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Commit 1d1551a

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Reading and writing JSON/binary JSON based surface data (.jmsh and .bmsh)
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‎nibabel/__init__.py‎

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from .cifti2 import Cifti2Header, Cifti2Image
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from .gifti import GiftiImage
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from .freesurfer import MGHImage
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from .jmesh import JMesh
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from .funcs import (squeeze_image, concat_images, four_to_three,
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as_closest_canonical)
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from .orientations import (io_orientation, orientation_affine,

‎nibabel/imageclasses.py‎

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from .spm99analyze import Spm99AnalyzeImage
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from .spm2analyze import Spm2AnalyzeImage
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from .volumeutils import Recoder
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from .jmesh import JMesh
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from .deprecated import deprecate_with_version
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from .optpkg import optional_package
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Cifti2Image, Nifti2Image, # Cifti2 before Nifti2
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Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
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Minc1Image, Minc2Image, MGHImage,
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PARRECImage, GiftiImage, AFNIImage]
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PARRECImage, GiftiImage, AFNIImage, JMesh]
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# DEPRECATED: mapping of names to classes and class functionality

‎nibabel/jmesh/__init__.py‎

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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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#
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# See COPYING file distributed along with the NiBabel package for the
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# copyright and license terms.
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#
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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"""JSON and BJData based JMesh format IO
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.. currentmodule:: nibabel.jmesh
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.. autosummary::
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:toctree: ../generated
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jmesh
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"""
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from .jmesh import load, save, JMesh, default_header

‎nibabel/jmesh/jmesh.py‎

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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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#
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# See COPYING file distributed along with the NiBabel package for the
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# copyright and license terms.
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#
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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# General JMesh Input - Output to and from the filesystem
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# Qianqian Fang <q.fang at neu.edu>
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##############
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__all__ = ['JMesh','read','write','default_header']
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from jdata import (load as jdload, save as jdsave)
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import numpy as np
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from ..filebasedimages import FileBasedImage
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default_header = {
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"JMeshVersion":"0.5",
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"Comment":"Created by NiPy with NeuroJSON JMesh specification",
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"AnnotationFormat":"https://neurojson.org/jmesh/draft2",
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"Parser":{
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"Python":[
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"https://pypi.org/project/jdata",
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"https://pypi.org/project/bjdata"
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],
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"MATLAB":[
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"https://github.com/NeuroJSON/jnifty",
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"https://github.com/NeuroJSON/jsonlab"
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],
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"JavaScript":"https://github.com/NeuroJSON/jsdata",
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"CPP":"https://github.com/NeuroJSON/json",
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"C":"https://github.com/NeuroJSON/ubj"
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}
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}
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class JMesh(FileBasedImage):
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"""JMesh: a simple data structure representing a brain surface
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* Description - JMesh defines a set of language-neutral JSON annotations for
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storage and exchange of mesh-related data. The details of the specification
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can be found in NeuroJSON's website at https://neurojson.org
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* Child Elements: [NA]
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* Text Content: [NA]
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Attributes
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----------
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info: a dict
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A dict object storing the metadata (`_DataInfo_`) section of the JMesh
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file
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node : 2-D list or numpy array
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A 2-D numpy.ndarray object to store the vertices of the mesh
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nodelabel : 1-D list or numpy array
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A 1-D numpy.ndarray object to store the label of each vertex
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face : 2-D list or numpy array
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A 2-D numpy.ndarray object to store the triangular elements of the
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mesh; indices start from 1
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facelabel : 1-D list or numpy array
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A 1-D numpy.ndarray object to store the label of each triangle
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raw : a dict
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The raw data loaded from the .jmsh or .bmsh file
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"""
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valid_exts = ('.jmsh', '.bmsh')
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files_types = (('image', '.jmsh'), ('image', '.bmsh'))
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makeable = False
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rw = True
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def __init__(self, info=None, node=None, nodelabel=None, face=None,
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facelabel=None):
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self.raw = {}
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if(not info is None):
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self.raw['_DataInfo_'] = info
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if(not nodelabel is None):
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self.raw['MeshVertex3'] = {'Data': node, 'Properties': {'Tag': nodelabel} }
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self.node = self.raw['MeshVertex3']['Data']
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self.nodelabel = self.raw['MeshVertex3']['Properties']['Tag']
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else:
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self.raw['MeshVertex3'] = node
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self.node = self.raw['MeshVertex3']
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if(not facelabel is None):
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self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel} }
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self.face = self.raw['MeshTri3']['Data']
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self.facelabel = self.raw['MeshTri3']['Properties']['Tag']
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else:
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self.raw['MeshTri3'] = face
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self.face = self.raw['MeshTri3']
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@classmethod
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def from_filename(self, filename, opt={}, **kwargs):
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self = read(filename, opt, **kwargs)
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return self
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@classmethod
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def to_filename(self, filename, opt={}, **kwargs):
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write(self, filename, opt, **kwargs)
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def read(filename, opt={}, **kwargs):
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""" Load a JSON or binary JData (BJData) based JMesh file
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Parameters
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----------
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filename : string
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The JMesh file to open, it has usually ending .gii
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opt: a dict that may contain below option keys
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ndarray: boolean, if True, node/face/nodelabel/facelabel are converted
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to numpy.ndarray, otherwise, leave those unchanged
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kwargs: additional keyword arguments for `json.load` when .jmsh file is being loaded
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Returns
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-------
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mesh : a JMesh object
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Return a JMesh object containing mesh data fields such as node, face, nodelabel etc
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"""
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opt.setdefault('ndarray',True)
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mesh = JMesh
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mesh.raw = jdload(filename, opt, **kwargs)
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#--------------------------------------------------
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# read metadata as `info`
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#--------------------------------------------------
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if('_DataInfo_' in mesh.raw):
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mesh.info = mesh.raw['_DataInfo_']
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#--------------------------------------------------
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# read vertices as `node` and `nodelabel`
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#--------------------------------------------------
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if('MeshVertex3' in mesh.raw):
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mesh.node = mesh.raw['MeshVertex3']
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elif('MeshNode' in mesh.raw):
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mesh.node = mesh.raw['MeshNode']
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else:
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raise Exception('JMesh', 'JMesh surface must contain node (MeshVertex3 or MeshNode)')
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if(isinstance(mesh.node, dict)):
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if(('Properties' in mesh.node) and ('Tag' in mesh.node['Properties'])):
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mesh.nodelabel = mesh.node['Properties']['Tag']
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if('Data' in mesh.node):
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mesh.node = mesh.node['Data']
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if(isinstance(mesh.node, np.ndarray) and mesh.node.ndim == 2 and mesh.node.shape[1] > 3):
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mesh.nodelabel = mesh.node[:,3:]
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mesh.node = mesh.node[:, 0:3]
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#--------------------------------------------------
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# read triangles as `face` and `facelabel`
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#--------------------------------------------------
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if('MeshTri3' in mesh.raw):
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mesh.face = mesh.raw['MeshTri3']
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elif('MeshSurf' in mesh.raw):
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mesh.face = mesh.raw['MeshSurf']
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if(isinstance(mesh.face, dict)):
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if(('Properties' in mesh.face) and ('Tag' in mesh.face['Properties'])):
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mesh.facelabel = mesh.face['Properties']['Tag']
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if('Data' in mesh.face):
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mesh.face = mesh.face['Data']
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if(isinstance(mesh.face, np.ndarray) and mesh.face.ndim == 2 and mesh.face.shape[1] > 3):
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mesh.facelabel = mesh.face[:,3:]
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mesh.face = mesh.face[:, 0:3]
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#--------------------------------------------------
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# convert to numpy ndarray
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#--------------------------------------------------
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if(opt['ndarray']):
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if hasattr(mesh, 'node') and (not mesh.node is None) and (not isinstance(mesh.node, np.ndarray)):
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mesh.node = np.array(mesh.node)
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if hasattr(mesh, 'face') and (not mesh.face is None) and (not isinstance(mesh.face, np.ndarray)):
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mesh.face = np.array(mesh.face)
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if hasattr(mesh, 'nodelabel') and (not mesh.nodelabel is None) and (not isinstance(mesh.nodelabel, np.ndarray)):
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mesh.nodelabel = np.array(mesh.nodelabel)
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if hasattr(mesh, 'facelabel') and (not mesh.facelabel is None) and (not isinstance(mesh.facelabel, np.ndarray)):
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mesh.facelabel = np.array(mesh.facelabel)
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return mesh
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def write(mesh, filename, opt={}, **kwargs):
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""" Save the current mesh to a new file
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Parameters
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----------
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mesh : a JMesh object
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filename : string
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Filename to store the JMesh file (.jmsh for JSON based JMesh and
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.bmsh for binary JMesh files)
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opt: a dict that may contain below option keys
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ndarray: boolean, if True, node/face/nodelabel/facelabel are converted
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to numpy.ndarray, otherwise, leave those unchanged
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kwargs: additional keyword arguments for `json.dump` when .jmsh file is being saved
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Returns
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-------
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None
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We update the mesh related data fields `MeshVetex3`, `MeshTri3` and metadata `_DataInfo_`
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from mesh.node, mesh.face and mesh.info, then save mesh.raw to JData files
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"""
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if not hasattr(mesh, 'raw') or mesh.raw is None:
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mesh.raw = {}
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if hasattr(mesh, 'info') and not mesh.info is None:
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mesh.raw['_DataInfo_']=mesh.info
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if hasattr(mesh, 'node') and not mesh.node is None:
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if(hasattr(mesh, 'facelabel') and not mesh.nodelabel is None):
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mesh.raw['MeshVertex3']={'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
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else:
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mesh.raw['MeshVertex3']=mesh.node
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if hasattr(mesh, 'info') and not mesh.face is None:
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if(hasattr(mesh, 'facelabel') and not mesh.facelabel is None):
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mesh.raw['MeshTri3']={'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
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else:
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mesh.raw['MeshTri3']=mesh.face
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return jdsave(mesh.raw, filename, opt, **kwargs)
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load = read
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save = write

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