more import defers, maybe fix python3 errors?

cortex/anat.py

@@ -5,7 +5,6 @@
 import subprocess as sp
 
 import numpy as np
-import nibabel
 
 #from . import utils
 from .database import db
@@ -28,6 +27,7 @@ def whitematter(outfile, subject, do_voxelize=False):
         else:
             voxelize(outfile, subject, surf="wm")
     except IOError:
+        import nibabel
         bet = db.get_anat(subject, type='brainmask').get_filename()
         try:
             cache = tempfile.mkdtemp()
@@ -56,6 +56,7 @@ def whitematter(outfile, subject, do_voxelize=False):
 
 def voxelize(outfile, subject, surf='wm', mp=True):
     '''Voxelize the whitematter surface to generate the white matter mask'''
+    import nibabel
     from . import polyutils
     nib = db.get_anat(subject, "raw")
     shape = nib.get_shape()

cortex/dataset/views.py

@@ -125,7 +125,7 @@ def to_json(self, simple=False):
         sdict = dict(
             state=self.state, 
             attrs=self.attrs.copy(), 
-            desc=self.description)
+            desc=self.description.decode())
         try:
             sdict.update(dict(
                 cmap=[self.cmap], 

cortex/openctm.pyx

@@ -28,7 +28,7 @@ attrmaps = [
 cdef class CTMfile:
     cdef CTMcontext ctx
 
-    cdef public bytes filename
+    cdef public object filename
     cdef public str mode
 
     cdef unsigned int length
@@ -38,7 +38,7 @@ cdef class CTMfile:
     cdef public dict attribs
     cdef public dict uvs
 
-    def __cinit__(self, bytes filename, str mode='r'):
+    def __cinit__(self, object filename, str mode='r'):
         cdef openctm.CTMenum err
         cdef char* name
         self.filename = filename
@@ -145,7 +145,7 @@ cdef class CTMfile:
 
         return pts, polys, norms
 
-    def save(self, str method='mg2', int level=9):
+    def save(self, method='mg2', int level=9):
         cdef char* cname = NULL
         cdef float* cnorms = NULL
         cdef openctm.CTMenum err

cortex/quickflat/composite.py

@@ -3,7 +3,6 @@
 from .. import dataset
 from ..database import db
 from ..options import config
-from ..svgoverlay import get_overlay
 from .utils import _get_height, _get_extents, _convert_svg_kwargs, _has_cmap, _get_images, _parse_defaults
 from .utils import make_flatmap_image, _make_hatch_image
 
@@ -194,6 +193,7 @@ def add_rois(fig, dataview, extents=None, height=None, with_labels=True, roi_lis
     img : matplotlib.image.AxesImage
         matplotlib axes image object for plotted data
     """
+    from ..svgoverlay import get_overlay
     if extents is None:
         extents = _get_extents(fig)
     if height is None:
@@ -240,6 +240,7 @@ def add_sulci(fig, dataview, extents=None, height=1024, with_labels=True, **kwar
     img : matplotlib.image.AxesImage
         matplotlib axes image object for plotted data
     """
+    from ..svgoverlay import get_overlay
     svgobject = db.get_overlay(dataview.subject)
     svg_kws = _convert_svg_kwargs(kwargs)
     layer_kws = _parse_defaults('sulci_paths')
@@ -292,6 +293,7 @@ def add_hatch(fig, hatch_data, extents=None, height=None, hatch_space=4, hatch_c
     -----
     Possibly to add: add hatch_width, hatch_offset arguments.
     """
+    from ..svgoverlay import get_overlay
     if extents is None:
         extents = _get_extents(fig)
     if height is None:
@@ -370,6 +372,7 @@ def add_custom(fig, dataview, svgfile, layer, extents=None, height=None, with_la
         matplotlib axes image object for plotted data
 
     """
+    from ..svgoverlay import get_overlay
     if height is None:
         height = _get_height(fig)
     if extents is None:
@@ -417,6 +420,7 @@ def add_cutout(fig, name, dataview, layers=None, height=None, extents=None):
     -------
 
     """
+    from ..svgoverlay import get_overlay
     if layers is None:
         layers = _get_images(fig)
     if height is None:

cortex/quickflat/utils.py

@@ -11,7 +11,6 @@
 from .. import dataset
 from ..database import db
 from ..options import config
-from ..svgoverlay import get_overlay
 
 
 def make_flatmap_image(braindata, height=1024, recache=False, **kwargs):

cortex/utils.py

@@ -11,7 +11,6 @@
 from .database import db
 from .volume import anat2epispace
 from .options import config
-from .freesurfer import fs_aseg_dict
 
 class DocLoader(object):
     def __init__(self, func, mod, package):
@@ -416,6 +415,7 @@ def get_aseg_mask(subject, aseg_name, xfmname=None, order=1, threshold=None, **k
     See also get_anat(subject, type='aseg')
 
     """
+    from .freesurfer import fs_aseg_dict
     aseg = db.get_anat(subject, type="aseg").get_data().T
 
     if not isinstance(aseg_name, (list, tuple)):