Zeropad Extension to 16 bytes, test writing

Also, fix _guess_implicit_VR method.

Author: kastman

nibabel/nifti1.py

@@ -390,7 +390,7 @@ class Nifti1DicomExtension(Nifti1Extension):
     def __init__(self, code, content):
         self._code = code
         self._raw_content = content
-        self._guess_implicit_VR()
+        self._is_implicit_VR = self._guess_implicit_VR()
         self._content = self._unmangle(content)
 
         super(Nifti1DicomExtension,self)
@@ -400,12 +400,12 @@ def _guess_implicit_VR(self):
         Representations (VRs) are included in the DICOM encoding or not.
         This reads where the first VR would be and checks it against a list of
         valid VRs"""
-        potential_vr = self._raw_content[8:12]
+        potential_vr = self._raw_content[4:6].decode()
         if potential_vr in dicom_converters.keys():
-            self._is_implicit_VR=False
+            implicit_VR=False
         else:
-            self._is_implicit_VR=True
-        return self._is_implicit_VR
+            implicit_VR=True
+        return implicit_VR
 
     def _is_little_endian(self):
         return True
@@ -415,19 +415,24 @@ def _unmangle(self,value):
         ds=read_dataset(raw_io,self._is_implicit_VR,self._is_little_endian)
         return ds
 
-    def _mangle(self):
+    def _mangle(self, value):
         raw_io=BytesIO()
         dio=DicomFileLike(raw_io)
         dio.is_implicit_VR = self._is_implicit_VR
         dio.is_little_endian = self._is_little_endian
-        ds_len=write_dataset(dio,self._content)
+        ds_len=write_dataset(dio,value)
         dio.seek(0)
         return dio.read(ds_len)
 
     def get_sizeondisk(self):
         """Return the size of the extension in the NIfTI file.
         """
-        return len(self._mangle())
+        size = len(self._mangle(self._content))
+        size += 8
+        # extensions size has to be a multiple of 16 bytes
+        size += 16 - (size % 16)
+        
+        return size
 
 try:
     from dicom.filereader import read_dataset

nibabel/tests/test_nifti1.py

@@ -44,6 +44,7 @@
 try:
     import dicom
     import struct
+    from io import BytesIO
 except ImportError:
     have_dicom = False
 else:
@@ -1087,29 +1088,37 @@ def test_nifti_dicom_extension():
     exts_container = hdr.extensions
 
     # create a single dicom tag (Patien ID, [0010,0020]) with Explicit VR
-    dcmbytes = struct.pack('<HH2sH4s',0x10,0x20,
+    dcmbytes_explicit = struct.pack('<HH2sH4s',0x10,0x20,
         'LO'.encode('utf-8'),4,'NiPy'.encode('utf-8'))
-    dcmext = Nifti1DicomExtension(2,dcmbytes)
+    dcmext = Nifti1DicomExtension(2,dcmbytes_explicit)
     assert_equal(dcmext.__class__, Nifti1DicomExtension)
+    assert_equal(dcmext._guess_implicit_VR(),False)
+    assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
-
+    assert_equal(dcmext._mangle(dcmext.get_content()),dcmbytes_explicit)
+    assert_equal(dcmext.get_sizeondisk() % 16, 0)
+    
     # create a single dicom tag (Patien ID, [0010,0020]) with Implicit VR
-    dcmbytes = struct.pack('<HHL4s',0x10,0x20,4,'NiPy'.encode('utf-8'))
-    dcmext = Nifti1DicomExtension(2,dcmbytes)
+    dcmbytes_implicit = struct.pack('<HHL4s',0x10,0x20,4,'NiPy'.encode('utf-8'))
+    dcmext = Nifti1DicomExtension(2,dcmbytes_implicit)
+    assert_equal(dcmext._guess_implicit_VR(),True)
+    assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
-    assert_equal(dcmext.get_sizeondisk(), len(dcmbytes))
-    assert_equal(dcmext._mangle(),dcmbytes)
+    assert_equal(dcmext._mangle(dcmext.get_content()),dcmbytes_implicit)
+    assert_equal(dcmext.get_sizeondisk() % 16, 0)
 
     # dicom extension access from nifti extensions
     assert_equal(exts_container.count('dicom'),0)
     exts_container.append(dcmext)
     assert_equal(exts_container.count('dicom'), 1)
     assert_equal(exts_container.get_codes(), [6, 6, 2])
-    assert_equal(dcmext.get_sizeondisk(), len(dcmbytes))
-    assert_equal(dcmext._mangle(),dcmbytes)
-    # assert_equal((exts_container.get_sizeondisk()) % 16, 0)
+    assert_equal(dcmext._mangle(dcmext.get_content()),dcmbytes_implicit)
+    assert_equal(dcmext.get_sizeondisk() % 16, 0)
+
+    raw_io = BytesIO()
+    dcmext.write_to(raw_io,False)
 
 class TestNifti1General(object):
     """ Test class to test nifti1 in general