@@ -10,31 +10,26 @@
 # Qianqian Fang <q.fang at neu.edu>
 ##############
 
-__all__ = ['JMesh','read','write','default_header']
+__all__ = ['JMesh', 'read', 'write', 'default_header']
 
-from jdata import (load as jdload, save as jdsave)
+from jdata import load as jdload, save as jdsave
 import numpy as np
 from ..filebasedimages import FileBasedImage
 
 default_header = {
-"JMeshVersion":"0.5",
-"Comment":"Created by NiPy with NeuroJSON JMesh specification",
-"AnnotationFormat":"https://neurojson.org/jmesh/draft2",
-"Parser":{
-"Python":[
-"https://pypi.org/project/jdata",
-"https://pypi.org/project/bjdata"
-],
-"MATLAB":[
-"https://.com/NeuroJSON/jnifty",
-"https://.com/NeuroJSON/jsonlab"
-],
-"JavaScript":"https://.com/NeuroJSON/jsdata",
-"CPP":"https://.com/NeuroJSON/json",
-"C":"https://.com/NeuroJSON/ubj"
-}
+'JMeshVersion': '0.5',
+'Comment': 'Created by NiPy with NeuroJSON JMesh specification',
+'AnnotationFormat': 'https://neurojson.org/jmesh/draft2',
+'Parser': {
+'Python': ['https://pypi.org/project/jdata', 'https://pypi.org/project/bjdata'],
+'MATLAB': ['https://.com/NeuroJSON/jnifty', 'https://.com/NeuroJSON/jsonlab'],
+'JavaScript': 'https://.com/NeuroJSON/jsdata',
+'CPP': 'https://.com/NeuroJSON/json',
+'C': 'https://.com/NeuroJSON/ubj',
+},
 }
 
+
 class JMesh(FileBasedImage):
 """JMesh: a simple data structure representing a brain surface
 
@@ -62,28 +57,28 @@ class JMesh(FileBasedImage):
 raw : a dict
 The raw data loaded from the .jmsh or .bmsh file
 """
+
 valid_exts = ('.jmsh', '.bmsh')
 files_types = (('image', '.jmsh'), ('image', '.bmsh'))
 makeable = False
 rw = True
 
-def __init__(self, info=None, node=None, nodelabel=None, face=None,
-facelabel=None):
+def __init__(self, info=None, node=None, nodelabel=None, face=None, facelabel=None):
 
 self.raw = {}
-if(not info is None):
+if not info is None:
 self.raw['_DataInfo_'] = info
 
-if(not nodelabel is None):
-self.raw['MeshVertex3'] = {'Data': node, 'Properties': {'Tag': nodelabel} }
+if not nodelabel is None:
+self.raw['MeshVertex3'] = {'Data': node, 'Properties': {'Tag': nodelabel}}
 self.node = self.raw['MeshVertex3']['Data']
 self.nodelabel = self.raw['MeshVertex3']['Properties']['Tag']
 else:
 self.raw['MeshVertex3'] = node
 self.node = self.raw['MeshVertex3']
 
-if(not facelabel is None):
-self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel} }
+if not facelabel is None:
+self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel}}
 self.face = self.raw['MeshTri3']['Data']
 self.facelabel = self.raw['MeshTri3']['Properties']['Tag']
 else:
@@ -99,8 +94,9 @@ def from_filename(self, filename, opt={}, **kwargs):
 def to_filename(self, filename, opt={}, **kwargs):
 write(self, filename, opt, **kwargs)
 
+
 def read(filename, opt={}, **kwargs):
-""" Load a JSON or binary JData (BJData) based JMesh file
+"""Load a JSON or binary JData (BJData) based JMesh file
 
 Parameters
 ----------
@@ -116,73 +112,90 @@ def read(filename, opt={}, **kwargs):
 mesh : a JMesh object
 Return a JMesh object containing mesh data fields such as node, face, nodelabel etc
 """
-opt.setdefault('ndarray',True)
+opt.setdefault('ndarray', True)
 
 mesh = JMesh
 mesh.raw = jdload(filename, opt, **kwargs)
 
-#--------------------------------------------------
+# --------------------------------------------------
 # read metadata as `info`
-#--------------------------------------------------
-if('_DataInfo_' in mesh.raw):
+# --------------------------------------------------
+if '_DataInfo_' in mesh.raw:
 mesh.info = mesh.raw['_DataInfo_']
 
-#--------------------------------------------------
+# --------------------------------------------------
 # read vertices as `node` and `nodelabel`
-#--------------------------------------------------
-if('MeshVertex3' in mesh.raw):
+# --------------------------------------------------
+if 'MeshVertex3' in mesh.raw:
 mesh.node = mesh.raw['MeshVertex3']
-elif('MeshNode' in mesh.raw):
+elif 'MeshNode' in mesh.raw:
 mesh.node = mesh.raw['MeshNode']
 else:
 raise Exception('JMesh', 'JMesh surface must contain node (MeshVertex3 or MeshNode)')
 
-if(isinstance(mesh.node, dict)):
-if(('Properties' in mesh.node) and ('Tag' in mesh.node['Properties'])):
+if isinstance(mesh.node, dict):
+if ('Properties' in mesh.node) and ('Tag' in mesh.node['Properties']):
 mesh.nodelabel = mesh.node['Properties']['Tag']
-if('Data' in mesh.node):
+if 'Data' in mesh.node:
 mesh.node = mesh.node['Data']
-if(isinstance(mesh.node, np.ndarray) and mesh.node.ndim == 2 and mesh.node.shape[1] > 3):
-mesh.nodelabel = mesh.node[:,3:]
+if isinstance(mesh.node, np.ndarray) and mesh.node.ndim == 2 and mesh.node.shape[1] > 3:
+mesh.nodelabel = mesh.node[:, 3:]
 mesh.node = mesh.node[:, 0:3]
 
-#--------------------------------------------------
+# --------------------------------------------------
 # read triangles as `face` and `facelabel`
-#--------------------------------------------------
-if('MeshTri3' in mesh.raw):
+# --------------------------------------------------
+if 'MeshTri3' in mesh.raw:
 mesh.face = mesh.raw['MeshTri3']
-elif('MeshSurf' in mesh.raw):
+elif 'MeshSurf' in mesh.raw:
 mesh.face = mesh.raw['MeshSurf']
 
-if(isinstance(mesh.face, dict)):
-if(('Properties' in mesh.face) and ('Tag' in mesh.face['Properties'])):
+if isinstance(mesh.face, dict):
+if ('Properties' in mesh.face) and ('Tag' in mesh.face['Properties']):
 mesh.facelabel = mesh.face['Properties']['Tag']
-if('Data' in mesh.face):
+if 'Data' in mesh.face:
 mesh.face = mesh.face['Data']
-if(isinstance(mesh.face, np.ndarray) and mesh.face.ndim == 2 and mesh.face.shape[1] > 3):
-mesh.facelabel = mesh.face[:,3:]
+if isinstance(mesh.face, np.ndarray) and mesh.face.ndim == 2 and mesh.face.shape[1] > 3:
+mesh.facelabel = mesh.face[:, 3:]
 mesh.face = mesh.face[:, 0:3]
 
-#--------------------------------------------------
+# --------------------------------------------------
 # convert to numpy ndarray
-#--------------------------------------------------
-if(opt['ndarray']):
-if hasattr(mesh, 'node') and (not mesh.node is None) and (not isinstance(mesh.node, np.ndarray)):
+# --------------------------------------------------
+if opt['ndarray']:
+if (
+hasattr(mesh, 'node')
+and (not mesh.node is None)
+and (not isinstance(mesh.node, np.ndarray))
+):
 mesh.node = np.array(mesh.node)
 
-if hasattr(mesh, 'face') and (not mesh.face is None) and (not isinstance(mesh.face, np.ndarray)):
+if (
+hasattr(mesh, 'face')
+and (not mesh.face is None)
+and (not isinstance(mesh.face, np.ndarray))
+):
 mesh.face = np.array(mesh.face)
 
-if hasattr(mesh, 'nodelabel') and (not mesh.nodelabel is None) and (not isinstance(mesh.nodelabel, np.ndarray)):
+if (
+hasattr(mesh, 'nodelabel')
+and (not mesh.nodelabel is None)
+and (not isinstance(mesh.nodelabel, np.ndarray))
+):
 mesh.nodelabel = np.array(mesh.nodelabel)
 
-if hasattr(mesh, 'facelabel') and (not mesh.facelabel is None) and (not isinstance(mesh.facelabel, np.ndarray)):
+if (
+hasattr(mesh, 'facelabel')
+and (not mesh.facelabel is None)
+and (not isinstance(mesh.facelabel, np.ndarray))
+):
 mesh.facelabel = np.array(mesh.facelabel)
 
 return mesh
 
+
 def write(mesh, filename, opt={}, **kwargs):
-""" Save the current mesh to a new file
+"""Save the current mesh to a new file
 
 Parameters
 ----------
@@ -207,20 +220,21 @@ def write(mesh, filename, opt={}, **kwargs):
 mesh.raw = {}
 
 if hasattr(mesh, 'info') and not mesh.info is None:
-mesh.raw['_DataInfo_']=mesh.info
+mesh.raw['_DataInfo_'] = mesh.info
 if hasattr(mesh, 'node') and not mesh.node is None:
-if(hasattr(mesh, 'facelabel') and not mesh.nodelabel is None):
-mesh.raw['MeshVertex3']={'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
+if hasattr(mesh, 'facelabel') and not mesh.nodelabel is None:
+mesh.raw['MeshVertex3'] = {'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
 else:
-mesh.raw['MeshVertex3']=mesh.node
+mesh.raw['MeshVertex3'] = mesh.node
 
 if hasattr(mesh, 'info') and not mesh.face is None:
-if(hasattr(mesh, 'facelabel') and not mesh.facelabel is None):
-mesh.raw['MeshTri3']={'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
+if hasattr(mesh, 'facelabel') and not mesh.facelabel is None:
+mesh.raw['MeshTri3'] = {'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
 else:
-mesh.raw['MeshTri3']=mesh.face
+mesh.raw['MeshTri3'] = mesh.face
 
 return jdsave(mesh.raw, filename, opt, **kwargs)
 
+
 load = read
 save = write