Merge branch 'bf/mesh_indices' into 'master'

Bf/mesh indices

See merge request fsl/fslpy!185

CHANGELOG.rst

@@ -34,6 +34,9 @@ Fixed
 * Improved the algorithm used by the :func:`.mesh.needsFixing` function.
 * The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
   output specification.
+* Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded
+  as floating point type.
+* Fixed a bug in the :func:`.resample` function.
 
 
 Deprecated

fsl/data/mesh.py

@@ -154,14 +154,6 @@ class Mesh(notifier.Notifier, meta.Meta):
     """
 
 
-    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)
-
-
     def __init__(self,
                  indices,
                  name='mesh',
@@ -189,7 +181,7 @@ class Mesh(notifier.Notifier, meta.Meta):
 
         self.__name       = name
         self.__dataSource = dataSource
-        self.__nvertices  = indices.max() + 1
+        self.__nvertices  = int(indices.max()) + 1
         self.__selected   = None
 
         # We potentially store two copies of
@@ -197,7 +189,7 @@ class Mesh(notifier.Notifier, meta.Meta):
         # orders. The vindices dict stores refs
         # to one or the other for each vertex
         # set.
-        self.__indices      = np.asarray(indices).reshape((-1, 3))
+        self.__indices      = np.asarray(indices, dtype=np.int32).reshape((-1, 3))
         self.__fixedIndices = None
         self.__vindices     = collections.OrderedDict()
 

fsl/utils/image/resample.py

@@ -47,9 +47,9 @@ def resampleToReference(image, reference, matrix=None, **kwargs):
     along the spatial (first three) dimensions.
 
     :arg image:     :class:`.Image` to resample
-    :arg matrix:    Optional world-to-world affine alignment matrix
     :arg reference: :class:`.Nifti` defining the space to resample ``image``
                     into
+    :arg matrix:    Optional world-to-world affine alignment matrix
     """
 
     oldShape = list(image.shape)
@@ -204,9 +204,10 @@ def resample(image,
     if matrix is None:
         matrix = affine.rescale(data.shape, newShape, origin)
 
-    # identity matrix? the image
-    # doesn't need to be resampled
-    if np.all(np.isclose(matrix, np.eye(len(newShape) + 1))):
+    # same shape and identity matrix? the
+    # image doesn't need to be resampled
+    if np.all(np.isclose(data.shape, newShape)) and \
+       np.all(np.isclose(matrix, np.eye(len(newShape) + 1))):
         return data, image.voxToWorldMat
 
     newShape = np.array(np.round(newShape), dtype=np.int)

requirements-extra.txt

 indexed_gzip>=0.7.0
 wxpython==4.*
 trimesh>=2.37.29
-rtree==0.8.3
+rtree>=0.8.3
 Pillow>=3.2.0