wip

mne/gui/_ieeg_locate_gui.py

@@ -48,42 +48,27 @@
 def _get_mri_head_trans(subject, subjects_dir):
     """Get the head to surface RAS transform using the Freesurfer recon."""
     lpa, nasion, rpa = get_mni_fiducials(subject, subjects_dir)
-    assert lpa['ident'] == FIFF.FIFFV_POINT_LPA
-    assert nasion['ident'] == FIFF.FIFFV_POINT_NASION
-    assert rpa['ident'] == FIFF.FIFFV_POINT_RPA
     montage = make_dig_montage(
         lpa=lpa['r'], nasion=nasion['r'], rpa=rpa['r'], coord_frame='mri')
     trans = compute_native_head_t(montage)
     return trans
 
 
 @requires_nibabel()
-def _reorient_image(img_data, vox_ras_t):
-    """Reorient an image to RAS."""
-    import nibabel as nib
-    ornt = nib.orientations.axcodes2ornt(
-        nib.orientations.aff2axcodes(vox_ras_t)).astype(int)
-    img_data = nib.orientations.apply_orientation(img_data, ornt)
-    vox_ras_t[:3, :3] = vox_ras_t[list(ornt[:, 0]), :3]
-    vox_ras_t[:3, 3] = vox_ras_t[list(ornt[:, 0]), 3]
-    vox_ras_t[:3, :3] *= ornt[:, 1]
-    vox_ras_t[:3, 3] *= ornt[:, 1]
-    return img_data, vox_ras_t
-
-
-@requires_nibabel()
-def _load_image(img, name, reorient=False, verbose=True):
+def _load_image(img, name, verbose=True):
     """Load data from a 3D image file (e.g. CT, MR)."""
     import nibabel as nib
     if not isinstance(img, nib.spatialimages.SpatialImage):
         if verbose:
-            print(f'Loading {img}')
+            logger.info(f'Loading {img}')
         _check_fname(img, overwrite='read', must_exist=True, name=name)
         img = nib.load(img)
-    img_data = np.array(img.dataobj)
-    vox_ras_t = img.affine
-    if reorient:
-        img_data, vox_ras_t = _reorient_image(img_data, vox_ras_t)
+    # get data reoriented to RAS and transform
+    orig_data = np.array(img.dataobj)
+    orig_mgh = nib.MGHImage(orig_data, img.affine)
+    vox_ras_t = orig_mgh.header.get_vox2ras_tkr()
+    img_canonical = nib.as_closest_canonical(img_mgh)
+    img_data, vox_ras_t = _reorient_image(img_data, vox_ras_t)
     return img_data, vox_ras_t
 
 
@@ -176,7 +161,7 @@ def _load_image_data(self, ct):
             op.join(self._subject_dir, 'mri', 'brain.mgz'),
             'MRI Image', reorient=True, verbose=self._verbose)
         self._ras_vox_t = np.linalg.inv(self._vox_ras_t)
-        self._T1_on = True
+        self._brain_on = True
 
         self._voxel_sizes = np.array(self._mri_data.shape)
         self._img_ranges = [[0, self._voxel_sizes[1], 0, self._voxel_sizes[2]],
@@ -287,14 +272,14 @@ def _plot_images(self):
         # Plot sagittal (0), coronal (1) or axial (2) view
         self._images = dict(mri=list(), ct=list(), chs=list(),
                             cursor=list(), cursor2=list())
+        ct_min, ct_max = np.nanmin(self._ct_data), np.nanmax(self._ct_data)
         self._ct_cutoff = int(round(np.quantile(
             self._ct_data[~np.isnan(self._ct_data)], _CT_MIN_DEFAULT))) \
-            if self._T1_on else 0  # only cut off by default if T1 is on
-        ct_min, ct_max = np.nanmin(self._ct_data), np.nanmax(self._ct_data)
-        ct_cmap = 'autumn_r' if self._T1_on else 'gray'
+            if self._brain_on else ct_min  # cut off by default if brain is on
+        ct_cmap = 'autumn_r' if self._brain_on else 'gray'
         for axis in range(3):
             self._plt._axes[axis].clear()
-            if self._T1_on:
+            if self._brain_on:
                 img_data = np.take(self._mri_data, self._current_slice[axis],
                                    axis=axis).T
                 self._images['mri'].append(self._plt._axes[axis].imshow(
@@ -658,7 +643,7 @@ def _update_ch_images(self, axis_selected=None, draw=False):
     def _update_mri_images(self, axis_selected=None, draw=False):
         """Update the MRI image(s)."""
         for axis in range(3) if axis_selected is None else [axis_selected]:
-            if self._T1_on:
+            if self._brain_on:
                 img_data = np.take(self._mri_data, self._current_slice[axis],
                                    axis=axis).T
             else:
@@ -682,7 +667,7 @@ def _update_ct_images(self, axis_selected=None, draw=False):
 
     def _update_images(self, axis=None, draw=True):
         """Update MRI, CT and channel images when general changes happen."""
-        if self._T1_on:
+        if self._brain_on:
             self._update_mri_images(axis_selected=axis)
         self._update_ct_images(axis_selected=axis)
         self._update_ch_images(axis_selected=axis)
@@ -779,8 +764,8 @@ def _key_press_event(self, event):
 
         if event.text() == 'b':
             # Toggle T1 scan on and off
-            self._T1_on = not self._T1_on
-            logger.info('Turning T1 ' + ('on' if self._T1_on else 'off'))
+            self._brain_on = not self._brain_on
+            logger.info('Turning T1 ' + ('on' if self._brain_on else 'off'))
             self._plot_images()
             # update slider on toggle
             self._ct_min_slider.setValue(self._ct_cutoff)