Update to work with pydicom 2.4+, 3.X, Python 3.10+ (#384)

* Update pydicom supported to >=2.4..0
* fix DVH repr problems with 'np.int(...) repr'
* collections.Callable -> collections.abc.Callable

* Resolve fixing of file_meta info

* Update workflows for testing pydicom 2.4, 3.X
* update some of the actions script versions

* Fix style and import issues

* Fix syntax

* Update Python versions in setup.py
* make pydicom versions in build name more obvious

* Fix force of old pydicom

* Update README to reflect Python 3.10 compatibility and badge changes

---------

Co-authored-by: Darcy Mason <darcymason@gmail.com>

Author: bastula

.github/workflows/build.yml

@@ -13,19 +13,22 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python-version: ["3.7", "3.8", "3.9", "3.10"]
-
+                python-version: ["3.10", "3.11", "3.12", "3.13"]
+                pydicom-version: ["pydicom-latest"]
+                include:
+                  - python-version: "3.10"
+                    pydicom-version: "pydicom==2.4.0"
         steps:
             - name: Checkout repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python-version }}
 
             - name: Cache Python dependencies
-              uses: actions/cache@v3
+              uses: actions/cache@v4
               with:
                   path: ~/.cache/pip
                   key: ${{ hashFiles('setup.py') }}
@@ -37,6 +40,11 @@ jobs:
                   pip install coverage
                   pip install coveralls
                   pip install codecov
+            
+            - name: Force pydicom version if needed
+              if: startsWith(matrix.pydicom-version, 'pydicom==')
+              run: |
+                  pip install -U "${{ matrix.pydicom-version }}"
 
             - name: Run tests via coverage
               run: |

.github/workflows/codacy.yml

@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout the repository to the GitHub Actions runner
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Execute Codacy Analysis CLI and generate a SARIF output with the security issues identified during the analysis
       - name: Run Codacy Analysis CLI

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2

.github/workflows/dependency-review.yml

@@ -15,6 +15,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout Repository'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@v3
+        uses: actions/dependency-review-action@v4

HISTORY.rst

@@ -5,6 +5,7 @@ History
 0.5.7 (unreleased)
 ------------------
 - Dropped support for Python 2.
+- pydicom 3.X supported (requirement now >= pydicom 2.4.0)
 
 0.5.6 (2023-05-08)
 ------------------

README.rst

@@ -16,13 +16,13 @@ Other information
 
 -  Free software: `BSD license <https://github.com/dicompyler/dicompyler-core/blob/master/LICENSE>`__
 -  Documentation: `Read the docs <https://dicompyler-core.readthedocs.io>`__
--  Tested on Python 3.7+
+-  Tested on Python 3.10+
 
 Dependencies
 ------------
 
 -  `numpy <http://www.numpy.org>`__ 1.2 or higher
--  `pydicom <https://pydicom.github.io>`__ 0.9.9 or higher (pydicom 1.0 compatible)
+-  `pydicom <https://pydicom.github.io>`__ 2.4.0 or higher
 -  `matplotlib <http://matplotlib.org>`__ 1.3.0 or higher (for DVH calculation)
 -  Optional:
 
@@ -85,7 +85,7 @@ This package was created with
    :target: http://mybinder.org/repo/bastula/dicom-notebooks
 .. |pypi| image:: https://img.shields.io/pypi/v/dicompyler-core.svg
    :target: https://pypi.python.org/pypi/dicompyler-core
-.. |Python Version| image:: https://img.shields.io/badge/python-3.7+-blue.svg
+.. |Python Version| image:: https://img.shields.io/badge/python-3.10+-blue.svg
    :target: https://pypi.python.org/pypi/dicompyler-core
 .. |GH Actions| image:: https://github.com/dicompyler/dicompyler-core/actions/workflows/build.yml/badge.svg
    :target: https://github.com/dicompyler/dicompyler-core/actions
@@ -97,8 +97,8 @@ This package was created with
    :target: https://app.codacy.com/gh/dicompyler/dicompyler-core/dashboard
 .. |Codecov| image:: https://codecov.io/gh/dicompyler/dicompyler-core/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/dicompyler/dicompyler-core
-.. |Total Lines| image:: https://img.shields.io/tokei/lines/github/dicompyler/dicompyler-core
-   :target: https://img.shields.io/tokei/lines/github/dicompyler/dicompyler-core
+.. |Total Lines| image:: https://img.shields.io/endpoint?url=https://ghloc.vercel.app/api/dicompyler/dicompyler-core/badge?style=flat&logoColor=white&label=Lines%20of%20Code
+   :target: https://ghloc.vercel.app/dicompyler/dicompyler-core?branch=master
 .. |Code Size| image:: https://img.shields.io/github/languages/code-size/dicompyler/dicompyler-core
    :target: https://img.shields.io/github/languages/code-size/dicompyler/dicompyler-core
 .. |Zenodo| image:: https://zenodo.org/badge/51550203.svg

dicompylercore/dicomparser.py

@@ -11,13 +11,10 @@
 
 import logging
 import numpy as np
-try:
-    from pydicom.dicomio import read_file
-    from pydicom.dataset import Dataset, validate_file_meta
-    from pydicom.pixel_data_handlers.util import pixel_dtype
-except ImportError:
-    from dicom import read_file
-    from dicom.dataset import Dataset
+from pydicom.dicomio import dcmread
+from pydicom.dataset import Dataset, validate_file_meta
+from pydicom.pixel_data_handlers.util import pixel_dtype
+from pydicom.uid import ImplicitVRLittleEndian, ExplicitVRBigEndian
 import random
 from numbers import Number
 from io import BytesIO
@@ -33,6 +30,40 @@
 logger = logging.getLogger('dicompylercore.dicomparser')
 
 
+def _fix_meta_info(dataset: Dataset) -> None:
+    """Ensure the file meta info exists and has the correct values
+    for transfer syntax and media storage UIDs.
+
+    Copied from pydicom 2.4 and edited
+
+    .. warning::
+
+        The transfer syntax for ``is_implicit_VR = False`` and
+        ``is_little_endian = True`` is ambiguous and will therefore not
+        be set.
+
+    Parameters
+    ----------
+    dataset: pydicom Dataset
+
+    """
+    dataset.ensure_file_meta()
+
+    if dataset.is_little_endian and dataset.is_implicit_VR:
+        dataset.file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
+    elif not dataset.is_little_endian and not dataset.is_implicit_VR:
+        dataset.file_meta.TransferSyntaxUID = ExplicitVRBigEndian
+    elif not dataset.is_little_endian and dataset.is_implicit_VR:
+        raise NotImplementedError(
+            "Implicit VR Big Endian is not a supported Transfer Syntax."
+        )
+
+    if 'SOPClassUID' in dataset:
+        dataset.file_meta.MediaStorageSOPClassUID = dataset.SOPClassUID
+    if 'SOPInstanceUID' in dataset:
+        dataset.file_meta.MediaStorageSOPInstanceUID = dataset.SOPInstanceUID
+
+
 class DicomParser:
     """Class to parse DICOM / DICOM RT files."""
 
@@ -59,7 +90,7 @@ def __init__(self, dataset, memmap_pixel_array=False):
         elif isinstance(dataset, (str, BytesIO, Path)):
             try:
                 with open(dataset, "rb") as fp:
-                    self.ds = read_file(fp, defer_size=100, force=True,
+                    self.ds = dcmread(fp, defer_size=100, force=True,
                                         stop_before_pixels=memmap_pixel_array)
                     if memmap_pixel_array:
                         self.offset = fp.tell() + 8
@@ -78,12 +109,14 @@ def __init__(self, dataset, memmap_pixel_array=False):
             raise AttributeError
 
         # Fix dataset file_meta if incorrect
+        self.ds.ensure_file_meta()
         try:
             validate_file_meta(self.ds.file_meta)
-        except ValueError:
+        except (AttributeError, ValueError):
             logger.debug('Fixing invalid File Meta for ' +
                          str(self.ds.SOPInstanceUID))
-            self.ds.fix_meta_info()
+            _fix_meta_info(self.ds)
+            validate_file_meta(self.ds.file_meta)
 
         # Remove the PixelData attribute if it is not set.
         # i.e. RTStruct does not contain PixelData and its presence can confuse

dicompylercore/dvh.py

@@ -108,16 +108,14 @@ def from_data(cls, data, binsize=1):
 
     def __repr__(self):
         """String representation of the class."""
-        return 'DVH(%s, %r bins: [%r:%r] %s, volume: %r %s, name: %r, ' \
-            'rx_dose: %d %s%s)' % \
-            (self.dvh_type, self.counts.size, self.bins.min(),
-                self.bins.max(), self.dose_units,
-                self.volume, self.volume_units,
-                self.name,
-                0 if not self.rx_dose else self.rx_dose,
-                self.dose_units,
-                ', *Notes: ' + self.notes if self.notes else '')
-
+        return (
+            f'DVH({self.dvh_type}, {self.counts.size} bins: '
+            f'[{self.bins.min()}:{self.bins.max()}] {self.dose_units}, '
+            f'volume: {self.volume} {self.volume_units}, name: {self.name}, '
+            f'rx_dose: {0 if not self.rx_dose else self.rx_dose} '
+            f'{self.dose_units}'
+            f'{", *Notes: " + self.notes if self.notes else ""})'
+        )
     def __eq__(self, other):
         """Comparison method between two DVH objects.
 

dicompylercore/util.py

@@ -132,7 +132,7 @@ def piecewise(x, condlist, funclist, *args, **kw):
     y = np.zeros(x.shape, x.dtype)
     for k in range(n):
         item = funclist[k]
-        if not isinstance(item, collections.Callable):
+        if not isinstance(item, collections.abc.Callable):
             y[condlist[k]] = item
         else:
             vals = x[condlist[k]]

docs/conf.py

@@ -44,7 +44,7 @@
               'sphinx.ext.napoleon']
 
 autodoc_mock_imports = [
-    'numpy', 'dicom', 'pydicom', 'pydicom', 'dicom',
+    'numpy', 'dicom', 'pydicom',
     'PIL', 'numpy.core', 'matplotlib', 'skimage', 'scipy']
 autodoc_member_order = 'bysource'