【Paddle Toolkit Development Competition No.6】Paddle 适配 deepali

jointContribution/deepali/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it using these metadata."
+title: "deepali: Image, point set, and surface registration in PyTorch"
+abstract: An open source research library for image, point set, and surface registration in PyTorch,
+  which is developed and maintained by the HeartFlow-Imperial College London research lab at the Biomedical Image Analysis Group.
+
+
+  Deepali is a Hindu/Sanskrit Indian given name, which means "joy" as in the gratification one may feel
+  working with code built on a modern tensor library with support for automatic differentiation, and
+  "chain of lamps" alluding to the application of the chain rule by torch.autograd, the concatenation
+  of spatial coordinate transformations, and furthermore the (sequential) composition of PyTorch modules.
+  In addition, the English words "deep" and "ali(-gnment)" partially contained in this name should highlight
+  that this project is not only suitable for traditional non-learning based registration, but in particular
+  facilitates deep learning based approaches to image alignment.
+type: software
+authors:
+  - given-names: Andreas
+    family-names: Schuh
+    affiliation: HeartFlow U.K. Ltd.
+    orcid: https://orcid.org/0000-0002-8214-116X
+  - given-names: Huaqi
+    family-names: Qiu
+    affiliation: Imperial College London
+  - name: HeartFlow Research
+doi: 10.5281/zenodo.8170161
+url: https://biomedia.github.io/deepali/
+repository-code: https://github.com/BioMedIA/deepali
+keywords:
+  - medical-imaging
+  - image-registration
+  - spatial-transformer-networks
+license: Apache-2.0

jointContribution/deepali/LICENSE

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jointContribution/deepali/README.md

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+
+Code from <https://github.com/BioMedIA/deepali>
+
+Install:
+
+``` shell
+# paddlepaddle develop
+python -m pip install --pre paddlepaddle-gpu -i https://www.paddlepaddle.org.cn/packages/nightly/cu118/
+
+# setup config file is pyproject.toml
+pip install .
+
+# test
+pytest tests/
+```

jointContribution/deepali/docs/_citations.bib

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+@article{rueckert_1999a,
+  author={Rueckert, D. and Sonoda, L.I. and Hayes, C. and Hill, D.L.G. and Leach, M.O. and Hawkes, D.J.},
+  title={Nonrigid registration using free-form deformations: application to breast MR images}, 
+  journal={IEEE Transactions on Medical Imaging}, 
+  year={1999},
+  volume={18},
+  number={8},
+  pages={712-721},
+  doi={10.1109/42.796284}
+}
+
+@misc{lee_2019a,
+  author={Matthew C. H. Lee and Ozan Oktay and Andreas Schuh and Michiel Schaap and Ben Glocker},
+  title={Image-and-Spatial Transformer Networks for Structure-Guided Image Registration},
+  year={2019},
+  eprint={1907.09200},
+  archivePrefix={arXiv},
+  primaryClass={cs.CV}
+}
+
+@article{sinclair_2022a,
+  author = {Matthew Sinclair and Andreas Schuh and Karl Hahn and Kersten Petersen and Ying Bai and James Batten and Michiel Schaap and Ben Glocker},
+  title = {Atlas-ISTN: Joint segmentation, registration and atlas construction with image-and-spatial transformer networks},
+  journal = {Medical Image Analysis},
+  volume = {78},
+  pages = {102383},
+  year = {2022},
+  issn = {1361-8415},
+  doi = {10.1016/j.media.2022.102383},
+}

jointContribution/deepali/docs/_config.yml

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+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# See the documentation for help and more options:
+# https://jupyterbook.org/customize/config.html
+
+#######################################################################################
+# Book settings
+title: deepali
+author: HeartFlow-Imperial College London
+copyright: "2020-2023"
+logo: _images/logo.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: auto
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - _citations.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/BioMedIA/deepali  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+
+# Add a Launch on Google Colab button
+launch_buttons:
+  colab_url: "https://colab.research.google.com"
+
+# By default MathJax version 2 is currently used. If you are using a lot of math,
+# you may want to try using version 3, which claims to improve load speeds by 60 - 80%.
+sphinx:
+  config:
+    add_module_names: false
+    autoapi_dirs:
+    - ../src/deepali
+    autoapi_add_toctree_entry: false
+    autoapi_generate_api_docs: true
+    autoapi_ignore:
+    - '*ignite*'  # deprecated
+    autoapi_keep_files: true
+    autoapi_member_order: bysource
+    autoapi_options:
+    - members
+    # - show-inheritance
+    - show-inheritance-diagram
+    - show-module-summary
+    autoapi_python_class_content: both
+    autoapi_python_use_implicit_namespaces: true
+    autoapi_root: reference/api
+    autoapi_type: python
+    autodoc_typehints: signature
+    autosummary_generate: true
+    bibtex_reference_style: author_year
+    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+    suppress_warnings:
+    - etoc.toctree
+  extra_extensions:
+  - autoapi.extension
+  - sphinx.ext.autodoc
+  - sphinx.ext.autosummary
+  - sphinx.ext.inheritance_diagram
+  - sphinx.ext.napoleon
+  - sphinx.ext.viewcode
+
+parse:
+  myst_enable_extensions:
+  - amsmath
+  - colon_fence
+  - dollarmath
+  - linkify
+  - substitution
+  - tasklist