MNT remove obsolete Python 2 syntax, add some types

cortex/__init__.py

@@ -30,7 +30,7 @@
     pass
 
 # Create deprecated interface for database
-class dep(object):
+class dep:
     def __getattr__(self, name):
         warnings.warn("cortex.surfs is deprecated, use cortex.db instead", Warning)
         return getattr(db, name)
@@ -41,8 +41,3 @@ def __dir__(self):
 surfs = dep()
 
 import sys
-if sys.version_info < (3,):
-    stdout = sys.stdout
-    reload(sys)
-    sys.setdefaultencoding('utf8')
-    sys.stdout = stdout

cortex/align.py

@@ -5,7 +5,6 @@
 import subprocess as sp
 import tempfile
 import warnings
-from builtins import input
 
 import numpy as np
 

cortex/appdirs.py

@@ -214,7 +214,7 @@ def user_log_dir(appname, appauthor=None, version=None, opinion=True):
     return path
 
 
-class AppDirs(object):
+class AppDirs:
     """Convenience wrapper for getting application dirs."""
     def __init__(self, appname, appauthor, version=None, roaming=False):
         self.appname = appname

cortex/brainctm.py

@@ -25,7 +25,7 @@
 from . import polyutils
 from .openctm import CTMfile
 
-class BrainCTM(object):
+class BrainCTM:
     def __init__(self, subject, decimate=False):
         self.subject = subject
         self.types = []
@@ -196,7 +196,7 @@ def save(self, path, method='mg2', external_svg=None,
                 fp.write(svg.toxml())
         return ptmap
 
-class Hemi(object):
+class Hemi:
     def __init__(self, pts, polys, norms=None):
         self.tf = tempfile.NamedTemporaryFile()
         self.tf.name = bytes(self.tf.name, 'ascii')
@@ -258,16 +258,16 @@ def __init__(self, pts, polys, fpolys, pia=None):
         idxmap[mask] = np.arange(mask.sum()).astype(np.uint32)
         #norms = polyutils.Surface(pts, polys).normals[mask]
         basepts = pts[mask] if pia is None else pia[mask]
-        super(DecimatedHemi, self).__init__(basepts, idxmap[allpolys])
+        super().__init__(basepts, idxmap[allpolys])
         self.aux[idxmap[mwidx], 0] = 1
         self.mask = mask
         self.idxmap = idxmap
 
     def setFlat(self, pts):
-        super(DecimatedHemi, self).setFlat(pts[self.mask])
+        super().setFlat(pts[self.mask])
 
     def addSurf(self, pts, **kwargs):
-        super(DecimatedHemi, self).addSurf(pts[self.mask], **kwargs)
+        super().addSurf(pts[self.mask], **kwargs)
 
 def make_pack(outfile, subj, types=("inflated",), method='raw', level=0,
               decimate=False, disp_layers=['rois'], 

cortex/database.py

@@ -10,7 +10,6 @@
 import shutil
 import tempfile
 import warnings
-from builtins import input
 from hashlib import sha1
 
 import numpy as np
@@ -33,7 +32,7 @@ def memofn(self, *args, **kwargs):
 
     return memofn
 
-class SubjectDB(object):
+class SubjectDB:
     def __init__(self, subj, filestore=default_filestore):
         self.subject = subj
         self._warning = None
@@ -61,7 +60,7 @@ def surfaces(self):
         self._surfaces = SurfaceDB(self.subject, filestore=self.filestore)
         return self._surfaces
 
-class SurfaceDB(object):
+class SurfaceDB:
     def __init__(self, subj, filestore=default_filestore):
         self.subject = subj
         self.types = {}
@@ -80,7 +79,7 @@ def __getattr__(self, attr):
             return self.types[attr]
         raise AttributeError(attr)
 
-class Surf(object):
+class Surf:
     def __init__(self, subject, surftype, filestore=default_filestore):
         self.subject, self.surftype = subject, surftype
         self.db = Database(filestore)
@@ -93,7 +92,7 @@ def show(self, hemisphere="both"):
         pts, polys = self.db.get_surf(self.subject, self.surftype, hemisphere, merge=True, nudge=True)
         return mlab.triangular_mesh(pts[:,0], pts[:,1], pts[:,2], polys)
 
-class XfmDB(object):
+class XfmDB:
     def __init__(self, subj, filestore=default_filestore):
         self.subject = subj
         self.filestore = filestore
@@ -108,7 +107,7 @@ def __repr__(self):
         xfms = "\n".join(sorted(self.xfms))
         return f"Available transforms for {self.subject}:\n{xfms}"
 
-class XfmSet(object):
+class XfmSet:
     def __init__(self, subj, name, filestore=default_filestore):
         self.subject = subj
         self.name = name
@@ -126,13 +125,13 @@ def __getattr__(self, attr):
     def __repr__(self):
         return "Types: {types}".format(types=", ".join(self._jsdat.keys()))
 
-class MaskSet(object):
+class MaskSet:
     def __init__(self, subj, name, filestore=default_filestore):
         self.subject = subj
         self.xfmname = name
         maskform = Database(filestore).get_paths(subj)['masks']
         maskpath = maskform.format(xfmname=name, type='*')
-        self._masks = dict((os.path.split(path)[1][5:-7], path) for path in glob.glob(maskpath))
+        self._masks = {os.path.split(path)[1][5:-7]: path for path in glob.glob(maskpath)}
 
     def __getitem__(self, item):
         import nibabel
@@ -141,7 +140,7 @@ def __getitem__(self, item):
     def __repr__(self):
         return "Masks: [{types}]".format(types=', '.join(self._masks.keys()))
 
-class Database(object):
+class Database:
     """
     Database()
 
@@ -180,7 +179,7 @@ def subjects(self):
         subjs = os.listdir(os.path.join(self.filestore))
         subjs = [s for s in subjs if os.path.isdir(os.path.join(self.filestore, s))]
         subjs = sorted(subjs)
-        self._subjects = dict([(sname, SubjectDB(sname, filestore=self.filestore)) for sname in subjs])
+        self._subjects = {sname: SubjectDB(sname, filestore=self.filestore) for sname in subjs}
         return self._subjects
 
     def reload_subjects(self):

cortex/dataset/braindata.py

@@ -15,7 +15,7 @@
 from ..database import db
 
 
-class BrainData(object):
+class BrainData:
     """
     Abstract base class for brain data.
 
@@ -38,7 +38,7 @@ def __init__(self, data: Union[npt.NDArray, str], subject: str, **kwargs):
         except NameError:
             subject = subject if isinstance(subject, str) else subject.decode('utf-8')
         self.subject = subject
-        super(BrainData, self).__init__(**kwargs)
+        super().__init__(**kwargs)
 
     @property
     def data(self):
@@ -86,7 +86,7 @@ def _write_hdf(self, h5, name=None):
     def to_json(self, simple=False):
         """Creates JSON description of this brain data.
         """
-        sdict = super(BrainData, self).to_json(simple=simple)
+        sdict = super().to_json(simple=simple)
         if simple:
             sdict.update(dict(name=self.name,
                 subject=self.subject,
@@ -144,11 +144,8 @@ class VolumeData(BrainData):
     def __init__(self, data: npt.NDArray, subject: str, xfmname: str, mask: Optional[npt.NDArray]=None, **kwargs):
         if self.__class__ == VolumeData:
             raise TypeError('Cannot directly instantiate VolumeData objects')
-        super(VolumeData, self).__init__(data, subject, **kwargs)
-        try:
-            basestring
-        except NameError:
-            xfmname = xfmname if isinstance(xfmname, str) else xfmname.decode('utf-8')
+        super().__init__(data, subject, **kwargs)
+        xfmname = xfmname if isinstance(xfmname, str) else xfmname.decode('utf-8')
         self.xfmname = xfmname
 
         self._check_size(mask)
@@ -158,13 +155,13 @@ def to_json(self, simple: bool=False):
         """Creates JSON description of this brain data.
         """
         if simple:
-            sdict = super(VolumeData, self).to_json(simple=simple)
+            sdict = super().to_json(simple=simple)
             sdict["shape"] = self.shape
             return sdict
 
         xfm = db.get_xfm(self.subject, self.xfmname, 'coord').xfm
         sdict = dict(xfm=[list(np.array(xfm).ravel())], data=[self.name])
-        sdict.update(super(VolumeData, self).to_json())
+        sdict.update(super().to_json())
         return sdict
 
     @classmethod
@@ -288,7 +285,7 @@ def __repr__(self):
         return "<%s data for (%s, %s)>"%(maskstr, self.subject, self.xfmname)
 
     def copy(self, data):
-        return super(VolumeData, self).copy(data, self.subject, self.xfmname, mask=self._mask)
+        return super().copy(data, self.subject, self.xfmname, mask=self._mask)
 
     @property
     def volume(self):
@@ -321,8 +318,8 @@ def save(self, filename, name=None):
         elif isinstance(filename, h5py.Group):
             self._write_hdf(filename, name=name)
 
-    def _write_hdf(self, h5, name=None):
-        node = super(VolumeData, self)._write_hdf(h5, name=name)
+    def _write_hdf(self, h5: Union[h5py.File, h5py.Group], name: Optional[str]=None) -> h5py.Dataset:
+        node = super()._write_hdf(h5, name=name)
 
         #write the mask into the file, as necessary
         if self._mask is not None:
@@ -367,7 +364,7 @@ class VertexData(BrainData):
     def __init__(self, data: npt.NDArray, subject: str, **kwargs):
         if self.__class__ == VertexData:
             raise TypeError('Cannot directly instantiate VertexData objects')
-        super(VertexData, self).__init__(data, subject, **kwargs)
+        super().__init__(data, subject, **kwargs)
         try:
             left, right = db.get_surf(self.subject, "wm")
         except IOError:
@@ -469,7 +466,7 @@ def copy(self, data: npt.NDArray) -> Self:
         it doesn't require reloading the surfaces from the database to check 
         numbers of vertices, etc.
         """
-        return super(VertexData, self).copy(data, self.subject)
+        return super().copy(data, self.subject)
 
     def volume(self, xfmname, projection='nearest', **kwargs):
         """
@@ -518,11 +515,11 @@ def __getitem__(self, idx):
     def to_json(self, simple: bool = False):
         if simple:
             sdict = dict(split=self.llen, frames=self.vertices.shape[0])
-            sdict.update(super(VertexData, self).to_json(simple=simple))
+            sdict.update(super().to_json(simple=simple))
             return sdict
 
         sdict = dict(data=[self.name])
-        sdict.update(super(VertexData, self).to_json())
+        sdict.update(super().to_json())
         return sdict
 
     @property

cortex/dataset/dataset.py

@@ -10,7 +10,7 @@
 from .views import normalize as _vnorm
 from .views import Dataview, Vertex, Volume, _from_hdf_data
 
-class Dataset(object):
+class Dataset:
     """
     Wrapper for multiple data objects. This often does not need to be used 
     explicitly--for example, if a dictionary of data objects is passed to 

cortex/dataset/view2D.py

@@ -171,14 +171,14 @@ def __init__(self, dim1: Union[npt.NDArray, Volume], dim2: Union[npt.NDArray, Vo
         vmax = self.dim1.vmax if vmax is None else vmax
         vmax2 = self.dim2.vmax if vmax2 is None else vmax2
 
-        super(Volume2D, self).__init__(description=description, cmap=cmap, vmin=vmin,
+        super().__init__(description=description, cmap=cmap, vmin=vmin,
                                        vmax=vmax, vmin2=vmin2, vmax2=vmax2, **kwargs)
 
     def __repr__(self):
         return "<2D volumetric data for (%s, %s)>"%(self.dim1.subject, self.dim1.xfmname)
 
     def _write_hdf(self, h5, name="data"):
-        viewnode = super(Volume2D, self)._write_hdf(h5, name)
+        viewnode = super()._write_hdf(h5, name)
         viewnode[7] = json.dumps([[self.dim1.xfmname, self.dim2.xfmname]])
         return viewnode
 
@@ -267,7 +267,7 @@ def __init__(self, dim1: Union[npt.NDArray, Vertex], dim2: Union[npt.NDArray, Ve
         vmax = self.dim1.vmax if vmax is None else vmax
         vmax2 = self.dim2.vmax if vmax2 is None else vmax2
 
-        super(Vertex2D, self).__init__(description=description, cmap=cmap,
+        super().__init__(description=description, cmap=cmap,
                                        vmin=vmin, vmax=vmax, vmin2=vmin2,
                                        vmax2=vmax2, **kwargs)
 

cortex/dataset/viewRGB.py

@@ -143,7 +143,7 @@ def _write_hdf(self, h5, name="data", xfmname=None):
         return viewnode
 
     def to_json(self, simple=False):
-        sdict = super(DataviewRGB, self).to_json(simple=simple)
+        sdict = super().to_json(simple=simple)
 
         if simple:
             sdict["name"] = self.name
@@ -558,7 +558,7 @@ def __init__(
         else:
             raise ValueError("Cannot handle different transforms per volume")
 
-        super(VolumeRGB, self).__init__(
+        super().__init__(
             subject, alpha, description=description, state=state, priority=priority
         )
 
@@ -591,7 +591,7 @@ def alpha(self, alpha: Optional[Union[npt.NDArray, Volume]]):
         self._alpha = alpha
 
     def to_json(self, simple=False):
-        sdict = super(VolumeRGB, self).to_json(simple=simple)
+        sdict = super().to_json(simple=simple)
         if simple:
             sdict["shape"] = self.red.shape
         else:
@@ -647,7 +647,7 @@ def name(self):
         return "__%s" % _hash(self.volume)[:16]
 
     def _write_hdf(self, h5, name="data"):
-        return super(VolumeRGB, self)._write_hdf(h5, name=name, xfmname=[self.xfmname])
+        return super()._write_hdf(h5, name=name, xfmname=[self.xfmname])
 
     @property
     def raw(self):
@@ -834,7 +834,7 @@ def __init__(
                 self.blue = Vertex(b, subject)
                 self.alpha = alpha
 
-        super(VertexRGB, self).__init__(
+        super().__init__(
             subject, alpha, description=description, state=state, priority=priority
         )
 
@@ -894,7 +894,7 @@ def vertices(self):
         return np.array(verts).transpose([1, 2, 0])
 
     def to_json(self, simple=False):
-        sdict = super(VertexRGB, self).to_json(simple=simple)
+        sdict = super().to_json(simple=simple)
 
         if simple:
             sdict.update(dict(split=self.red.llen, frames=self.vertices.shape[0]))