diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 0347a5df351c952d247feb8efaa3416d70d62c36..912d98a07979aa01b3feb25ff2b4cf8cd355ac3e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -12,6 +12,20 @@ Added
* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
Cottaar).
+* New :func:`.makeWriteable` function which ensures that a ``numpy.array`` is
+ writeable, and creates a copy if necessary
+
+
+Changed
+^^^^^^^
+
+
+* The :class:`.GiftiMesh` class no longer creates copies of the mesh
+ vertex/index arrays. This means that, with ``numpy>=1.16`` these arrays
+ will be flagged as read-only.
+* The :class:`.Mesh` class handles vertex data sets requiring different
+ triangle unwinding orders, at the cost of potentially having to store
+ two copies of the mesh indices.
Fixed
diff --git a/fsl/data/__init__.py b/fsl/data/__init__.py
index c1890b375baadbf3a78f1ac8437145040cab8570..3c5afc3f2d09c49b5c1e5be18d20b7b5eab0cc56 100644
--- a/fsl/data/__init__.py
+++ b/fsl/data/__init__.py
@@ -9,4 +9,5 @@ models, constants, and other data-like things used throughout ``fslpy``.
"""
-from .utils import guessType # noqa
+from .utils import (guessType, # noqa
+ makeWriteable)
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index abd41f7d43e468136c08be7e418ec8cbdb0bda9f..aa8b20ed7b8cedf7a168c901458f0aa85e8d770e 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -211,8 +211,8 @@ def loadGiftiMesh(filename):
raise ValueError('{}: GIFTI surface files must contain '
'at least one pointset array'.format(filename))
- vertices = [np.array(ps.data) for ps in pointsets]
- indices = np.array(triangles[0].data)
+ vertices = [ps.data for ps in pointsets]
+ indices = triangles[0].data
if len(vdata) == 0: vdata = None
else: vdata = prepareGiftiVertexData(vdata, filename)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index f5ca20adea3747ca53945755f61c85dc28c539d1..e581c96037108376d1ba551b46f32d9b8720c0df 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -98,6 +98,12 @@ class Mesh(notifier.Notifier, meta.Meta):
selectedVertices
vertexSets
+ .. note:: Internally the ``Mesh`` class may store two versions of the
+ triangles, with opposite unwinding orders. It keeps track of the
+ required triangle unwinding order for each vertex set, so that
+ the :meth:`indices` method will return the appropriate copy for
+ the currently selected vertex set.
+
**Vertex data**
@@ -183,19 +189,17 @@ class Mesh(notifier.Notifier, meta.Meta):
self.__name = name
self.__dataSource = dataSource
- self.__indices = np.asarray(indices).reshape((-1, 3))
- self.__nvertices = self.__indices.max() + 1
-
- # 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
+ self.__nvertices = indices.max() + 1
+ self.__selected = None
+
+ # We potentially store two copies of
+ # the indices, with opposite unwinding
+ # orders. The vindices dict stores refs
+ # to one or the other for each vertex
+ # set.
+ self.__indices = np.asarray(indices).reshape((-1, 3))
+ self.__fixedIndices = None
+ self.__vindices = collections.OrderedDict()
# All of these are populated
# in the addVertices method
@@ -287,7 +291,7 @@ class Mesh(notifier.Notifier, meta.Meta):
@property
def indices(self):
"""The ``(M, 3)`` triangles of this mesh. """
- return self.__indices
+ return self.__vindices[self.__selected]
@property
@@ -297,7 +301,7 @@ class Mesh(notifier.Notifier, meta.Meta):
"""
selected = self.__selected
- indices = self.__indices
+ indices = self.__vindices[selected]
vertices = self.__vertices[selected]
fnormals = self.__faceNormals.get(selected, None)
@@ -315,7 +319,7 @@ class Mesh(notifier.Notifier, meta.Meta):
"""
selected = self.__selected
- indices = self.__indices
+ indices = self.__vindices[selected]
vertices = self.__vertices[selected]
vnormals = self.__vertNormals.get(selected, None)
@@ -334,10 +338,8 @@ class Mesh(notifier.Notifier, meta.Meta):
``((xlow, ylow, zlow), (xhigh, yhigh, zhigh))``
"""
-
lo = self.__loBounds[self.__selected]
hi = self.__hiBounds[self.__selected]
-
return lo, hi
@@ -411,26 +413,26 @@ class Mesh(notifier.Notifier, meta.Meta):
self.nvertices))
self.__vertices[key] = vertices
+ self.__vindices[key] = self.__indices
self.__loBounds[key] = lo
self.__hiBounds[key] = hi
if select:
self.vertices = key
- # 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
+ if fixWinding:
+ indices = self.__indices
+ normals = self.normals
+ needsFix = needsFixing(vertices, indices, normals, lo, hi)
# See needsFixing documentation
if needsFix:
- indices[:, [1, 2]] = indices[:, [2, 1]]
+ if self.__fixedIndices is None:
+ self.__fixedIndices = indices[:, [0, 2, 1]]
- for k, fn in self.__faceNormals.items():
- self.__faceNormals[k] = fn * -1
+ self.__vindices[ key] = self.__fixedIndices
+ self.__faceNormals[key] = normals * -1
return vertices
diff --git a/fsl/data/utils.py b/fsl/data/utils.py
index e0fae151e05c02d5ecfe6289e5e1779ee9276a61..d902dc18a2b77c753c7d43f09d70398ebb25b71a 100644
--- a/fsl/data/utils.py
+++ b/fsl/data/utils.py
@@ -10,7 +10,7 @@ with the data types defined in the :mod:`fsl.data` package.
import os.path as op
-
+import numpy as np
def guessType(path):
"""A convenience function which, given the name of a file or directory,
@@ -77,3 +77,14 @@ def guessType(path):
# Otherwise, I don't
# know what to do
return None, path
+
+
+def makeWriteable(array):
+ """Updates the given ``numpy.array`` so that it is writeable. If this
+ is not possible, a copy is created and returned.
+ """
+ try:
+ array.flags['WRITEABLE'] = True
+ except ValueError:
+ array = np.array(array)
+ return array
diff --git a/tests/test_fsl_data_utils.py b/tests/test_fsl_data_utils.py
index 3fd02a8f948d921fda54c0ca9481a83154d371fc..1ef030bd228dbc263a0b390329a646f162e186a3 100644
--- a/tests/test_fsl_data_utils.py
+++ b/tests/test_fsl_data_utils.py
@@ -9,6 +9,8 @@ import shutil
import os
import os.path as op
+import numpy as np
+
import fsl.utils.tempdir as tempdir
import fsl.data.utils as dutils
@@ -105,3 +107,22 @@ def test_guessType():
asrt('norecognise.txt', None)
os.remove('norecognise')
os.remove('norecognise.txt')
+
+
+def test_makeWriteable():
+ robuf = bytes( b'\01\02\03\04')
+ wbuf = bytearray(b'\01\02\03\04')
+
+ roarr = np.ndarray((4,), dtype=np.uint8, buffer=robuf)
+ warr = np.ndarray((4,), dtype=np.uint8, buffer=wbuf)
+
+ warr.flags['WRITEABLE'] = False
+
+ rocopy = dutils.makeWriteable(roarr)
+ wcopy = dutils.makeWriteable(warr)
+
+ assert rocopy.base is not roarr.base
+ assert wcopy .base is warr .base
+
+ rocopy[1] = 100
+ wcopy[ 1] = 100
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
index 8b97bfa1c180cd301af462a2f067aff02c04e4b1..20ff3cdb772878e1ece865f6fc98f7b813fa1824 100644
--- a/tests/test_mesh.py
+++ b/tests/test_mesh.py
@@ -417,3 +417,29 @@ def test_planeIntersection():
assert lines.shape == (0, 2, 3)
assert faces.shape == (0, )
assert dists.shape == (0, 2, 3)
+
+
+def test_mesh_different_winding_orders():
+
+ verts1 = CUBE_VERTICES
+ verts2 = -CUBE_VERTICES
+ tris = CUBE_TRIANGLES_CCW
+ trisfixed = CUBE_TRIANGLES_CW
+
+ mnofix = fslmesh.Mesh(tris)
+ mfix = fslmesh.Mesh(tris)
+
+ mnofix.addVertices(verts1, key='v1', fixWinding=False)
+ mnofix.addVertices(verts2, key='v2', fixWinding=False)
+ mfix .addVertices(verts1, key='v1', fixWinding=True)
+ mfix .addVertices(verts2, key='v2', fixWinding=True)
+
+ mnofix.vertices = 'v1'
+ assert np.all(mnofix.indices == tris)
+ mnofix.vertices = 'v2'
+ assert np.all(mnofix.indices == tris)
+
+ mfix.vertices = 'v1'
+ assert np.all(mfix.indices == tris)
+ mfix.vertices = 'v2'
+ assert np.all(mfix.indices == trisfixed)