upload files

03-第四期/代码资料/DeepReg-main/.dockerignore

+# logs
+# logs
+logs/
+
+# data folders

03-第四期/代码资料/DeepReg-main/.flake8

+[flake8]
+[flake8]
+ignore = E203, E266, E501, W503
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/01_bug_report.md

+---
+---
+name: 🐜 Bug report
+about: Something isn't working.
+---
+
+## Subject of the issue
+
+Describe your issue here.
+
+If the bug is confirmed, would you be willing to submit a PR? _(Help can be provided if
+you need assistance submitting a PR)_
+
+Yes / No
+
+## Your environment
+
+- DeepReg version (commit hash)
+
+  Please use `git rev-parse HEAD` to get the hash of the current commit. Using
+  `pip list` will provide the fixed tag version inside `setup.py`, therefore it is not
+  accurate.
+
+  We recommend installing DeepReg using
+  [Anaconda](https://docs.anaconda.com/anaconda/install/) /
+  [Miniconda](https://docs.conda.io/en/latest/miniconda.html) in a separate virtual
+  environment.
+
+- OS (e.g. Ubuntu 20.04, MacOS 10.15, etc.)
+
+  We do not officially support windows.
+
+- Python Version (3.7, 3.8, etc.)
+
+  We support only Python 3.7 officially.
+
+- TensorFlow
+
+  - TensorFlow Version (2.2, 2.3, etc.)
+  - CUDA Version (10.1, etc.) if available.
+  - cuDNN Version
+
+  We support only TensorFlow 2.3 officially.
+
+  If using GPU, please check https://www.tensorflow.org/install/source#gpu to verify the
+  GPU support.
+
+## Steps to reproduce
+
+Tell us how to reproduce this issue. Please provide a working demo.
+
+## Expected behaviour
+
+Tell us what should happen.
+
+## Actual behaviour
+
+Tell us what happens instead.

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/02_feature_request.md

+---
+---
+name: 💡 Feature request
+about: It would be nice to have some new feature.
+---
+
+## Subject of the feature
+
+What are you trying to do and how would you want to do it differently?
+
+Is it something you currently you cannot do?
+
+Is this related to an issue/problem?
+
+Has the feature been requested before? If yes, please provide a link to the issue.
+
+If the feature request is approved, would you be willing to submit a PR? _(Help can be
+provided if you need assistance submitting a PR)_
+
+Yes / No

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/03_docs_request.md

+---
+---
+name: 📝 Documentation request
+about: Some documentation is missing or incorrect.
+---
+
+## Subject of the documentation
+
+What are you trying to do and which part of the code is hard to understand or incorrect
+or missing? Please provide a link to the readthedocs page and code if available.
+
+If the documentation request is approved, would you be willing to submit a PR? _(Help
+can be provided if you need assistance submitting a PR)_
+
+Yes / No

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/04_test_request.md

+---
+---
+name: 🧪 Test request
+about: Some code is not covered by test.
+---
+
+## Subject of the code / test
+
+What are you trying to do and which part of the code is not tested? Please provide a
+link to the code if available.
+
+If the test request is approved, would you be willing to submit a PR? _(Help can be
+provided if you need assistance submitting a PR)_
+
+Yes / No

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/05_other.md

+---
+---
+name: 😀 Other
+about: Anything not covered by previous options.
+---
+
+## Subject of the issue
+
+Please describe the issue, it can be a question or any other discussions.

03-第四期/代码资料/DeepReg-main/.github/ISSUE_TEMPLATE/config.yml

+blank_issues_enabled: false
+blank_issues_enabled: false
+contact_links:
+  - name: Documentation
+    url: https://deepreg.readthedocs.io/en/latest/
+    about: Please check the documentation here.
+  - name: Contribution Guidelines
+    url: https://deepreg.readthedocs.io/en/latest/contributing/guide.html
+    about: Please check the guidelines for contributing here.

03-第四期/代码资料/DeepReg-main/.github/PULL_REQUEST_TEMPLATE.md

+# Description
+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include
+relevant motivation and context. List any dependencies that are required for this
+change.
+
+Fixes #<issue_number>
+
+## Type of change
+
+What types of changes does your code introduce to DeepReg?
+
+_Please check the boxes that apply after submitting the pull request._
+
+- [ ] Bugfix (non-breaking change which fixes an issue)
+- [ ] Code style update (formatting, renaming)
+- [ ] Refactoring (no functional changes, no api changes)
+- [ ] Documentation Update (fix or improvement on the documentation)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Other (if none of the other choices apply)
+
+## Checklist
+
+_Please check the boxes that apply after submitting the pull request._
+
+_If you're unsure about any of them, don't hesitate to ask. We're here to help! This is
+simply a reminder of what we are going to look for before merging your code._
+
+- [ ] I have
+      [installed pre-commit](https://deepreg.readthedocs.io/en/latest/contributing/setup.html)
+      using `pre-commit install` and formatted all changed files. If you are not
+      certain, run `pre-commit run --all-files`.
+- [ ] My commits' message styles matches
+      [our requested structure](https://deepreg.readthedocs.io/en/latest/contributing/commit.html),
+      e.g. `Issue #<issue number>: detailed message`.
+- [ ] I have updated the
+      [change log file](https://github.com/DeepRegNet/DeepReg/blob/main/CHANGELOG.md)
+      regarding my changes.
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] I have added necessary documentation (if appropriate)

03-第四期/代码资料/DeepReg-main/.github/stale.yml

+# Number of days of inactivity before an issue becomes stale
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 60
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 14
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had recent
+  activity. It will be closed if no further activity occurs. Thank you for your
+  contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

03-第四期/代码资料/DeepReg-main/.github/workflows/pre-commit.yml

+name: pre-commit
+name: pre-commit
+
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: pre-commit/action@v2.0.0

03-第四期/代码资料/DeepReg-main/.github/workflows/python-integration-test.yml

+name: Integration Test
+name: Integration Test
+
+on:
+  workflow_dispatch:
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  integration-test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.7"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Ubuntu system dependencies
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install graphviz
+      - name: Install Mac OS system dependencies
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: |
+          brew install graphviz
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install codecov==2.1.11
+          pip install -e .
+      - name: Test examples
+        run: |
+          pytest test/integration/test_examples.py
+      - name: Test demos
+        run: |
+          pytest test/integration/test_demos.py

03-第四期/代码资料/DeepReg-main/.github/workflows/python-publish.yml

+# This workflows will upload a Python Package using Twine when a release is created
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+
+      - name: Bump setup.py Version
+        run: perl -pi -e "s/0\.0\.0/${GITHUB_REF##*/v}/g" ./setup.py
+
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

03-第四期/代码资料/DeepReg-main/.github/workflows/python-unit-test.yml

+name: Unit Test
+name: Unit Test
+
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  unit-test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.7", "3.6"]
+        exclude:
+          # excludes py3.6 on MacOS to save time/energy
+          - os: macos-latest
+            python-version: "3.6"
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Ubuntu system dependencies
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install graphviz
+      - name: Install Mac OS system dependencies
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: |
+          brew install graphviz
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install codecov==2.1.11
+          pip install -e .
+      - name: Linting
+        # W9006 can't be checked like this as we need to ignore ValueError
+        run: |
+          pylint --disable=all --enable=C0103,C0301,R1725,W0107,W9012,W9015 *
+          pylint --exit-zero *
+        timeout-minutes: 10
+      - name: Unit test with pytest
+        run: |
+          pytest --cov-report=xml --cov=deepreg --durations=20 --durations-min=1.0 ./test/unit/
+        timeout-minutes: 20
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.7' }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml

03-第四期/代码资料/DeepReg-main/.gitignore

+# Byte-compiled / optimized / DLL files
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+docs/_site/*
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# intellij
+.idea/
+
+# logs
+logs/
+
+# data folders
+*.tfrecords
+
+# demo dataset folders and zip files
+demos/*/dataset
+demos/*/*.zip
+
+# demo test folders
+demos/*/logs_reg
+demos/*/logs_train
+demos/*/logs_predict
+
+# test folders
+deepreg_download_temp_dir/

03-第四期/代码资料/DeepReg-main/.isort.cfg

+[settings]
+[settings]
+known_third_party = git,h5py,matplotlib,nibabel,numpy,pandas,pytest,scipy,setuptools,sphinx_rtd_theme,tensorflow,testfixtures,tqdm,yaml
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88

03-第四期/代码资料/DeepReg-main/.pre-commit-config.yaml

+repos:
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: check-ast # Simply check whether the files parse as valid python
+      - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
+      - id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types
+      - id: check-docstring-first # Check a common error of defining a docstring after code
+      - id: check-merge-conflict # Check for files that contain merge conflict strings
+      - id: check-yaml # Check yaml files
+      - id: check-vcs-permalinks # Ensure that links to vcs websites are permalinks
+      - id: debug-statements # Check for debugger imports and py37+ `breakpoint()` calls in python source
+      - id: detect-private-key # Detect the presence of private keys
+      - id: end-of-file-fixer # Ensure that a file is either empty, or ends with one newline
+      - id: mixed-line-ending # Replace or checks mixed line ending
+      - id: trailing-whitespace # This hook trims trailing whitespace
+  - repo: https://github.com/asottile/seed-isort-config
+    rev: v2.2.0
+    hooks:
+      - id: seed-isort-config
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.8.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+        language_version: python3.7
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.812
+    hooks:
+      - id: mypy
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.2.1
+    hooks:
+      - id: prettier
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.0
+    hooks:
+      - id: flake8
+#  - repo: https://github.com/pycqa/pydocstyle
+#    rev: 5.1.1 # pick a git hash / tag to point to
+#    hooks:
+#      - id: pydocstyle

03-第四期/代码资料/DeepReg-main/.prettierignore

+docs/joss_paper/paper.md
+docs/joss_paper/paper.md

03-第四期/代码资料/DeepReg-main/.prettierrc

+{
+{
+  "printWidth": 88,
+  "proseWrap": "always",
+  "useTabs": false,
+  "tabWidth": 2
+}

03-第四期/代码资料/DeepReg-main/.readthedocs.yml

+# .readthedocs.yml
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .

03-第四期/代码资料/DeepReg-main/.zenodo.json

+{
+{
+  "description": "DeepReg is a freely available, community-supported open-source toolkit for research and education in medical image registration using deep learning.",
+  "license": "Apache-2.0",
+  "title": "DeepReg: a deep learning toolkit for medical image registration",
+  "upload_type": "software",
+  "keywords": [
+    "Deep Learning",
+    "Image Fusion",
+    "Medical Image Registration",
+    "Neural Networks"
+  ],
+  "creators": [
+    {
+      "orcid": "0000-0002-1184-7421",
+      "name": "Fu, Yunguan"
+    },
+    {
+      "orcid": "0000-0001-5685-971X",
+      "name": "Monta\u00f1a-Brown, Nina"
+    },
+    {
+      "orcid": "0000-0002-5004-0663",
+      "name": "Saeed, Shaheer U."
+    },
+    {
+      "orcid": "0000-0002-0539-3638",
+      "name": "Casamitjana, Adri\u00e0"
+    },
+    {
+      "orcid": "0000-0001-6838-335X",
+      "name": "Baum, Zachary M. C."
+    },
+    {
+      "orcid": "0000-0002-0398-4995",
+      "name": "Delaunay, R\u00e9mi"
+    },
+    {
+      "orcid": "0000-0003-4401-5311",
+      "name": "Yang, Qianye"
+    },
+    {
+      "orcid": "0000-0002-2608-2580",
+      "name": "Grimwood, Alexander"
+    },
+    {
+      "orcid": "0000-0002-8903-1561",
+      "name": "Min, Zhe"
+    },
+    {
+      "orcid": "0000-0002-7150-9918",
+      "name": "Blumberg, Stefano B."
+    },
+    {
+      "orcid": "0000-0001-7569-173X",
+      "name": "Iglesias, Juan Eugenio"
+    },
+    {
+      "orcid": "0000-0003-2916-655X",
+      "name": "Barratt, Dean C."
+    },
+    {
+      "orcid": "0000-0001-9217-5438",
+      "name": "Bonmati, Ester"
+    },
+    {
+      "orcid": "0000-0003-2439-350X",
+      "name": "Alexander, Daniel C."
+    },
+    {
+      "orcid": "0000-0002-5565-1252",
+      "name": "Clarkson, Matthew J."
+    },
+    {
+      "orcid": "0000-0003-1794-0456",
+      "name": "Vercauteren, Tom"
+    },
+    {
+      "orcid": "0000-0003-4902-0486",
+      "name": "Hu, Yipeng"
+    }
+  ],
+  "access_right": "open"
+}

03-第四期/代码资料/DeepReg-main/CHANGELOG.md

+# Change Log
+# Change Log
+
+All notable changes to this project will be documented in this file. It's a team effort
+to make them as straightforward as possible.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project
+adheres to [Semantic Versioning](http://semver.org/).
+
+## [1.0.0-rc1] - In Progress
+
+Release comment: refactoring of models means that old checkpoint files are no longer
+compatible with the updates.
+
+### Added
+
+- Added `num_parallel_calls` option in config for data preprocessing.
+- Added tests for Dice score, Jaccard Index, and cross entropy losses.
+- Added statistics on inputs, DDF and TRE into tensorboard.
+- Added example for using custom loss.
+- Added tests on Mac OS.
+- Added tests for python 3.6 and 3.7.
+- Added support to custom layer channels in U-Net.
+- Added support to multiple loss functions for each loss type: "image", "label" and
+  "regularization".
+- Added LNCC computation using separable 1-D filters for all kernels available
+
+### Changed
+
+- Updated pre-trained models for unpaired_ct_abdomen demo to new version
+- Changed dataset config so that `format` and `labeled` are defined per split.
+- Reduced TensorFlow logging level.
+- Used `DEEPREG_LOG_LEVEL` to control logging in DeepReg.
+- Increased all EPS to 1e-5.
+- Clarify the suggestion in doc to use all-zero masks for missing labels.
+- Moved contributor list to a separate page.
+- Changed `no-test` flag to `full` for demo scripts.
+- Renamed `neg_weight` to `background_weight`.
+- Renamed `log_dir` to `exp_name` and `log_root` to `log_dir` respectively.
+- Uniformed local-net, global-net, u-net under a single u-net structure.
+- Simplified custom layer definitions.
+- Removed multiple unnecessary custom layers and use tf.keras.layers whenever possible.
+- Refactored BSplines interpolation independently of the backbone network and available
+  only for DDF and DVF models.
+
+### Fixed
+
+- Fixed using GPU remotely
+- Fixed LNCC loss regarding INF values.
+- Removed loss weight checks to be more robust.
+- Fixed import error under python 3.6.
+- Fixed the residual module in local net architecture, compatible for previous
+  checkpoints.
+- Broken link in README to seminar video.
+
+## [0.1.2] - 2021-01-31
+
+Release comment: This is mainly a bugfix release, although some of the tasks in
+1.0.0-rc1 have been included in this release, with or without public-facing
+accessibility (see details below).
+
+### Added
+
+- Added global NCC loss
+- Added the docs on registry for backbone models.
+- Added backward compatible config parser.
+- Added tests so that test coverage is 100%.
+- Added config file docs with details on how new config works.
+- Added DDF data augmentation.
+- Added the registry for backbone models and losses.
+- Added pylint with partial check (C0103,C0301,R1725,W0107,W9012,W9015) to CI.
+- Added badges for code quality and maintainability.
+- Added additional links (CoC, PyPI) and information (contributing, citing) to project
+  README.md.
+- Added CMIC seminar where DeepReg was introduced to the project README.md.
+- Added deepreg_download entry point to access non-release folders required for Quick
+  Start.
+
+### Changed
+
+- Refactored optimizer configuration.
+- Refactored affine transform data augmentation.
+- Modified the implementation of resampler to support zero boundary condition.
+- Refactored loss functions into classes.
+- Use CheckpointManager callback for saving and support training restore.
+- Changed distribute strategy to default for <= 1 GPU.
+- Migrated from Travis-CI to GitHub Actions.
+- Simplified configuration for backbone models and losses.
+- Simplified contributing documentation.
+- Uniform kernel size for LNCC loss.
+- Improved demo configurations with the updated pre-trained models for:
+  grouped_mask_prostate_longitudinal, paried_mrus_prostate, unpaired_us_prostate_cv,
+  grouped_mr_heart, unpaired_ct_lung, paired_ct_lung.
+
+### Fixed
+
+- Fixed several dead links in the documentation.
+- Fixed a bug due to typo when image loss weight is zero, label loss is not applied.
+- Fixed warp CLI tool by saving outputs in Nifti1 format.
+- Fixed optimiser storage and loading from checkpoints.
+- Fixed bias initialization for theta in GlobalNet.
+- Removed invalid `first` argument in DataLoader for sample_index generator.
+- Fixed build error when downloading data from the private repository.
+- Fixed the typo for CLI tools in documents.
+
+## [0.1.0] - 2020-11-02
+
+### Added
+
+- Added option to change the kernel size and type for LNCC image similarity loss.
+- Added visualization tool for generating gifs from model outputs.
+- Added the max_epochs argument for training to overwrite configuration.
+- Added the log_root argument for training and prediction to customize the log file
+  location.
+- Added more meaningful error messages for data loading.
+- Added integration tests for all demos.
+- Added environment.yml file for Conda environment creation.
+- Added Dockerfile.
+- Added the documentation about using UCL cluster with DeepReg.
+
+### Changed
+
+- Updated TensorFlow version to 2.3.1.
+- Updated the pre-trained models in MR brain demo.
+- Updated instruction on Conda environment creation.
+- Updated the documentation regarding pre-commit and unit-testing.
+- Updated the issue and pull-request templates.
+- Updated the instructions for all demos.
+- Updated pre-commit hooks version.
+- Updated JOSS paper to address reviewers' comments.
+- Migrated from travis-ci.org to travis-ci.com.
+
+### Fixed
+
+- Fixed prediction error when number of samples cannot be divided by batch size exactly.
+- Fixed division by zero handling in multiple image/label losses.
+- Fixed tensor comparison in unit tests and impacted tests.
+- Removed normalization of DDF/DVF when saving in Nifti formats.
+- Fixed invalid link in the quick start page.
+
+## [0.1.0b1] - 2020-09-01
+
+Initial beta release.

03-第四期/代码资料/DeepReg-main/Dockerfile

+FROM tensorflow/tensorflow:2.3.1-gpu
+FROM tensorflow/tensorflow:2.3.1-gpu
+
+# install miniconda
+ENV CONDA_DIR=/root/miniconda3
+ENV PATH=${CONDA_DIR}/bin:${PATH}
+ARG PATH=${CONDA_DIR}/bin:${PATH}
+RUN apt-get update
+RUN apt-get install -y wget git && rm -rf /var/lib/apt/lists/*
+RUN wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-latest-Linux-x86_64.sh
+
+# directory for following operations
+WORKDIR /app
+
+# clone DeepReg
+RUN git clone https://github.com/DeepRegNet/DeepReg.git
+WORKDIR DeepReg
+RUN git pull
+
+# install conda env
+RUN conda env create -f environment.yml \
+    && conda init bash \
+    && echo "conda activate deepreg" >> /root/.bashrc
+
+# install deepreg
+ENV CONDA_PIP="${CONDA_DIR}/envs/deepreg/bin/pip"
+RUN ${CONDA_PIP} install -e .

03-第四期/代码资料/DeepReg-main/MANIFEST.in

+include README.md
+include README.md
+include requirements.txt

03-第四期/代码资料/DeepReg-main/README.md

+<p align="center">
+<p align="center">
+  <img src="https://raw.githubusercontent.com/DeepRegNet/DeepReg/main/docs/asset/deepreg_logo_purple.svg"
+    alt="deepreg_logo" title="DeepReg" width="200"/>
+</p>
+
+<table align="center">
+  <tr>
+    <td>
+      <b>Package</b>
+    </td>
+    <td>
+      <a href="https://opensource.org/licenses/Apache-2.0">
+      <img src="https://img.shields.io/badge/License-Apache%202.0-blue.svg" alt="License">
+      </a>
+      <a href="https://pypi.python.org/pypi/DeepReg/">
+      <img src="https://img.shields.io/pypi/v/deepreg.svg" alt="PyPI Version">
+      </a>
+      <a href="https://pypi.python.org/pypi/DeepReg/">
+      <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/deepreg">
+      </a>
+      <a href="https://pepy.tech/project/deepreg">
+      <img src="https://static.pepy.tech/personalized-badge/deepreg?period=total&units=none&left_color=grey&right_color=orange&left_text=Downloads"
+        alt="PyPI downloads">
+      </a>
+    </td>
+  </tr>
+  <tr>
+    <td>
+      <b>Documentation</b>
+    </td>
+    <td>
+      <a href="https://deepreg.readthedocs.io/en/latest/?badge=latest">
+      <img src="https://readthedocs.org/projects/deepreg/badge/?version=latest" alt="Documentation Status">
+      </a>
+    </td>
+  </tr>
+  <tr>
+    <td>
+      <b>Code</b>
+    </td>
+    <td>
+      <a href="https://github.com/DeepRegNet/DeepReg/actions?query=workflow%3A%22Unit+Test%22">
+      <img src="https://github.com/deepregnet/deepreg/workflows/Unit%20Test/badge.svg?branch=main" alt="Unit Test">
+      </a>
+      <a href="https://github.com/DeepRegNet/DeepReg/actions?query=workflow%3A%22Integration+Test%22">
+      <img src="https://github.com/deepregnet/deepreg/workflows/Integration%20Test/badge.svg?branch=main" alt="Integration Test">
+      </a>
+      <a href="https://codecov.io/github/DeepRegNet/DeepReg">
+      <img src="https://codecov.io/gh/DeepRegNet/DeepReg/branch/main/graph/badge.svg" alt="Coverage Status">
+      </a>
+      <a href="https://github.com/psf/black">
+      <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code Style">
+      </a>
+      <a href="https://scrutinizer-ci.com/g/DeepRegNet/DeepReg/">
+      <img src="https://scrutinizer-ci.com/g/DeepRegNet/DeepReg/badges/quality-score.png" alt="Code Quality">
+      </a>
+      <a href="https://codeclimate.com/github/DeepRegNet/DeepReg/maintainability">
+      <img src="https://api.codeclimate.com/v1/badges/65245e28aa8f2cd7c6b6/maintainability" alt="Code Maintainability">
+      </a>
+    </td>
+  </tr>
+  <tr>
+    <td>
+      <b>Papers</b>
+    </td>
+    <td>
+      <a href="https://joss.theoj.org/papers/7e6de472bc82a70d7618e23f618960b3"><img
+        src="https://joss.theoj.org/papers/7e6de472bc82a70d7618e23f618960b3/status.svg"
+        alt="JOSS Paper"></a>
+      <a href="https://zenodo.org/badge/latestdoi/269365590"><img src="https://zenodo.org/badge/269365590.svg"
+        alt="DOI"></a>
+    </td>
+  </tr>
+</table>
+
+# DeepReg
+
+**DeepReg is a freely available, community-supported open-source toolkit for research
+and education in medical image registration using deep learning.**
+
+- TensorFlow 2-based for efficient training and rapid deployment;
+- Implementing major unsupervised and weakly-supervised algorithms, with their
+  combinations and variants;
+- Focusing on growing and diverse clinical applications, with all DeepReg Demos using
+  open-accessible data;
+- Simple built-in command line tools requiring minimal programming and scripting;
+- Open, permissible and research-and-education-driven, under the Apache 2.0 license.
+
+---
+
+## Getting Started
+
+- [DeepReg.Net](http://deepreg.net/)
+- [Documentation, Tutorials, and Quick Start](https://deepreg.readthedocs.io/)
+- [Medical Image Registration Demos using DeepReg](https://deepreg.readthedocs.io/en/latest/demo/introduction.html)
+- [Issue Tracker](https://github.com/DeepRegNet/DeepReg/issues/new/choose)
+
+## Contributing
+
+Get involved, and help make DeepReg better! We want your help - **Really**.
+
+**Being a contributor doesn't just mean writing code.** Equally important to the
+open-source process is writing or proof-reading documentation, suggesting or
+implementing tests, or giving feedback about the project. You might see the errors and
+assumptions that have been glossed over. If you can write any code at all, you can
+contribute code to open-source. We are constantly trying out new skills, making
+mistakes, and learning from those mistakes. That's how we all improve, and we are happy
+to help others learn with us.
+
+### Code of Conduct
+
+This project is released with a
+[Code of Conduct](https://github.com/DeepRegNet/DeepReg/blob/main/docs/CODE_OF_CONDUCT.md).
+By participating in this project, you agree to abide by its terms.
+
+### Where Should I Start?
+
+For guidance on making a contribution to DeepReg, see our
+[Contribution Guidelines](https://deepreg.readthedocs.io/en/latest/contributing/guide.html).
+
+Have a registration application with openly accessible data? Consider
+[contributing a DeepReg Demo](https://deepreg.readthedocs.io/en/latest/contributing/demo.html).
+
+## MICCAI 2020 Educational Challenge
+
+Our [MICCAI Educational Challenge](https://miccai-sb.github.io/materials.html)
+submission on DeepReg is an Award Winner!
+
+Check it out
+[here](https://github.com/DeepRegNet/DeepReg/blob/main/docs/Intro_to_Medical_Image_Registration.ipynb) -
+you can also
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/DeepRegNet/DeepReg/blob/main/docs/Intro_to_Medical_Image_Registration.ipynb)
+
+## Overview Video
+
+Members of the DeepReg dev team presented "The Road to DeepReg" at the Centre for
+Medical Imaging Computing (CMIC) seminar series at University College London on the 4th
+of November 2020. You can access the talk
+[here](https://www.youtube.com/watch?v=jDEyWXZM3CE&feature=youtu.be).
+
+## Citing DeepReg
+
+DeepReg is research software, made by a
+[team of academic researchers](https://deepreg.readthedocs.io/en/latest/#contributors).
+Citations and use of our software help us justify the effort which has gone into, and
+will keep going into, maintaining and growing this project.
+
+If you have used DeepReg in your research, please consider citing us:
+
+> Fu _et al._, (2020). DeepReg: a deep learning toolkit for medical image registration.
+> _Journal of Open Source Software_, **5**(55), 2705,
+> https://doi.org/10.21105/joss.02705
+
+Or with BibTex:
+
+```
+@article{Fu2020,
+  doi = {10.21105/joss.02705},
+  url = {https://doi.org/10.21105/joss.02705},
+  year = {2020},
+  publisher = {The Open Journal},
+  volume = {5},
+  number = {55},
+  pages = {2705},
+  author = {Yunguan Fu and Nina Montaña Brown and Shaheer U. Saeed and Adrià Casamitjana and Zachary M. C. Baum and Rémi Delaunay and Qianye Yang and Alexander Grimwood and Zhe Min and Stefano B. Blumberg and Juan Eugenio Iglesias and Dean C. Barratt and Ester Bonmati and Daniel C. Alexander and Matthew J. Clarkson and Tom Vercauteren and Yipeng Hu},
+  title = {DeepReg: a deep learning toolkit for medical image registration},
+  journal = {Journal of Open Source Software}
+}
+```

03-第四期/代码资料/DeepReg-main/config/test/affine.yaml

+train:
+train:
+  method: "ddf" # ddf / dvf / conditional
+  backbone:
+    name: "global"
+    num_channel_initial: 1
+    depth: 4
+  loss:
+    image:
+      name: "lncc"
+      weight: 0.1
+    label:
+      weight: 1.0
+      name: "dice"
+      scales: [0, 1, 2, 4, 8, 16, 32]
+    regularization:
+      weight: 0.5
+      name: "bending"
+  preprocess:
+    batch_size: 2
+    shuffle_buffer_num_batch: 1
+    num_parallel_calls: -1 # number elements to process asynchronously in parallel during preprocessing, -1 means unlimited, heuristically it should be set to the number of CPU cores available
+  optimizer:
+    name: "Adam"
+    learning_rate: 1.0e-5
+  epochs: 2
+  save_period: 2

03-第四期/代码资料/DeepReg-main/config/test/conditional.yaml

+train:
+train:
+  method: "conditional" # ddf / dvf / conditional

03-第四期/代码资料/DeepReg-main/config/test/ddf.yaml

+train:
+train:
+  method: "ddf" # ddf / dvf / conditional
+  backbone:
+    name: "local"
+    num_channel_initial: 1
+    extract_levels: [0, 1, 2, 3, 4]
+  loss:
+    image:
+      name: "lncc"
+      weight: 0.1
+    label:
+      weight: 1.0
+      name: "dice"
+      scales: [0, 1, 2, 4, 8, 16, 32]
+    regularization:
+      weight: 0.5
+      name: "bending"
+  preprocess:
+    data_augmentation:
+      name: "affine"
+    batch_size: 2
+    shuffle_buffer_num_batch: 1
+    num_parallel_calls: -1 # number elements to process asynchronously in parallel during preprocessing, -1 means unlimited, heuristically it should be set to the number of CPU cores available
+  optimizer:
+    name: "Adam"
+    learning_rate: 1.0e-5
+  epochs: 2
+  save_period: 2

03-第四期/代码资料/DeepReg-main/config/test/demo_paired.yaml

+dataset:
+dataset:
+  moving_image_shape: [16, 16, 16]
+  fixed_image_shape: [8, 8, 8]
+train:
+  epochs: 1
+  save_period: 1

03-第四期/代码资料/DeepReg-main/config/test/demo_unpaired_grouped.yaml

+dataset:
+dataset:
+  image_shape: [16, 16, 16]
+train:
+  epochs: 1
+  save_period: 1

03-第四期/代码资料/DeepReg-main/config/test/dvf.yaml

+train:
+train:
+  method: "dvf" # ddf / dvf / conditional

03-第四期/代码资料/DeepReg-main/config/test/grouped_h5.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/h5/grouped/train"
+    format: "h5"
+    labeled: true
+  valid:
+    dir: "data/test/h5/grouped/test"
+    format: "h5"
+    labeled: true
+  test:
+    dir: "data/test/h5/grouped/test"
+    format: "h5"
+    labeled: true
+  type: "grouped" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]
+  intra_group_prob: 1
+  intra_group_option: "forward"
+  sample_image_in_group: true

03-第四期/代码资料/DeepReg-main/config/test/grouped_mr_heart_v011.yaml

+dataset:
+dataset:
+  dir:
+    train: "demos/grouped_mr_heart/dataset/train"
+    valid: "demos/grouped_mr_heart/dataset/val"
+    test: "demos/grouped_mr_heart/dataset/test"
+  format: "nifti"
+  type: "grouped" # paired / unpaired / grouped
+  labeled: false
+  intra_group_prob: 1
+  intra_group_option: "unconstrained" # forward / backward / unconstrained
+  sample_image_in_group: true
+  image_shape: [128, 128, 28]
+
+train:
+  # define neural network structure
+  model:
+    method: "ddf" # the registration method, value should be ddf / dvf / conditional
+    backbone: "local" # value should be local / global / unet
+    local:
+      num_channel_initial: 32 # number of initial channel in local net, controls the size of the network
+      extract_levels: [0, 1, 2, 3, 4]
+
+  # define the loss function for training
+  loss:
+    dissimilarity:
+      image:
+        name: "gmi"
+        weight: 1.0
+      label:
+        weight: 0.0
+        name: "multi_scale"
+        multi_scale:
+          loss_type: "dice"
+          loss_scales: [0, 1, 2, 4, 8, 16]
+        single_scale:
+          loss_type: "cross-entropy"
+    regularization:
+      weight: 0.25 # weight of regularization loss
+      energy_type: "gradient-l2" # value should be bending / gradient-l1 / gradient-l2
+
+  # define the optimizer
+  optimizer:
+    name: "adam" # value should be adam / sgd / rms
+    adam:
+      learning_rate: 1.0e-4
+
+  preprocess:
+    batch_size: 4
+    shuffle_buffer_num_batch: 1 # shuffle_buffer_size = batch_size * shuffle_buffer_num_batch
+
+  # other training hyper-parameters
+  epochs: 4000 # number of training epochs
+  save_period: 1000 # the model will be saved every `save_period` epochs.

03-第四期/代码资料/DeepReg-main/config/test/grouped_nifti.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/nifti/grouped/train"
+    format: "nifti"
+    labeled: true
+  valid:
+    dir: "data/test/nifti/grouped/test"
+    format: "nifti"
+    labeled: true
+  test:
+    dir: "data/test/nifti/grouped/test"
+    format: "nifti"
+    labeled: true
+  type: "grouped" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]
+  intra_group_prob: 1
+  intra_group_option: "forward"
+  sample_image_in_group: true

03-第四期/代码资料/DeepReg-main/config/test/labeled.yaml

+dataset:
+dataset:
+  train:
+    labeled: true
+  valid:
+    labeled: true
+  test:
+    labeled: true

03-第四期/代码资料/DeepReg-main/config/test/paired_h5.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/h5/paired/train"
+    format: "h5"
+    labeled: true
+  valid:
+    dir: "data/test/h5/paired/test"
+    format: "h5"
+    labeled: true
+  test:
+    dir: "data/test/h5/paired/test"
+    format: "h5"
+    labeled: true
+  type: "paired" # paired / unpaired / grouped
+  moving_image_shape: [16, 16, 16]
+  fixed_image_shape: [8, 8, 8]

03-第四期/代码资料/DeepReg-main/config/test/paired_nifti.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/nifti/paired/train"
+    format: "nifti"
+    labeled: true
+  valid:
+    dir: "data/test/nifti/paired/test"
+    format: "nifti"
+    labeled: true
+  test:
+    dir: "data/test/nifti/paired/test"
+    format: "nifti"
+    labeled: true
+  type: "paired" # paired / unpaired / grouped
+  moving_image_shape: [16, 16, 16]
+  fixed_image_shape: [8, 8, 8]

03-第四期/代码资料/DeepReg-main/config/test/unlabeled.yaml

+dataset:
+dataset:
+  train:
+    labeled: false
+  valid:
+    labeled: false
+  test:
+    labeled: false

03-第四期/代码资料/DeepReg-main/config/test/unpaired_h5.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/h5/unpaired/train"
+    format: "h5"
+    labeled: true
+  valid:
+    dir: "data/test/h5/unpaired/test"
+    format: "h5"
+    labeled: true
+  test:
+    dir: "data/test/h5/unpaired/test"
+    format: "h5"
+    labeled: true
+  type: "unpaired" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]

03-第四期/代码资料/DeepReg-main/config/test/unpaired_nifti.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/nifti/unpaired/train"
+    format: "nifti"
+    labeled: true
+  valid:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  test:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  type: "unpaired" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]

03-第四期/代码资料/DeepReg-main/config/test/unpaired_nifti_multi_dirs.yaml

+dataset:
+dataset:
+  train:
+    dir:
+      - "data/test/nifti/unpaired/train"
+      - "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  valid:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  test:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  type: "unpaired" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]

03-第四期/代码资料/DeepReg-main/config/test/unpaired_nifti_no_valid.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/nifti/unpaired/train"
+    format: "nifti"
+    labeled: true
+  valid:
+  test:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  type: "unpaired" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]

03-第四期/代码资料/DeepReg-main/config/unpaired_labeled_ddf.yaml

+dataset:
+dataset:
+  train:
+    dir: "data/test/nifti/unpaired/train"
+    format: "nifti"
+    labeled: true
+  valid:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  test:
+    dir: "data/test/nifti/unpaired/test"
+    format: "nifti"
+    labeled: true
+  type: "unpaired" # paired / unpaired / grouped
+  image_shape: [16, 16, 16]
+
+train:
+  # define neural network structure
+  method: "ddf" # options include "ddf", "dvf", "conditional"
+  backbone:
+    name: "local" # options include "local", "unet" and "global"
+    num_channel_initial: 1 # number of initial channel in local net, controls the size of the network
+    extract_levels: [0, 1, 2, 3, 4] # this defines the resolution levels used to compose the output ddf, e.g. one does not use the highest resolution level can be specified as [0,1,2,3]
+
+  # define the loss function for training
+  loss:
+    image:
+      name: "lncc" # other options include "lncc", "ssd" and "gmi", for local normalised cross correlation,
+      weight: 0.1
+    label:
+      weight: 1.0
+      name: "dice" # options include "dice", "cross-entropy", "mean-squared", "generalised_dice" and "jaccard"
+      scales: [0, 1, 2, 4, 8, 16, 32]
+    regularization:
+      weight: 0.5 # weight of regularization loss
+      name: "bending" # options include "bending", "gradient"
+
+  # define the optimizer
+  optimizer:
+    name: "Adam"
+    learning_rate: 1.0e-5
+
+  # define the hyper-parameters for preprocessing
+  preprocess:
+    data_augmentation:
+      name: "affine"
+    batch_size: 2
+    shuffle_buffer_num_batch: 1 # shuffle_buffer_size = batch_size * shuffle_buffer_num_batch
+    num_parallel_calls: -1 # number elements to process asynchronously in parallel during preprocessing, -1 means unlimited, heuristically it should be set to the number of CPU cores available
+
+  # other training hyper-parameters
+  epochs: 2 # number of training epochs
+  save_period: 2 # the model will be saved every `save_period` epochs.