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run blue to format jmesh new units
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@fangq
fangq committed Feb 19, 2023
1 parent 9e19045 commit 9de951c
Showing 1 changed file with 77 additions and 63 deletions.
140 changes: 77 additions & 63 deletions nibabel/jmesh/jmesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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://github.com/NeuroJSON/jnifty",
"https://github.com/NeuroJSON/jsonlab"
],
"JavaScript":"https://github.com/NeuroJSON/jsdata",
"CPP":"https://github.com/NeuroJSON/json",
"C":"https://github.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://github.com/NeuroJSON/jnifty', 'https://github.com/NeuroJSON/jsonlab'],
'JavaScript': 'https://github.com/NeuroJSON/jsdata',
'CPP': 'https://github.com/NeuroJSON/json',
'C': 'https://github.com/NeuroJSON/ubj',
},
}


class JMesh(FileBasedImage):
"""JMesh: a simple data structure representing a brain surface
Expand Down Expand Up @@ -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:
Expand All @@ -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
----------
Expand All @@ -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
----------
Expand All @@ -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

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