Use write_dataset for pydicom < 0.9.9 compat

Author: kastman

nibabel/nifti1.py

@@ -462,14 +462,25 @@ def _unmangle(self,value):
 
     def _mangle(self, value):
         bio=BytesIO()
-        write_file(bio,value)
-        bio.seek(0)
-        return bio.read()
+        dio=DicomFileLike(bio)
+        if self._preamble:
+            dio.write(self._preamble)  # blank 128 byte preamble
+            _write_file_meta_info(dio, self._meta)
+
+        # Set file VR, endian. MUST BE AFTER writing META INFO (which changes to Explicit LittleEndian)
+        dio.is_implicit_VR = self._is_implicit_VR
+        dio.is_little_endian = self._is_little_endian
+
+        write_dataset(dio, value)
+        # write_file(bio,value)
+        dio.seek(0)
+        return dio.read()
 
 try:
     from dicom.dataset import FileDataset
     from dicom.filereader import read_dataset,read_preamble,_read_file_meta_info
-    from dicom.filewriter import write_file
+    from dicom.filewriter import write_dataset,_write_file_meta_info
+    from dicom.filebase import DicomFileLike
     from dicom.values import converters as dicom_converters
     import dicom.UID
     from io import BytesIO

nibabel/tests/test_nifti1.py

@@ -1096,6 +1096,7 @@ def test_nifti_dicom_extension():
     assert_equal(dcmext._guess_implicit_VR(),False)
     assert_equal(dcmext._is_implicit_VR,False)
     assert_equal(dcmext._is_little_endian,True)
+    assert_equal(dcmext._check_encoding(),(False,True))
     assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
@@ -1108,6 +1109,7 @@ def test_nifti_dicom_extension():
     assert_equal(dcmext._guess_implicit_VR(),True)
     assert_equal(dcmext._is_implicit_VR,True)
     assert_equal(dcmext._is_little_endian,True)
+    assert_equal(dcmext._check_encoding(),(True,True))
     assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
@@ -1126,14 +1128,15 @@ def test_nifti_dicom_extension():
     with open(dicom_file,'rb') as dim:
         dcmbytes_full = dim.read()
     dcmext = Nifti1DicomExtension(2,dcmbytes_full)
+    assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext._is_implicit_VR,True)
     assert_equal(dcmext._is_little_endian,True)
-    assert_equal(dcmext.get_code(),2)
+    assert_equal(dcmext._check_encoding(),(True,True))
     assert_equal(dcmext.get_content().PatientID, '1234')
     assert_equal(len(dcmext.get_content().values()), 139)
-    # assert_equal(
-    #     dcmext.get_content().file_meta,
-    #     dicom.filereader.read_file_meta_info(dicom_file))
+    assert_equal(
+        dcmext.get_content().file_meta.TransferSyntaxUID,
+        dicom.filereader.read_file_meta_info(dicom_file).TransferSyntaxUID)
     assert_equal(dcmext.get_sizeondisk() % 16, 0)
 
     # make it round-tripable