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fangqfangq
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run blue to format jmesh new units
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‎nibabel/jmesh/jmesh.py

+77-63
Original file line numberDiff line numberDiff line change
@@ -10,31 +10,26 @@
1010
# Qianqian Fang <q.fang at neu.edu>
1111
##############
1212

13-
__all__ = ['JMesh','read','write','default_header']
13+
__all__ = ['JMesh', 'read', 'write', 'default_header']
1414

15-
from jdata import (load as jdload, save as jdsave)
15+
from jdata import load as jdload, save as jdsave
1616
import numpy as np
1717
from ..filebasedimages import FileBasedImage
1818

1919
default_header = {
20-
"JMeshVersion":"0.5",
21-
"Comment":"Created by NiPy with NeuroJSON JMesh specification",
22-
"AnnotationFormat":"https://neurojson.org/jmesh/draft2",
23-
"Parser":{
24-
"Python":[
25-
"https://pypi.org/project/jdata",
26-
"https://pypi.org/project/bjdata"
27-
],
28-
"MATLAB":[
29-
"https://github.com/NeuroJSON/jnifty",
30-
"https://github.com/NeuroJSON/jsonlab"
31-
],
32-
"JavaScript":"https://github.com/NeuroJSON/jsdata",
33-
"CPP":"https://github.com/NeuroJSON/json",
34-
"C":"https://github.com/NeuroJSON/ubj"
35-
}
20+
'JMeshVersion': '0.5',
21+
'Comment': 'Created by NiPy with NeuroJSON JMesh specification',
22+
'AnnotationFormat': 'https://neurojson.org/jmesh/draft2',
23+
'Parser': {
24+
'Python': ['https://pypi.org/project/jdata', 'https://pypi.org/project/bjdata'],
25+
'MATLAB': ['https://github.com/NeuroJSON/jnifty', 'https://github.com/NeuroJSON/jsonlab'],
26+
'JavaScript': 'https://github.com/NeuroJSON/jsdata',
27+
'CPP': 'https://github.com/NeuroJSON/json',
28+
'C': 'https://github.com/NeuroJSON/ubj',
29+
},
3630
}
3731

32+
3833
class JMesh(FileBasedImage):
3934
"""JMesh: a simple data structure representing a brain surface
4035
@@ -62,28 +57,28 @@ class JMesh(FileBasedImage):
6257
raw : a dict
6358
The raw data loaded from the .jmsh or .bmsh file
6459
"""
60+
6561
valid_exts = ('.jmsh', '.bmsh')
6662
files_types = (('image', '.jmsh'), ('image', '.bmsh'))
6763
makeable = False
6864
rw = True
6965

70-
def __init__(self, info=None, node=None, nodelabel=None, face=None,
71-
facelabel=None):
66+
def __init__(self, info=None, node=None, nodelabel=None, face=None, facelabel=None):
7267

7368
self.raw = {}
74-
if(not info is None):
69+
if not info is None:
7570
self.raw['_DataInfo_'] = info
7671

77-
if(not nodelabel is None):
78-
self.raw['MeshVertex3'] = {'Data': node, 'Properties': {'Tag': nodelabel} }
72+
if not nodelabel is None:
73+
self.raw['MeshVertex3'] = {'Data': node, 'Properties': {'Tag': nodelabel}}
7974
self.node = self.raw['MeshVertex3']['Data']
8075
self.nodelabel = self.raw['MeshVertex3']['Properties']['Tag']
8176
else:
8277
self.raw['MeshVertex3'] = node
8378
self.node = self.raw['MeshVertex3']
8479

85-
if(not facelabel is None):
86-
self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel} }
80+
if not facelabel is None:
81+
self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel}}
8782
self.face = self.raw['MeshTri3']['Data']
8883
self.facelabel = self.raw['MeshTri3']['Properties']['Tag']
8984
else:
@@ -99,8 +94,9 @@ def from_filename(self, filename, opt={}, **kwargs):
9994
def to_filename(self, filename, opt={}, **kwargs):
10095
write(self, filename, opt, **kwargs)
10196

97+
10298
def read(filename, opt={}, **kwargs):
103-
""" Load a JSON or binary JData (BJData) based JMesh file
99+
"""Load a JSON or binary JData (BJData) based JMesh file
104100
105101
Parameters
106102
----------
@@ -116,73 +112,90 @@ def read(filename, opt={}, **kwargs):
116112
mesh : a JMesh object
117113
Return a JMesh object containing mesh data fields such as node, face, nodelabel etc
118114
"""
119-
opt.setdefault('ndarray',True)
115+
opt.setdefault('ndarray', True)
120116

121117
mesh = JMesh
122118
mesh.raw = jdload(filename, opt, **kwargs)
123119

124-
#--------------------------------------------------
120+
# --------------------------------------------------
125121
# read metadata as `info`
126-
#--------------------------------------------------
127-
if('_DataInfo_' in mesh.raw):
122+
# --------------------------------------------------
123+
if '_DataInfo_' in mesh.raw:
128124
mesh.info = mesh.raw['_DataInfo_']
129125

130-
#--------------------------------------------------
126+
# --------------------------------------------------
131127
# read vertices as `node` and `nodelabel`
132-
#--------------------------------------------------
133-
if('MeshVertex3' in mesh.raw):
128+
# --------------------------------------------------
129+
if 'MeshVertex3' in mesh.raw:
134130
mesh.node = mesh.raw['MeshVertex3']
135-
elif('MeshNode' in mesh.raw):
131+
elif 'MeshNode' in mesh.raw:
136132
mesh.node = mesh.raw['MeshNode']
137133
else:
138134
raise Exception('JMesh', 'JMesh surface must contain node (MeshVertex3 or MeshNode)')
139135

140-
if(isinstance(mesh.node, dict)):
141-
if(('Properties' in mesh.node) and ('Tag' in mesh.node['Properties'])):
136+
if isinstance(mesh.node, dict):
137+
if ('Properties' in mesh.node) and ('Tag' in mesh.node['Properties']):
142138
mesh.nodelabel = mesh.node['Properties']['Tag']
143-
if('Data' in mesh.node):
139+
if 'Data' in mesh.node:
144140
mesh.node = mesh.node['Data']
145-
if(isinstance(mesh.node, np.ndarray) and mesh.node.ndim == 2 and mesh.node.shape[1] > 3):
146-
mesh.nodelabel = mesh.node[:,3:]
141+
if isinstance(mesh.node, np.ndarray) and mesh.node.ndim == 2 and mesh.node.shape[1] > 3:
142+
mesh.nodelabel = mesh.node[:, 3:]
147143
mesh.node = mesh.node[:, 0:3]
148144

149-
#--------------------------------------------------
145+
# --------------------------------------------------
150146
# read triangles as `face` and `facelabel`
151-
#--------------------------------------------------
152-
if('MeshTri3' in mesh.raw):
147+
# --------------------------------------------------
148+
if 'MeshTri3' in mesh.raw:
153149
mesh.face = mesh.raw['MeshTri3']
154-
elif('MeshSurf' in mesh.raw):
150+
elif 'MeshSurf' in mesh.raw:
155151
mesh.face = mesh.raw['MeshSurf']
156152

157-
if(isinstance(mesh.face, dict)):
158-
if(('Properties' in mesh.face) and ('Tag' in mesh.face['Properties'])):
153+
if isinstance(mesh.face, dict):
154+
if ('Properties' in mesh.face) and ('Tag' in mesh.face['Properties']):
159155
mesh.facelabel = mesh.face['Properties']['Tag']
160-
if('Data' in mesh.face):
156+
if 'Data' in mesh.face:
161157
mesh.face = mesh.face['Data']
162-
if(isinstance(mesh.face, np.ndarray) and mesh.face.ndim == 2 and mesh.face.shape[1] > 3):
163-
mesh.facelabel = mesh.face[:,3:]
158+
if isinstance(mesh.face, np.ndarray) and mesh.face.ndim == 2 and mesh.face.shape[1] > 3:
159+
mesh.facelabel = mesh.face[:, 3:]
164160
mesh.face = mesh.face[:, 0:3]
165161

166-
#--------------------------------------------------
162+
# --------------------------------------------------
167163
# convert to numpy ndarray
168-
#--------------------------------------------------
169-
if(opt['ndarray']):
170-
if hasattr(mesh, 'node') and (not mesh.node is None) and (not isinstance(mesh.node, np.ndarray)):
164+
# --------------------------------------------------
165+
if opt['ndarray']:
166+
if (
167+
hasattr(mesh, 'node')
168+
and (not mesh.node is None)
169+
and (not isinstance(mesh.node, np.ndarray))
170+
):
171171
mesh.node = np.array(mesh.node)
172172

173-
if hasattr(mesh, 'face') and (not mesh.face is None) and (not isinstance(mesh.face, np.ndarray)):
173+
if (
174+
hasattr(mesh, 'face')
175+
and (not mesh.face is None)
176+
and (not isinstance(mesh.face, np.ndarray))
177+
):
174178
mesh.face = np.array(mesh.face)
175179

176-
if hasattr(mesh, 'nodelabel') and (not mesh.nodelabel is None) and (not isinstance(mesh.nodelabel, np.ndarray)):
180+
if (
181+
hasattr(mesh, 'nodelabel')
182+
and (not mesh.nodelabel is None)
183+
and (not isinstance(mesh.nodelabel, np.ndarray))
184+
):
177185
mesh.nodelabel = np.array(mesh.nodelabel)
178186

179-
if hasattr(mesh, 'facelabel') and (not mesh.facelabel is None) and (not isinstance(mesh.facelabel, np.ndarray)):
187+
if (
188+
hasattr(mesh, 'facelabel')
189+
and (not mesh.facelabel is None)
190+
and (not isinstance(mesh.facelabel, np.ndarray))
191+
):
180192
mesh.facelabel = np.array(mesh.facelabel)
181193

182194
return mesh
183195

196+
184197
def write(mesh, filename, opt={}, **kwargs):
185-
""" Save the current mesh to a new file
198+
"""Save the current mesh to a new file
186199
187200
Parameters
188201
----------
@@ -207,20 +220,21 @@ def write(mesh, filename, opt={}, **kwargs):
207220
mesh.raw = {}
208221

209222
if hasattr(mesh, 'info') and not mesh.info is None:
210-
mesh.raw['_DataInfo_']=mesh.info
223+
mesh.raw['_DataInfo_'] = mesh.info
211224
if hasattr(mesh, 'node') and not mesh.node is None:
212-
if(hasattr(mesh, 'facelabel') and not mesh.nodelabel is None):
213-
mesh.raw['MeshVertex3']={'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
225+
if hasattr(mesh, 'facelabel') and not mesh.nodelabel is None:
226+
mesh.raw['MeshVertex3'] = {'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
214227
else:
215-
mesh.raw['MeshVertex3']=mesh.node
228+
mesh.raw['MeshVertex3'] = mesh.node
216229

217230
if hasattr(mesh, 'info') and not mesh.face is None:
218-
if(hasattr(mesh, 'facelabel') and not mesh.facelabel is None):
219-
mesh.raw['MeshTri3']={'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
231+
if hasattr(mesh, 'facelabel') and not mesh.facelabel is None:
232+
mesh.raw['MeshTri3'] = {'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
220233
else:
221-
mesh.raw['MeshTri3']=mesh.face
234+
mesh.raw['MeshTri3'] = mesh.face
222235

223236
return jdsave(mesh.raw, filename, opt, **kwargs)
224237

238+
225239
load = read
226240
save = write

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