0], name + ext)
         np.savetxt(fname, self.current["events"][:, [0, 2]], fmt="%d",
                    delimiter=",", header="pos,type", comments="")
+        print("Events exported: ", fname)
 
     def export_annotations(self, fname):
         """Export annotations to a CSV file."""
@@ -190,6 +192,7 @@ def export_annotations(self, fname):
             for a in zip(anns.description, anns.onset, anns.duration):
                 f.write(",".join([a[0], str(a[1]), str(a[2])]))
                 f.write("\n")
+        print("Annotations exported: ", fname)
 
     def export_ica(self, fname):
         name, ext = splitext(split(fname)[-1])
@@ -478,12 +481,41 @@ def convert_beer_lambert(self):
             "data = mne.preprocessing.nirs.beer_lambert_law(data)")
 
     @data_changed
-    def set_reference(self, ref):
+    def set_reference(self, ref, bichan=None):
         self.current["reference"] = ref
         if ref == "average":
             self.current["name"] += " (average ref)"
             self.current["data"].set_eeg_reference(ref)
             self.history.append('data.set_eeg_reference("average")')
+        if ref == "bipolar":
+            self.current["name"] += " (original + bipolar ref)"
+
+            anodes = [i[1:-1].split(', ').pop(0)
+                      .rstrip("'\"").lstrip("\"'").strip() for i in bichan]
+            cathodes = [i[1:-1].split(', ').pop(1)
+                        .rstrip("'\"").lstrip("\"'").strip() for i in bichan]
+            anodes_ch_names = []
+            cathodes_ch_names = []
+
+            for anode in anodes:
+                for ch_name in self.current["data"].info["ch_names"]:
+                    if anode in ch_name:
+                        anodes_ch_names.append(ch_name)
+            for cathode in cathodes:
+                for ch_name in self.current["data"].info["ch_names"]:
+                    if cathode in ch_name:
+                        cathodes_ch_names.append(ch_name)
+
+            self.current["data"] = mne.set_bipolar_reference(
+                self.current["data"],
+                anode=anodes_ch_names,
+                cathode=cathodes_ch_names,
+                drop_refs=False)
+            d = {x: x.strip() for x in
+                 self.current["data"].info["ch_names"] if "EEG" in x}
+            mne.rename_channels(self.current["data"].info, d)
+            self.history.append(f'data.set_bipolar_reference({ref})')
+
         else:
             self.current["name"] += " (" + ",".join(ref) + ")"
             if set(ref) - set(self.current["data"].info["ch_names"]):