Merge pull request #152 from Eric89GXL/py3k

MRG: Py3k support

Author: larsoner

.travis.yml

@@ -15,15 +15,15 @@ env:
 before_install:
     - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
     - chmod +x miniconda.sh
-    - ./miniconda.sh -b
+    - ./miniconda.sh -b -p /home/travis/miniconda
     - export PATH=/home/travis/miniconda/bin:$PATH
     - conda update --yes conda
 
 install:
     - conda create -n testenv --yes pip python=$PYTHON
     - source activate testenv
     # Pillow (or PIL/imaging) is necessary for scipy.misc.imsave to exist
-    - conda install --yes --quiet ipython==1.1.0 numpy scipy mayavi matplotlib nose imaging
+    - conda install --yes --quiet numpy scipy mayavi matplotlib nose imaging
     - if [ "${DEPS}" == "full" ]; then
         travis_retry sudo apt-get update -qq;
         travis_retry sudo apt-get install mencoder;

examples/plot_meg_inverse_solution.py

@@ -24,6 +24,14 @@
 """
 brain = Brain(subject_id, hemi, surface, size=(800, 400))
 
+"""
+label for time annotation in milliseconds
+"""
+
+
+def time_label(t):
+    return 'time=%0.2f ms' % (t * 1e3)
+
 """
 read MNE dSPM inverse solution
 """
@@ -49,11 +57,6 @@
     """
     colormap = 'hot'
 
-    """
-    label for time annotation in milliseconds
-    """
-    time_label = lambda t: 'time=%0.2f ms' % (t * 1e3)
-
     brain.add_data(data, colormap=colormap, vertices=vertices,
                    smoothing_steps=10, time=time, time_label=time_label,
                    hemi=hemi)

setup.py

@@ -6,9 +6,11 @@
 #                         Martin Luessi
 #                         Eric Larson
 
+import os
+from setuptools import setup
+
 descr = """PySurfer: cortical surface visualization using Python."""
 
-import os
 # deal with MPL sandbox violations during easy_install
 os.environ['MPLCONFIGDIR'] = '.'
 
@@ -32,10 +34,9 @@
 DOWNLOAD_URL = 'https://github.com/nipy/PySurfer'
 VERSION = version
 
-def check_dependencies():
 
-    needed_deps = ["IPython",
-                   "numpy", "scipy", "matplotlib",
+def check_dependencies():
+    needed_deps = ["numpy", "scipy", "matplotlib",
                    "mayavi",
                    ]
     missing_deps = []
@@ -50,8 +51,6 @@ def check_dependencies():
         raise ImportError("Missing dependencies: %s" % missing)
 
 
-from setuptools import setup
-
 if __name__ == "__main__":
     if os.path.exists('MANIFEST'):
         os.remove('MANIFEST')
@@ -64,7 +63,6 @@ def check_dependencies():
                             'clean'))):
         check_dependencies()
 
-
     setup(name=DISTNAME,
           maintainer=MAINTAINER,
           include_package_data=True,
@@ -79,6 +77,9 @@ def check_dependencies():
           classifiers=['Intended Audience :: Science/Research',
                        'Intended Audience :: Developers',
                        'Programming Language :: Python :: 2.7',
+                       'Programming Language :: Python :: 3.3',
+                       'Programming Language :: Python :: 3.4',
+                       'Programming Language :: Python :: 3.5',
                        'License :: OSI Approved',
                        'Programming Language :: Python',
                        'Topic :: Software Development',

surfer/io.py

@@ -176,7 +176,8 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
         cmd = ['bash', '-c', 'source {} && env'.format(
                os.path.join(env['FREESURFER_HOME'], 'FreeSurferEnv.sh'))]
         envout = check_output(cmd)
-        env = dict(line.split('=', 1) for line in envout.split('\n')
+        env = dict(line.split('=', 1)
+                   for line in envout.decode('utf-8').split('\n')
                    if '=' in line)
 
     # Set the basic commands
@@ -199,7 +200,7 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
         proj_flag += "-"
         proj_flag += projsum
     if hasattr(projarg, "__iter__"):
-        proj_arg = map(str, projarg)
+        proj_arg = list(map(str, projarg))
     else:
         proj_arg = [str(projarg)]
     cmd_list.extend([proj_flag] + proj_arg)

surfer/viz.py

@@ -82,9 +82,9 @@ def make_montage(filename, fnames, orientation='h', colorbar=None,
     #          dimension-dependent-attributeerror-in-pil-fromarray-function
     fnames = [f if isinstance(f, string_types) else f.copy() for f in fnames]
     if isinstance(fnames[0], string_types):
-        images = map(Image.open, fnames)
+        images = list(map(Image.open, fnames))
     else:
-        images = map(Image.fromarray, fnames)
+        images = list(map(Image.fromarray, fnames))
     # get bounding box for cropping
     boxes = []
     for ix, im in enumerate(images):
@@ -566,7 +566,7 @@ def _get_one_brain(self, d, name):
                              'or brain.brains.' % name)
         if isinstance(d, dict):
             out = dict()
-            for key, value in d.iteritems():
+            for key, value in d.items():
                 out[key] = value[0]
         else:
             out = d[0]
@@ -595,7 +595,7 @@ def contour(self):
     @property
     def annot(self):
         """Wrap to annot"""
-        return self._get_one_brain(self.annot_list, 'contour')
+        return self._get_one_brain(self.annot_list, 'annot')
 
     @property
     def texts(self):
@@ -879,9 +879,11 @@ def add_data(self, array, min=None, max=None, thresh=None,
             if not self.n_times == len(time):
                 raise ValueError('time is not the same length as '
                                  'array.shape[1]')
-            if isinstance(time_label, basestring):
+            if isinstance(time_label, string_types):
                 time_label_fmt = time_label
-                time_label = lambda x: time_label_fmt % x
+
+                def time_label(x):
+                    return time_label_fmt % x
             data["time_label"] = time_label
             data["time"] = time
             data["time_idx"] = 0
@@ -1374,7 +1376,7 @@ def add_contour_overlay(self, source, min=None, max=None,
         scalar_data = _prepare_data(scalar_data)
 
         # Maybe get rid of an old overlay
-        if hasattr(self, "contour") and remove_existing:
+        if remove_existing:
             for c in self.contour_list:
                 c['surface'].remove()
                 if c['colorbar'] is not None:
@@ -2234,7 +2236,7 @@ def animate(self, views, n_steps=180., fname=None, use_cache=False,
             Column index of the brain to use
         """
         brain = self.brain_matrix[row, col]
-        gviews = map(brain._xfm_view, views)
+        gviews = list(map(brain._xfm_view, views))
         allowed = ('lateral', 'caudal', 'medial', 'rostral')
         if not len([v for v in gviews if v in allowed]) == len(gviews):
             raise ValueError('Animate through %s views.' % ' '.join(allowed))