RF+TST: drop CIFTI Matrix check, add tests

CIFTI matrix check was incorrect, metadata never required.  However, we
do need to have one or more MatrixIndicesMap entries referring to all
the axes in the data matrix.  Need to think about how to do this check,
as the XML generator does not know how many data dimensions we have.

Author: matthew-brett

nibabel/cifti2/cifti2.py

@@ -867,6 +867,23 @@ def _to_xml_element(self):
 
 
 class Cifti2Matrix(xml.XmlSerializable, collections.MutableSequence):
+    """ CIFTI2 Matrix object
+
+    This is a list-like container where the elements are instances of
+    :class:`Cifti2MatrixIndicesMap`.
+
+    * Description: contains child elements that describe the meaning of the
+      values in the matrix.
+    * Attributes: [NA]
+    * Child Elements
+    * MetaData (0 .. 1)
+    * MatrixIndicesMap (1 .. N)
+    * Text Content: [NA]
+    * Parent Element: CIFTI
+
+    For each matrix (data) dimension, exactly one MatrixIndicesMap element must
+    list it in the AppliesToMatrixDimension attribute.
+    """
     def __init__(self):
         self._mims = []
         self.metadata = None
@@ -909,11 +926,9 @@ def insert(self, index, value):
         self._mims.insert(index, value)
 
     def _to_xml_element(self):
-        if (len(self) == 0 and self.metadata is None):
-            raise CIFTI2HeaderError(
-                'Matrix element requires either a MatrixIndicesMap or a Metadata element'
-            )
-
+        # From the spec: "For each matrix dimension, exactly one
+        # MatrixIndicesMap element must list it in the AppliesToMatrixDimension
+        # attribute."
         mat = xml.Element('Matrix')
         if self.metadata:
             mat.append(self.metadata._to_xml_element())
@@ -970,9 +985,9 @@ def __init__(self,
         Parameters
         ----------
         dataobj : object
-            Object containing image data.  It should be some object that returns
-            an array from ``np.asanyarray``.  It should have a ``shape``
-            attribute or property.
+            Object containing image data.  It should be some object that
+            returns an array from ``np.asanyarray``.  It should have a
+            ``shape`` attribute or property.
         header : Cifti2Header instance
             Header with data for / from XML part of CIFTI2 format.
         nifti_header : None or mapping or NIfTI2 header instance, optional
@@ -985,6 +1000,11 @@ def __init__(self,
         super(Cifti2Image, self).__init__(dataobj, header=header,
                                           extra=extra, file_map=file_map)
         self._nifti_header = Nifti2Header.from_header(nifti_header)
+        # if NIfTI header not specified, get data type from input array
+        if nifti_header is None:
+            if hasattr(dataobj, 'dtype'):
+                self._nifti_header.set_data_dtype(dataobj.dtype)
+        self.update_headers()
 
     @property
     def nifti_header(self):
@@ -1055,6 +1075,7 @@ def to_file_map(self, file_map=None):
         None
         """
         from .parse_cifti2 import Cifti2Extension
+        self.update_headers()
         header = self._nifti_header
         extension = Cifti2Extension(content=self.header.to_xml())
         header.extensions.append(extension)
@@ -1066,6 +1087,26 @@ def to_file_map(self, file_map=None):
         img = Nifti2Image(data, None, header)
         img.to_file_map(file_map or self.file_map)
 
+    def update_headers(self):
+        ''' Harmonize CIFTI2 and NIfTI headers with image data
+
+        >>> import numpy as np
+        >>> data = np.zeros((2,3,4))
+        >>> img = Cifti2Image(data)
+        >>> img.shape == (2, 3, 4)
+        True
+        >>> img.update_headers()
+        >>> img.nifti_header.get_data_shape() == (2, 3, 4)
+        True
+        '''
+        self._nifti_header.set_data_shape(self._dataobj.shape)
+
+    def get_data_dtype(self):
+        return self._nifti_header.get_data_dtype()
+
+    def set_data_dtype(self, dtype):
+        self._nifti_header.set_data_dtype(dtype)
+
 
 def load(filename):
     """ Load cifti2 from `filename`

nibabel/cifti2/tests/test_cifti2.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 from nibabel import cifti2 as ci
+from nibabel.nifti2 import Nifti2Header
 from nibabel.cifti2.cifti2 import _float_01
 
 from nose.tools import assert_true, assert_equal, assert_raises, assert_is_none
@@ -292,3 +293,19 @@ def test_underscoring():
 
     for camel, underscored in pairs:
         assert_equal(ci.cifti2._underscore(camel), underscored)
+
+
+class TestCifti2ImageAPI(_TDA):
+    """ Basic validation for Cifti2Image instances
+    """
+    # A callable returning an image from ``image_maker(data, header)``
+    image_maker = ci.Cifti2Image
+    # A callable returning a header from ``header_maker()``
+    header_maker = ci.Cifti2Header
+    # A callable returning a nifti header
+    ni_header_maker = Nifti2Header
+    example_shapes = ((2,), (2, 3), (2, 3, 4))
+    standard_extension = '.nii'
+
+    def make_imaker(self, arr, header=None, ni_header=None):
+        return lambda: self.image_maker(arr.copy(), header, ni_header)

nibabel/tests/test_filebasedimages.py

@@ -60,15 +60,15 @@ class TestFBImageAPI(GenericImageAPI):
     can_save = True
     standard_extension = '.npy'
 
+    def make_imaker(self, arr, header=None):
+        return lambda: self.image_maker(arr, header)
+
     def obj_params(self):
         # Create new images
-        def make_imaker(arr, header=None):
-            return lambda: self.image_maker(arr, header)
-
         for shape, dtype in product(self.example_shapes, self.example_dtypes):
             arr = np.arange(np.prod(shape), dtype=dtype).reshape(shape)
             hdr = self.header_maker()
-            func = make_imaker(arr.copy(), hdr)
+            func = self.make_imaker(arr.copy(), hdr)
             params = dict(
                 dtype=dtype,
                 data=arr,