RF: Replace deprecated pydicom.dicomio.read_file with dcmread

Author: effigies

nibabel/nicom/dicomreaders.py

@@ -53,7 +53,7 @@ def read_mosaic_dir(dicom_path, globber='*.dcm', check_is_dwi=False, dicom_kwarg
        If True, raises an error if we don't find DWI information in the
        DICOM headers.
     dicom_kwargs : None or dict
-       Extra keyword arguments to pass to the pydicom ``read_file`` function.
+       Extra keyword arguments to pass to the pydicom ``dcmread`` function.
 
     Returns
     -------

nibabel/nicom/dicomwrappers.py

@@ -44,9 +44,9 @@ def wrapper_from_file(file_like, *args, **kwargs):
        filename string or file-like object, pointing to a valid DICOM
        file readable by ``pydicom``
     \*args : positional
-        args to ``dicom.read_file`` command.
+        args to ``dicom.dcmread`` command.
     \*\*kwargs : keyword
-        args to ``dicom.read_file`` command.  ``force=True`` might be a
+        args to ``dicom.dcmread`` command.  ``force=True`` might be a
         likely keyword argument.
 
     Returns
@@ -55,7 +55,7 @@ def wrapper_from_file(file_like, *args, **kwargs):
        DICOM wrapper corresponding to DICOM data type
     """
     with ImageOpener(file_like) as fobj:
-        dcm_data = pydicom.read_file(fobj, *args, **kwargs)
+        dcm_data = pydicom.dcmread(fobj, *args, **kwargs)
     return wrapper_from_data(dcm_data)
 
 

nibabel/nicom/tests/test_dicomreaders.py

@@ -41,7 +41,7 @@ def test_passing_kwds():
         # This should not raise an error
         data2, aff2, bs2, gs2 = func(IO_DATA_PATH, dwi_glob, dicom_kwargs=dict(force=True))
         assert_array_equal(data, data2)
-        # This should raise an error in pydicom.dicomio.read_file
+        # This should raise an error in pydicom.filereader.dcmread
         with pytest.raises(TypeError):
             func(IO_DATA_PATH, dwi_glob, dicom_kwargs=dict(not_a_parameter=True))
         # These are invalid dicoms, so will raise an error unless force=True

nibabel/nicom/tests/test_dicomwrappers.py

@@ -23,8 +23,8 @@
 DATA_FILE = pjoin(IO_DATA_PATH, 'siemens_dwi_1000.dcm.gz')
 DATA_FILE_PHILIPS = pjoin(IO_DATA_PATH, 'philips_mprage.dcm.gz')
 if have_dicom:
-    DATA = pydicom.read_file(gzip.open(DATA_FILE))
-    DATA_PHILIPS = pydicom.read_file(gzip.open(DATA_FILE_PHILIPS))
+    DATA = pydicom.dcmread(gzip.open(DATA_FILE))
+    DATA_PHILIPS = pydicom.dcmread(gzip.open(DATA_FILE_PHILIPS))
 else:
     DATA = None
     DATA_PHILIPS = None
@@ -170,7 +170,7 @@ def test_wrapper_from_data():
 
 @dicom_test
 def test_wrapper_args_kwds():
-    # Test we can pass args, kwargs to read_file
+    # Test we can pass args, kwargs to dcmread
     dcm = didw.wrapper_from_file(DATA_FILE)
     data = dcm.get_data()
     # Passing in non-default arg for defer_size

nibabel/pydicom_compat.py

@@ -35,7 +35,7 @@
 if have_dicom:
     # Values not imported by default
     import pydicom.values  # type: ignore
-    from pydicom.dicomio import read_file  # noqa:F401
+    from pydicom.dicomio import dcmread as read_file  # noqa:F401
     from pydicom.sequence import Sequence  # noqa:F401
 
     tag_for_keyword = pydicom.datadict.tag_for_keyword