Merge branch 'main' into seg

.circleci/config.yml

@@ -42,7 +42,7 @@ jobs:
         - run:
             name: Get Python running
             command: |
-              pip install --upgrade PyQt6 sphinx-gallery pydata-sphinx-theme numpydoc scikit-learn nilearn autoreject git+https://github.com/pyvista/pyvista@main memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube
+              pip install --upgrade PyQt6 "PyQt6-Qt6!=6.6.1" sphinx-gallery pydata-sphinx-theme numpydoc scikit-learn nilearn mne-bids autoreject git+https://github.com/pyvista/pyvista@main memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube
               pip install -ve ./mne-python .
         - run:
             name: Check Qt

.github/workflows/tests.yml

@@ -20,20 +20,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.11"]  # Newest supported version (dipy not out for 3.11 yet!)
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11"]
         mne-version: [mne-main]
         qt: [PyQt6]
         include:
-          # macOS (can be moved above once Dipy releases 3.11 wheels)
           - os: macos-latest
             python-version: "3.10"
-            mne-version: mne-main  # TODO: Set back to mne-stable once 1.4 is out (we need its pytest fixtures)
+            mne-version: mne-stable
             qt: PyQt6
           # Old (and PyQt5)
           - os: ubuntu-latest
-            python-version: "3.8"
-            mne-version: mne-main  # TODO: Set back to mne-stable once 1.4 is out (we need its pytest fixtures)
+            python-version: "3.9"
+            mne-version: mne-stable
             qt: PyQt5
           # PySide2
           - os: ubuntu-latest
@@ -63,7 +62,7 @@ jobs:
       if: "matrix.mne-version == 'mne-main'"
       run: git clone --single-branch --branch main https://github.com/mne-tools/mne-python.git
     - run: pip install -ve ./mne-python
-    - run: pip install -v ${{ matrix.qt }}
+    - run: pip install -v ${{ matrix.qt }} "PyQt6-Qt6!=6.6.1"
     - run: pip install -ve .[tests]
     - run: mne sys_info
     - run: |

examples/ieeg_locate.py

@@ -43,6 +43,7 @@
 import mne
 import mne_gui_addons as mne_gui
 from mne.datasets import fetch_fsaverage
+import mne_bids
 
 # paths to mne datasets: sample sEEG and FreeSurfer's fsaverage subject,
 # which is in MNI space
@@ -384,6 +385,38 @@ def plot_overlay(image, compare, title, thresh=None):
 )
 # The `raw` object is modified to contain the channel locations
 
+# %%
+# In a real case, we would not already have contact locations. We would have
+# to click through the slices to find spots of hyperintensity and associate
+# those with channel names from the recording. If we have surgical plans for
+# where these contacts were targeted, we can try to do this contact detection
+# and association automatically. Here, we will fake the surgical plans using
+# the locations that have already been found but, in practice, you would enter
+# these manually from the planning documentation.
+
+montage = raw.get_montage()
+montage.apply_trans(subj_trans)  # convert to surface RAS
+# convert to scanner RAS
+mne_bids.convert_montage_to_ras(
+    montage, subject="sample_seeg", subjects_dir=misc_path / "seeg"
+)
+
+raw.set_montage(None)  # clear already found montage
+# fake surgical plans from already-found contact locations
+targets = {
+    "".join([letter for letter in ch if not letter.isdigit()]): pos
+    for ch, pos in montage.get_positions()["ch_pos"].items()
+    if [letter for letter in ch if letter.isdigit()] == ["1"]
+}
+mne_gui.locate_ieeg(
+    raw.info,
+    subj_trans,
+    CT_aligned,
+    subject="sample_seeg",
+    subjects_dir=misc_path / "seeg",
+    targets=targets,
+)
+
 # %%
 # Let's do a quick sidebar and show what this looks like for ECoG as well.
 
@@ -415,6 +448,45 @@ def plot_overlay(image, compare, title, thresh=None):
     subjects_dir=misc_path / "ecog",
 )
 
+# %%
+# Similarly for ECoG, we can try to automatically detect contact locations.
+# In the case of ECoG, there can often be a lot of contacts so this can be
+# a big time saver.
+
+montage = raw_ecog.get_montage()
+montage.apply_trans(subj_trans_ecog)  # convert to surface RAS
+# convert to scanner RAS
+mne_bids.convert_montage_to_ras(
+    montage, subject="sample_ecog", subjects_dir=misc_path / "ecog"
+)
+
+raw_ecog.set_montage(None)  # clear already found montage
+# fake surgical plans from already-found contact locations
+targets = dict()
+ch_pos = montage.get_positions()["ch_pos"]
+for elec in set(
+    [
+        "".join([letter for letter in ch if not letter.isdigit()])
+        for ch in raw_ecog.ch_names
+    ]
+):
+    names = [ch for ch in raw_ecog.ch_names if ch.replace(elec, "").isdigit()]
+    ch1 = [name for name in names if name.replace(elec, "") == "1"][0]
+    ch2 = [name for name in names if name.replace(elec, "") == "2"][0]
+    targets[elec] = (
+        ch_pos[ch1],
+        ch_pos[ch2],
+    )  # use second channel so grid counts the right way
+
+mne_gui.locate_ieeg(
+    raw_ecog.info,
+    subj_trans_ecog,
+    CT_aligned_ecog,
+    subject="sample_ecog",
+    subjects_dir=misc_path / "ecog",
+    targets=targets,
+)
+
 # %%
 # For ECoG, we typically want to account for "brain shift" or shrinking of the
 # brain away from the skull/dura due to changes in pressure during the

mne_gui_addons/__init__.py

@@ -27,6 +27,7 @@ def locate_ieeg(
     subject=None,
     subjects_dir=None,
     groups=None,
+    targets=None,
     show=True,
     block=False,
     verbose=None,
@@ -51,6 +52,12 @@ def locate_ieeg(
         like ``LAMY`` precedes a numeric index like ``7``. If the channels
         are formatted improperly, group plotting will work incorrectly.
         Group assignments can be adjusted in the GUI.
+    targets : dict | None
+        An optional dictionary with group (electrode/grid) names as keys
+        and a list containing 1) the planned target location for the first
+        electrode contact and 2) the next contact or planned entry point
+        (for sEEG). Including only the target location is also an option.
+        If not provided, automatic contact locations will not be found.
     show : bool
         Show the GUI if True.
     block : bool
@@ -74,6 +81,7 @@ def locate_ieeg(
         subject=subject,
         subjects_dir=subjects_dir,
         groups=groups,
+        targets=targets,
         show=show,
         verbose=verbose,
     )

mne_gui_addons/_core.py

@@ -489,9 +489,11 @@ def _configure_status_bar(self, hbox=None):
     def _update_camera(self, render=False):
         """Update the camera position."""
         self._renderer.set_camera(
-            focalpoint=tuple(self._ras),
-            reset_camera=False,
+            focalpoint=tuple(apply_trans(self._scan_ras_mri_t, self._ras)),
+            distance="auto",
         )
+        if render:
+            self._renderer._update()
 
     def _on_scroll(self, event):
         """Process mouse scroll wheel event to zoom."""