Merge pull request #1280 from effigies/mnt/deprecate-pydicom_compat

MNT: Deprecate nibabel.pydicom_compat

Author: effigies

nibabel/dft.py

@@ -238,7 +238,7 @@ def __getattribute__(self, name):
         return val
 
     def dicom(self):
-        return pydicom.read_file(self.files[0])
+        return pydicom.dcmread(self.files[0])
 
 
 def _get_subdirs(base_dir, files_dict=None, followlinks=False):
@@ -347,7 +347,7 @@ def _update_dir(c, dir, files, studies, series, storage_instances):
 
 def _update_file(c, path, fname, studies, series, storage_instances):
     try:
-        do = pydicom.read_file(f'{path}/{fname}')
+        do = pydicom.dcmread(f'{path}/{fname}')
     except pydicom.filereader.InvalidDicomError:
         logger.debug('        not a DICOM file')
         return None

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

@@ -21,11 +21,19 @@
 """
 from __future__ import annotations
 
+import warnings
 from typing import Callable
 
 from .deprecated import deprecate_with_version
 from .optpkg import optional_package
 
+warnings.warn(
+    "We will remove the 'pydicom_compat' module from nibabel 7.0. "
+    "Please consult pydicom's documentation for any future needs.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
 pydicom, have_dicom, _ = optional_package('pydicom')
 
 read_file: Callable | None = None
@@ -35,7 +43,7 @@
 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

nibabel/tests/test_removalschedule.py

@@ -6,6 +6,7 @@
 from ..pkg_info import cmp_pkg_version
 
 MODULE_SCHEDULE = [
+    ('7.0.0', ['nibabel.pydicom_compat']),
     ('5.0.0', ['nibabel.keywordonly', 'nibabel.py3k']),
     ('4.0.0', ['nibabel.trackvis']),
     ('3.0.0', ['nibabel.minc', 'nibabel.checkwarns']),

tox.ini

@@ -99,9 +99,8 @@ deps =
   full,pre,dev: pillow >=8.1
   full,pre,dev: indexed_gzip >=1.4
   full,pre,dev: pyzstd >=0.14.3
-  full,pre,dev: pydicom >=2.1
-  # pydicom master seems to be breaking things
-  # pre: pydicom @ git+https://github.com/pydicom/pydicom.git@main
+  full,pre: pydicom >=2.1
+  dev: pydicom @ git+https://github.com/pydicom/pydicom.git@main
 
 commands =
   pytest --doctest-modules --doctest-plus \