Support channel groups for rawless subjects

meggie/datatypes/epochs/epochs.py

@@ -60,6 +60,11 @@ def params(self):
         """Returns additional information stored."""
         return self._params
 
+    @property
+    def info(self):
+        """Returns info."""
+        return self.content.info
+
     def delete_content(self):
         """Deletes the fif file from the files system"""
         os.remove(self._path)

meggie/experiment.py

@@ -13,6 +13,7 @@
 from meggie.utilities.filemanager import open_raw
 from meggie.utilities.filemanager import save_raw
 from meggie.utilities.channels import get_default_channel_groups
+from meggie.utilities.channels import find_montage_info
 from meggie.utilities.validators import validate_name
 from meggie.utilities.uid import generate_uid
 
@@ -81,23 +82,26 @@ def channel_groups(self):
         """Returns channel groups for experiment. If not set,
         uses defaults."""
         channel_groups = self._channel_groups.copy()
+        specs = find_all_datatype_specs()
 
-        # if channel groups not found, use defaults..
+        # if channel groups not found, look for defaults..
         if not channel_groups.get("eeg"):
-            if self.active_subject and self.active_subject.has_raw:
-                raw = self.active_subject.get_raw(preload=False)
-                try:
-                    channel_groups["eeg"] = get_default_channel_groups(raw, "eeg")
-                except Exception:
-                    pass
+            if self.active_subject:
+                info = find_montage_info(self.active_subject, specs.keys(), "eeg")
+                if info:
+                    try:
+                        channel_groups["eeg"] = get_default_channel_groups(info, "eeg")
+                    except Exception:
+                        pass
 
         if not channel_groups.get("meg"):
-            if self.active_subject and self.active_subject.has_raw:
-                raw = self.active_subject.get_raw(preload=False)
-                try:
-                    channel_groups["meg"] = get_default_channel_groups(raw, "meg")
-                except Exception:
-                    pass
+            if self.active_subject:
+                info = find_montage_info(self.active_subject, specs.keys(), "meg")
+                if info:
+                    try:
+                        channel_groups["meg"] = get_default_channel_groups(info, "meg")
+                    except Exception:
+                        pass
 
         return channel_groups
 

meggie/mainwindow/dialogs/channelGroupsDialogMain.py

@@ -15,6 +15,8 @@
 from meggie.utilities.messaging import exc_messagebox
 from meggie.utilities.channels import get_default_channel_groups
 from meggie.utilities.channels import get_triplet_from_mag
+from meggie.utilities.channels import find_montage_info
+from meggie.mainwindow.dynamic import find_all_datatype_specs
 
 from meggie.mainwindow.dialogs.channelGroupsDialogUi import Ui_channelGroupsDialog
 
@@ -93,17 +95,18 @@ def on_pushButtonReset_clicked(self, checked=None):
             messagebox(self.parent, "To reset, active subject is needed")
             return
 
-        raw = subject.get_raw()
+        specs = find_all_datatype_specs()
 
         if self.ui.radioButtonEEG.isChecked():
-            self.eeg_channel_groups = get_default_channel_groups(raw, "eeg")
+            info = find_montage_info(subject, specs.keys(), "eeg")
+            self.eeg_channel_groups = get_default_channel_groups(info, "eeg")
             self.ui.listWidgetChannelGroups.clear()
             for ch_name in sorted(self.eeg_channel_groups.keys()):
                 self.ui.listWidgetChannelGroups.addItem(ch_name)
 
         else:
-            meg_defaults = get_default_channel_groups(raw, "meg")
-            self.meg_channel_groups = meg_defaults
+            info = find_montage_info(subject, specs.keys(), "meg")
+            self.meg_channel_groups = get_default_channel_groups(info, "meg")
             self.ui.listWidgetChannelGroups.clear()
             for ch_name in sorted(self.meg_channel_groups.keys()):
                 self.ui.listWidgetChannelGroups.addItem(ch_name)
@@ -123,16 +126,17 @@ def on_pushButtonSetChannels_clicked(self, checked=None):
             messagebox(self.parent, "Select a channel group first")
             return
 
-        raw = subject.get_raw()
+        specs = find_all_datatype_specs()
 
         if self.ui.radioButtonEEG.isChecked():
-            if mne.pick_types(raw.info, meg=False, eeg=True).size == 0:
+            info = find_montage_info(subject, specs.keys(), "eeg")
+            if mne.pick_types(info, meg=False, eeg=True).size == 0:
                 messagebox(self.parent, "No EEG channels found")
                 return
 
             ch_names = self.eeg_channel_groups[selected_item.text()]
             try:
-                ch_idxs = [raw.info["ch_names"].index(ch_name) for ch_name in ch_names]
+                ch_idxs = [info["ch_names"].index(ch_name) for ch_name in ch_names]
             except ValueError:
                 messagebox(
                     self.parent,
@@ -144,7 +148,7 @@ def on_pushButtonSetChannels_clicked(self, checked=None):
 
             try:
                 fig, selection = mne.viz.plot_sensors(
-                    raw.info,
+                    info,
                     kind="select",
                     ch_type="eeg",
                     ch_groups=ch_groups,
@@ -156,13 +160,14 @@ def on_pushButtonSetChannels_clicked(self, checked=None):
                 return
 
         else:
-            if mne.pick_types(raw.info, meg=True, eeg=False).size == 0:
+            info = find_montage_info(subject, specs.keys(), "meg")
+            if mne.pick_types(info, meg=True, eeg=False).size == 0:
                 messagebox(self.parent, "No MEG channels found")
                 return
 
             ch_names = self.meg_channel_groups[selected_item.text()]
             try:
-                ch_idxs = [raw.info["ch_names"].index(ch_name) for ch_name in ch_names]
+                ch_idxs = [info["ch_names"].index(ch_name) for ch_name in ch_names]
             except ValueError:
                 messagebox(
                     self.parent,
@@ -173,7 +178,7 @@ def on_pushButtonSetChannels_clicked(self, checked=None):
             ch_groups = [[], ch_idxs]
 
             fig, selection = mne.viz.plot_sensors(
-                raw.info,
+                info,
                 kind="select",
                 ch_type="mag",
                 ch_groups=ch_groups,

meggie/utilities/channels.py

@@ -31,7 +31,7 @@ def is_montage_set(info, ch_type):
     ch_names = [ch_name for idx, ch_name in enumerate(info["ch_names"]) if idx in picks]
 
     if not ch_names:
-        raise Exception("Data does not contain channels of type " + str(ch_type))
+        return False
 
     info_filt = filter_info(info, ch_names)
 
@@ -52,7 +52,45 @@ def ensure_montage(subject, inst, ch_type):
         inst.set_montage(montage)
 
 
-def get_default_channel_groups(raw, ch_type):
+def find_montage_info(subject, datatypes, ch_type):
+    """Try to find channel locations first from raw and then from any dataobject.
+
+    Parameters
+    ----------
+    subject : meggie.subject.Subject
+        The subject to find the montage info in
+    ch_type : str
+        Should be 'meg' or 'eeg'.
+    datatypes : list
+        List of datatypes to look into
+
+    Returns
+    -------
+    info : mne.Info | None
+        Info containing channel locations.
+    """
+
+    if subject.has_raw:
+        raw = subject.get_raw(preload=False)
+        if is_montage_set(raw.info, ch_type):
+            return raw.info
+
+    for datatype in datatypes:
+        objects = getattr(subject, datatype, {})
+        for key, item in objects.items():
+            try:
+                info = item.info
+            except NotImplementedError:
+                continue
+
+            if is_montage_set(info, ch_type):
+                return info
+
+    # Did not find anything..
+    return None
+
+
+def get_default_channel_groups(info, ch_type):
     """Returns channels grouped by standard locations
     (Left-frontal, Right-occipital, etc.). Grouping is done via
     geometric division from mne, to have a generic ability
@@ -74,21 +112,19 @@ def get_default_channel_groups(raw, ch_type):
     """
 
     if ch_type == "meg":
-        picks = mne.pick_types(raw.info, meg=True, eeg=False)
+        picks = mne.pick_types(info, meg=True, eeg=False)
     else:
-        picks = mne.pick_types(raw.info, meg=False, eeg=True)
+        picks = mne.pick_types(info, meg=False, eeg=True)
 
-    ch_names = [
-        ch_name for idx, ch_name in enumerate(raw.info["ch_names"]) if idx in picks
-    ]
+    ch_names = [ch_name for idx, ch_name in enumerate(info["ch_names"]) if idx in picks]
     if not ch_names:
         return {}
 
     # check if there is no montage set..
-    if not is_montage_set(raw.info, ch_type):
+    if not is_montage_set(info, ch_type):
         return {}
 
-    info_filt = filter_info(raw.info, ch_names)
+    info_filt = filter_info(info, ch_names)
 
     regions = _divide_to_regions(info_filt, add_stim=False)
 

meggie/utilities/tests/test_channels.py

@@ -33,7 +33,7 @@ def test_default_channel_groups():
 
     raw = mne.io.read_raw_fif(sample_fname)
 
-    assert get_default_channel_groups(raw, "eeg")["Left-frontal"] == [
+    assert get_default_channel_groups(raw.info, "eeg")["Left-frontal"] == [
         "EEG 001",
         "EEG 004",
         "EEG 005",
@@ -77,8 +77,8 @@ def test_average_to_channel_groups():
 
     ch_names = info["ch_names"][:20]
 
-    meg_channel_groups = get_default_channel_groups(raw, "meg")
-    eeg_channel_groups = get_default_channel_groups(raw, "eeg")
+    meg_channel_groups = get_default_channel_groups(raw.info, "meg")
+    eeg_channel_groups = get_default_channel_groups(raw.info, "eeg")
 
     # find out to which channel group each of the channels belongs to
     results = []