update: pydicom v3 (#273)

Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>

Author: vsoch

.github/workflows/main.yaml

@@ -11,7 +11,7 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup black environment
         run: conda create --quiet --name black black
@@ -26,14 +26,13 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup conda environment
         run: |
           conda create --quiet --name testing
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate testing
-          pip install matplotlib
           pip install .
 
       - name: Test deid

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
+- Update to use pydicom 3 [#267](https://github.com/pydicom/deid/pull/267) (0.4.0)
 - Refactor INCLUDE_REQUIRES and provide max pydicom version [#267](https://github.com/pydicom/deid/pull/267) (0.3.25)
 - Support pydicom.Dataset objects created from BytesIO [#265](https://github.com/pydicom/deid/pull/265) (0.3.24)
 - Exception with missing filters for non-string VR [#256](https://github.com/pydicom/deid/issues/256) (0.3.23)

deid/config/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 from deid.config.standards import actions, formats, sections

deid/config/standards.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 # Supported formats

deid/config/utils.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 # pylint: skip-file

deid/data/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import os

deid/dicom/actions/jitter.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 from deid.logger import bot

deid/dicom/actions/uids.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import uuid

deid/dicom/fields.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import re

deid/dicom/filter.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import re
@@ -23,7 +23,7 @@ def apply_filter(dicom, field, filter_name, value):
 
     Parameters
     ==========
-    dicom: the pydicom.dataset Dataset (pydicom.read_file)
+    dicom: the pydicom.dataset Dataset
     field: the name of the field to apply the filter to,
       or the tag number as a string '0xGGGGEEEE'
     filer_name: the name of the filter to apply (e.g., contains)

deid/dicom/groups.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 

deid/dicom/header.py

@@ -1,12 +1,11 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 
 import os
 
-from pydicom import read_file
-
+import deid.dicom.utils as utils
 from deid.dicom.parser import DicomParser
 from deid.dicom.utils import save_dicom
 from deid.logger import bot
@@ -68,7 +67,7 @@ def remove_private_identifiers(
         dicom_files = [dicom_files]
 
     for dicom_file in dicom_files:
-        dicom = read_file(dicom_file, force=force)
+        dicom = utils.dcmread(dicom_file, force=force)
         dicom.remove_private_tags()
         dicom_name = os.path.basename(dicom_file)
         bot.debug("Removed private identifiers for %s" % dicom_name)

deid/dicom/parser.py

@@ -1,17 +1,17 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import os
 import re
 from copy import deepcopy
 from io import BytesIO
 
-from pydicom import read_file
 from pydicom.dataelem import DataElement
 from pydicom.dataset import Dataset
 from pydicom.tag import Tag
 
+import deid.dicom.utils as utils
 from deid.config import DeidRecipe
 from deid.config.standards import actions as valid_actions
 from deid.dicom.actions import deid_funcs, jitter_timestamp
@@ -99,7 +99,7 @@ def load(self, dicom_file, force=True):
             # If we must read the file, the path must exist
             if not os.path.exists(dicom_file):
                 bot.exit("%s does not exist." % dicom_file)
-            self.dicom = read_file(dicom_file, force=force)
+            self.dicom = utils.dcmread(dicom_file, force=force)
 
         # Set class variables that might be helpful later
         df = self.dicom.get("filename")

deid/dicom/pixels/clean.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 
@@ -13,7 +13,6 @@
 import matplotlib
 import numpy
 from numpy.typing import NDArray
-from pydicom import read_file
 from pydicom.pixel_data_handlers.util import get_expected_length
 
 from deid.config import DeidRecipe
@@ -245,7 +244,7 @@ def save_dicom(self, output_folder=None, image_type="cleaned"):
         # Having clean also means has dicom image
         if hasattr(self, image_type):
             dicom_name = self._get_clean_name(output_folder)
-            dicom = read_file(self.dicom_file, force=True)
+            dicom = utils.dcmread(self.dicom_file, force=True)
             # If going from compressed, change TransferSyntax
             if dicom.file_meta.TransferSyntaxUID.is_compressed is True:
                 dicom.decompress()

deid/dicom/pixels/detect.py

@@ -1,13 +1,14 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 
 from typing import List, Optional, Union
 
-from pydicom import FileDataset, read_file
+from pydicom import FileDataset
 from pydicom.sequence import Sequence
 
+import deid.dicom.utils as utils
 from deid.config import DeidRecipe
 from deid.dicom.filter import apply_filter
 from deid.logger import bot
@@ -111,10 +112,7 @@ def _has_burned_pixels_single(dicom_file, force: bool, deid):
             ]
         }
     """
-    if isinstance(dicom_file, FileDataset):
-        dicom = dicom_file
-    else:
-        dicom = read_file(dicom_file, force=force)
+    dicom = utils.load_dicom(dicom_file, force=force)
 
     # Return list with lookup as dicom_file
     results = []

deid/dicom/tags.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import re
@@ -123,7 +123,7 @@ def update_tag(dicom, field, value):
 
     Parameters
     ==========
-    dicom: the pydicom.dataset Dataset (pydicom.read_file)
+    dicom: the pydicom.dataset Dataset
     field: the name of the field to update
     value: the value to set, if name is a valid tag
 
@@ -157,7 +157,7 @@ def get_private(dicom):
 
     Parameters
     ==========
-    dicom: the pydicom.dataset Dataset (pydicom.read_file)
+    dicom: the pydicom.dataset Dataset
     """
     datasets = [dicom]
     private_tags = []
@@ -188,7 +188,7 @@ def has_private(dicom):
 
     Parameters
     ==========
-    dicom: the pydicom.dataset Dataset (pydicom.read_file)
+    dicom: the pydicom.dataset Dataset
 
     """
     private_tags = len(get_private(dicom))

deid/dicom/utils.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import os
@@ -106,8 +106,12 @@ def save_dicom(dicom, dicom_file, output_folder=None, overwrite=False):
     return output_dicom
 
 
-def load_dicom(dcm_file):
+def load_dicom(dcm_file, force=True):
     if isinstance(dcm_file, FileDataset):
         return dcm_file
     else:
-        return pydicom.read_file(dcm_file, force=True)
+        return pydicom.dcmread(dcm_file, force=force)
+
+
+def dcmread(filename, **kwargs):
+    return pydicom.dcmread(filename, **kwargs)

deid/dicom/validate.py

@@ -1,9 +1,8 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
-from pydicom import read_file
-
+import deid.dicom.utils as utils
 from deid.logger import bot
 
 
@@ -28,7 +27,7 @@ def validate_dicoms(dcm_files, force=False):
     for dcm_file in dcm_files:
         try:
             with open(dcm_file, "rb") as filey:
-                read_file(filey, force=force)
+                utils.dcmread(filey, force=force)
             valids.append(dcm_file)
         except Exception:
             bot.warning("Cannot read input file {0!s}, skipping.".format(dcm_file))

deid/logger/message.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 

deid/main/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import argparse

deid/main/identifiers.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 

deid/main/inspect.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import datetime

deid/tests/Xtest_dicom_header.py

@@ -1,16 +1,12 @@
 #!/usr/bin/env python
 
-__author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
-__license__ = "MIT"
-
-
 import os
 import shutil
 import tempfile
 import unittest
 
 from deid.data import get_dataset
+from deid.dicom import utils
 from deid.utils import get_installdir
 
 
@@ -47,15 +43,14 @@ def test_get_identifiers(self):
 
     def test_replace_identifiers(self):
         print("Testing deid.dicom replace_identifiers")
-        from pydicom import read_file
 
         from deid.dicom import get_identifiers, replace_identifiers
 
         dicom_files = get_dicom(self.dataset, return_dir=True)
         ids = get_identifiers(dicom_files)
 
         # Before blanking, 28 fields don't have blanks
-        notblanked = read_file(dicom_files[0])
+        notblanked = utils.dcmread(dicom_files[0])
         notblanked_fields = [
             x for x in notblanked.dir() if notblanked.get(x) != ""
         ]  # 28
@@ -64,21 +59,20 @@ def test_replace_identifiers(self):
         updated_files = replace_identifiers(dicom_files, ids, output_folder=self.tmpdir)
 
         # After replacing only 9 don't have blanks
-        blanked = read_file(updated_files[0])
+        blanked = utils.dcmread(updated_files[0])
         blanked_fields = [x for x in blanked.dir() if blanked.get(x) != ""]
         self.assertTrue(len(blanked_fields) == 9)
 
 
 def get_dicom(dataset, return_dir=False):
     """helper function to load a dicom"""
-    from pydicom import read_file
 
     from deid.dicom import get_files
 
     dicom_files = get_files(dataset)
     if return_dir:
         return list(dicom_files)
-    return read_file(next(dicom_files))
+    return utils.dcmread(next(dicom_files))
 
 
 if __name__ == "__main__":