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Image data with type int64 will error in future. #35

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adamltyson opened this issue Jul 27, 2022 · 1 comment
Closed

Image data with type int64 will error in future. #35

adamltyson opened this issue Jul 27, 2022 · 1 comment
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bug Something isn't working old-imio Issue was open on imio before it was merged into this package. Now concerns the image_io submodule.

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@adamltyson
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 imio.save.py:31: FutureWarning: Image data has type int64, which may cause incompatibilities with other tools. This will error in NiBabel 5.0. This warning can be silenced by passing the dtype argument to Nifti1Image().
    img = nib.Nifti1Image(img, affine_transform)
@adamltyson adamltyson added the bug Something isn't working label Jul 27, 2022
@adamltyson adamltyson self-assigned this Jul 27, 2022
@adamltyson adamltyson removed their assignment Jan 10, 2023
@dstansby dstansby mentioned this issue Jan 30, 2023
Merged
@willGraham01 willGraham01 transferred this issue from brainglobe/imio Feb 9, 2024
@willGraham01 willGraham01 added the old-imio Issue was open on imio before it was merged into this package. Now concerns the image_io submodule. label Feb 9, 2024
adamltyson added a commit that referenced this issue Feb 9, 2024
@willGraham01 @crousseau
@adamltyson @jaimergp @JulesScholler @dstansby @allcontributors @pre-commit-ci @alessandrofelder @IgorTatarnikov
Merge imio in as image_io submodule (#33)
5a2a2d6 
* Initial commit

* bump

* bump

* bump

* add bump2version

* Bump version: 0.0.2 → 0.0.3

* add pre commit hooks

* update testing

* reorder ci

* fix non-istropic loading error

* Bump version: 0.0.3 → 0.0.4

* Gh actions (#3)

* add gh actions

* Update testing

* update testing

* add lint

* coveralls

* coveralls

* deploy

* Bump version: 0.0.4 → 0.0.5

* update readme

* transfer to brainglobe

* run tests on PR

* update coverage

* support python 3.9

* Bump version: 0.0.5 → 0.0.6

* update bump2version

* Bump version: 0.0.6 → 0.1.0-rc0

* Bump version: 0.1.0-rc0 → 0.1.0

* Update setup.py

* add missing import

* Update README.md

* fix linting

* Exclude tests from packaged distributions (#6)

* Update pre commit

* reformat

* Python 3.10 compatibility

* Bump version: 0.1.0 → 0.2.0-rc0

* update GH actions

* Bump version: 0.2.0-rc0 → 0.2.0-rc1

* Bump version: 0.2.0-rc1 → 0.2.0

* Revert older changes

* Fix deprecation of tifffile.imsave replaced by tifffile.imwrite. (#8)

Co-authored-by: Jules Scholler <[email protected]>

* Bump version: 0.2.1 → 0.2.2-rc0

* Bump version: 0.2.2-rc0 → 0.2.2

* Add link to contributing guide

* Add tox and use brainglobe/actions (#10)

* Add tox and use brainglobe actions for testing

* Update pre-commit

* run pre-commit

* Update tox.ini

* Bump version: 0.2.2 → 0.2.3-rc0

* Bump version: 0.2.3-rc0 → 0.2.3

* Long description (#11)

* Add long description for PyPI

* Bump version: 0.2.3 → 0.2.4-rc0

* Bump version: 0.2.4-rc0 → 0.2.4

* Change coverage badge to codecov.

* Test on recent python versions (#13)

* Test on recent python versions

* Bump pre-commit versions

* Fix dtype issue

* Remove straggling mention of 3.7

* Replace brainglobe > NI actions (#14)

* Use standard pre-commit config  (#15)

* Add standard pre-commit config

* pre-commit fixes

* Use pyproject.toml (#16)

* Filter warnings in pytest (#17)

* Filter warnings in pytest

* Filter nptyping warnings

* Add all-contributors

* Update README.md

Co-authored-by: David Stansby <[email protected]>

* docs: add crousseau as a contributor for code, ideas, and test (#25)

* docs: update README.md [skip ci]

* docs: create .all-contributorsrc [skip ci]

* Remove badge

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* Don't skip CI for all-contrbutors-bot

* Update .all-contributorsrc

* docs: add jaimergp as a contributor for code (#23)

* docs: update README.md [skip ci]

* docs: create .all-contributorsrc [skip ci]

* Update README.md

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* docs: add JulesScholler as a contributor for code (#22)

* docs: update README.md [skip ci]

* docs: create .all-contributorsrc [skip ci]

* Update README.md

* Update .all-contributorsrc

* Update .all-contributorsrc

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* docs: add dstansby as a contributor for test, code, and 3 more (#21)

* docs: update README.md [skip ci]

* docs: create .all-contributorsrc [skip ci]

* Update README.md

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* docs: add adamltyson as a contributor for code, infra, and 2 more (#24)

* docs: update README.md [skip ci]

* docs: create .all-contributorsrc [skip ci]

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

* Update README.md

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* Update doc links (#27)

* [pre-commit.ci] pre-commit autoupdate (#28)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.240...v0.0.272)
- [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0)
- [github.com/pre-commit/mirrors-mypy: v0.991 → v1.3.0](pre-commit/mirrors-mypy@v0.991...v1.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update dependency (imlib -> brainglobe-utils) (#29)

* [pre-commit.ci] pre-commit autoupdate (#31)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.4.1](pre-commit/mirrors-mypy@v1.3.0...v1.4.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* remove all contributors (#32)

* [pre-commit.ci] pre-commit autoupdate (#33)

updates:
- https:/charliermarsh/ruff-pre-commit → https:/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#34)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update CI workflow to use NIU actions (#35)

* [pre-commit.ci] pre-commit autoupdate (#36)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278)
- [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#37)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#38)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.280 → v0.0.281](astral-sh/ruff-pre-commit@v0.0.280...v0.0.281)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#39)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.281...v0.0.282)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#40)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)
- [github.com/pre-commit/mirrors-mypy: v1.4.1 → v1.5.0](pre-commit/mirrors-mypy@v1.4.1...v1.5.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#41)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)
- [github.com/pre-commit/mirrors-mypy: v1.5.0 → v1.5.1](pre-commit/mirrors-mypy@v1.5.0...v1.5.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#42)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Set pre-commit autoupdate frequency to monthly (#43)

* [pre-commit.ci] pre-commit autoupdate (#44)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#45)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.292](astral-sh/ruff-pre-commit@v0.0.287...v0.0.292)
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#48)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.4](astral-sh/ruff-pre-commit@v0.0.292...v0.1.4)
- [github.com/psf/black: 23.9.1 → 23.10.1](psf/black@23.9.1...23.10.1)
- [github.com/pre-commit/mirrors-mypy: v1.5.1 → v1.6.1](pre-commit/mirrors-mypy@v1.5.1...v1.6.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#49)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.4...v0.1.6)
- [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0)
- [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.1](pre-commit/mirrors-mypy@v1.6.1...v1.7.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#50)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.6...v0.1.9)
- [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](pre-commit/mirrors-mypy@v1.7.1...v1.8.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update GH actions badge (#51)

* Update test_and_deploy.yml (#52)

See neuroinformatics-unit/movement#108

Co-authored-by: Igor Tatarnikov <[email protected]>

* Add manifest (#54)

* Update CI workflows with manifest

* Allow workflow to be dispatchable

* Add pyarrow dependency to prevent future pandas failures

* [pre-commit.ci] pre-commit autoupdate (#53)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* refactor image_io as submodule

* Deprecated alias warning is still present

* Fix an actual circular import because of wildcard import

* Fix buggy html logo - wrong escape backslash

---------

Co-authored-by: crousseau <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Jaime Rodríguez-Guerra <[email protected]>
Co-authored-by: Jules Scholler <[email protected]>
Co-authored-by: Jules Scholler <[email protected]>
Co-authored-by: David Stansby <[email protected]>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: Igor Tatarnikov <[email protected]>
@adamltyson
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Looking into this, I don't think we should do anything about this because int64 nii files do cause issues with other software.

I can't remember when this warning was raised, but I think it's unlikely that software should be saving int64 niis. Anyway this will now error with the latest version of nibabel, so if it occurs, we can address it.

@adamltyson adamltyson closed this as not planned Won't fix, can't repro, duplicate, stale May 14, 2024
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bug Something isn't working old-imio Issue was open on imio before it was merged into this package. Now concerns the image_io submodule.
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