Merge branch 'main' of https://github.com/mne-tools/mne-python into c…

…oreg-ui-fiducial-io-widgets

doc/changes/latest.inc

@@ -92,6 +92,8 @@ Enhancements
 
 - All methods of :class:`mne.Report` with a ``tags`` parameter now also accept a single tag passed as a string (previously, you needed to pass a tuple of strings, even for a single tag) (:gh:`10183`, by `Richard Höchenberger`_)
 
+- :meth:`mne.Report.add_trans` has gained a new parameter, ``alpha``, to control the level of opacity of the rendered head (:gh:`10247`, by `Richard Höchenberger`_)
+
 - The new convenience function :func:`mne.event.match_event_names` allows for straightforward checking if a specific event name or a group of events is present in a collection of event names (:gh:`10233` by `Richard Höchenberger`_)
 
 Bugs

mne/html_templates/report/epochs.html.jinja

@@ -17,9 +17,9 @@
     aria-labelledby="accordion-header-{{ id }}">
     <div class="accordion-body">
       {{ repr | safe }}
+      {{ drop_log | safe }}
       {{ metadata | safe }}
       {{ erp_imgs | safe }}
-      {{ drop_log | safe }}
       {{ psd | safe }}
       {{ ssp_projs | safe }}
     </div>

mne/report/report.py

@@ -437,7 +437,7 @@ def _get_bem_contour_figs_as_arrays(
     return out
 
 
-def _iterate_trans_views(function, **kwargs):
+def _iterate_trans_views(function, alpha, **kwargs):
     """Auxiliary function to iterate over views in trans fig."""
     from ..viz import create_3d_figure
     from ..viz.backends.renderer import MNE_3D_BACKEND_TESTING
@@ -447,9 +447,11 @@ def _iterate_trans_views(function, **kwargs):
     from ..viz.backends.renderer import backend
     try:
         try:
-            return _itv(function, fig, surfaces=['head-dense'], **kwargs)
+            return _itv(
+                function, fig, surfaces={'head-dense': alpha}, **kwargs
+            )
         except IOError:
-            return _itv(function, fig, surfaces=['head'], **kwargs)
+            return _itv(function, fig, surfaces={'head': alpha}, **kwargs)
     finally:
         backend._close_3d_figure(fig)
 
@@ -1241,7 +1243,7 @@ def add_inverse_operator(self, inverse_operator, title, *, subject=None,
 
     @fill_doc
     def add_trans(self, trans, *, info, title, subject=None, subjects_dir=None,
-                  tags=('coregistration',), replace=False):
+                  alpha=None, tags=('coregistration',), replace=False):
         """Add a coregistration visualization to the report.
 
         Parameters
@@ -1259,6 +1261,10 @@ def add_trans(self, trans, *, info, title, subject=None, subjects_dir=None,
             report creation.
         subjects_dir : path-like | None
             The FreeSurfer ``SUBJECTS_DIR``.
+        alpha : float | None
+            The level of opacity to apply to the head surface. If a float, must
+            be between 0 and 1 (inclusive), where 1 means fully opaque. If
+            ``None``, will use the MNE-Python default value.
         %(report_tags)s
         %(report_replace)s
 
@@ -1273,6 +1279,7 @@ def add_trans(self, trans, *, info, title, subject=None, subjects_dir=None,
             info=info,
             subject=subject,
             subjects_dir=subjects_dir,
+            alpha=alpha,
             title=title,
             tags=tags
         )
@@ -3484,8 +3491,8 @@ def _render_cov(self, cov, *, info, image_format, tags):
 
         return htmls
 
-    def _render_trans(self, *, trans, info, subject, subjects_dir, title,
-                      tags):
+    def _render_trans(self, *, trans, info, subject, subjects_dir, alpha,
+                      title, tags):
         """Render trans (only PNG)."""
         if not isinstance(trans, Transform):
             trans = read_trans(trans)
@@ -3497,7 +3504,7 @@ def _render_trans(self, *, trans, info, subject, subjects_dir, title,
                       meg=['helmet', 'sensors'], show_axes=True,
                       coord_frame='mri')
         img, caption = _iterate_trans_views(
-            function=plot_alignment, **kwargs)
+            function=plot_alignment, alpha=alpha, **kwargs)
 
         dom_id = self._get_dom_id()
         html = _html_image_element(

tutorials/intro/70_report.py

@@ -306,14 +306,15 @@
 # "coregistration") can be visualized via :meth:`mne.Report.add_trans`. The
 # method expects the transformation either as a `~mne.transforms.Transform`
 # object or as a path to a ``trans.fif`` file, the FreeSurfer subject name and
-# subjects directory, and a title.
+# subjects directory, and a title. The ``alpha`` parameter can be used to
+# control the transparency of the head, where a value of 1 means fully opaque.
 
 trans_path = sample_dir / 'sample_audvis_raw-trans.fif'
 
 report = mne.Report(title='Coregistration example')
 report.add_trans(
     trans=trans_path, info=raw_path, subject='sample',
-    subjects_dir=subjects_dir, title='Coregistration'
+    subjects_dir=subjects_dir, alpha=1.0, title='Coregistration'
 )
 report.save('report_coregistration.html', overwrite=True)