Merge pull request #249 from satra/enh/cifti2

MRG: CIFTI2 spec reader and writer

Initial read / write capability for CIFTI2.   The API may change in the future, before a first release, please be careful.

Author: matthew-brett

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "nibabel-data/parrec_oblique"]
 	path = nibabel-data/parrec_oblique
 	url = https://github.com/grlee77/parrec_oblique.git
+[submodule "nibabel-data/nitest-cifti2"]
+	path = nibabel-data/nitest-cifti2
+	url = https://github.com/demianw/nibabel-nitest-cifti2.git

nibabel-data/nitest-cifti2

@@ -51,6 +51,7 @@
 from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
 from .minc1 import Minc1Image
 from .minc2 import Minc2Image
+from .cifti2 import Cifti2Header, Cifti2Image
 # Deprecated backwards compatiblity for MINC1
 from .deprecated import ModuleProxy as _ModuleProxy
 minc = _ModuleProxy('nibabel.minc')

nibabel/__init__.py

@@ -27,6 +27,8 @@
 """
 import warnings
 
+import numpy as np
+
 from .volumeutils import array_from_file, apply_read_scaling
 from .fileslice import fileslice
 from .keywordonly import kw_only_meth
@@ -111,8 +113,12 @@ def shape(self):
         return self._shape
 
     @property
-    def is_proxy(self):
-        return True
+    def dtype(self):
+        return self._dtype
+
+    @property
+    def offset(self):
+        return self._offset
 
     @property
     def slope(self):
@@ -123,8 +129,8 @@ def inter(self):
         return self._inter
 
     @property
-    def offset(self):
-        return self._offset
+    def is_proxy(self):
+        return True
 
     def get_unscaled(self):
         ''' Read of data from file
@@ -164,3 +170,10 @@ def is_proxy(obj):
         return obj.is_proxy
     except AttributeError:
         return False
+
+
+def reshape_dataobj(obj, shape):
+    """ Use `obj` reshape method if possible, else numpy reshape function
+    """
+    return (obj.reshape(shape) if hasattr(obj, 'reshape')
+            else np.reshape(obj, shape))

nibabel/arrayproxy.py

@@ -0,0 +1,27 @@
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""CIfTI format IO
+
+.. currentmodule:: nibabel.cifti2
+
+.. autosummary::
+   :toctree: ../generated
+
+   cifti2
+"""
+
+from .parse_cifti2 import Cifti2Extension
+from .cifti2 import (Cifti2MetaData, Cifti2Header, Cifti2Image, Cifti2Label,
+                     Cifti2LabelTable, Cifti2VertexIndices,
+                     Cifti2VoxelIndicesIJK, Cifti2BrainModel, Cifti2Matrix,
+                     Cifti2MatrixIndicesMap, Cifti2NamedMap, Cifti2Parcel,
+                     Cifti2Surface,
+                     Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ,
+                     Cifti2Vertices, Cifti2Volume, CIFTI_BRAIN_STRUCTURES,
+                     Cifti2HeaderError, CIFTI_MODEL_TYPES, load, save)