Merge pull request #311 from ImagingDataCommons/v0.24.0dev

WIP: V0.24.0dev

.github/workflows/run_unit_tests.yml

@@ -7,15 +7,15 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
+    branches: [ "master", "v*dev" ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         dependencies: [".", "'.[libjpeg]'"]
 
     steps:

bin/create_iods_modules.py

@@ -83,10 +83,15 @@ def _create_modules(directory):
         except KeyError:
             logger.error(f'keyword not found for attribute "{tag}"')
             continue
+        try:
+            kw_path = [dictionary_keyword(t) for t in path]
+        except KeyError:
+            logger.error(f'keyword in path of attribute "{tag}" not found')
+            continue
         mapping = {
             'keyword': keyword,
             'type': item['type'],
-            'path': [dictionary_keyword(t) for t in path],
+            'path': kw_path,
         }
         modules[item['moduleId']].append(mapping)
     return modules

docs/conf.py

@@ -13,6 +13,7 @@
 import os
 import sys
 import pkg_resources
+import datetime
 
 source_dir = os.path.dirname(__file__)
 pkg_dir = os.path.join(source_dir, '..', '..', 'src', 'highdicom')
@@ -21,7 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'highdicom'
-copyright = '2020-2022, Herrmann Lab'
+copyright = f'2020-{datetime.datetime.now().year}, highdicom contributors'
 author = 'Markus D. Herrmann'
 
 # The full version, including alpha/beta/rc tags

docs/installation.rst

@@ -16,7 +16,7 @@ Requirements
 Installation
 ------------
 
-Pre-build package available at PyPi:
+Pre-built package available at PyPi:
 
 .. code-block:: none
 

docs/package.rst

@@ -75,6 +75,15 @@ highdicom.utils module
    :undoc-members:
    :show-inheritance:
 
+highdicom.pixels module
++++++++++++++++++++++++
+
+.. automodule:: highdicom.pixels
+   :members:
+   :inherited-members: pydicom.dataset.Dataset,pydicom.sequence.Sequence,Dataset,Sequence,list,str,DataElementSequence,enum.Enum,Enum,
+   :special-members: __call__
+   :undoc-members:
+   :show-inheritance:
 
 .. _highdicom-legacy-subpackage:
 

docs/seg.rst

@@ -447,7 +447,7 @@ segments. Note that passing a "label map" is purely a convenience provided by
 (`highdicom` splits the label map into multiple single-segment frames and
 stores these, as required by the standard).
 
-Therefore, The following snippet produces an equivalent SEG image to the
+Therefore, the following snippet produces an equivalent SEG image to the
 previous snippet, but passes the mask as a label map rather than as a stack of
 segments.
 

pyproject.toml

@@ -4,12 +4,13 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "highdicom"
-version = "0.23.1"
+version = "0.24.0"
 description = "High-level DICOM abstractions."
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
     { name = "Markus D. Herrmann" },
+    { name = "Christopher P. Bridge" },
 ]
 maintainers = [
     { name = "Markus D. Herrmann" },
@@ -27,6 +28,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Multimedia :: Graphics",
     "Topic :: Scientific/Engineering :: Information Analysis",
 ]
@@ -35,6 +37,7 @@ dependencies = [
     "pillow>=8.3",
     "pydicom>=3.0.1",
     "pyjpegls>=1.0.0",
+    "typing-extensions>=4.0.0",
 ]
 
 [project.optional-dependencies]
@@ -62,6 +65,12 @@ homepage = "https://github.com/imagingdatacommons/highdicom"
 documentation = "https://highdicom.readthedocs.io/"
 repository = "https://github.com/ImagingDataCommons/highdicom.git"
 
+[tool.setuptools.packages.find]
+where = [ "src" ]
+
+[tool.setuptools.package-data]
+highdicom = [ "**/*.icc" ]
+
 [tool.pytest.ini_options]
 minversion = "7"
 addopts = ["--doctest-modules", "-ra", "--strict-config", "--strict-markers"]

src/highdicom/__init__.py

@@ -34,50 +34,72 @@
     VOILUTTransformation,
 )
 from highdicom.enum import (
+    AxisHandedness,
     AnatomicalOrientationTypeValues,
     CoordinateSystemNames,
     ContentQualificationValues,
     DimensionOrganizationTypeValues,
     LateralityValues,
+    PadModes,
     PatientSexValues,
     PhotometricInterpretationValues,
+    PixelIndexDirections,
     PixelRepresentationValues,
     PlanarConfigurationValues,
     PatientOrientationValuesBiped,
     PatientOrientationValuesQuadruped,
     PresentationLUTShapeValues,
     RescaleTypeValues,
+    RGBColorChannels,
     UniversalEntityIDTypeValues,
     VOILUTFunctionValues,
 )
 from highdicom import frame
+from highdicom.image import (
+    Image,
+    imread,
+    get_volume_from_series,
+)
 from highdicom import io
+from highdicom import pixels
 from highdicom import spatial
 from highdicom.uid import UID
 from highdicom import utils
 from highdicom.version import __version__
+from highdicom.volume import (
+    RGB_COLOR_CHANNEL_DESCRIPTOR,
+    ChannelDescriptor,
+    Volume,
+    VolumeGeometry,
+    VolumeToVolumeTransformer,
+)
+
 
 __all__ = [
-    'LUT',
-    'UID',
-    'VOILUT',
+    'RGB_COLOR_CHANNEL_DESCRIPTOR',
     'AlgorithmIdentificationSequence',
     'AnatomicalOrientationTypeValues',
+    'AxisHandedness',
+    'ChannelDescriptor',
     'ContentCreatorIdentificationCodeSequence',
     'ContentQualificationValues',
     'CoordinateSystemNames',
     'DimensionOrganizationTypeValues',
+    'Image',
     'IssuerOfIdentifier',
+    'LUT',
     'LateralityValues',
     'ModalityLUT',
     'ModalityLUTTransformation',
+    'PadModes',
     'PaletteColorLUT',
     'PaletteColorLUTTransformation',
     'PatientOrientationValuesBiped',
     'PatientOrientationValuesQuadruped',
     'PatientSexValues',
     'PhotometricInterpretationValues',
     'PixelMeasuresSequence',
+    'PixelIndexDirections',
     'PixelRepresentationValues',
     'PlanarConfigurationValues',
     'PlaneOrientationSequence',
@@ -87,6 +109,7 @@
     'PresentationLUTTransformation',
     'ReferencedImageSequence',
     'RescaleTypeValues',
+    'RGBColorChannels',
     'SOPClass',
     'SegmentedPaletteColorLUT',
     'SpecimenCollection',
@@ -95,21 +118,29 @@
     'SpecimenProcessing',
     'SpecimenSampling',
     'SpecimenStaining',
+    'UID',
     'UniversalEntityIDTypeValues',
+    'VOILUT',
     'VOILUTFunctionValues',
     'VOILUTTransformation',
+    'Volume',
+    'VolumeGeometry',
+    'VolumeToVolumeTransformer',
     '__version__',
     'ann',
     'color',
     'frame',
+    'imread',
     'io',
     'ko',
     'legacy',
+    'pixels',
     'pm',
     'pr',
     'sc',
     'seg',
     'spatial',
     'sr',
     'utils',
+    'get_volume_from_series',
 ]