Merge pull request #93 from dengemann/fix_color_bar

BUG/WIP: positive only overlays + multiple hemis

Author: larsoner

surfer/tests/test_viz.py

@@ -1,5 +1,6 @@
 import numpy as np
 import os
+import os.path as op
 from os.path import join as pjoin
 from numpy.testing import assert_raises, assert_array_equal
 from tempfile import mktemp
@@ -12,10 +13,11 @@
 subj_dir = utils._get_subjects_dir()
 subject_id = 'fsaverage'
 std_args = [subject_id, 'lh', 'inflated']
-data_dir = pjoin(os.path.split(__file__)[0], '..', '..',
-                 'examples', 'example_data')
+data_dir = pjoin(op.dirname(__file__), '..', '..', 'examples', 'example_data')
 small_brain = dict(size=100)
 
+overlay_fname = pjoin(data_dir, 'lh.sig.nii.gz')
+
 
 def has_freesurfer():
     if 'FREESURFER_HOME' not in os.environ:
@@ -42,11 +44,16 @@ def test_offscreen():
 def test_image():
     """Test image saving
     """
+    tmp_name = mktemp() + '.png'
+
     mlab.options.backend = 'auto'
+    subject_id, _, surf = std_args
+    brain = Brain(subject_id, 'both', surf=surf, config_opts=small_brain)
+    brain.add_overlay(overlay_fname, hemi='lh', min=5, max=20, sign="pos")
+    brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
+
     brain = Brain(*std_args, config_opts=small_brain)
-    tmp_name = mktemp() + '.png'
     brain.save_image(tmp_name)
-    brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
     brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
     brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')
     brain.save_montage(tmp_name, [['l', 'v'], ['m', 'f']])

surfer/viz.py

@@ -1621,8 +1621,9 @@ def _get_colorbars(self, row, col):
         if len(self.overlays_dict) > 0:
             for name, obj in self.overlays_dict.items():
                 for bar in ["pos_bar", "neg_bar"]:
-                    try:
-                        colorbars.append(getattr(obj[ind], bar))
+                    try:  # deal with positive overlays
+                        this_ind = min(len(obj) - 1, ind)
+                        colorbars.append(getattr(obj[this_ind], bar))
                     except AttributeError:
                         pass
         return colorbars