tst: added basic io tests

Author: satra

nibabel/cifti/__init__.py

@@ -18,7 +18,7 @@
 """
 
 from .parse_cifti_fast import create_cifti_image
-from .cifti import (CiftiMetaData, CiftiHeader, CiftiLabel,
+from .cifti import (CiftiMetaData, CiftiHeader, CiftiImage, CiftiLabel,
                     CiftiLabelTable, CiftiNVPair, CiftiVertexIndices,
                     CiftiVoxelIndicesIJK, CiftiBrainModel, CiftiMatrix,
                     CiftiMatrixIndicesMap, CiftiNamedMap, CiftiParcel,

nibabel/cifti/cifti.py

@@ -263,10 +263,9 @@ def __init__(self, brainStructure=None, surfaceNumberOfVertices=None):
     def to_xml(self, prefix='', indent='    '):
         if self.brainStructure is None:
             return ''
-        res = ('%s<Surface BrainStructure="%s" '
-               'SurfaceNumberOfVertices"%s" />\n') % (prefix,
-                                                      self.brainStructure,
-                                                      self.surfaceNumberOfVertices)
+        res = ('%s<Surface BrainStructure="%s" SurfaceNumberOfVertices="%s" '
+               '/>\n') % (prefix, self.brainStructure,
+                          self.surfaceNumberOfVertices)
         return res
 
 class CiftiVoxelIndicesIJK(object):
@@ -740,8 +739,10 @@ def from_header(klass, header=None):
 class CiftiImage(object):
     header_class = CiftiHeader
 
-    def __init__(self, data, header, nifti_header):
-        self.header = header
+    def __init__(self, data=None, header=None, nifti_header=None):
+        self.header = CiftiHeader()
+        if header is not None:
+            self.header = header
         self.data = data
         self.extra = nifti_header
 

nibabel/cifti/parse_cifti_fast.py

@@ -361,10 +361,7 @@ def parse_cifti_string(cifti_string):
     out = Outputter()
     for name in HANDLER_NAMES:
         setattr(parser, name, getattr(out, name))
-    try:
-        parser.Parse(cifti_string, True)
-    except ExpatError:
-        print('An expat error occured while parsing the  Cifti file.')
+    parser.Parse(cifti_string, True)
     return out.header
 
 def create_cifti_image(nifti2_image, cifti_header, intent_code):
@@ -374,6 +371,8 @@ def create_cifti_image(nifti2_image, cifti_header, intent_code):
         if ext.get_code() == 32:
             nifti_header.extensions.remove(ext)
             break
+    with open('test.xml', 'wt') as fp:
+        fp.writelines(cifti_header)
     header = parse_cifti_string(cifti_header)
     img = CiftiImage(data, header, nifti_header)
     return img

nibabel/cifti/tests/test_ciftiio.py

@@ -0,0 +1,96 @@
+# 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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+from __future__ import division, print_function, absolute_import
+
+from os.path import join as pjoin, dirname
+import sys
+
+import numpy as np
+
+from ... import cifti as ci
+
+from ...tmpdirs import InTemporaryDirectory
+
+from numpy.testing import assert_array_equal, assert_array_almost_equal
+
+from nose.tools import (assert_true, assert_false, assert_equal,
+                        assert_raises)
+
+
+IO_DATA_PATH = pjoin(dirname(__file__), 'data')
+
+DATA_FILE1 = pjoin(IO_DATA_PATH, '')
+DATA_FILE2 = pjoin(IO_DATA_PATH,
+                   'Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii')
+DATA_FILE3 = pjoin(IO_DATA_PATH,
+                   'Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii')
+DATA_FILE4 = pjoin(IO_DATA_PATH,
+                   'Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii')
+DATA_FILE5 = pjoin(IO_DATA_PATH,
+                   'Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii')
+DATA_FILE6 = pjoin(IO_DATA_PATH, 'ones.dscalar.nii')
+
+datafiles = [DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5, DATA_FILE6]
+
+def test_read_ordering():
+    # DATA_FILE1 has an expected darray[0].data shape of (3,3).  However if we
+    # read another image first (DATA_FILE2) then the shape is wrong
+    # Read an image
+    img2 = ci.load(DATA_FILE6)
+    assert_equal(img2.data.shape, (91282,))
+
+
+def test_version():
+    for i, dat in enumerate(datafiles):
+        img = ci.load(dat)
+        assert_equal(img.header.version, '2')
+
+'''
+def test_dataarray1():
+    img1 = gi.read(DATA_FILE1)
+    # Round trip
+    with InTemporaryDirectory():
+        gi.write(img1, 'test.gii')
+        bimg = gi.read('test.gii')
+    for img in (img1, bimg):
+        assert_array_almost_equal(img.darrays[0].data, DATA_FILE1_darr1)
+        assert_array_almost_equal(img.darrays[1].data, DATA_FILE1_darr2)
+        me=img.darrays[0].meta.get_metadata()
+        assert_true('AnatomicalStructurePrimary' in me)
+        assert_true('AnatomicalStructureSecondary' in me)
+        assert_equal(me['AnatomicalStructurePrimary'], 'CortexLeft')
+        assert_array_almost_equal(img.darrays[0].coordsys.xform, np.eye(4,4))
+        assert_equal(xform_codes.niistring[img.darrays[0].coordsys.dataspace],'NIFTI_XFORM_TALAIRACH')
+        assert_equal(xform_codes.niistring[img.darrays[0].coordsys.xformspace],'NIFTI_XFORM_TALAIRACH')
+'''
+
+
+def test_readwritedata():
+    with InTemporaryDirectory():
+        for name in datafiles:
+            img = ci.load(name)
+            img.to_filename('test.nii')
+            img2 = ci.load('test.nii')
+            assert_equal(img.header.matrix.numMIM,img2.header.matrix.numMIM)
+            assert_array_almost_equal(img.data,
+                                      img2.data)
+
+
+def test_newmetadata():
+    img = ci.CiftiImage()
+    attr = ci.CiftiNVPair(name = 'mykey', value = 'val1')
+    newmeta = ci.CiftiMetaData(attr)
+    img.header.matrix.meta = newmeta
+    myme = img.header.matrix.meta.get_metadata()
+    assert_true('mykey' in myme)
+    newmeta = ci.CiftiMetaData.from_dict( {'mykey1' : 'val2'} )
+    img.header.matrix.meta = newmeta
+    myme = img.header.matrix.meta.get_metadata()
+    assert_true('mykey1' in myme)
+    assert_false('mykey' in myme)

nibabel/nifti2.py

@@ -237,16 +237,26 @@ def from_file_map(klass, file_map):
         img = super(Nifti2Image, klass).from_file_map(file_map)
         hdr = img.get_header()
         intent_code = hdr.get_intent('code')[0]
+        img.is_cifti = False
         if intent_code >= 3000 and intent_code < 3100:
-            cifti_header = None
-            if  hdr.extensions is not None:
-                for extension in hdr.extensions:
-                    if extension.get_code() == 32:
-                        cifti_header = extension.get_content()
-            if cifti_header is None:
-                raise ValueError(('Nifti2 header does not contain a CIFTI '
-                                  'extension'))
-            img = create_cifti_image(img, cifti_header, intent_code)
+            img.is_cifti = True
+            img = img.to_cifti()
+        return img
+
+    def to_cifti(self):
+        if not self.is_cifti:
+            TypeError('Nifti2 image is not a CIFTI file')
+        hdr = self.get_header()
+        intent_code = hdr.get_intent('code')[0]
+        cifti_header = None
+        if hdr.extensions is not None:
+            for extension in hdr.extensions:
+                if extension.get_code() == 32:
+                    cifti_header = extension.get_content()
+        if cifti_header is None:
+            raise ValueError(('Nifti2 header does not contain a CIFTI '
+                              'extension'))
+        img = create_cifti_image(self, cifti_header, intent_code)
         return img
 
 def load(filename):