MRG: Fix label colors (#229)

* FIX: Label colors

* FIX: Nicks fix is better

* ENH: Bump to VTK from pip

* FIX: Travis

Author: larsoner

environment.yml

@@ -1,23 +1,22 @@
 name: mne
 channels:
 - defaults
-- clinicalgraphics  # Needed for VTK
 dependencies:
-- python=3.6.1
+- python>=3.6
 - pip
 - mkl
 - numpy
 - scipy
 - matplotlib
 - pyqt=5
-- vtk>=7
 - nose
 - coverage
 - pytest
 - pytest-cov
 - flake8
 - pygments
 - pip:
+  - vtk
   - "git+https://github.com/enthought/traits.git@a7a83182048c08923953e302658b51b68c802132"
   - "git+https://github.com/enthought/pyface.git@13a064de48adda3c880350545717d8cf8929afad"
   - "git+https://github.com/enthought/traitsui.git@ee8ef0a34dfc1db18a8e2c0301cc18d96b7a3e2f"

examples/plot_label.py

@@ -26,7 +26,7 @@
 brain.add_label("BA1_exvivo", color="blue", scalar_thresh=.5)
 
 # Or you can give a path to a label in an arbitrary location
-subj_dir = os.environ["SUBJECTS_DIR"]
+subj_dir = brain.subjects_dir
 label_file = os.path.join(subj_dir, subject_id,
                           "label", "%s.MT_exvivo.label" % hemi)
 brain.add_label(label_file)

surfer/tests/test_viz.py

@@ -81,10 +81,12 @@ def test_image():
     brain.close()
 
     brain = Brain(*std_args, size=100)
+    if sys.platform == 'darwin' and os.getenv('TRAVIS', '') == 'true':
+        raise SkipTest('image saving on OSX travis is not supported')
     brain.save_image(tmp_name)
     brain.save_image(tmp_name, 'rgba', True)
     brain.screenshot()
-    if not os.getenv('TRAVIS', 'false') == 'true':
+    if os.getenv('TRAVIS', '') != 'true':
         # for some reason these fail on Travis sometimes
         brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
         brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')
@@ -340,6 +342,8 @@ def test_movie():
                    smoothing_steps=10, time=time, time_label='time=%0.2f ms')
     brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
 
+    if sys.platform == 'darwin' and os.getenv('TRAVIS', '') == 'true':
+        raise SkipTest('movie saving on OSX Travis is not supported')
     # save movies with different options
     tempdir = mkdtemp()
     try:

surfer/viz.py

@@ -3257,7 +3257,10 @@ def add_label(self, label, label_name, color, alpha):
         color = colorConverter.to_rgba(color, alpha)
         cmap = np.array([(0, 0, 0, 0,), color])
         l_m = surf.module_manager.scalar_lut_manager
-        l_m.load_lut_from_list(cmap)
+        # for some reason (traits?) using `load_lut_from_list` here does
+        # not work (.data_range needs to be tweaked in this case),
+        # but setting the table directly does:
+        l_m.lut.table = np.round(cmap * 255).astype(np.uint8)
         return array_id, surf
 
     def add_morphometry(self, morph_data, colormap, measure,