Commit fd5fdfe4 authored by Paul McCarthy's avatar Paul McCarthy
Browse files

model.Model named to mesh.TriangleMesh. Indices are now shape (M, 3), instead

of (M*3,). New gifti module for basic gifti surface support.
parent 69c0f766
#!/usr/bin/env python
#
# gifti.py - GIFTI file support.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
# Michiel Cottar <michiel.cottaar@ndcn.ox.ac.uk>
#
"""This class provides classes and functions for working with GIFTI files.
The GIFTI file format specification can be found at
http://www.nitrc.org/projects/gifti/
Support is currently very basic - only the following classes/functions
are available:
.. autosummary::
:nosignatures:
GiftiSurface
extractGiftiSurface
"""
import os.path as op
import fsl.utils.path as fslpath
from . import mesh
class GiftiSurface(mesh.TriangleMesh):
"""Class which represents a GIFTI surface image. This is essentially
just a 3D model made of triangles.
In addition to the ``vertices`` and ``indices`` provided by the
:class:`.TriangleMesh` class (from which the ``GiftiSurface`` class
derives), a ``GiftiSurface`` instance has the following attributes:
============== ====================================================
``name`` A name, typically the file name sans-suffix.
``dataSource`` Full path to the GIFTI file.
``surfImg`` Reference to the loaded ``nibabel.gifti.GiftiImage``
============== ====================================================
"""
def __init__(self, infile):
"""Load the given GIFTI file using ``nibabel``, and extracts surface
data using the :func:`extractGiftiSurface` function.
:arg infile: A GIFTI surface file
"""
import nibabel as nib
surfimg = nib.load(infile)
vertices, indices = extractGiftiSurface(surfimg)
mesh.TriangleMesh.__init__(self, vertices, indices)
name = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
infile = op.abspath(infile)
self.name = name
self.dataSource = infile
self.surfImg = surfimg
ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
"""
EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI surface file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`.
"""
def extractGiftiSurface(surfimg):
"""Extracts surface data from the given ``nibabel.gifti.GiftiImage``.
The image is expected to contain the following``<DataArray>`` elements:
- one comprising ``NIFTI_INTENT_POINTSET`` data (the surface vertices)
- one comprising ``NIFTI_INTENT_TRIANGLE`` data (vertex indices
defining the triangles).
A ``ValueError`` will be raised if this is not the case.
:arg surfimg: A ``GiftiImage`` containing surface data.
:returns: A tuple containing these values:
- A :math:`N\\times 3` ``numpy`` array containing :math:`N`
vertices.
- A :math:`M\\times 3` ``numpy`` array containing the
vertex indices for :math:`M` triangles.
"""
from nibabel import gifti
codes = gifti.gifti.intent_codes.code
indices = None
vertices = None
for darray in surfimg.darrays:
if darray.intent == codes['pointset']:
if vertices is not None:
raise ValueError('multiple arrays with intent "{}"'.format(
darray.intent))
vertices = darray.data
elif darray.intent == codes['triangle']:
if indices is not None:
raise ValueError('multiple arrays with intent "{}"'.format(
darray.intent))
indices = darray.data
if vertices is None:
raise ValueError('no array with intent "pointset" found')
if indices is None:
raise ValueError('no array witbh intent "triangle"found')
return vertices, indices
#!/usr/bin/env python
#
# model.py - The Model class, for VTK polygon data.
# mesh.py - The TriangleMesh class.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`Model` class, which represents a 3D model.
"""This module provides the :class:`TriangleMesh` class, which represents a
3D model made of triangles.
.. note:: I/O support is very limited - currently, the only supported file
.. note:: I/O support is very limited - currently, the only supported file
type is the VTK legacy file format, containing the ``POLYDATA``
dataset. the :class:`Model` class assumes that every polygon defined
in an input file is a triangle (i.e. refers to three vertices).
dataset. the :class:`TriangleMesh` class assumes that every polygon
defined in an input file is a triangle (i.e. refers to three
vertices).
See http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf
for an overview of the VTK legacy file format.
In the future, I may or may not add support for more complex meshes.
"""
......@@ -29,22 +33,41 @@ from . import image as fslimage
log = logging.getLogger(__name__)
class Model(object):
"""The ``Model`` class represents a 3D model. A model is defined by a
collection of vertices and indices. The indices index into the list of
class TriangleMesh(object):
"""The ``TriangleMesh`` class represents a 3D model. A mesh is defined by
a collection of vertices and indices. The indices index into the list of
vertices, and define a set of triangles which make the model.
A ``TriangleMesh`` instance has the following attributes:
============== ====================================================
``name`` A name, typically the file name sans-suffix.
``dataSource`` Full path to the mesh file (or ``None`` if there is
no file associated with this mesh).
``vertices`` A :math:`N\times 3` ``numpy `` array containing
the vertices.
``indices`` A :meth:`M\times 3` ``numpy`` array containing
the vertex indices for :math:`M` triangles
============== ====================================================
"""
def __init__(self, data, indices=None):
"""Create a ``Model`` instance.
"""Create a ``TriangleMesh`` instance.
:arg data: Can either be a file name, or a :math:`N\\times 3`
``numpy`` array containing vertex data. If ``data`` is
a file name, it is passed to the
:func:`loadVTKPolydataFile` function.
:arg indices: A list of indices into the vertex data.
:arg indices: A list of indices into the vertex data, defining
the triangles.
"""
if isinstance(data, six.string_types):
......@@ -58,34 +81,36 @@ class Model(object):
self.name = op.basename(infile)
self.dataSource = infile
else:
self.name = 'Model'
self.dataSource = 'Model'
self.name = 'TriangleMesh'
self.dataSource = None
if indices is None:
indices = np.arange(data.shape[0], dtype=np.uint32)
indices = np.arange(data.shape[0])
self.vertices = np.array(data, dtype=np.float32)
self.indices = indices
self.vertices = np.array(data)
self.indices = np.array(indices).reshape((-1, 3))
self.__loBounds = self.vertices.min(axis=0)
self.__hiBounds = self.vertices.max(axis=0)
def __repr__(self):
"""Rewturns a string representation of this ``Model`` instance. """
"""Returns a string representation of this ``TriangleMesh`` instance.
"""
return '{}({}, {})'.format(type(self).__name__,
self.name,
self.dataSource)
def __str__(self):
"""Rewturns a string representation of this ``Model`` instance. """
"""Returns a string representation of this ``TriangleMesh`` instance.
"""
return self.__repr__()
def getBounds(self):
"""Returns a tuple of values which define a minimal bounding box that
will contain all vertices in this ``Model`` instance. The bounding
box is arranged like so:
will contain all vertices in this ``TriangleMesh`` instance. The
bounding box is arranged like so:
``((xlow, ylow, zlow), (xhigh, yhigh, zhigh))``
"""
......@@ -93,7 +118,8 @@ class Model(object):
ALLOWED_EXTENSIONS = ['.vtk']
"""A list of file extensions which could contain :class:`Model` data. """
"""A list of file extensions which could contain :class:`TriangleMesh` data.
"""
EXTENSION_DESCRIPTIONS = ['VTK polygon model file']
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment