Revert "Read full datasets (with TransferSyntax)"

This reverts commit 32fd4b1.

Author: kastman

nibabel/nifti1.py

@@ -390,52 +390,9 @@ class Nifti1DicomExtension(Nifti1Extension):
     def __init__(self, code, content):
         self._code = code
         self._raw_content = content
-        self._bio = BytesIO(content)
+        self._is_implicit_VR = self._guess_implicit_VR()
         self._content = self._unmangle(content)
 
-    def _check_encoding(self):
-        """DICOM Data can be stored in the header either as a valid DICOM
-        object, with a preamble, meta info, transfer syntax etc., or as a
-        set of naked tags.  Check for meta info and transfer synatx here
-        and fall back to heuristics if metainfo is missing."""
-        self._bio.seek(0)
-        self._preamble = read_preamble(self._bio,True)  # Attempt to read preamble,
-                                                        # skip if missing w/o error
-
-        if self._preamble:
-            self._meta,_is_implicit_VR,_is_little_endian = self._check_meta()
-        else:
-            self._meta = None
-            _is_implicit_VR = self._guess_implicit_VR()
-            _is_little_endian = self._guess_little_endian()
-        return _is_implicit_VR,_is_little_endian
-
-
-    def _check_meta(self):
-        """Check the DICOM Transfer Syntax and set encoding appropriately.
-        Extracted from dicom.filereader.read_partial, see there for detail"""
-        file_meta_dataset = _read_file_meta_info(self._bio)
-        transfer_syntax = file_meta_dataset.TransferSyntaxUID
-        if transfer_syntax == dicom.UID.ImplicitVRLittleEndian:
-            is_implicit_VR = True
-            is_little_endian = True
-        elif transfer_syntax == dicom.UID.ExplicitVRLittleEndian:
-            is_implicit_VR = False
-            is_little_endian = True
-        elif transfer_syntax == dicom.UID.ExplicitVRBigEndian:
-            is_implicit_VR = False
-            is_little_endian = False
-        elif transfer_syntax == dicom.UID.DeflatedExplicitVRLittleEndian:
-            zipped = fileobj.read()
-            unzipped = zlib.decompress(zipped, -zlib.MAX_WBITS)
-            self._bio = BytesIO(unzipped)  # a file-like object
-            is_implicit_VR = False
-            is_little_endian = True
-        else:
-            is_implicit_VR = False
-            is_little_endian = True
-        return file_meta_dataset, is_implicit_VR, is_little_endian
-
     def _guess_implicit_VR(self):
         """Without a DICOM Transfer Syntax, it's difficult to tell if Value
         Representations (VRs) are included in the DICOM encoding or not.
@@ -448,30 +405,28 @@ def _guess_implicit_VR(self):
             implicit_VR=True
         return implicit_VR
 
-    def _guess_little_endian(self):
+    def _is_little_endian(self):
         return True
 
     def _unmangle(self,value):
-        self._is_implicit_VR, self._is_little_endian = self._check_encoding()
-
-        ds=read_dataset(self._bio,self._is_implicit_VR,self._is_little_endian)
-        content = FileDataset(
-            self._bio,ds,self._preamble,self._meta,self._is_implicit_VR,self._is_little_endian
-        )
-        return content
+        raw_io=BytesIO(value)
+        ds=read_dataset(raw_io,self._is_implicit_VR,self._is_little_endian)
+        return ds
 
     def _mangle(self, value):
-        bio=BytesIO()
-        write_file(bio,value)
-        bio.seek(0)
-        return bio.read()
+        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,value)
+        dio.seek(0)
+        return dio.read(ds_len)
 
 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.filereader import read_dataset
+    from dicom.filewriter import write_dataset
+    from dicom.filebase import DicomFileLike
     from dicom.values import converters as dicom_converters
-    import dicom.UID
     from io import BytesIO
 except ImportError:
     """Fall back to standard reader if pydicom unavailable."""

nibabel/tests/test_nifti1.py

@@ -40,7 +40,6 @@
 
 header_file = os.path.join(data_path, 'nifti1.hdr')
 image_file = os.path.join(data_path, 'example4d.nii.gz')
-dicom_file = os.path.join(data_path, '0.dcm')
 
 try:
     import dicom
@@ -1094,8 +1093,6 @@ def test_nifti_dicom_extension():
     dcmext = Nifti1DicomExtension(2,dcmbytes_explicit)
     assert_equal(dcmext.__class__, Nifti1DicomExtension)
     assert_equal(dcmext._guess_implicit_VR(),False)
-    assert_equal(dcmext._is_implicit_VR,False)
-    assert_equal(dcmext._is_little_endian,True)
     assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
@@ -1106,8 +1103,6 @@ def test_nifti_dicom_extension():
     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._is_implicit_VR,True)
-    assert_equal(dcmext._is_little_endian,True)
     assert_equal(dcmext.get_code(),2)
     assert_equal(dcmext.get_content().PatientID, 'NiPy')
     assert_equal(len(dcmext.get_content().values()), 1)
@@ -1122,24 +1117,8 @@ def test_nifti_dicom_extension():
     assert_equal(dcmext._mangle(dcmext.get_content()),dcmbytes_implicit)
     assert_equal(dcmext.get_sizeondisk() % 16, 0)
 
-    # Use a full dicom file with metadata as a header
-    with open(dicom_file,'rb') as dim:
-        dcmbytes_full = dim.read()
-    dcmext = Nifti1DicomExtension(2,dcmbytes_full)
-    assert_equal(dcmext._is_implicit_VR,True)
-    assert_equal(dcmext._is_little_endian,True)
-    assert_equal(dcmext.get_code(),2)
-    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_sizeondisk() % 16, 0)
-    
-    # make it round-tripable
-    assert_equal(dcmext._mangle(dcmext.get_content()),dcmbytes_full)
-
-    dcmext.write_to(BytesIO(),False)
+    raw_io = BytesIO()
+    dcmext.write_to(raw_io,False)
 
 class TestNifti1General(object):
     """ Test class to test nifti1 in general