diff --git a/nibabel/__init__.py b/nibabel/__init__.py index 50dca14515..ac7f39ae7c 100644 --- a/nibabel/__init__.py +++ b/nibabel/__init__.py @@ -70,6 +70,7 @@ ) from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage +from .jmesh import JMesh # isort: split diff --git a/nibabel/imageclasses.py b/nibabel/imageclasses.py index e2dbed129d..31424fef96 100644 --- a/nibabel/imageclasses.py +++ b/nibabel/imageclasses.py @@ -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 = [ @@ -36,6 +37,7 @@ PARRECImage, GiftiImage, AFNIImage, + JMesh ] # Image classes known to require spatial axes to be first in index ordering. diff --git a/nibabel/jmesh/__init__.py b/nibabel/jmesh/__init__.py new file mode 100644 index 0000000000..f555d6a70a --- /dev/null +++ b/nibabel/jmesh/__init__.py @@ -0,0 +1,19 @@ +# 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 diff --git a/nibabel/jmesh/jmesh.py b/nibabel/jmesh/jmesh.py new file mode 100644 index 0000000000..c3a9e85add --- /dev/null +++ b/nibabel/jmesh/jmesh.py @@ -0,0 +1,226 @@ +# 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 +############## + +__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(not info is None): + self.raw['_DataInfo_'] = info + + 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} } + 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 (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)): + mesh.face = np.array(mesh.face) + + 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)): + 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 not mesh.info is None: + 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}} + else: + 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}} + else: + mesh.raw['MeshTri3']=mesh.face + + return jdsave(mesh.raw, filename, opt, **kwargs) + +load = read +save = write