Remove kludgy support for older versions of pydicom and dcmstack

nipy · Apr 11, 2023 · e9252c1 · e9252c1
1 parent 591d1a9
commit e9252c1
Show file tree

Hide file tree

Showing 8 changed files with 8 additions and 51 deletions.
diff --git a/heudiconv/bids.py b/heudiconv/bids.py
@@ -16,9 +16,9 @@
 import warnings
 
 import numpy as np
+import pydicom as dcm
 
 from . import __version__, dicoms
-from .external.pydicom import dcm
 from .parser import find_files
 from .utils import (
     create_file_if_missing,

diff --git a/heudiconv/dicoms.py b/heudiconv/dicoms.py
@@ -8,7 +8,8 @@
 from typing import List, Optional
 import warnings
 
-from .external.pydicom import dcm
+import pydicom as dcm
+
 from .utils import SeqInfo, get_typed_attr, load_json, set_readonly
 
 with warnings.catch_warnings():
@@ -505,9 +506,9 @@ def embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, bids_info):
     import json
     import os.path
 
+    import dcmstack as ds
     import nibabel as nb
 
-    from heudiconv.external.dcmstack import ds
     from heudiconv.utils import save_json
 
     stack = ds.parse_and_stack(dcmfiles, force=True).values()

diff --git a/heudiconv/external/dcmstack.py b/heudiconv/external/dcmstack.py
diff --git a/heudiconv/external/pydicom.py b/heudiconv/external/pydicom.py
diff --git a/heudiconv/heuristics/multires_7Tbold.py b/heudiconv/heuristics/multires_7Tbold.py
@@ -20,7 +20,7 @@ def filter_dicom(dcmdata):
 def extract_moco_params(basename, _outypes, dicoms):
     if "_rec-dico" not in basename:
         return
-    from dicom import read_file as dcm_read
+    from pydicom import read_file as dcm_read
 
     # get acquisition time for all dicoms
     dcm_times = [

diff --git a/heudiconv/info.py b/heudiconv/info.py
@@ -29,7 +29,7 @@
     "filelock>=3.0.12",
     "nibabel",
     "nipype >=1.2.3",
-    "pydicom",
+    "pydicom >= 1.0.0",
 ]
 
 TESTS_REQUIRES = [

diff --git a/heudiconv/tests/test_dicoms.py b/heudiconv/tests/test_dicoms.py
@@ -3,6 +3,7 @@
 import json
 import os.path as op
 
+import pydicom as dcm
 import pytest
 
 from heudiconv.cli.run import main as runner
@@ -15,7 +16,6 @@
     group_dicoms_into_seqinfos,
     parse_private_csa_header,
 )
-from heudiconv.external.pydicom import dcm
 
 from .utils import TESTS_DATA_PATH, assert_cwd_unchanged
 

diff --git a/heudiconv/tests/test_regression.py b/heudiconv/tests/test_regression.py
@@ -4,10 +4,10 @@
 import os.path as op
 import re
 
+import pydicom as dcm
 import pytest
 
 from heudiconv.cli.run import main as runner
-from heudiconv.external.pydicom import dcm
 from heudiconv.utils import load_json
 
 # testing utilities