mesh.py 25.9 KB
Newer Older
1
2
#!/usr/bin/env python
#
3
# mesh.py - The TriangleMesh class.
4
5
6
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
7
"""This module provides the :class:`Mesh` class, which represents a
8
3D model made of triangles.
9

10
See also the following modules:
11

12
  .. autosummary::
13

14
15
16
17
     fsl.data.vtk
     fsl.data.gifti
     fsl.data.freesurfer

18
19
A handful of standalone functions are provided in this module, for doing
various things with meshes:
20
21
22
23
24
25
26

  .. autosummary::
     :nosignatures:

     calcFaceNormals
     calcVertexNormals
     needsFixing
27
28
"""

29

30
import logging
31
32
33
34
import collections

import six
import deprecation
35

36
37
import os.path as op
import numpy   as np
38

39
import fsl.utils.meta      as meta
40
import fsl.utils.notifier  as notifier
41
import fsl.utils.memoize   as memoize
42
import fsl.utils.transform as transform
43

44
45
46
47

log = logging.getLogger(__name__)


48
49
class Mesh(notifier.Notifier, meta.Meta):
    """The ``Mesh`` class represents a 3D model. A mesh is defined by a
50
    collection of ``N`` vertices, and ``M`` triangles.  The triangles are
Paul McCarthy's avatar
Paul McCarthy committed
51
    defined by ``(M, 3)`` indices into the list of vertices.
52
53


54
    A ``Mesh`` instance has the following attributes:
55

56

57
58
    ============== ====================================================
    ``name``       A name, typically the file name sans-suffix.
59

60
61
    ``dataSource`` Full path to the mesh file (or ``None`` if there is
                   no file associated with this mesh).
62

63
64
65
66
67
    ``vertices``   A ``(n, 3)`` array containing the currently selected
                   vertices. You can assign  a vertex set key to this
                   attribute to change the selected vertex set.

    ``bounds``     The lower and upper bounds
68

69
70
    ``indices``    A ``(m, 3)`` array containing the vertex indices
                   for ``m`` triangles
71

72
73
    ``normals``    A  ``(m, 3)`` array containing face normals for the
                   triangles
74

75
76
    ``vnormals``   A ``(n, 3)`` array containing vertex normals for the
                   the current vertices.
77
78
    ============== ====================================================

79

80
81
82
83
84
85
86
87
    **Vertex sets**


    A ``Mesh`` object can be associated with multiple sets of vertices, but
    only one set of triangles. Vertices can be added via the
    :meth:`addVertices` method. Each vertex set must be associated with a
    unique key - you can then select the current vertex set via the
    :meth:`vertices` property. Most ``Mesh`` methods will raise a ``KeyError``
88
89
90
91
92
93
    if you have not added any vertex sets, or selected a vertex set. The
    following methods are available for managing vertex sets:

    .. autosummary::
       :nosignatures:

94
       loadVertices
95
96
       addVertices
       selectedVertices
97
       vertexSets
98
99
100
101
102
103
104


    **Vertex data**


    A ``Mesh`` object can store vertex-wise data. The following methods can be
    used for adding/retrieving vertex data:
105
106
107
108

    .. autosummary::
       :nosignatures:

109
       loadVertexData
110
       addVertexData
111
       getVertexData
112
       vertexDataSets
113
       clearVertexData
114

115

116
    **Notification**
117

118

119
120
121
122
123
124
    The ``Mesh`` class inherits from the :class:`Notifier` class. Whenever the
    ``Mesh`` vertex set is changed, a notification is emitted via the
    ``Notifier`` interface, with a topic of ``'vertices'``. When this occurs,
    the :meth:`vertices`, :meth:`bounds`, :meth:`normals` and :attr:`vnormals`
    properties will all change so that they return data specific to the newly
    selected vertex set.
125
126


127
    **Metadata*
128

129

130
131
    The ``Mesh`` class also inherits from the :class:`Meta` class, so
    any metadata associated with the ``Mesh`` may be added via those methods.
132

133

134
    **Geometric queries**
135

136

137
138
    If the ``trimesh`` library is present, the following methods may be used
    to perform geometric queries on a mesh:
139

140
141
    .. autosummary::
       :nosignatures:
142

143
144
145
146
       rayIntersection
       planeIntersection
       nearestVertex
    """
147
148


149
150
151
152
153
154
155
156
    def __new__(cls, *args, **kwargs):
        """Create a ``Mesh``. We must override ``__new__``, otherwise the
        :class:`Meta` and :class:`Notifier` ``__new__`` methods will not be
        called correctly.
        """
        return super(Mesh, cls).__new__(cls, *args, **kwargs)


157
158
159
160
161
162
    def __init__(self,
                 indices,
                 name='mesh',
                 dataSource=None,
                 vertices=None,
                 fixWinding=False):
163
164
165
166
        """Create a ``Mesh`` instance.

        Before a ``Mesh`` can be used, some vertices must be added via the
        :meth:`addVertices` method.
167

168
169
170
171
172
        :arg indices:    A list of indices into the vertex data, defining the
                         mesh triangles.

        :arg name:       A name for this ``Mesh``.

173
174
175
176
        :arg dataSource: The data source for this ``Mesh``.

        :arg vertices:   Initial vertex set to add - given the key
                         ``'default'``.
177
178
179

        :arg fixWinding: Ignored if ``vertices is None``. Passed through to the
                         :meth:`addVertices` method along with ``vertices``.
180
181
        """

182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
        self.__name       = name
        self.__dataSource = dataSource
        self.__indices    = np.asarray(indices).reshape((-1, 3))

        # This attribute is used to store
        # the currently selected vertex set,
        # used as a kety into all of the
        # dictionaries below.
        self.__selected = None

        # Flag used to keep track of whether
        # the triangle winding order has been
        # "fixed" - see the addVertices method.
        self.__fixed = False

        # All of these are populated
        # in the addVertices method
        self.__vertices = collections.OrderedDict()
        self.__loBounds = collections.OrderedDict()
        self.__hiBounds = collections.OrderedDict()

        # These get populated on
        # normals/vnormals accesses
        self.__faceNormals = collections.OrderedDict()
        self.__vertNormals = collections.OrderedDict()

        # this gets populated in
        # the addVertexData method
        self.__vertexData  = collections.OrderedDict()

        # this gets populated
        # in the trimesh method
        self.__trimesh = collections.OrderedDict()

216
217
218
        # Add initial vertex
        # set if provided
        if vertices is not None:
219
            self.addVertices(vertices, fixWinding=fixWinding)
220

221

222
223
224
225
226
227
228
229
230
231
232
233
234
    def __repr__(self):
        """Returns a string representation of this ``Mesh`` instance. """
        return '{}({}, {})'.format(type(self).__name__,
                                   self.name,
                                   self.dataSource)


    def __str__(self):
        """Returns a string representation of this ``Mesh`` instance.
        """
        return self.__repr__()


235
236
237
238
239
240
241
242
243
244
    @property
    def name(self):
        """Returns the name of this ``Mesh``. """
        return self.__name


    @property
    def dataSource(self):
        """Returns the data source of this ``Mesh``. """
        return self.__dataSource
245
246


247
248
249
    @property
    def vertices(self):
        """The ``(N, 3)`` vertices of this mesh. """
250
251
252
        return self.__vertices[self.__selected]


253
    @vertices.setter
254
255
256
    def vertices(self, key):
        """Select the current vertex set - a ``KeyError`` is raised
        if no vertex set with the specified ``key`` has been added.
257
258
259
260

        When the current vertex set is changed, a notification is emitted
        through the :class:`.Notifier` interface, with the topic
        ``'vertices'``.
261
262
263
264
265
        """

        # Force a key error if
        # the key is invalid
        self.__vertices[key]
266

267
268
269
        if self.__selected != key:
            self.__selected = key
            self.notify(topic='vertices')
270

271
272
273
274

    @property
    def indices(self):
        """The ``(M, 3)`` triangles of this mesh. """
275
        return self.__indices
276
277


278
279
280
281
282
    @property
    def normals(self):
        """A ``(M, 3)`` array containing surface normals for every
        triangle in the mesh, normalised to unit length.
        """
283

284
285
286
287
        selected = self.__selected
        indices  = self.__indices
        vertices = self.__vertices[selected]
        fnormals = self.__faceNormals.get(selected, None)
288

289
290
291
        if fnormals is None:
            fnormals = calcFaceNormals(vertices, indices)
            self.__faceNormals[selected] = fnormals
292

293
        return fnormals
294
295
296
297


    @property
    def vnormals(self):
298
        """A ``(N, 3)`` array containing normals for every vertex
299
300
301
        in the mesh.
        """

302
303
304
305
        selected = self.__selected
        indices  = self.__indices
        vertices = self.__vertices[selected]
        vnormals = self.__vertNormals.get(selected, None)
306

307
308
309
        if vnormals is None:
            vnormals = calcVertexNormals(vertices, indices, self.normals)
            self.__vertNormals[selected] = vnormals
310

311
        return vnormals
312
313


314
315
    @property
    def bounds(self):
316
        """Returns a tuple of values which define a minimal bounding box that
317
318
        will contain all of the currently selected vertices in this
        ``Mesh`` instance. The bounding box is arranged like so:
319
320
321
322

            ``((xlow, ylow, zlow), (xhigh, yhigh, zhigh))``
        """

323
324
325
326
        lo = self.__loBounds[self.__selected]
        hi = self.__hiBounds[self.__selected]

        return lo, hi
327
328


329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
    def loadVertices(self, infile, key=None, **kwargs):
        """Loads vertex data from the given ``infile``, and adds it as a vertex
        set with the given ``key``. This implementation supports loading vertex
        data from white-space delimited text files via ``numpy.loadtxt``, but
        sub-classes may override this method to support additional file types.


        :arg infile: File to load data from.

        :arg key:    Key to pass to :meth:`addVertices`. If not provided,
                     set to ``infile`` (converted to an absolute path)

        All of the other arguments are passed through to :meth:`addVertices`.

        :returns:    The loaded vertices.
        """

        infile = op.abspath(infile)

        if key is None:
            key = infile

        vertices = np.loadtxt(infile)
        vertices = vertices.reshape(self.vertices.shape)

        self.addVertices(vertices, key, **kwargs)

        return vertices


359
    def addVertices(self, vertices, key=None, select=True, fixWinding=False):
360
        """Adds a set of vertices to this ``Mesh``.
361

362
363
        :arg vertices:   A `(n, 3)` array containing ``n`` vertices, compatible
                         with the indices specified in :meth:`__init__`.
364

365
366
        :arg key:        A key for this vertex set. If ``None`` defaults to
                         ``'default'``.
367
368
369
370
371
372
373

        :arg select:     If ``True`` (the default), this vertex set is
                         made the currently selected vertex set.

        :arg fixWinding: Defaults to ``False``. If ``True``, the vertex
                         winding order of every triangle is is fixed so they
                         all have outward-facing normal vectors.
374
375
        """

376
377
378
        if key is None:
            key = 'default'

379
380
381
        vertices = np.asarray(vertices)
        lo       = vertices.min(axis=0)
        hi       = vertices.max(axis=0)
382

383
384
385
        self.__vertices[key] = vertices
        self.__loBounds[key] = lo
        self.__hiBounds[key] = hi
386

387
388
        if select:
            self.vertices = key
389

390
391
392
393
394
395
        # indices already fixed?
        if fixWinding and (not self.__fixed):
            indices      = self.indices
            normals      = self.normals
            needsFix     = needsFixing(vertices, indices, normals, lo, hi)
            self.__fixed = True
396

397
398
399
400
401
402
403
404
405
            # See needsFixing documentation
            if needsFix:

                indices[:, [1, 2]] = indices[:, [2, 1]]

                for k, fn in self.__faceNormals.items():
                    self.__faceNormals[k] = fn * -1


406
    def vertexSets(self):
407
408
409
        """Returns a list containing the keys of all vertex sets. """
        return list(self.__vertices.keys())

410
411
412
413
414
415

    def selectedVertices(self):
        """Returns the key of the currently selected vertex set. """
        return self.__selected


416
417
418
419
420
421
422
423
424
425
    def loadVertexData(self, infile, key=None):
        """Loads vertex-wise data from the given ``infile``, and adds it with
        the given ``key``. This implementation supports loading data from
        whitespace-delimited text files via ``numpy.loadtxt``, but sub-classes
        may override this method to support additional file types.

        :arg infile: File to load data from.

        :arg key:    Key to pass to :meth:`addVertexData`. If not provided,
                     set to ``infile`` (converted to an absolute path)
426
427

        :returns:    The loaded vertex data.
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
        """

        infile = op.abspath(infile)

        if key is None:
            key = infile

        nvertices  = self.vertices.shape[0]
        vertexData = np.loadtxt(infile)
        vertexData = vertexData.reshape(nvertices, -1)

        self.addVertexData(key, vertexData)

        return vertexData


444
445
446
447
    def addVertexData(self, key, vdata):
        """Adds a vertex-wise data set to the ``Mesh``. It can be retrieved
        by passing the specified ``key`` to the :meth:`getVertexData` method.
        """
448
449
450

        nvertices = self.vertices.shape[0]

451
452
453
        if vdata.ndim not in (1, 2) or vdata.shape[0] != nvertices:
            raise ValueError('{}: incompatible vertex data '
                             'shape: {}'.format(key, vdata.shape))
454
455

        self.__vertexData[key] = vdata.reshape(nvertices, -1)
456
457


458
459
460
461
    def getVertexData(self, key):
        """Returns the vertex data for the given ``key`` from the
        internal vertex data cache. If there is no vertex data iwth the
        given key, a ``KeyError`` is raised.
462
463
        """

464
        return self.__vertexData[key]
465
466
467
468


    def clearVertexData(self):
        """Clears the internal vertex data cache - see the
469
        :meth:`addVertexData` and :meth:`getVertexData` methods.
470
        """
471
        self.__vertexData = collections.OrderedDict()
472
473


474
475
476
477
478
    def vertexDataSets(self):
        """Returns a list of keys for all loaded vertex data sets. """
        return list(self.__vertexData.keys())


479
480
481
482
483
484
    @memoize.Instanceify(memoize.memoize)
    def trimesh(self):
        """Reference to a ``trimesh.Trimesh`` object which can be used for
        geometric operations on the mesh.

        If the ``trimesh`` or ``rtree`` libraries are not available, this
485
486
        function returns ``None``, and none of the geometric query methods
        will do anything.
487
488
489
490
491
492
493
494
495
496
497
498
499
500
        """

        # trimesh is an optional dependency - rtree
        # is a depedendency of trimesh which is a
        # wrapper around libspatialindex, without
        # which trimesh can't be used for calculating
        # ray-mesh intersections.
        try:
            import trimesh
            import rtree   # noqa
        except ImportError:
            log.warning('trimesh is not available')
            return None

501
502
503
504
505
506
507
        tm = self.__trimesh.get(self.__selected, None)

        if tm is None:
            tm = trimesh.Trimesh(self.vertices,
                                 self.indices,
                                 process=False,
                                 validate=False)
508

509
            self.__trimesh[self.__selected] = tm
510

511
        return tm
512
513


514
    def rayIntersection(self, origins, directions, vertices=False):
515
516
517
518
519
        """Calculate the intersection between the mesh, and the rays defined by
        ``origins`` and ``directions``.

        :arg origins:    Sequence of ray origins
        :arg directions: Sequence of ray directions
520
521
522
523
524
525
526
527
528
        :returns:        A tuple containing:

                           - A ``(n, 3)`` array containing the coordinates
                             where the mesh was intersected by each of the
                             ``n`` rays.

                           - A ``(n,)`` array containing the indices of the
                             triangles that were intersected by each of the
                             ``n`` rays.
529
530
531
532
533
        """

        trimesh = self.trimesh()

        if trimesh is None:
534
            return np.zeros((0, 3)), np.zeros((0,))
535

536
        tris, rays, locs = trimesh.ray.intersects_id(
537
538
539
            origins,
            directions,
            return_locations=True,
540
            multiple_hits=False)
541

Paul McCarthy's avatar
Paul McCarthy committed
542
        if len(tris) == 0:
543
544
            return np.zeros((0, 3)), np.zeros((0,))

545
546
        # sort by ray. I'm Not sure if this is
        # needed - does trimesh do it for us?
547
        rayIdxs = np.asarray(np.argsort(rays), np.int)
548
549
        locs    = locs[rayIdxs]
        tris    = tris[rayIdxs]
550

551
        return locs, tris
552
553


554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
    def nearestVertex(self, points):
        """Identifies the nearest vertex to each of the provided points.

        :arg points: A ``(n, 3)`` array containing the points to query.

        :returns:    A tuple containing:

                      - A ``(n, 3)`` array containing the nearest vertex for
                        for each of the ``n`` input points.

                      - A ``(n,)`` array containing the indices of each vertex.

                      - A ``(n,)`` array containing the distance from each
                        point to the nearest vertex.
        """

        trimesh = self.trimesh()

        if trimesh is None:
573
            return np.zeros((0, 3)), np.zeros((0, )), np.zeros((0, ))
574
575
576
577
578
579
580

        dists, idxs = trimesh.nearest.vertex(points)
        verts       = self.vertices[idxs, :]

        return verts, idxs, dists


581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
    def planeIntersection(self,
                          normal,
                          origin,
                          distances=False):
        """Calculate the intersection of this ``TriangleMesh`` with
        the plane defined by ``normal`` and ``origin``.

        :arg normal:    Vector defining the plane orientation

        :arg origin:    Point defining the plane location

        :arg distances: If ``True``, barycentric coordinates for each
                        intersection line vertex are calculated and returned,
                        giving their respective distance from the intersected
                        triangle vertices.

        :returns:       A tuple containing
                          - A ``(m, 2, 3)`` array containing ``m`` vertices:
                            of a set of lines, defining the plane intersection

                          - A ``(m,)`` array containing the indices of the
                            ``m`` triangles that were intersected.

                          - (if ``distances is True``) A ``(m, 2, 3)`` arra
                            containing the barycentric coordinates of each
                            line vertex with respect to its intersected
                            triangle.
        """

        trimesh = self.trimesh()

        if trimesh is None:
            return np.zeros((0, 3)), np.zeros((0, 3))

        import trimesh.intersections as tmint
        import trimesh.triangles     as tmtri

        lines, faces = tmint.mesh_plane(
            trimesh,
            plane_normal=normal,
            plane_origin=origin,
            return_faces=True)

        if not distances:
            return lines, faces

        # Calculate the barycentric coordinates
        # (distance from triangle vertices) for
        # each intersection line

        triangles = self.vertices[self.indices[faces]].repeat(2, axis=0)
        points    = lines.reshape((-1, 3))

        if triangles.size > 0:
            dists = tmtri.points_to_barycentric(triangles, points)
            dists = dists.reshape((-1, 2, 3))
        else:
            dists = np.zeros((0, 2, 3))

        return lines, faces, dists


643
644
645
def calcFaceNormals(vertices, indices):
    """Calculates face normals for the mesh described by ``vertices`` and
    ``indices``.
646

647
648
649
650
    :arg vertices: A ``(n, 3)`` array containing the mesh vertices.
    :arg indices:  A ``(m, 3)`` array containing the mesh triangles.
    :returns:      A ``(m, 3)`` array containing normals for every triangle in
                   the mesh.
651
    """
652

653
654
655
    v0 = vertices[indices[:, 0]]
    v1 = vertices[indices[:, 1]]
    v2 = vertices[indices[:, 2]]
656

657
658
    fnormals = np.cross((v1 - v0), (v2 - v0))
    fnormals = transform.normalise(fnormals)
659

660
    return fnormals
661

662

663
664
665
def calcVertexNormals(vertices, indices, fnormals):
    """Calculates vertex normals for the mesh described by ``vertices``
    and ``indices``.
666

667
668
669
670
671
672
    :arg vertices: A ``(n, 3)`` array containing the mesh vertices.
    :arg indices:  A ``(m, 3)`` array containing the mesh triangles.
    :arg fnormals: A ``(m, 3)`` array containing the face/triangle normals.
    :returns:      A ``(n, 3)`` array containing normals for every vertex in
                   the mesh.
    """
673

674
    vnormals = np.zeros((vertices.shape[0], 3), dtype=np.float)
675

676
677
678
679
680
    # TODO make fast. I can't figure
    # out how to use np.add.at to
    # accumulate the face normals for
    # each vertex.
    for i in range(indices.shape[0]):
681

682
        v0, v1, v2 = indices[i]
683

684
685
686
        vnormals[v0, :] += fnormals[i]
        vnormals[v1, :] += fnormals[i]
        vnormals[v2, :] += fnormals[i]
687

688
689
    # normalise to unit length
    return transform.normalise(vnormals)
690
691


692
693
694
def needsFixing(vertices, indices, fnormals, loBounds, hiBounds):
    """Determines whether the triangle winding order, for the mesh described by
    ``vertices`` and ``indices``, needs to be flipped.
695

696
697
698
    If this function returns ``True``, the given ``indices`` and ``fnormals``
    need to be adjusted so that all face normals are facing outwards from the
    centre of the mesh. The necessary adjustments are as follows::
699

700
701
        indices[:, [1, 2]] = indices[:, [2, 1]]
        fnormals           = fnormals * -1
702

703
704
705
706
707
    :arg vertices: A ``(n, 3)`` array containing the mesh vertices.
    :arg indices:  A ``(m, 3)`` array containing the mesh triangles.
    :arg fnormals: A ``(m, 3)`` array containing the face/triangle normals.
    :arg loBounds: A ``(3, )`` array contaning the low vertex bounds.
    :arg hiBounds: A ``(3, )`` array contaning the high vertex bounds.
708

709
710
    :returns:      ``True`` if the ``indices`` and ``fnormals`` need to be
                   adjusted, ``False`` otherwise.
711
712
    """

713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
    # Define a viewpoint which is
    # far away from the mesh.
    camera = loBounds - (hiBounds - loBounds)

    # Find the nearest vertex
    # to the viewpoint
    dists = np.sqrt(np.sum((vertices - camera) ** 2, axis=1))
    ivert = np.argmin(dists)
    vert  = vertices[ivert]

    # Pick a triangle that
    # this vertex is in and
    # ges its face normal
    itri = np.where(indices == ivert)[0][0]
    n    = fnormals[itri, :]

    # Make sure the angle between the
    # normal, and a vector from the
    # vertex to the camera is positive
    # If it isn't, we need to flip the
    # triangle winding order.
    return np.dot(n, transform.normalise(camera - vert)) < 0
735
736
737


class TriangleMesh(Mesh):
738
    """Deprecated - use :class:`fsl.data.mesh.Mesh`, or one of its sub-classes
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
    instead.
    """


    @deprecation.deprecated(deprecated_in='1.6.0',
                            removed_in='2.0.0',
                            details='Use fsl.data.mesh.Mesh, or one '
                                    'of its sub-classes instead')
    def __init__(self, data, indices=None, fixWinding=False):

        import fsl.data.vtk as fslvtk

        if isinstance(data, six.string_types):
            name       = op.basename(data)
            dataSource = data
            mesh       = fslvtk.VTKMesh(data, fixWinding=False)
            vertices   = mesh.vertices
            indices    = mesh.indices

        else:
            name       = 'TriangleMesh'
            dataSource = None
            vertices   = data

        Mesh.__init__(self, indices, name=name, dataSource=dataSource)
        self.addVertices(vertices, 'default', fixWinding=fixWinding)


    @deprecation.deprecated(deprecated_in='1.6.0',
                            removed_in='2.0.0',
                            details='Use the Mesh class instead')
    def loadVertexData(self, dataSource, vertexData=None):

        nvertices = self.vertices.shape[0]

        # Currently only white-space delimited
        # text files are supported
        if vertexData is None:
            vertexData = np.loadtxt(dataSource)
            vertexData.reshape(nvertices, -1)

        if vertexData.shape[0] != nvertices:
            raise ValueError('Incompatible size: {}'.format(dataSource))

        self.addVertexData(dataSource, vertexData)

        return vertexData


788
789
790
791
792
793
794
795
    @deprecation.deprecated(deprecated_in='1.6.0',
                            removed_in='2.0.0',
                            details='Use bounds instead')
    def getBounds(self):
        """Deprecated - use :meth:`bounds` instead. """
        return self.bounds


796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
    @deprecation.deprecated(deprecated_in='1.6.0',
                            removed_in='2.0.0',
                            details='Use the Mesh class instead')
    def getVertexData(self, dataSource):
        try:
            return Mesh.getVertexData(self, dataSource)
        except KeyError:
            return self.loadVertexData(dataSource)


@deprecation.deprecated(deprecated_in='1.6.0',
                        removed_in='2.0.0',
                        details='Use fsl.data.vtk.loadVTKPolydataFile instead')
def loadVTKPolydataFile(*args, **kwargs):
    """Deprecated - use :func:`fsl.data.vtk.loadVTKPolydataFile` instead. """
    import fsl.data.vtk as fslvtk
    return fslvtk.loadVTKPolydataFile(*args, **kwargs)


@deprecation.deprecated(deprecated_in='1.6.0',
                        removed_in='2.0.0',
                        details='Use fsl.data.vtk.getFIRSTPrefix instead')
def getFIRSTPrefix(*args, **kwargs):
    """Deprecated - use :func:`fsl.data.vtk.getFIRSTPrefix` instead. """
    import fsl.data.vtk as fslvtk
    return fslvtk.getFIRSTPrefix(*args, **kwargs)


@deprecation.deprecated(deprecated_in='1.6.0',
                        removed_in='2.0.0',
                        details='Use fsl.data.vtk.findReferenceImage instead')
def findReferenceImage(*args, **kwargs):
    """Deprecated - use :func:`fsl.data.vtk.findReferenceImage` instead. """
    import fsl.data.vtk as fslvtk
    return fslvtk.findReferenceImage(*args, **kwargs)
831
832
833
834
835
836
837
838
839
840


ALLOWED_EXTENSIONS = ['.vtk']
"""Deprecated, will be removed in fslpy 2.0.0. Use
:attr:`fsl.data.vtk.ALLOWED_EXTENSIONS` instead."""


EXTENSION_DESCRIPTIONS = ['VTK polygon model file']
"""Deprecated, will be removed in fslpy 2.0.0. Use
:attr:`fsl.data.vtk.EXTENSION_DESCRIPTIONS` instead."""