Alternative construction of objects from existing data sets

.gitignore

@@ -108,3 +108,7 @@ venv.bak/
 
 #IntelliJ
 .idea
+
+# Visual Studio Code
+.vscode
+

bin/create_iods_modules.py

@@ -6,7 +6,7 @@
 import os
 import sys
 
-from pydicom.datadict import dictionary_keyword, repeater_has_tag
+from pydicom.datadict import dictionary_keyword
 from pydicom.tag import Tag
 
 logger = logging.getLogger(__name__)
@@ -28,21 +28,23 @@ def _load_json_from_file(filename):
 def _dump_json(data):
     return json.dumps(data, indent=4, sort_keys=True)
 
+
 def _create_sop_to_iods(directory):
     filename = os.path.join(directory, 'sops.json')
     sops = _load_json_from_file(filename)
 
     filename = os.path.join(directory, 'ciods.json')
     ciods = _load_json_from_file(filename)
 
-    sop_id_to_ciod_name = {sop['id'] :sop['ciod'] for sop in sops}
-    ciod_name_to_ciod_id = {ciod['name'] :ciod['id'] for ciod in ciods}
+    sop_id_to_ciod_name = {sop['id']: sop['ciod'] for sop in sops}
+    ciod_name_to_ciod_id = {ciod['name']: ciod['id'] for ciod in ciods}
     sop_id_to_ciod_id = {
         sop_id: ciod_name_to_ciod_id[sop_id_to_ciod_name[sop_id]]
         for sop_id in sop_id_to_ciod_name
     }
     return sop_id_to_ciod_id
 
+
 def _create_iods(directory):
     filename = os.path.join(directory, 'ciod_to_modules.json')
     ciod_to_modules = _load_json_from_file(filename)
@@ -110,31 +112,40 @@ def _create_modules(directory):
 
     iods = _create_iods(directory)
     iods_docstr = '\n'.join([
-        '"""DICOM information object definitions (IODs)',
+        '"""DICOM Information Object Definitions (IODs)',
         f'auto-generated on {current_date} at {current_time}.',
-        '"""'
+        '"""',
+        'from typing import Dict, List'
     ])
     sop_to_iods = _create_sop_to_iods(directory)
     iods_filename = os.path.join(PGK_PATH, '_iods.py')
     with open(iods_filename, 'w') as fp:
         fp.write(iods_docstr)
         fp.write('\n\n')
         iods_formatted = _dump_json(iods).replace('null', 'None')
-        fp.write('IOD_MODULE_MAP = {}'.format(iods_formatted))
+        fp.write(
+            'IOD_MODULE_MAP: Dict[str, List[Dict[str, str]]] = {}'.format(
+                iods_formatted
+            )
+        )
         fp.write('\n\n')
         sop_to_iods_formatted = _dump_json(sop_to_iods).replace('null', 'None')
         fp.write('SOP_CLASS_UID_IOD_KEY_MAP = {}'.format(sop_to_iods_formatted))
 
-
     modules = _create_modules(directory)
-    modules_docstr = (
+    modules_docstr = '\n'.join([
         '"""DICOM modules'
         f'auto-generated on {current_date} at {current_time}.'
-        '"""'
-    )
+        '"""',
+        'from typing import Dict, List, Sequence, Union'
+    ])
     modules_filename = os.path.join(PGK_PATH, '_modules.py')
     with open(modules_filename, 'w') as fp:
         fp.write(modules_docstr)
         fp.write('\n\n')
         modules_formatted = _dump_json(modules).replace('null', 'None')
-        fp.write('MODULE_ATTRIBUTE_MAP = {}'.format(modules_formatted))
+        fp.write(
+            'MODULE_ATTRIBUTE_MAP: Dict[str, List[Dict[str, Union[str, Sequence[str]]]]] = {}'.format(  # noqa: E501
+                modules_formatted
+            )
+        )

data/test_files/README.md

@@ -0,0 +1,29 @@
+# Test Files
+
+These files are used for automated tests of the highdicom library. Note that
+many more test files are available as part of the pydicom package.
+
+### Images
+* `ct_image.dcm` - A small CT image.
+* `sm_image.dcm` - A slide microscopy image.
+
+### Segmentation Images
+* `seg_image_ct_binary.dcm` - Segmentation image of `BINARY` type derived
+  from the series of small CT images in the pydicom test files
+  (`dicomdirtests/77654033/CT2/*`) using the highdicom library.
+* `seg_image_ct_binary_overlap.dcm` - Segmentation image of `BINARY` type derived
+  from the series of small CT images in the pydicom test files
+  (`dicomdirtests/77654033/CT2/*`) using the highdicom library. This example
+  contains 2 overlapping segments.
+* `seg_image_ct_binary_fractional.dcm` - Segmentation image of `FRACTIONAL`
+  type but with binary values (i.e. only 0.0 and 1.0) derived from the series
+  of small CT images in the pydicom test files (`dicomdirtests/77654033/CT2/*`)
+  using the highdicom library.
+* `seg_image_ct_true_fractional.dcm` - Segmentation image of `FRACTIONAL`
+  type with true fractional values derived from the series
+  of small CT images in the pydicom test files (`dicomdirtests/77654033/CT2/*`)
+  using the highdicom library.
+
+### Structured Report Documents
+* `sr_document.dcm` - A simple SR document following TID 1500 describing
+   measurements of a CT image.

docs/package.rst

@@ -23,15 +23,6 @@ highdicom.color module
    :undoc-members:
    :show-inheritance:
 
-highdicom.enum module
-+++++++++++++++++++++
-
-.. automodule:: highdicom.enum
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
 highdicom.frame module
 ++++++++++++++++++++++
 

requirements_test.txt

@@ -1,5 +1,5 @@
-mypy==0.800
-pytest==6.2.2
-pytest-cov==2.11.1
+mypy==0.910
+pytest==6.2.4
+pytest-cov==2.12.1
 pytest-flake8==1.0.7
 git+https://github.com/numpy/numpy-stubs@201115370a0c011d879d69068b60509accc7f750#egg=numpy-stubs

setup.py

@@ -38,8 +38,8 @@
     package_dir={'': 'src'},
     python_requires='>=3.6',
     install_requires=[
-        'pydicom>=1.4,!=2.1.0,!=2.1.1',
+        'pydicom>=2.2.1',
         'numpy>=1.19',
-        'pillow>=6.0'
+        'pillow>=8.3'
     ],
 )

src/highdicom/__init__.py

@@ -1,4 +1,5 @@
 from highdicom import legacy
+from highdicom import pm
 from highdicom import sc
 from highdicom import seg
 from highdicom import sr
@@ -15,6 +16,20 @@
     SpecimenSampling,
     SpecimenStaining,
 )
+from highdicom.enum import (
+    CoordinateSystemNames,
+    ContentQualificationValues,
+    DimensionOrganizationTypeValues,
+    PatientSexValues,
+    PhotometricInterpretationValues,
+    PlanarConfigurationValues,
+    PixelRepresentationValues,
+    LateralityValues,
+    AnatomicalOrientationTypeValues,
+    PatientOrientationValuesBiped,
+    PatientOrientationValuesQuadruped,
+    UniversalEntityIDTypeValues
+)
 from highdicom import frame
 from highdicom import io
 from highdicom import spatial
@@ -23,23 +38,36 @@
 
 __all__ = [
     'AlgorithmIdentificationSequence',
-    'color',
-    'frame',
-    'io',
+    'AnatomicalOrientationTypeValues',
+    'ContentQualificationValues',
+    'CoordinateSystemNames',
+    'DimensionOrganizationTypeValues',
     'IssuerOfIdentifier',
-    'legacy',
+    'LateralityValues',
+    'PatientOrientationValuesBiped',
+    'PatientOrientationValuesQuadruped',
+    'PatientSexValues',
+    'PhotometricInterpretationValues',
     'PixelMeasuresSequence',
-    'PlanePositionSequence',
+    'PixelRepresentationValues',
+    'PlanarConfigurationValues',
     'PlaneOrientationSequence',
-    'sc',
-    'seg',
-    'spatial',
+    'PlanePositionSequence',
     'SpecimenCollection',
     'SpecimenDescription',
     'SpecimenPreparationStep',
     'SpecimenSampling',
     'SpecimenStaining',
-    'sr',
     'UID',
+    'UniversalEntityIDTypeValues',
+    'color',
+    'frame',
+    'io',
+    'legacy',
+    'pm',
+    'sc',
+    'seg',
+    'spatial',
+    'sr',
     'utils',
 ]