ENH: Add show hide menu with freesurfer atlas (#27)

.circleci/config.yml

@@ -42,8 +42,7 @@ jobs:
         - run:
             name: Get Python running
             command: |
-              # TO DO: sphinx-gallery main -> stable on 0.17 release
-              pip install --upgrade PyQt6!=6.6.0 "PyQt6-Qt6!=6.6.0,!=6.7.0" git+https://github.com/sphinx-gallery/sphinx-gallery.git pydata-sphinx-theme numpydoc scikit-learn nilearn mne-bids autoreject pyvista memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube darkdetect qdarkstyle
+              pip install --upgrade PyQt6!=6.6.0 "PyQt6-Qt6!=6.6.0,!=6.7.0" sphinx-gallery pydata-sphinx-theme numpydoc scikit-learn nilearn mne-bids autoreject pyvista memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube darkdetect qdarkstyle
               pip install -ve ./mne-python .
         - run:
             name: Check Qt

mne_gui_addons/_core.py

@@ -10,8 +10,8 @@
 import numpy as np
 from functools import partial
 
-from qtpy import QtCore
-from qtpy.QtCore import Slot, Qt
+from qtpy import QtCore, QtGui
+from qtpy.QtCore import Slot, Signal, Qt
 from qtpy.QtWidgets import (
     QMainWindow,
     QGridLayout,
@@ -21,6 +21,8 @@
     QMessageBox,
     QWidget,
     QLineEdit,
+    QComboBox,
+    QPushButton,
 )
 
 from matplotlib import patheffects
@@ -29,6 +31,7 @@
 from matplotlib.patches import Rectangle
 from matplotlib.colors import LinearSegmentedColormap
 
+from mne import read_freesurfer_lut
 from mne.viz.backends.renderer import _get_renderer
 from mne.viz.utils import safe_event
 from mne.surface import _read_mri_surface, _marching_cubes
@@ -151,6 +154,17 @@ def make_label(name):
     return label
 
 
+class ComboBox(QComboBox):
+    """Dropdown menu that emits a click when popped up."""
+
+    clicked = Signal()
+
+    def showPopup(self):
+        """Override show popup method to emit click."""
+        self.clicked.emit()
+        super(ComboBox, self).showPopup()
+
+
 class SliceBrowser(QMainWindow):
     """Navigate between slices of an MRI, CT, etc. image."""
 
@@ -173,6 +187,10 @@ def __init__(
         super(SliceBrowser, self).__init__()
         self.setAttribute(Qt.WA_DeleteOnClose, True)
 
+        atlas_ids, colors = read_freesurfer_lut()
+        self._fs_lut = {atlas_id: colors[name] for name, atlas_id in atlas_ids.items()}
+        self._atlas_ids = {val: key for key, val in atlas_ids.items()}
+
         self._verbose = verbose
         # if bad/None subject, will raise an informative error when loading MRI
         subject = os.environ.get("SUBJECT") if subject is None else subject
@@ -203,13 +221,15 @@ def __init__(
         self._configure_ui()
 
     def _configure_ui(self):
+        toolbar = self._configure_toolbar()
         bottom_hbox = self._configure_status_bar()
 
         # Put everything together
         plot_ch_hbox = QHBoxLayout()
         plot_ch_hbox.addLayout(self._plt_grid)
 
         main_vbox = QVBoxLayout()
+        main_vbox.addLayout(toolbar)
         main_vbox.addLayout(plot_ch_hbox)
         main_vbox.addLayout(bottom_hbox)
 
@@ -219,25 +239,27 @@ def _configure_ui(self):
 
     def _load_image_data(self, base_image=None):
         """Get image data to display and transforms to/from vox/RAS."""
+        self._using_atlas = False
         if self._subject_dir is None:
             # if the recon-all is not finished or the CT is not
             # downsampled to the MRI, the MRI can not be used
-            self._mr_data = None
-            self._head = None
-            self._lh = self._rh = None
+            self._mr_data = self._head = self._lh = self._rh = None
+            self._mr_scan_ras_ras_vox_t = None
         else:
-            mri_img = (
-                "brain"
-                if op.isfile(op.join(self._subject_dir, "mri", "brain.mgz"))
-                else "T1"
+            mr_base_fname = op.join(self._subject_dir, "mri", "{}.mgz")
+            mr_fname = (
+                mr_base_fname.format("brain")
+                if op.isfile(mr_base_fname.format("brain"))
+                else mr_base_fname.format("T1")
             )
             (
                 self._mr_data,
                 mr_vox_mri_t,
                 mr_vox_scan_ras_t,
                 mr_ras_vox_scan_ras_t,
                 self._mr_vol_info,
-            ) = _load_image(op.join(self._subject_dir, "mri", f"{mri_img}.mgz"))
+            ) = _load_image(mr_fname)
+            self._mr_scan_ras_ras_vox_t = np.linalg.inv(mr_ras_vox_scan_ras_t)
 
         # ready alternate base image if provided, otherwise use brain/T1
         self._base_mr_aligned = True
@@ -417,23 +439,25 @@ def _plot_images(self):
                 [1],
             )[0]
             rr = apply_trans(self._ras_vox_scan_ras_t, rr)  # base image vox -> RAS
-            self._renderer.mesh(
+            self._mc_actor, _ = self._renderer.mesh(
                 *rr.T,
                 triangles=tris,
                 color="gray",
                 opacity=0.2,
                 reset_camera=False,
                 render=False,
             )
+            self._head_actor = None
         else:
-            self._renderer.mesh(
+            self._head_actor, _ = self._renderer.mesh(
                 *self._head["rr"].T,
                 triangles=self._head["tris"],
                 color="gray",
                 opacity=0.2,
                 reset_camera=False,
                 render=False,
             )
+            self._mc_actor = None
         if self._lh is not None and self._rh is not None and self._base_mr_aligned:
             self._lh_actor, _ = self._renderer.mesh(
                 *self._lh["rr"].T,
@@ -460,6 +484,51 @@ def _plot_images(self):
         self._draw()
         self._renderer._update()
 
+    def _configure_toolbar(self, hbox=None):
+        """Make a bar at the top with tools on it."""
+        hbox = QHBoxLayout() if hbox is None else hbox
+
+        help_button = QPushButton("Help")
+        help_button.released.connect(self._show_help)
+        hbox.addWidget(help_button)
+
+        hbox.addStretch(6)
+
+        self._toggle_show_selector = ComboBox()
+
+        # add title, not selectable
+        self._toggle_show_selector.addItem("Show/Hide")
+        model = self._toggle_show_selector.model()
+        model.itemFromIndex(model.index(0, 0)).setSelectable(False)
+        # color differently
+        color = QtGui.QColor("gray")
+        brush = QtGui.QBrush(color)
+        brush.setStyle(QtCore.Qt.SolidPattern)
+        model.setData(model.index(0, 0), brush, QtCore.Qt.BackgroundRole)
+
+        if self._base_mr_aligned and hasattr(self, "_toggle_show_brain"):
+            self._toggle_show_selector.addItem("Show brain slices")
+            self._toggle_show_selector.addItem("Show atlas slices")
+
+        if hasattr(self, "_toggle_show_mip"):
+            self._toggle_show_selector.addItem("Show max intensity proj")
+
+        if hasattr(self, "_toggle_show_max"):
+            self._toggle_show_selector.addItem("Show local maxima")
+
+        if self._head_actor is not None:
+            self._toggle_show_selector.addItem("Hide 3D head")
+
+        if self._lh_actor is not None and self._rh_actor is not None:
+            self._toggle_show_selector.addItem("Hide 3D brain")
+
+        if self._mc_actor is not None:
+            self._toggle_show_selector.addItem("Hide 3D rendering")
+
+        self._toggle_show_selector.currentIndexChanged.connect(self._toggle_show)
+        hbox.addWidget(self._toggle_show_selector)
+        return hbox
+
     def _configure_status_bar(self, hbox=None):
         """Make a bar at the bottom with information in it."""
         hbox = QHBoxLayout() if hbox is None else hbox
@@ -539,6 +608,51 @@ def _update_VOX(self, event):
         if ras is not None:
             self._set_ras(ras)
 
+    def _toggle_show(self):
+        """Show or hide objects in the 3D rendering."""
+        text = self._toggle_show_selector.currentText()
+        if text == "Show/Hide":
+            return
+        idx = self._toggle_show_selector.currentIndex()
+        show_hide, item = text.split(" ")[0], " ".join(text.split(" ")[1:])
+        show_hide_opp = "Show" if show_hide == "Hide" else "Hide"
+        if "slices" in item:
+            # atlas shown and brain already on or brain already on and atlas shown
+            if show_hide == "Show" and "mri" in self._images:
+                idx2, item2 = (2, "atlas") if self._using_atlas else (1, "brain")
+                self._toggle_show_selector.setItemText(idx2, f"Show {item2} slices")
+                self._toggle_show_brain()
+            mr_base_fname = op.join(self._subject_dir, "mri", "{}.mgz")
+            if show_hide == "Show" and "atlas" in item and not self._using_atlas:
+                if op.isfile(mr_base_fname.format("wmparc")):
+                    self._mr_data = _load_image(mr_base_fname.format("wmparc"))[0]
+                else:
+                    self._mr_data = _load_image(mr_base_fname.format("aparc+aseg"))[0]
+                self._using_atlas = True
+            if show_hide == "Show" and "brain" in item and self._using_atlas:
+                if op.isfile(mr_base_fname.format("brain")):
+                    self._mr_data = _load_image(mr_base_fname.format("brain"))[0]
+                else:
+                    self._mr_data = _load_image(mr_base_fname.format("T1"))[0]
+                self._using_atlas = False
+            self._toggle_show_brain()
+            self._update_moved()
+        elif item == "max intensity proj":
+            self._toggle_show_mip()
+        elif item == "local maxima":
+            self._toggle_show_max()
+        else:
+            actors = {
+                "3D head": [self._head_actor],
+                "3D brain": [self._lh_actor, self._rh_actor],
+                "3D rendering": [self._mc_actor],
+            }[item]
+            for actor in actors:
+                actor.SetVisibility(show_hide == "Show")
+            self._renderer._update()
+        self._toggle_show_selector.setItemText(idx, f"{show_hide_opp} {item}")
+        self._toggle_show_selector.setCurrentIndex(0)  # back to title
+
     def _convert_text(self, text, text_kind):
         text = text.replace("\n", "")
         vals = text.split(",")
@@ -720,9 +834,16 @@ def _update_moved(self):
         self._VOX_textbox.setText(
             "{:3d}, {:3d}, {:3d}".format(*self._vox.round().astype(int))
         )
-        self._intensity_label.setText(
-            "intensity = {:.2f}".format(self._base_data[tuple(self._current_slice)])
+        intensity_text = "intensity = {:.2f}".format(
+            self._base_data[tuple(self._current_slice)]
         )
+        if self._using_atlas:
+            vox = (
+                apply_trans(self._mr_scan_ras_ras_vox_t, self._ras).round().astype(int)
+            )
+            label = self._atlas_ids[int(self._mr_data[tuple(vox)])]
+            intensity_text += f" ({label})"
+        self._intensity_label.setText(intensity_text)
 
     @safe_event
     def closeEvent(self, event):