ENH: Add kwargs in Brain.add_* and pass it to mayavi modules (#276)

* Feat: add kwargs in Brain.add_* and pass it to mayavi modules, so that we could directly manipulate mayavi display settings, like point resolution and overlay opacity.

* Fix: Fix code styles which failed in the flake test.

* Modify test_viz to pass the kwargs to the mayavi module.

* fix flake test.

* Specifying `kwargs` as `mlab_kws` and make the documentation more clear.

* Revert "Specifying `kwargs` as `mlab_kws` and make the documentation more clear."

This reverts commit c7a5912.

* Link mayavi documents.

* Give detailed explanations about the kwargs passed to the functions.

* Revert "Link mayavi documents."

This reverts commit 2c86a04.

* Change the position of line breaking.

* Fix the typo and unavailable links.

* Fix render errors.

* Revert "Fix render errors."

This reverts commit ac0b7b8.

* Fix render error.

* Improve code rendering.

* Revert "Fix render error."

This reverts commit bbf7631.

* Fix line breaking error.

* Revert "Fix line breaking error."

This reverts commit 6efccac.

* Fix line breaking error.

* Revert "Fix line breaking error."

This reverts commit a7abf61.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit 6a9cdf1.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit c7f6a9f.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit de31e5f.

* Fix render error

Force line breaking to avoid render error.

* Render undocumented function as plain code.

* Fix sectioning.

* FIX: Formatting

Author: DingkunLiu

.gitignore

@@ -7,6 +7,7 @@
 *.orig
 *.mov
 build
+.idea/
 
 dist/
 doc/_build/

doc/_static/navy.css

@@ -546,4 +546,8 @@ ul.keywordmatches li.goodmatch a {
     div.sphx-glr-footer-example a code span:last-child {
 	font-size: unset;
     }
-}
+}
+
+table.longtable.align-default {
+    width: 100%;
+}

surfer/tests/test_viz.py

@@ -153,7 +153,7 @@ def test_annot():
     view = get_view(brain)
 
     for a, b, p in zip(annots, borders, alphas):
-        brain.add_annotation(a, b, p)
+        brain.add_annotation(a, b, p, opacity=0.8)
     check_view(brain, view)
 
     brain.set_surf('white')
@@ -226,7 +226,11 @@ def test_foci():
     coords = [[-36, 18, -3],
               [-43, 25, 24],
               [-48, 26, -2]]
-    brain.add_foci(coords, map_surface="white", color="gold", name='test1')
+    brain.add_foci(coords,
+                   map_surface="white",
+                   color="gold",
+                   name='test1',
+                   resolution=25)
 
     subj_dir = utils._get_subjects_dir()
     annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
@@ -398,7 +402,7 @@ def test_overlay():
     brain = Brain(*std_args)
     brain.add_overlay(overlay_file)
     brain.overlays["sig"].remove()
-    brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
+    brain.add_overlay(overlay_file, min=5, max=20, sign="pos", opacity=0.7)
     sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
     sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))