Implementation of Microscopy Bulk Simple Annotations (#114)

* Catch errors in module generation script

* Update IOD and module mappings

* Minor reformatting of code in seg package

* Implement Microscopy Bulk Simple Annotations

* Increase package version

* Update pydicom dependency

* Fixed annotation module import files (#115)

* Copy patient, study, and specimen information

* Update README

Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com>
Co-authored-by: Christopher Bridge <chrisbridge44@gmail.com>

Author: 3 people

README.md

@@ -4,8 +4,10 @@
 
 # High DICOM
 
-A library that provides high-level DICOM abstractions for the Python programming language to facilitate the creation and handling of DICOM objects for image-derived information, including image annotations and image analysis results.
+A library that provides high-level DICOM abstractions for the Python programming language to facilitate the creation and handling of DICOM objects for image-derived information, including image annotations, and image analysis results.
 It currently provides tools for creating and decoding the following DICOM information object definitions (IODs):
+* Annotations
+* Parametric Maps
 * Segmentation images
 * Structured Reports
 * Secondary Capture images
@@ -31,4 +33,4 @@ The developers gratefully acknowledge their support:
 * The [MGH & BWH Center for Clinical Data Science](https://www.ccds.io/)
 * [Quantitative Image Informatics for Cancer Research (QIICR)](http://qiicr.org)
 * [Radiomics](http://radiomics.io)
-* The [NCI Imaging Data Commons](https://imagingdatacommons.github.io/)
+* The [NCI Imaging Data Commons](https://imaging.datacommons.cancer.gov/)

bin/create_iods_modules.py

@@ -38,10 +38,13 @@ def _create_sop_to_iods(directory):
 
     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
-    }
+    sop_id_to_ciod_id = {}
+    for sop_id in sop_id_to_ciod_name:
+        ciod_name = sop_id_to_ciod_name[sop_id]
+        try:
+            sop_id_to_ciod_id[sop_id] = ciod_name_to_ciod_id[ciod_name]
+        except KeyError:
+            logger.error(f'could not map IOD "{ciod_name}"')
     return sop_id_to_ciod_id
 
 

docs/package.rst

@@ -80,6 +80,16 @@ highdicom.legacy package
    :undoc-members:
    :show-inheritance:
 
+.. _highdicom-ann-subpackage:
+
+highdicom.ann package
+---------------------
+
+.. automodule:: highdicom.ann
+   :members:
+   :special-members: __call__
+   :undoc-members:
+   :show-inheritance:
 
 .. _highdicom-seg-subpackage:
 

requirements_docs.txt

@@ -1,5 +1,5 @@
 sphinx-autodoc-typehints==1.12.0
-sphinx-pyreverse==0.0.16
-sphinx-rtd-theme==0.5.2
+sphinx-pyreverse==0.0.17
+sphinx-rtd-theme==1.0.0
 sphinxcontrib-autoprogram==0.1.7
 sphinxcontrib-websupport==1.2.4

setup.py

@@ -38,7 +38,7 @@
     package_dir={'': 'src'},
     python_requires='>=3.6',
     install_requires=[
-        'pydicom>=2.2.1',
+        'pydicom>=2.2.2',
         'numpy>=1.19',
         'pillow>=8.3'
     ],

src/highdicom/__init__.py

@@ -3,6 +3,7 @@
 from highdicom import sc
 from highdicom import seg
 from highdicom import sr
+from highdicom import ann
 from highdicom import color
 from highdicom.content import (
     AlgorithmIdentificationSequence,
@@ -60,6 +61,7 @@
     'SpecimenStaining',
     'UID',
     'UniversalEntityIDTypeValues',
+    'ann',
     'color',
     'frame',
     'io',