Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Support more types, and support dask. #36

Open
3 of 6 tasks
adamltyson opened this issue Sep 15, 2021 · 1 comment
Open
3 of 6 tasks

Support more types, and support dask. #36

adamltyson opened this issue Sep 15, 2021 · 1 comment
Labels
enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed old-imio Issue was open on imio before it was merged into this package. Now concerns the image_io submodule.

Comments

@adamltyson
Copy link
Member

adamltyson commented Sep 15, 2021 •
edited
Loading

Moving issue from brainglobe/cellfinder#184

Imio should read more types with an option to return a dask array rather than numpy.

Some ideas include:

  • Path to directory of tiffs
  • Path to text file of tiffs
  • 3D tiff
  • h5/BDV
  • npy
  • OME-Zarr
@adamltyson adamltyson added enhancement New feature or request help wanted Extra attention is needed good first issue Good for newcomers labels Sep 15, 2021
This was referenced Sep 15, 2021
Merged
Closed
@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 <jules.scholler@wysscenter.ch>

* 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 <dstansby@gmail.com>

* 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 <code@adamltyson.com>

* 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 <code@adamltyson.com>

* 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 <code@adamltyson.com>

* 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 <code@adamltyson.com>

* 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 <code@adamltyson.com>

* 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://github.com/charliermarsh/ruff-pre-commit → https://github.com/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 <61896994+IgorTatarnikov@users.noreply.github.com>

* 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 <c.rousseau@ucl.ac.uk>
Co-authored-by: Adam Tyson <adam.tyson@ucl.ac.uk>
Co-authored-by: Adam Tyson <code@adamltyson.com>
Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com>
Co-authored-by: Jules Scholler <jules.scholler@gmail.com>
Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch>
Co-authored-by: David Stansby <dstansby@gmail.com>
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 <alessandrofelder@users.noreply.github.com>
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
@adamltyson
Copy link
Member Author

This has progressed very slightly with #73. At some point, read_z_stack and read_with_dask should be combined with load_any etc. I didn't do it in #73 because there's already enough downstream effects of that PR.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement New feature or request good first issue Good for newcomers help wanted Extra attention is needed old-imio Issue was open on imio before it was merged into this package. Now concerns the image_io submodule.
Projects
Core development
Status: Backlog
Milestone
No milestone
Development

No branches or pull requests
2 participants
@adamltyson @willGraham01