From ae6cfc3a15ab150cb1c75d34f18a91112fbc4ee7 Mon Sep 17 00:00:00 2001 From: Aditya Panchal Date: Mon, 8 May 2023 10:08:21 -0500 Subject: [PATCH] Update history for version 0.5.6. --- .gitignore | 126 +++++++++++++++++++++++----------------------- .readthedocs.yaml | 10 ++-- AUTHORS.rst | 3 +- HISTORY.rst | 23 +++++++-- LICENSE | 62 +++++++++++------------ SECURITY.md | 10 ++-- docs/conf.py | 12 ++--- 7 files changed, 132 insertions(+), 114 deletions(-) diff --git a/.gitignore b/.gitignore index cf5229d..55f0c4f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,62 +1,64 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*,cover -.hypothesis/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Mac OS X cruft -.DS_Store +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Mac OS X cruft +.DS_Store + +.mypy_cache diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 453b68c..5db50e5 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,10 +1,10 @@ version: 2 build: - os: "ubuntu-20.04" - tools: - python: "3.9" + os: "ubuntu-22.04" + tools: + python: "3.11" formats: all python: - install: - - requirements: requirements_dev.txt + install: + - requirements: requirements_dev.txt diff --git a/AUTHORS.rst b/AUTHORS.rst index a8756c8..4e70a9b 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -10,4 +10,5 @@ Development Lead Contributors ------------ -* Roy Keyes +* Roy Keyes (Original co-author of dicompyler) +* See :doc:`history` for additional contributors diff --git a/HISTORY.rst b/HISTORY.rst index 93eee6d..305d2f9 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,18 +2,33 @@ History ======= -0.5.6 (unreleased) +0.5.7 (unreleased) ------------------ -* Added ``dose`` module with ``DVH`` class for Pythonic access to RT Dose `(#164) `__ `[Dan Cutright] `__ +0.5.6 (2023-05-08) +------------------ + +.. warning:: This version will be the last version to support Python 2.x and support will be dropped in version 0.5.7. +- Dropped support for Python 3.5 & 3.6 and added support for Python 3.9 & 3.10. +- Made changes to codebase to support recent versions of numpy, Shapely and scikit-image dependencies. +- Added ``dose`` module with ``DVH`` class for Pythonic access to RT Dose. `(#164) `__ `[Dan Cutright] `__ +- Added decubitus orientation and related changes. `(#285) `__ `[Darcy Mason] `__ +- Fix a bug if Pixel Data attribute was set for non image based SOP Classes (i.e. RT Structure Set). `(#214) `__ `[Dan Cutright] `__ + +dvhcalc +~~~~~~~ +- Implement interpolation for non square pixels in DVH calculation. `(#124) `__ +- Fix a bug where the DVHDoseScaling attribute was not applied properly to RT Dose DVHs. `(#301) `__ `[Christian Velten] `__ +- Fix a bug where floating point pixel spacing wasn't rounded in DVH calculations. `(#318) `__ `[Samuel Ouellet] `__ dose ~~~~~~~ -* Added RT Dose grid summmation with interpolation (from DVHA) `(#164) `__ `[Dan Cutright] `__ +- Added RT Dose grid summmation with interpolation (from DVHA). `(#164) `__ `[Dan Cutright] `__ dicomparser ~~~~~~~~~~~ -* Initial implementation of memory mapped access to pixel data. `(#131) `__ +- Initial implementation of memory mapped access to pixel data. `(#131) `__ +- Ensure that all files read have a valid File Meta header. 0.5.5 (2019-05-31) ------------------ diff --git a/LICENSE b/LICENSE index 8c67586..389e3b0 100644 --- a/LICENSE +++ b/LICENSE @@ -1,31 +1,31 @@ -Copyright (c) 2009-2016 Aditya Panchal and dicompyler-core contributors - -All rights reserved. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are -met: - - Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - - Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the - distribution. - - The name of Aditya Panchal may not be used to endorse or promote - products derived from this software without specific prior written - permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A -PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER -OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +Copyright (c) 2009-2023 Aditya Panchal and dicompyler-core contributors + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the + distribution. + + The name of Aditya Panchal may not be used to endorse or promote + products derived from this software without specific prior written + permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A +PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER +OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/SECURITY.md b/SECURITY.md index ef496b8..cf825fb 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -2,11 +2,11 @@ ## Supported Versions -| Version | Supported | -| ------- | ------------------ | -| master (0.5.6) | :white_check_mark: | -| 0.5.5 | :white_check_mark: | -| < 0.5.4 | :x: | +| Version | Supported | +| -------------- | ------------------ | +| master (0.5.7) | :white_check_mark: | +| 0.5.6 | :white_check_mark: | +| < 0.5.5 | :x: | ## Reporting a Vulnerability diff --git a/docs/conf.py b/docs/conf.py index a3965bf..2660b01 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,6 +13,7 @@ # All configuration values have a default; values that are commented out # serve to show the default. +import dicompylercore import sys import os @@ -31,7 +32,6 @@ # version is used. sys.path.insert(0, project_root) -import dicompylercore # -- General configuration --------------------------------------------- @@ -45,7 +45,7 @@ autodoc_mock_imports = [ 'numpy', 'dicom', 'pydicom', 'pydicom', 'dicom', - 'PIL', 'numpy', 'matplotlib', 'skimage', 'scipy'] + 'PIL', 'numpy.core', 'matplotlib', 'skimage', 'scipy'] autodoc_member_order = 'bysource' # Add any paths that contain templates here, relative to this directory. @@ -62,7 +62,7 @@ # General information about the project. project = u'dicompyler-core' -copyright = u'2016-2020, Aditya Panchal' +copyright = u'2016-2023, Aditya Panchal' # The version info for the project you're documenting, acts as replacement # for |version| and |release|, also used in various other places throughout @@ -201,13 +201,13 @@ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). - #'papersize': 'letterpaper', + # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). - #'pointsize': '10pt', + # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. - #'preamble': '', + # 'preamble': '', } # Grouping the document tree into LaTeX files. List of tuples