Merge pull request #104 from Eric89GXL/peps

larsoner · larsoner · commit cf81e8840951 · 2014-04-11T14:36:31.000-07:00
FIX: PEP8
diff --git a/examples/plot_basics.py b/examples/plot_basics.py
@@ -5,7 +5,7 @@
 Initialize a basic visualization session.
 
 """
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
diff --git a/examples/plot_fmri_activation.py b/examples/plot_fmri_activation.py
@@ -9,7 +9,7 @@
 
 """
 
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
diff --git a/examples/plot_fmri_activation_volume.py b/examples/plot_fmri_activation_volume.py
@@ -13,7 +13,7 @@
 
 """
 
-print __doc__
+print(__doc__)
 
 import os
 from surfer import Brain, project_volume_data
diff --git a/examples/plot_fmri_conjunction.py b/examples/plot_fmri_conjunction.py
@@ -11,7 +11,7 @@
 
 """
 
-print __doc__
+print(__doc__)
 
 import os.path as op
 import numpy as np
diff --git a/examples/plot_foci.py b/examples/plot_foci.py
@@ -7,7 +7,7 @@
 according to coordinates or vertex ids.
 
 """
-print __doc__
+print(__doc__)
 
 import os
 import os.path as op
diff --git a/examples/plot_label.py b/examples/plot_label.py
@@ -6,7 +6,7 @@
 with a large amount of control over the visual representation.
 
 """
-print __doc__
+print(__doc__)
 
 import os
 from surfer import Brain
diff --git a/examples/plot_label_foci.py b/examples/plot_label_foci.py
@@ -7,7 +7,7 @@
 that label and the focus that defines its center.
 
 """
-print __doc__
+print(__doc__)
 
 from surfer import Brain, utils
 
diff --git a/examples/plot_meg_inverse_solution.py b/examples/plot_meg_inverse_solution.py
@@ -5,7 +5,7 @@
 Data were computed using mne-python (http://martinos.org/mne)
 
 """
-print __doc__
+print(__doc__)
 
 import os
 import numpy as np
@@ -68,5 +68,5 @@
 """
 uncomment these lines to use the interactive TimeViewer GUI
 """
-#from surfer import TimeViewer
-#viewer = TimeViewer(brain)
+# from surfer import TimeViewer
+# viewer = TimeViewer(brain)
diff --git a/examples/plot_morphometry.py b/examples/plot_morphometry.py
@@ -7,7 +7,7 @@
 
 """
 
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
diff --git a/examples/plot_parc_values.py b/examples/plot_parc_values.py
@@ -8,7 +8,7 @@
 quickly summarize the analysis.
 
 """
-print __doc__
+print(__doc__)
 
 import os
 import numpy as np
diff --git a/examples/plot_parcellation.py b/examples/plot_parcellation.py
@@ -5,7 +5,7 @@
 Display a Freesurfer cortical parcellation from an annotation file.
 
 """
-print __doc__
+print(__doc__)
 
 import os
 from os.path import join as pjoin
diff --git a/examples/plot_resting_correlations.py b/examples/plot_resting_correlations.py
@@ -9,7 +9,7 @@
 the data.
 
 """
-print __doc__
+print(__doc__)
 
 import os
 from surfer import Brain, io
diff --git a/examples/plot_topographic_contours.py b/examples/plot_topographic_contours.py
@@ -6,7 +6,7 @@
 
 """
 
-print __doc__
+print(__doc__)
 
 import os.path as op
 from surfer import Brain
diff --git a/examples/rotate_animation.py b/examples/rotate_animation.py
@@ -4,7 +4,7 @@
 ============================
 
 """
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
@@ -32,4 +32,4 @@
 try:
     brain.animate(['l', 'd'])
 except ValueError as e:
-    print e
+    print(e)
diff --git a/examples/save_views.py b/examples/save_views.py
@@ -6,7 +6,7 @@
 Save some views in png files.
 
 """
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
diff --git a/examples/show_views.py b/examples/show_views.py
@@ -6,7 +6,7 @@
 Among the views available are lateral, rostral, caudal, frontal etc.
 
 """
-print __doc__
+print(__doc__)
 
 from surfer import Brain
 
diff --git a/surfer/utils.py b/surfer/utils.py
@@ -18,6 +18,13 @@
 logger = logging.getLogger('surfer')
 
 
+# Py3k compat
+if sys.version[0] == '2':
+    string_types = basestring  # noqa
+else:
+    string_types = str
+
+
 class Surface(object):
     """Container for surface object
 
@@ -226,12 +233,12 @@ def set_log_level(verbose=None, return_old_level=False):
             verbose = 'INFO'
         else:
             verbose = 'WARNING'
-    if isinstance(verbose, basestring):
+    if isinstance(verbose, string_types):
         verbose = verbose.upper()
         logging_types = dict(DEBUG=logging.DEBUG, INFO=logging.INFO,
                              WARNING=logging.WARNING, ERROR=logging.ERROR,
                              CRITICAL=logging.CRITICAL)
-        if not verbose in logging_types:
+        if verbose not in logging_types:
             raise ValueError('verbose must be of a valid type')
         verbose = logging_types[verbose]
     logger = logging.getLogger('surfer')
@@ -565,7 +572,7 @@ def coord_to_label(subject_id, coord, label, hemi='lh', n_steps=30,
     data = np.zeros(n_vertices)
     data[foci_vtxs] = 1.
     smooth_mat = smoothing_matrix(np.arange(n_vertices), adj_mat, 1)
-    for _ in xrange(n_steps):
+    for _ in range(n_steps):
         data = smooth_mat * data
     idx = np.where(data.ravel() > 0)[0]
     # Write label
diff --git a/surfer/viz.py b/surfer/viz.py
@@ -15,7 +15,8 @@
 
 from . import utils, io
 from .config import config
-from .utils import Surface, verbose, create_color_lut, _get_subjects_dir
+from .utils import (Surface, verbose, create_color_lut, _get_subjects_dir,
+                    string_types)
 
 
 import logging
@@ -73,8 +74,8 @@ def make_montage(filename, fnames, orientation='h', colorbar=None,
     # This line is only necessary to overcome a PIL bug, see:
     #     http://stackoverflow.com/questions/10854903/what-is-causing-
     #          dimension-dependent-attributeerror-in-pil-fromarray-function
-    fnames = [f if isinstance(f, basestring) else f.copy() for f in fnames]
-    if isinstance(fnames[0], basestring):
+    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)
     else:
         images = map(Image.fromarray, fnames)
@@ -197,7 +198,7 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen):
             orig_val = mlab.options.offscreen
             mlab.options.offscreen = True
             figures = [[mlab.figure(size=(h / n_row, w / n_col))
-                        for _ in xrange(n_col)] for __ in xrange(n_row)]
+                        for _ in range(n_col)] for __ in range(n_row)]
             mlab.options.offscreen = orig_val
             _v = None
         else:
@@ -235,7 +236,7 @@ def __init__(self, n_row, n_col, width, height, title, **traits):
         self.n_col = n_col
         self.width = width
         self.height = height
-        for fi in xrange(n_row * n_col):
+        for fi in range(n_row * n_col):
             name = 'mlab_view%03g' % fi
             self.mlab_names.append(name)
             self.add_trait(name, Instance(MlabSceneModel, ()))
@@ -259,9 +260,9 @@ def _get_gen_view(self):
         from traitsui.api import (View, Item, VGroup, HGroup)
         ind = 0
         va = []
-        for ri in xrange(self.n_row):
+        for ri in range(self.n_row):
             ha = []
-            for ci in xrange(self.n_col):
+            for ci in range(self.n_col):
                 ha += [Item(name=self.mlab_names[ind], style='custom',
                             resizable=True, show_label=False,
                             editor=SceneEditor(scene_class=MayaviScene))]
@@ -319,7 +320,7 @@ def __init__(self, subject_id, hemi, surf, curv=True, title=None,
                  views=['lat'], show_toolbar=False, offscreen=False):
         col_dict = dict(lh=1, rh=1, both=1, split=2)
         n_col = col_dict[hemi]
-        if not hemi in col_dict.keys():
+        if hemi not in col_dict.keys():
             raise ValueError('hemi must be one of [%s], not %s'
                              % (', '.join(col_dict.keys()), hemi))
         # Get the subjects directory from parameter or env. var
@@ -654,7 +655,7 @@ def _read_scalar_data(self, source, hemi, name=None, cast=True):
             as a source
         """
         # If source is a string, try to load a file
-        if isinstance(source, basestring):
+        if isinstance(source, string_types):
             if name is None:
                 basename = os.path.basename(source)
                 if basename.endswith(".gz"):
@@ -750,7 +751,7 @@ def add_overlay(self, source, min=None, max=None, sign="abs", name=None,
         # load data here
         scalar_data, name = self._read_scalar_data(source, hemi, name=name)
         min, max = self._get_display_range(scalar_data, min, max, sign)
-        if not sign in ["abs", "pos", "neg"]:
+        if sign not in ["abs", "pos", "neg"]:
             raise ValueError("Overlay sign must be 'abs', 'pos', or 'neg'")
         old = OverlayData(scalar_data, self.geo[hemi], min, max, sign)
         ol = []
@@ -1026,7 +1027,7 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
         -----
         To remove previously added labels, run Brain.remove_labels().
         """
-        if isinstance(label, basestring):
+        if isinstance(label, string_types):
             hemi = self._check_hemi(hemi)
             if color is None:
                 color = "crimson"
@@ -1665,7 +1666,7 @@ def close(self):
                     mlab.close(f)
                     self._figures[ri][ci] = None
 
-        #should we tear down other variables?
+        # should we tear down other variables?
         if self._v is not None:
             self._v.dispose()
             self._v = None
@@ -1703,7 +1704,7 @@ def save_single_image(self, filename, row=-1, col=-1):
         ftype = filename[filename.rfind('.') + 1:]
         good_ftypes = ['png', 'jpg', 'bmp', 'tiff', 'ps',
                        'eps', 'pdf', 'rib', 'oogl', 'iv', 'vrml', 'obj']
-        if not ftype in good_ftypes:
+        if ftype not in good_ftypes:
             raise ValueError("Supported image types are %s"
                              % " ".join(good_ftypes))
         mlab.draw(brain._f)
@@ -1832,7 +1833,7 @@ def save_imageset(self, prefix, views,  filetype='png', colorbar='auto',
         images_written: list
             all filenames written
         """
-        if isinstance(views, basestring):
+        if isinstance(views, string_types):
             raise ValueError("Views must be a non-string sequence"
                              "Use show_view & save_image for a single view")
         if colorbar == 'auto':
@@ -2044,7 +2045,7 @@ class _Hemisphere(object):
     """Object for visualizing one hemisphere with mlab"""
     def __init__(self, subject_id, hemi, surf, figure, geo, curv, title,
                  config_opts, subjects_dir, bg_color, offset, backend):
-        if not hemi in ['lh', 'rh']:
+        if hemi not in ['lh', 'rh']:
             raise ValueError('hemi must be either "lh" or "rh"')
         # Set the identifying info
         self.subject_id = subject_id
@@ -2084,7 +2085,7 @@ def __init__(self, subject_id, hemi, surf, figure, geo, curv, title,
 
     def show_view(self, view=None, roll=None, distance=None):
         """Orient camera to display view"""
-        if isinstance(view, basestring):
+        if isinstance(view, string_types):
             try:
                 vd = self._xfm_view(view, 'd')
                 view = dict(azimuth=vd['v'][0], elevation=vd['v'][1])
@@ -2099,7 +2100,7 @@ def show_view(self, view=None, roll=None, distance=None):
             view['figure'] = self._f
             view['distance'] = distance
             # DO NOT set focal point, can screw up non-centered brains
-            #view['focalpoint'] = (0.0, 0.0, 0.0)
+            # view['focalpoint'] = (0.0, 0.0, 0.0)
             mlab.view(**view)
         if roll is not None:
             mlab.roll(roll=roll, figure=self._f)
@@ -2126,7 +2127,7 @@ def _xfm_view(self, view, out='s'):
             's' to return string, 'd' to return dict
 
         """
-        if not view in self.viewdict:
+        if view not in self.viewdict:
             good_view = [k for k in self.viewdict if view == k[:len(view)]]
             if len(good_view) == 0:
                 raise ValueError('No views exist with this substring')
@@ -2496,7 +2497,7 @@ class TimeViewer(HasTraits):
     brain : Brain (or list of Brain)
         brain(s) to control
     """
-     # Nested import of traisui for setup.py without X server
+    # Nested import of traisui for setup.py without X server
     from traitsui.api import (View, Item, VSplit, HSplit, Group)
     min_time = Int(0)
     max_time = Int(1E9)
