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ENH: Reading and writing JSON/binary JSON based surface data (.jmsh and .bmsh)#1114

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4 changes: 3 additions & 1 deletionmin-requirements.txt
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# Auto-generated by tools/update_requirements.py
numpy ==1.19
packaging ==17
setuptools
importlib_resources; python_version < '3.9'
jdata ==0.5
bjdata ==0.4
1 change: 1 addition & 0 deletionsnibabel/__init__.py
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Expand Up@@ -70,6 +70,7 @@
)
from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage
from .jmesh import JMesh

# isort: split

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2 changes: 2 additions & 0 deletionsnibabel/imageclasses.py
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Expand Up@@ -19,6 +19,7 @@
from .parrec import PARRECImage
from .spm2analyze import Spm2AnalyzeImage
from .spm99analyze import Spm99AnalyzeImage
from .jmesh import JMesh

# Ordered by the load/save priority.
all_image_classes = [
Expand All@@ -36,6 +37,7 @@
PARRECImage,
GiftiImage,
AFNIImage,
JMesh,
]

# Image classes known to require spatial axes to be first in index ordering.
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19 changes: 19 additions & 0 deletionsnibabel/jmesh/__init__.py
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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""JSON and BJData based JMesh format IO

.. currentmodule:: nibabel.jmesh

.. autosummary::
:toctree: ../generated

jmesh
"""

from .jmesh import load, save, JMesh, default_header
240 changes: 240 additions & 0 deletionsnibabel/jmesh/jmesh.py
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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
# General JMesh Input - Output to and from the filesystem
# Qianqian Fang <q.fang at neu.edu>
##############

__all__ = ['JMesh', 'read', 'write', 'default_header']

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',
},
}


class JMesh(FileBasedImage):
"""JMesh: a simple data structure representing a brain surface

* Description - JMesh defines a set of language-neutral JSON annotations for
storage and exchange of mesh-related data. The details of the specification
can be found in NeuroJSON's website at https://neurojson.org

* Child Elements: [NA]
* Text Content: [NA]

Attributes
----------
info: a dict
A dict object storing the metadata (`_DataInfo_`) section of the JMesh
file
node : 2-D list or numpy array
A 2-D numpy.ndarray object to store the vertices of the mesh
nodelabel : 1-D list or numpy array
A 1-D numpy.ndarray object to store the label of each vertex
face : 2-D list or numpy array
A 2-D numpy.ndarray object to store the triangular elements of the
mesh; indices start from 1
facelabel : 1-D list or numpy array
A 1-D numpy.ndarray object to store the label of each triangle
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):

self.raw = {}
if info is not None:
self.raw['_DataInfo_'] = info

if nodelabel is not 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 facelabel is not None:
self.raw['MeshTri3'] = {'Data': face, 'Properties': {'Tag': facelabel}}
self.face = self.raw['MeshTri3']['Data']
self.facelabel = self.raw['MeshTri3']['Properties']['Tag']
else:
self.raw['MeshTri3'] = face
self.face = self.raw['MeshTri3']

@classmethod
def from_filename(self, filename, opt={}, **kwargs):
self = read(filename, opt, **kwargs)
return self

@classmethod
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

Parameters
----------
filename : string
The JMesh file to open, it has usually ending .gii
opt: a dict that may contain below option keys
ndarray: boolean, if True, node/face/nodelabel/facelabel are converted
to numpy.ndarray, otherwise, leave those unchanged
kwargs: additional keyword arguments for `json.load` when .jmsh file is being loaded

Returns
-------
mesh : a JMesh object
Return a JMesh object containing mesh data fields such as node, face, nodelabel etc
"""
opt.setdefault('ndarray', True)

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

# --------------------------------------------------
# read metadata as `info`
# --------------------------------------------------
if '_DataInfo_' in mesh.raw:
mesh.info = mesh.raw['_DataInfo_']

# --------------------------------------------------
# read vertices as `node` and `nodelabel`
# --------------------------------------------------
if 'MeshVertex3' in mesh.raw:
mesh.node = mesh.raw['MeshVertex3']
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']):
mesh.nodelabel = mesh.node['Properties']['Tag']
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:]
mesh.node = mesh.node[:, 0:3]

# --------------------------------------------------
# read triangles as `face` and `facelabel`
# --------------------------------------------------
if 'MeshTri3' in mesh.raw:
mesh.face = mesh.raw['MeshTri3']
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']):
mesh.facelabel = mesh.face['Properties']['Tag']
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:]
mesh.face = mesh.face[:, 0:3]

# --------------------------------------------------
# convert to numpy ndarray
# --------------------------------------------------
if opt['ndarray']:
if (
hasattr(mesh, 'node')
and (mesh.node is not None)
and (not isinstance(mesh.node, np.ndarray))
):
mesh.node = np.array(mesh.node)

if (
hasattr(mesh, 'face')
and (mesh.face is not None)
and (not isinstance(mesh.face, np.ndarray))
):
mesh.face = np.array(mesh.face)

if (
hasattr(mesh, 'nodelabel')
and (mesh.nodelabel is not None)
and (not isinstance(mesh.nodelabel, np.ndarray))
):
mesh.nodelabel = np.array(mesh.nodelabel)

if (
hasattr(mesh, 'facelabel')
and (mesh.facelabel is not 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

Parameters
----------
mesh : a JMesh object
filename : string
Filename to store the JMesh file (.jmsh for JSON based JMesh and
.bmsh for binary JMesh files)
opt: a dict that may contain below option keys
ndarray: boolean, if True, node/face/nodelabel/facelabel are converted
to numpy.ndarray, otherwise, leave those unchanged
kwargs: additional keyword arguments for `json.dump` when .jmsh file is being saved

Returns
-------
None

We update the mesh related data fields `MeshVetex3`, `MeshTri3` and metadata `_DataInfo_`
from mesh.node, mesh.face and mesh.info, then save mesh.raw to JData files
"""

if not hasattr(mesh, 'raw') or mesh.raw is None:
mesh.raw = {}

if hasattr(mesh, 'info') and mesh.info is not None:
mesh.raw['_DataInfo_'] = mesh.info
if hasattr(mesh, 'node') and mesh.node is not None:
if hasattr(mesh, 'facelabel') and mesh.nodelabel is not None:
mesh.raw['MeshVertex3'] = {'Data': mesh.node, 'Properties': {'Tag': mesh.nodelabel}}
else:
mesh.raw['MeshVertex3'] = mesh.node

if hasattr(mesh, 'info') and mesh.face is not None:
if hasattr(mesh, 'facelabel') and mesh.facelabel is not None:
mesh.raw['MeshTri3'] = {'Data': mesh.face, 'Properties': {'Tag': mesh.facelabel}}
else:
mesh.raw['MeshTri3'] = mesh.face

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


load = read
save = write
2 changes: 2 additions & 0 deletionspyproject.toml
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Expand Up@@ -14,6 +14,8 @@ dependencies = [
"numpy >=1.19",
"packaging >=17",
"importlib_resources; python_version < '3.9'",
"jdata >=0.5",
"bjdata >=0.4",
]
classifiers = [
"Development Status :: 5 - Production/Stable",
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4 changes: 3 additions & 1 deletionrequirements.txt
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@@ -1,4 +1,6 @@
# Auto-generated by tools/update_requirements.py
numpy >=1.19
packaging >=17
setuptools
importlib_resources; python_version < '3.9'
jdata >=0.5
bjdata >=0.4
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