Add basic support for montages without raw, montages are ensured on d…

…emand for evokeds etc.

meggie/actions/evoked_plot/__init__.py

@@ -49,8 +49,8 @@ def handler(self, subject, params):
             else:
                 chs = list(get_channels_by_type(info).keys())
                 if "eeg" in chs:
-                    plot_evoked_topo(evoked, ch_type="eeg")
+                    plot_evoked_topo(subject, evoked, ch_type="eeg")
                 if "grad" in chs or "mag" in chs:
-                    plot_evoked_topo(evoked, ch_type="meg")
+                    plot_evoked_topo(subject, evoked, ch_type="meg")
         except Exception as exc:
             exc_messagebox(self.window, exc)

meggie/actions/evoked_plot/controller/evoked.py

@@ -9,6 +9,7 @@
 from meggie.utilities.plotting import color_cycle
 from meggie.utilities.plotting import create_channel_average_plot
 from meggie.utilities.channels import average_to_channel_groups
+from meggie.utilities.channels import ensure_montage
 from meggie.utilities.plotting import set_figure_title
 
 from meggie.utilities.units import get_unit
@@ -66,7 +67,7 @@ def plot_fun(ax_idx, ax):
     plt.show()
 
 
-def plot_evoked_topo(evoked, ch_type):
+def plot_evoked_topo(subject, evoked, ch_type):
     """Plots evoked time courses arranged as a topography"""
     evokeds = []
     labels = []
@@ -88,6 +89,8 @@ def plot_evoked_topo(evoked, ch_type):
 
         evok = evok.copy().drop_channels(dropped_names)
 
+        ensure_montage(subject, evok, ch_type)
+
         evokeds.append(evok)
         labels.append(key)
 
@@ -100,6 +103,7 @@ def plot_evoked_topo(evoked, ch_type):
     ]
 
     fig, axes = plt.subplots()
+
     mne.viz.plot_evoked_topo(evokeds, color=colors, legend=False, show=False, axes=axes)
     axes.legend(handles=lines, loc="upper right")
     title = "{0}_{1}".format(evoked.name, ch_type)

meggie/actions/raw_measurement_info/__init__.py

@@ -23,7 +23,7 @@ def run(self):
             rereferenced = subject.rereferenced
 
             try:
-                eeg_montage_set = is_montage_set(raw, "eeg")
+                eeg_montage_set = is_montage_set(raw.info, "eeg")
             except Exception:
                 eeg_montage_set = False
 

meggie/actions/raw_montage/__init__.py

@@ -23,8 +23,6 @@ def handler(self, subject, params):
         @threaded
         def montage_fun():
             """ """
-            raw = subject.get_raw()
-
             head_size = params["head_size"]
 
             if params["custom"] is True:
@@ -38,7 +36,11 @@ def montage_fun():
                     montage_name, head_size=head_size
                 )
 
-            raw.set_montage(montage)
+            if subject.has_raw:
+                raw = subject.get_raw()
+                raw.set_montage(montage)
+
+            subject.save_montage(montage)
             subject.save()
 
         montage_fun(do_meanwhile=self.window.update_ui)

meggie/actions/raw_montage/configuration.json

@@ -3,5 +3,5 @@
     "name": "Montage",
     "entry": "Montage",
     "description": "Apply a montage to the EEG dataset, enabling the creation of topographical plots.",
-    "tags": ["eeg", "raw"]
+    "tags": ["eeg"]
 }

meggie/actions/spectrum_plot/controller/spectrum.py

@@ -11,6 +11,7 @@
 from meggie.utilities.channels import average_to_channel_groups
 from meggie.utilities.channels import iterate_topography
 from meggie.utilities.channels import filter_info
+from meggie.utilities.channels import ensure_montage
 from meggie.utilities.plotting import set_figure_title
 from meggie.utilities.units import get_power_unit
 
@@ -88,6 +89,8 @@ def plot_spectrum_topo(subject, name, log_transformed=True, ch_type="meg"):
 
     info = filter_info(info, picked_channels)
 
+    ensure_montage(subject, info, ch_type)
+
     colors = color_cycle(len(data))
 
     def individual_plot(ax, info_idx, names_idx):

meggie/actions/tfr_plot/controller/tfr.py

@@ -7,6 +7,7 @@
 
 from meggie.utilities.plotting import create_channel_average_plot
 from meggie.utilities.channels import average_to_channel_groups
+from meggie.utilities.channels import ensure_montage
 from meggie.utilities.plotting import set_figure_title
 
 
@@ -139,6 +140,8 @@ def plot_tfr_topo(
     # apply baseline here to get better vmin and vmax values
     tfr.apply_baseline(baseline=bline, mode=mode)
 
+    ensure_montage(subject, tfr, ch_type)
+
     values = tfr.data.flatten()
     vmax = np.percentile(np.abs(values), 99)
     vmin = -vmax

meggie/actions/tfr_plot_tse/controller/tfr.py

@@ -11,6 +11,7 @@
 from meggie.utilities.channels import average_to_channel_groups
 from meggie.utilities.channels import iterate_topography
 from meggie.utilities.channels import filter_info
+from meggie.utilities.channels import ensure_montage
 from meggie.utilities.units import get_power_unit
 
 
@@ -75,6 +76,8 @@ def plot_tse_topo(
 
     info = filter_info(info, picked_channels)
 
+    ensure_montage(subject, info, ch_type)
+
     ch_names = meggie_tfr.ch_names
     colors = color_cycle(len(tses))
 

meggie/experiment.py

@@ -84,15 +84,15 @@ def channel_groups(self):
 
         # if channel groups not found, use defaults..
         if not channel_groups.get("eeg"):
-            if self.active_subject:
+            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 not channel_groups.get("meg"):
-            if self.active_subject:
+            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")

meggie/subject.py

@@ -126,14 +126,15 @@ def get_raw(self, preload=True, verbose="warning"):
 
     def save(self):
         """Saves the data to the existing path."""
-        try:
-            filemanager.save_raw(self._raw, self.raw_path)
-        except Exception:
-            raise Exception(
-                "Could not save the raw file. Please ensure "
-                "that the entire experiment folder has "
-                "write permissions."
-            )
+        if self.has_raw:
+            try:
+                filemanager.save_raw(self._raw, self.raw_path)
+            except Exception:
+                raise Exception(
+                    "Could not save the raw file. Please ensure "
+                    "that the entire experiment folder has "
+                    "write permissions."
+                )
 
     def release_memory(self):
         """Releases data from the memory."""
@@ -191,3 +192,31 @@ def ensure_folders(self):
                 "Please ensure that the experiment folder "
                 "has write permissions everywhere."
             )
+
+    def save_montage(self, montage):
+
+        ch_names = montage.ch_names
+        with open(os.path.join(self.path, "montage_channels.txt"), "w") as f:
+            for ch_name in ch_names:
+                f.write(ch_name + "\n")
+
+        montage.save(os.path.join(self.path, "montage.fif"), overwrite=True)
+
+    def read_montage(self):
+        montage_path = os.path.join(self.path, "montage.fif")
+        channels_path = os.path.join(self.path, "montage_channels.txt")
+        if os.path.exists(montage_path) and os.path.exists(channels_path):
+            ch_names = []
+            with open(channels_path, "r") as f:
+                for line in f:
+                    ch_names.append(line.strip())
+
+            montage = mne.channels.read_dig_fif(montage_path)
+
+            mapping = {}
+            for idx, name in enumerate(montage.ch_names):
+                mapping[name] = ch_names[idx]
+
+            montage.rename_channels(mapping)
+
+            return montage

meggie/utilities/channels.py

@@ -7,13 +7,13 @@
 from mne.channels import _divide_to_regions
 
 
-def is_montage_set(raw, ch_type):
+def is_montage_set(info, ch_type):
     """Checks whether channel locations are found in the info for given channel type.
 
     Parameters
     ----------
-    raw : mne.io.Raw
-        Raw containing info which contains channel information.
+    info : mne.Info
+        Info containing channel information.
     ch_type : str
         Should be 'meg' or 'eeg'.
 
@@ -24,18 +24,16 @@ def is_montage_set(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:
         raise Exception("Data does not contain channels of type " + str(ch_type))
 
-    info_filt = filter_info(raw.info, ch_names)
+    info_filt = filter_info(info, ch_names)
 
     # check if there is no montage set..
     ch_norms = []
@@ -47,6 +45,13 @@ def is_montage_set(raw, ch_type):
     return True
 
 
+def ensure_montage(subject, inst, ch_type):
+    """Checks if the subject contains a montage that could be used for inst."""
+    montage = subject.read_montage()
+    if montage:
+        inst.set_montage(montage)
+
+
 def get_default_channel_groups(raw, ch_type):
     """Returns channels grouped by standard locations
     (Left-frontal, Right-occipital, etc.). Grouping is done via
@@ -80,7 +85,7 @@ def get_default_channel_groups(raw, ch_type):
         return {}
 
     # check if there is no montage set..
-    if not is_montage_set(raw, ch_type):
+    if not is_montage_set(raw.info, ch_type):
         return {}
 
     info_filt = filter_info(raw.info, ch_names)