Fix overlapping in patches aggregator #832
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Codecov Report
@@ Coverage Diff @@
## main #832 +/- ##
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- Coverage 93.87% 93.86% -0.02%
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Files 72 72
Lines 4524 4514 -10
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- Hits 4247 4237 -10
Misses 277 277
Continue to review full report at Codecov.
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Phew, this was a tough one. Thanks for reporting, @Hsuxu. May I add you to the list of contributors? |
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Of course. |
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@all-contributors please add @Hsuxu for bug. |
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I've put up a pull request to add @Hsuxu! 🎉 |
justusschock
added a commit
to justusschock/torchio
that referenced
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Jun 28, 2022
Use type of current instance instead of hardcoded subject type fix copy behavior Stop running some unstable tests on CI (fepegar#796) * Print output messages during testing * Skip MedMNIST tests on GitHub Actions * Fix AttributeError * Add reason for skipping test Add support to specify the interpolation type for label images (fepegar#791) * Add label_interpolation option in spatial transforms and augmentations * Add label_interpolation option in spatial transforms and augmentations * Adds missing backtick * update docs 782 * Minor docs edits Co-authored-by: Fernando Pérez-García <[email protected]> docs: add snavalm as a contributor for code (fepegar#802) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.71 → 0.18.72 Add py.typed marker file for type checking (fepegar#808) docs: add jcreinhold as a contributor for code (fepegar#809) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.72 → 0.18.73 Fix overlapping in patches aggregator (fepegar#832) Bump version: 0.18.73 → 0.18.74 Update announcement docs: add Hsuxu as a contributor for bug (fepegar#833) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Add check for shapes of input batch and output location Add support for torch >= 1.11 (fepegar#838) * added support for pytorch>=1.11.0 * Replace type with isinstance Co-authored-by: Fernando Pérez-García <[email protected]> Bump version: 0.18.74 → 0.18.75 docs: add snipdome as a contributor for bug (fepegar#839) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Remove redundant tests in GitHub actions (fepegar#850) Fix new SimpleITK release breaking tests (fepegar#852) Bump version: 0.18.75 → 0.18.76 Disable fail-fast in CI matrix strategy Fix wrong mapping in SequentialLabels transform (fepegar#841) docs: add iamSmallY as a contributor for bug (fepegar#855) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Fix SimpleITK version in docs requirements Fix examples format in docstrings Improve documentation and tests for label transforms (fepegar#857) * Improve documentation and tests for label transforms * Add parametrization with duplicated values in dict Add example of RandomLabelsToImage Add example of RandomGamma Use sphinx-opengraph for documentation Improve quality of figures from plot directive [pre-commit.ci] pre-commit autoupdate (fepegar#859) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.2.0](pre-commit/pre-commit-hooks@v4.0.1...v4.2.0) - [github.com/pycqa/flake8: 3.9.2 → 4.0.1](PyCQA/flake8@3.9.2...4.0.1) - [github.com/asottile/pyupgrade: v2.29.0 → v2.32.0](asottile/pyupgrade@v2.29.0...v2.32.0) * Fix pre-commit not installing flake8 This commit address the comments by @asottile in pre-commit-ci/issues#118. Thanks, @asottile! Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fernando Pérez-García <[email protected]> Validate arguments of add/remove_image Return figure in plot_volume function (fepegar#872) Co-authored-by: Derk <[email protected]> docs: add guigautier as a contributor for ideas (fepegar#875) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Update flake8 error codes [pre-commit.ci] pre-commit autoupdate (fepegar#874) updates: - [github.com/asottile/pyupgrade: v2.32.0 → v2.32.1](asottile/pyupgrade@v2.32.0...v2.32.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fernando Pérez-García <[email protected]> Stop upgrading pip in CI (fepegar#877) Update bug report template docs: add AyedSamy as a contributor for bug (fepegar#878) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Add tests for Python 3.10 (fepegar#880) * Add tests for Python 3.10 * Fix Python version in YAML Use PyTorch to compute Fourier transforms (fepegar#389) * Use PyTorch for FFT if available * Make sure tensor in on CPU before calling numpy() Remove support for Python 3.6 (fepegar#881) * Remove support for Python 3.6 * Fix Python version Add support to use different numbers of samples in the queue (fepegar#795) docs: add jmlipman as a contributor for ideas, code (fepegar#882) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Juan Miguel <[email protected]> Fix computation of kernels in `Blur` transform (fepegar#861) * Fix size of Gaussian kernel for blurring * Fix typo in docstring Add support to pass label keys for dict input (fepegar#879) * Add support to pass label keys for dict input * Add reference to @josegcpa's code Co-authored-by: josegcpa <[email protected]> docs: add josegcpa as a contributor for ideas (fepegar#883) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.76 → 0.18.77 Fix support for NiBabel inputs Remove unnecessary check Remove error for multichannel NiBabel input Cover method to print queue memory Add gallery example for custom resampling transform docs: add saikhu as a contributor for bug (fepegar#887) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Move package code to `src` directory (fepegar#896) * Move package to src directory * Update setup.py * Update setup.py * Move requirements * Include requirements file in MANIFEST.in * Stop using requirements file * Fix warning in docs Remove setup.py script and add pyproject.toml config file (fepegar#898) * Remove setup.py and add pyproject.toml * Add version to setup config * Remove bumpversion config for setup.py * Fix path to __init__ * Stop removing trailing whitespaces from setup.cfg See peritus/bumpversion#78 * Update version replacing in bumpversion config * Fix tox configuration for pyproject.toml * Add keywords * Remove requirements file * Update authors config Bump version: 0.18.77 → 0.18.78 Enable verbose mode for publishing GHA Fix version Fix version not being updated As it seems that bump2version is not able to modify its own config file. Add citation file [pre-commit.ci] pre-commit autoupdate (fepegar#902) updates: - [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](pre-commit/pre-commit-hooks@v4.2.0...v4.3.0) - [github.com/asottile/pyupgrade: v2.32.1 → v2.34.0](asottile/pyupgrade@v2.32.1...v2.34.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Fix warning in RTD documentation build (fepegar#903) Add hook for trailing commas (fepegar#904) * Add hook for trailing commas * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix flake8 issues Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Disable Binder buttons in Sphinx gallery (fepegar#905) * Disable Binder buttons in Sphinx gallery * Update RTD config to use pip installation * Fix extra requirements string * Add missing doc requirement Add checks for TOML and YAML files Add support to mask 4D images with 3D masks (fepegar#908) * Add failing test * Add support to mask 4D images with 3D masks * Improve docstring Co-authored-by: cbri92 <[email protected]> Co-authored-by: valabregue <[email protected]> docs: add cbri92 as a contributor for bug (fepegar#909) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.78 → 0.18.79 Add fftshift to fourier_transform with torch.fft (fepegar#912) This makes the behavior of fourier_transform and inv_fourier_transform consistent with earlier versions of torchio. It is also independent of whether torch or numpy is used to perform the transform. Solves fepegar#911 docs: add iimog as a contributor for bug (fepegar#913) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.79 → 0.18.80 Remove incorrect Contributors badge Stop ignoring some missing imports for mypy Fix tox running on Python 3.7 only (fepegar#915) Create dependabot.yml (fepegar#917) Test all Python versions in Ubuntu only (fepegar#918) * Test all Python versions in Ubuntu only * Fix exclusions Bump actions/setup-python from 2 to 4 (fepegar#919) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v4) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Ignore some files in MANIFEST (fepegar#916) * Ignore some files in MANIFEST * Always publish to TestPyPI * Skip existing TestPyPI versions Bump actions/checkout from 2 to 3 (fepegar#920) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v3) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Update fpg.py Proper copy of subclass copies [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci fix parenthesis imports Fix proper subject subclass copy old-style type annotations linting [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Fix proper subject subclass copy
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Fixes #813.
Description
This PR fixes a bug in the aggregator. When certain conditions were met, overlapping patches were over-cropped, causing spatial shifting between the input and output volumes during inference with a grid sampler and an aggregator.
Checklist
CONTRIBUTINGdocs and have a developer setup (especially important arepre-commitandpytest)pytestmake htmlinside thedocs/folder