Move Surface to utils

Surface was not imported in utils, which was breaking coord_to_label.
I could not perform a relative import of io from utils (I do not understand
that bug, but there were some other reports of similar issues with package
modules named io on Google).

Anyway, tests pass and docs build with the reorganization.

Author: mwaskom

surfer/__init__.py

@@ -1,6 +1,5 @@
-from io import Surface
 from viz import Brain, TimeViewer
-from utils import verbose, set_log_level, set_log_file
+from utils import Surface, verbose, set_log_level, set_log_file
 
 __version__ = "0.5.dev"
 

surfer/io.py

@@ -1,5 +1,4 @@
 import os
-from os.path import join as pjoin
 from tempfile import mktemp
 
 from subprocess import Popen, PIPE
@@ -11,9 +10,6 @@
 import logging
 logger = logging.getLogger('surfer')
 
-from .config import config
-from .utils import _get_subjects_dir
-
 
 def read_scalar_data(filepath):
     """Load in scalar data from an image.
@@ -243,115 +239,3 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
     surf_data = read_scalar_data(out_file)
     os.remove(out_file)
     return surf_data
-
-
-class Surface(object):
-    """Container for surface object
-
-    Attributes
-    ----------
-    subject_id : string
-        Name of subject
-    hemi : {'lh', 'rh'}
-        Which hemisphere to load
-    surf : string
-        Name of the surface to load (eg. inflated, orig ...)
-    data_path : string
-        Path where to look for data
-    x: 1d array
-        x coordinates of vertices
-    y: 1d array
-        y coordinates of vertices
-    z: 1d array
-        z coordinates of vertices
-    coords : 2d array of shape [n_vertices, 3]
-        The vertices coordinates
-    faces : 2d array
-        The faces ie. the triangles
-    subjects_dir : str | None
-        If not None, this directory will be used as the subjects directory
-        instead of the value set using the SUBJECTS_DIR environment variable.
-    """
-
-    def __init__(self, subject_id, hemi, surf, subjects_dir=None,
-                 offset=None):
-        """Surface
-
-        Parameters
-        ----------
-        subject_id : string
-            Name of subject
-        hemi : {'lh', 'rh'}
-            Which hemisphere to load
-        surf : string
-            Name of the surface to load (eg. inflated, orig ...)
-        offset : float | None
-            If 0.0, the surface will be offset such that the medial
-            wall is aligned with the origin. If None, no offset will
-            be applied. If != 0.0, an additional offset will be used.
-        """
-        if hemi not in ['lh', 'rh']:
-            raise ValueError('hemi must be "lh" or "rh')
-        self.subject_id = subject_id
-        self.hemi = hemi
-        self.surf = surf
-        self.offset = offset
-
-        subjects_dir = _get_subjects_dir(subjects_dir)
-        self.data_path = pjoin(subjects_dir, subject_id)
-
-    def load_geometry(self):
-        surf_path = pjoin(self.data_path, "surf",
-                          "%s.%s" % (self.hemi, self.surf))
-        self.coords, self.faces = nib.freesurfer.read_geometry(surf_path)
-        if self.offset is not None:
-            if self.hemi == 'lh':
-                self.coords[:, 0] -= (np.max(self.coords[:, 0]) + self.offset)
-            else:
-                self.coords[:, 0] -= (np.min(self.coords[:, 0]) + self.offset)
-
-    def save_geometry(self):
-        surf_path = pjoin(self.data_path, "surf",
-                          "%s.%s" % (self.hemi, self.surf))
-        nib.freesurfer.write_geometry(surf_path, self.coords, self.faces)
-
-    @property
-    def x(self):
-        return self.coords[:, 0]
-
-    @property
-    def y(self):
-        return self.coords[:, 1]
-
-    @property
-    def z(self):
-        return self.coords[:, 2]
-
-    def load_curvature(self):
-        """Load in curvature values from the ?h.curv file."""
-        curv_path = pjoin(self.data_path, "surf", "%s.curv" % self.hemi)
-        self.curv = nib.freesurfer.read_morph_data(curv_path)
-        self.bin_curv = np.array(self.curv > 0, np.int)
-
-    def load_label(self, name):
-        """Load in a Freesurfer .label file.
-
-        Label files are just text files indicating the vertices included
-        in the label. Each Surface instance has a dictionary of labels, keyed
-        by the name (which is taken from the file name if not given as an
-        argument.
-
-        """
-        label = nib.freesurfer.read_label(pjoin(self.data_path, 'label',
-                                          '%s.%s.label' % (self.hemi, name)))
-        label_array = np.zeros(len(self.x), np.int)
-        label_array[label] = 1
-        try:
-            self.labels[name] = label_array
-        except AttributeError:
-            self.labels = {name: label_array}
-
-    def apply_xfm(self, mtx):
-        """Apply an affine transformation matrix to the x,y,z vectors."""
-        self.coords = np.dot(np.c_[self.coords, np.ones(len(self.coords))],
-                                     mtx.T)[:, :3]

surfer/tests/test_io.py renamed to surfer/tests/test_utils.py

@@ -3,19 +3,18 @@
 import numpy as np
 from numpy.testing import assert_array_almost_equal
 
-from surfer import io
-from surfer.utils import requires_fsaverage
+from surfer import utils
 
-subj_dir = io._get_subjects_dir()
+subj_dir = utils._get_subjects_dir()
 subject_id = 'fsaverage'
 data_path = pjoin(subj_dir, subject_id)
 
 
-@requires_fsaverage
+@utils.requires_fsaverage
 def test_surface():
     """Test IO for Surface class"""
     for subjects_dir in [None, subj_dir]:
-        surface = io.Surface('fsaverage', 'lh', 'inflated',
+        surface = utils.Surface('fsaverage', 'lh', 'inflated',
                              subjects_dir=subjects_dir)
         surface.load_geometry()
         surface.load_label('BA1')

surfer/tests/test_viz.py

@@ -6,11 +6,11 @@
 import nibabel as nib
 
 from surfer import Brain
-from surfer import io
+from surfer import io, utils
 from surfer.utils import requires_fsaverage
 from mayavi import mlab
 
-subj_dir = io._get_subjects_dir()
+subj_dir = utils._get_subjects_dir()
 subject_id = 'fsaverage'
 std_args = [subject_id, 'lh', 'inflated']
 data_dir = pjoin(os.path.split(__file__)[0], '..', '..',

surfer/utils.py

@@ -7,13 +7,127 @@
 from functools import wraps
 
 import numpy as np
+import nibabel as nib
 from scipy import sparse
 from scipy.spatial.distance import cdist
+
 from .config import config
 
 logger = logging.getLogger('surfer')
 
 
+class Surface(object):
+    """Container for surface object
+
+    Attributes
+    ----------
+    subject_id : string
+        Name of subject
+    hemi : {'lh', 'rh'}
+        Which hemisphere to load
+    surf : string
+        Name of the surface to load (eg. inflated, orig ...)
+    data_path : string
+        Path where to look for data
+    x: 1d array
+        x coordinates of vertices
+    y: 1d array
+        y coordinates of vertices
+    z: 1d array
+        z coordinates of vertices
+    coords : 2d array of shape [n_vertices, 3]
+        The vertices coordinates
+    faces : 2d array
+        The faces ie. the triangles
+    subjects_dir : str | None
+        If not None, this directory will be used as the subjects directory
+        instead of the value set using the SUBJECTS_DIR environment variable.
+    """
+
+    def __init__(self, subject_id, hemi, surf, subjects_dir=None,
+                 offset=None):
+        """Surface
+
+        Parameters
+        ----------
+        subject_id : string
+            Name of subject
+        hemi : {'lh', 'rh'}
+            Which hemisphere to load
+        surf : string
+            Name of the surface to load (eg. inflated, orig ...)
+        offset : float | None
+            If 0.0, the surface will be offset such that the medial
+            wall is aligned with the origin. If None, no offset will
+            be applied. If != 0.0, an additional offset will be used.
+        """
+        if hemi not in ['lh', 'rh']:
+            raise ValueError('hemi must be "lh" or "rh')
+        self.subject_id = subject_id
+        self.hemi = hemi
+        self.surf = surf
+        self.offset = offset
+
+        subjects_dir = _get_subjects_dir(subjects_dir)
+        self.data_path = op.join(subjects_dir, subject_id)
+
+    def load_geometry(self):
+        surf_path = op.join(self.data_path, "surf",
+                          "%s.%s" % (self.hemi, self.surf))
+        self.coords, self.faces = nib.freesurfer.read_geometry(surf_path)
+        if self.offset is not None:
+            if self.hemi == 'lh':
+                self.coords[:, 0] -= (np.max(self.coords[:, 0]) + self.offset)
+            else:
+                self.coords[:, 0] -= (np.min(self.coords[:, 0]) + self.offset)
+
+    def save_geometry(self):
+        surf_path = op.join(self.data_path, "surf",
+                          "%s.%s" % (self.hemi, self.surf))
+        nib.freesurfer.write_geometry(surf_path, self.coords, self.faces)
+
+    @property
+    def x(self):
+        return self.coords[:, 0]
+
+    @property
+    def y(self):
+        return self.coords[:, 1]
+
+    @property
+    def z(self):
+        return self.coords[:, 2]
+
+    def load_curvature(self):
+        """Load in curvature values from the ?h.curv file."""
+        curv_path = op.join(self.data_path, "surf", "%s.curv" % self.hemi)
+        self.curv = nib.freesurfer.read_morph_data(curv_path)
+        self.bin_curv = np.array(self.curv > 0, np.int)
+
+    def load_label(self, name):
+        """Load in a Freesurfer .label file.
+
+        Label files are just text files indicating the vertices included
+        in the label. Each Surface instance has a dictionary of labels, keyed
+        by the name (which is taken from the file name if not given as an
+        argument.
+
+        """
+        label = nib.freesurfer.read_label(op.join(self.data_path, 'label',
+                                          '%s.%s.label' % (self.hemi, name)))
+        label_array = np.zeros(len(self.x), np.int)
+        label_array[label] = 1
+        try:
+            self.labels[name] = label_array
+        except AttributeError:
+            self.labels = {name: label_array}
+
+    def apply_xfm(self, mtx):
+        """Apply an affine transformation matrix to the x,y,z vectors."""
+        self.coords = np.dot(np.c_[self.coords, np.ones(len(self.coords))],
+                                     mtx.T)[:, :3]
+
+
 ###############################################################################
 # LOGGING (courtesy of mne-python)
 

surfer/viz.py

@@ -13,11 +13,10 @@
 from mayavi.core.ui.api import SceneEditor
 from mayavi.core.ui.mayavi_scene import MayaviScene
 
-from . import io
-from . import utils
-from .io import Surface, _get_subjects_dir
+from . import utils, io
 from .config import config
-from .utils import verbose
+from .utils import Surface, verbose, _get_subjects_dir
+
 
 import logging
 logging.basicConfig()  # suppress "No handlers found for logger" error
@@ -1233,8 +1232,8 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
         if map_surface is None:
             foci_coords = np.atleast_2d(coords)
         else:
-            foci_surf = io.Surface(self.subject_id, hemi, map_surface,
-                                   subjects_dir=self.subjects_dir)
+            foci_surf = Surface(self.subject_id, hemi, map_surface,
+                                subjects_dir=self.subjects_dir)
             foci_surf.load_geometry()
             foci_vtxs = utils.find_closest_vertices(foci_surf.coords, coords)
             foci_coords = self.geo[hemi].coords[foci_vtxs]