ENH: Add to annot

Author: larsoner

examples/plot_parcellation.py

@@ -17,7 +17,6 @@
 surface = 'inflated'
 view = 'frontal'
 
-
 """
 Bring up the visualization
 """
@@ -46,4 +45,4 @@
 annot_path = pjoin(subjects_dir, subject_id, "label", "lh.aparc.annot")
 brain.add_annotation(annot_path, hemi='lh', borders=False, alpha=.75)
 annot_path = pjoin(subjects_dir, subject_id, "label", "rh.aparc.a2009s.annot")
-brain.add_annotation(annot_path, hemi='rh', remove_existing=False)
+brain.add_annotation(annot_path, hemi='rh', borders=2, remove_existing=False)

surfer/tests/test_viz.py

@@ -89,11 +89,12 @@ def test_annot():
     """
     mlab.options.backend = 'test'
     annots = ['aparc', 'aparc.a2005s']
-    borders = [True, False]
+    borders = [True, False, 2]
     alphas = [1, 0.5]
     brain = Brain(*std_args)
     for a, b, p in zip(annots, borders, alphas):
         brain.add_annotation(a, b, p)
+    assert_raises(ValueError, brain.add_annotation, 'aparc', borders=-1)
     brain.close()
 
 

surfer/viz.py

@@ -905,8 +905,10 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
         ----------
         annot : str
             Either path to annotation file or annotation name
-        borders : bool
-            Show only borders of regions
+        borders : bool | int
+            Show only label borders. If int, specify the number of steps
+            (away from the true border) along the cortical mesh to include
+            as part of the border definition.
         alpha : float in [0, 1]
             Alpha level to control opacity
         hemi : str | None
@@ -960,13 +962,7 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
                                                         orig_ids=True)
 
             # Maybe zero-out the non-border vertices
-            if borders:
-                n_vertices = labels.size
-                edges = utils.mesh_edges(self.geo[hemi].faces)
-                border_edges = labels[edges.row] != labels[edges.col]
-                show = np.zeros(n_vertices, dtype=np.int)
-                show[np.unique(edges.row[border_edges])] = 1
-                labels *= show
+            self._to_borders(labels, hemi, borders)
 
             # Handle null labels properly
             # (tksurfer doesn't use the alpha channel, so sometimes this
@@ -1012,8 +1008,8 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
             scalar >= thresh)
         borders : bool | int
             Show only label borders. If int, specify the number of steps
-            along the cortical mesh to include in the border definition
-            (higher numbers create thicker borders).
+            (away from the true border) along the cortical mesh to include
+            as part of the border definition.
         hemi : str | None
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
@@ -1095,8 +1091,22 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
                 i += 1
             label_name = name % i
 
+        self._to_borders(label, hemi, borders, restrict_idx=ids)
+
+        # make a list of all the plotted labels
+        ll = []
+        views = self._toggle_render(False)
+        for brain in self._brain_list:
+            if brain['hemi'] == hemi:
+                ll.append(brain['brain'].add_label(label, label_name,
+                          color, alpha))
+        self.labels_dict[label_name] = ll
+        self._toggle_render(True, views)
+
+    def _to_borders(self, label, hemi, borders, restrict_idx=None):
+        """Helper to potentially convert a label/parc to borders"""
         if not isinstance(borders, (bool, int)) or borders < 0:
-            raise TypeError('borders must be a bool or positive integer')
+            raise ValueError('borders must be a bool or positive integer')
         if borders:
             n_vertices = label.size
             edges = utils.mesh_edges(self.geo[hemi].faces)
@@ -1107,22 +1117,13 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
                 for _ in range(borders):
                     keep_idx = np.in1d(self.geo[hemi].faces.ravel(), keep_idx)
                     keep_idx.shape = self.geo[hemi].faces.shape
-                    keep_idx = self.geo[hemi].faces[np.any(keep_idx,
-                                                           axis=1)].ravel()
-                keep_idx = keep_idx[np.in1d(keep_idx, ids)]
+                    keep_idx = self.geo[hemi].faces[np.any(keep_idx, axis=1)]
+                    keep_idx = np.unique(keep_idx)
+                if restrict_idx is not None:
+                    keep_idx = keep_idx[np.in1d(keep_idx, restrict_idx)]
             show[keep_idx] = 1
             label *= show
 
-        # make a list of all the plotted labels
-        ll = []
-        views = self._toggle_render(False)
-        for brain in self._brain_list:
-            if brain['hemi'] == hemi:
-                ll.append(brain['brain'].add_label(label, label_name,
-                          color, alpha))
-        self.labels_dict[label_name] = ll
-        self._toggle_render(True, views)
-
     def remove_labels(self, labels=None, hemi=None):
         """Remove one or more previously added labels from the image.