[ENH, WIP] Add localization for microgrids

doc/conf.py

@@ -36,8 +36,8 @@
     "matplotlib": ("https://matplotlib.org/stable", None),
     "nibabel": ("https://nipy.org/nibabel", None),
     "dipy": (
-        "https://dipy.org/documentation/latest/",
-        "https://dipy.org/documentation/latest/objects.inv/",
+        "https://docs.dipy.org/latest/objects.inv",
+        "https://docs.dipy.org/stable/objects.inv",
     ),
     "mne": ("https://mne.tools/stable", None),
     "mne_bids": ("https://mne.tools/mne-bids/stable", None),

examples/locate_microgrid.py

@@ -0,0 +1,41 @@
+"""
+.. _ex-ieeg-microgrid:
+
+==================================
+Locating an intracranial microgrid
+==================================
+
+For intracranial grids that are too small for even high-resolution
+computed tomography (CT) images to detect, the contacts must be
+aligned with an intraoperative image such as from a surgical
+microscope as shown below.
+"""
+
+# Authors: Alex Rockhill <[email protected]>
+#
+# License: BSD-3-Clause
+
+import numpy as np
+import nibabel as nib
+import mne
+import mne_gui_addons as mne_gui
+
+# path to sample sEEG
+misc_path = mne.datasets.misc.data_path()
+subjects_dir = misc_path / "ecog"
+
+# GUI requires pyvista backend
+mne.viz.set_3d_backend("pyvistaqt")
+
+# we need two things:
+# 1) The electrophysiology file which contains the channels names
+# that we would like to associate with positions in the brain
+# 2) A scope image of the grid
+raw = mne.io.read_raw(misc_path / "ecog" / "sample_ecog_ieeg.fif")
+trans = mne.coreg.estimate_head_mri_t("sample_ecog", subjects_dir)
+
+raw.set_montage(None)  # remove macro channels
+
+gui = mne_gui.locate_ieeg(
+    raw.info, trans, subject="sample_ecog", subjects_dir=subjects_dir
+)

mne_gui_addons/__init__.py

@@ -23,7 +23,7 @@
 def locate_ieeg(
     info,
     trans,
-    base_image,
+    base_image=None,
     subject=None,
     subjects_dir=None,
     groups=None,
@@ -38,10 +38,11 @@ def locate_ieeg(
     ----------
     %(info_not_none)s
     %(trans_not_none)s
-    base_image : path-like | nibabel.spatialimages.SpatialImage
+    base_image : path-like | nibabel.spatialimages.SpatialImage | None
         The CT or MR image on which the electrode contacts can located. It
         must be aligned to the Freesurfer T1 if ``subject`` and
-        ``subjects_dir`` are provided. Path-like inputs and nibabel image
+        ``subjects_dir`` are provided. If aligning a grid to the pial surface,
+        the T1 will be used by default. Path-like inputs and nibabel image
         objects are supported.
     %(subject)s
     %(subjects_dir)s

mne_gui_addons/_core.py

@@ -21,6 +21,7 @@
     QMessageBox,
     QWidget,
     QLineEdit,
+    QSlider,
 )
 
 from matplotlib import patheffects
@@ -180,6 +181,10 @@ def __init__(
         self._subject_dir = (
             op.join(subjects_dir, subject) if subject and subjects_dir else None
         )
+        if self._subject_dir is None and base_image is None:
+            raise ValueError(
+                "`subjects_dir` must be provided if no `base_image` is provided"
+            )
         self._load_image_data(base_image=base_image)
 
         # GUI design
@@ -363,6 +368,7 @@ def _plot_images(self):
                     img_data,
                     cmap="gray",
                     aspect="auto",
+                    interpolation="spline16",
                     zorder=1,
                     vmin=img_min,
                     vmax=img_max,
@@ -416,7 +422,10 @@ def _plot_images(self):
                 [1],
             )[0]
             rr = apply_trans(self._ras_vox_scan_ras_t, rr)  # base image vox -> RAS
-            self._renderer.mesh(
+
+            self._head = dict(rr=rr, tris=tris)
+
+            self._head_actor, _ = self._renderer.mesh(
                 *rr.T,
                 triangles=tris,
                 color="gray",
@@ -425,7 +434,7 @@ def _plot_images(self):
                 render=False,
             )
         else:
-            self._renderer.mesh(
+            self._head_actor, _ = self._renderer.mesh(
                 *self._head["rr"].T,
                 triangles=self._head["tris"],
                 color="gray",
@@ -437,15 +446,15 @@ def _plot_images(self):
             self._lh_actor, _ = self._renderer.mesh(
                 *self._lh["rr"].T,
                 triangles=self._lh["tris"],
-                color="white",
+                color="gray",
                 opacity=0.2,
                 reset_camera=False,
                 render=False,
             )
             self._rh_actor, _ = self._renderer.mesh(
                 *self._rh["rr"].T,
                 triangles=self._rh["tris"],
-                color="white",
+                color="gray",
                 opacity=0.2,
                 reset_camera=False,
                 render=False,
@@ -699,6 +708,17 @@ def keyPressEvent(self, event):
                 )
             self._set_ras(ras)
 
+    def _make_slider(self, smin, smax, sval, sfun=None):
+        slider = QSlider(QtCore.Qt.Horizontal)
+        slider.setMinimum(int(round(smin)))
+        slider.setMaximum(int(round(smax)))
+        slider.setValue(int(round(sval)))
+        slider.setTracking(False)  # only update on release
+        if sfun is not None:
+            slider.valueChanged.connect(sfun)
+        slider.keyPressEvent = self.keyPressEvent
+        return slider
+
     def _on_click(self, event, axis):
         """Move to view on MRI and CT on click."""
         if event.inaxes is self._figs[axis].axes[0]:
@@ -721,6 +741,7 @@ def _update_moved(self):
         self._intensity_label.setText(
             "intensity = {:.2f}".format(self._base_data[tuple(self._current_slice)])
         )
+        self._update_camera(render=True)
 
     @safe_event
     def closeEvent(self, event):