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Allow free rotation of the atlas #36

Merged
merged 37 commits into from
Jul 26, 2024
Merged

Allow free rotation of the atlas #36

merged 37 commits into from
Jul 26, 2024

Commits on Jan 15, 2024

  1. Fixed contents margins

    @IgorTatarnikov
    IgorTatarnikov committed Jan 15, 2024
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  2. Scaling of sample image added to adjust moving image dropdown

    @IgorTatarnikov
    IgorTatarnikov committed Jan 15, 2024
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  3. Added brainglobe-utils as dependency

    @IgorTatarnikov
    IgorTatarnikov committed Jan 15, 2024
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  4. Merge branch 'move-to-dropdown-parent' into scale-moving-image-resolu… 

    …tion
    @IgorTatarnikov
    IgorTatarnikov committed Jan 15, 2024
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Commits on Jan 16, 2024

  1. Added error message when no images selected

    @IgorTatarnikov
    IgorTatarnikov committed Jan 16, 2024
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  2. Atlas rotation working using scipy

    @IgorTatarnikov
    IgorTatarnikov committed Jan 16, 2024
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  3. Pitch, yaw, roll implemented using one affine transform

    @IgorTatarnikov
    IgorTatarnikov committed Jan 16, 2024
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  4. Dask loading for both the reference atlas and the rotation

    @IgorTatarnikov
    IgorTatarnikov committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. Added a 'Reset Atlas' button, blocked while dask computes the rotatio… 

    …n to avoid race conditions
    @IgorTatarnikov
    IgorTatarnikov committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. Rotate atlas button also greyed out while daks processes the rotation

    @IgorTatarnikov
    IgorTatarnikov committed Jan 18, 2024
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Commits on Feb 2, 2024

  1. Use the update upload_pypi action (#29) 

    See neuroinformatics-unit/movement#108
    @IgorTatarnikov
    IgorTatarnikov authored Feb 2, 2024
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Commits on Feb 6, 2024

  1. Resolved merge conflicts

    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  2. Added elastix Logs directory to .gitignore

    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  3. Fixed tests

    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  4. Moved run_registration to be imported just as run button is clicked t… 

    …o avoid long boot times
    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  5. Atlas rotation works again (might relate to napari 0.4.19

    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  6. Added test for atlas_rotation_signal from AdjustMovingImage view

    @IgorTatarnikov
    IgorTatarnikov committed Feb 6, 2024
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  7. [pre-commit.ci] pre-commit autoupdate (#30) 

    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>
    @pre-commit-ci
    pre-commit-ci[bot] authored Feb 6, 2024
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Commits on Apr 4, 2024

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

    updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.5](astral-sh/ruff-pre-commit@v0.2.0...v0.3.5)
- [github.com/psf/black: 24.1.1 → 24.3.0](psf/black@24.1.1...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](pre-commit/mirrors-mypy@v1.8.0...v1.9.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    @pre-commit-ci
    pre-commit-ci[bot] authored Apr 4, 2024
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Commits on Apr 12, 2024

  1. Import header from brainglobe-utils (#33) 

    * import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency
    @K-Meech
    K-Meech authored Apr 12, 2024
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Commits on Apr 22, 2024

  1. Update requirements (#34) 

    * import header from brainglobe-utils

* split package name over two lines

* remove brainglobe png from manifest

* add brainglobe-utils dependency

* Switched from bg-atlasapi to brainglobe-atlasapi

* Added lxml_html_clean explicitly to requirements

* Pinned itk to 5.4rc2 for now as 5.4rc3 cased a seg fault

* Undo itk pin

---------

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
    @IgorTatarnikov @K-Meech
    IgorTatarnikov and K-Meech authored Apr 22, 2024
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  2. add codecov token (#35)

    @K-Meech
    K-Meech authored Apr 22, 2024
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Commits on Apr 23, 2024

  1. Added tests for calculate_rotated_bounding_box

    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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  2. Fixed docstrings for functions in utils.py

    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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  3. Keep track of napari layers for the atlas and atlas annotations in th… 

    …e napari widget class
    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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  4. Added tests for atlas rotation

    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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  5. Fixed pre-commit

    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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  6. Fixed merge conflicts

    @IgorTatarnikov
    IgorTatarnikov committed Apr 23, 2024
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Commits on Jun 27, 2024

  1. Add test for reset_atlas in adjust_moving_image_view

    @IgorTatarnikov
    IgorTatarnikov committed Jun 27, 2024
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  2. Add caching

    @IgorTatarnikov
    IgorTatarnikov committed Jun 27, 2024
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  3. Update the function calls in test_adjust_moving_image_view

    @IgorTatarnikov
    IgorTatarnikov committed Jun 27, 2024
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Commits on Jul 26, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
    @IgorTatarnikov @alessandrofelder
    IgorTatarnikov and alessandrofelder authored Jul 26, 2024
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  2. Applied suggestions from code review

    @IgorTatarnikov
    IgorTatarnikov committed Jul 26, 2024
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jul 26, 2024
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  4. Fixed merge conflicts

    @IgorTatarnikov
    IgorTatarnikov committed Jul 26, 2024
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  5. Applied suggestions from code review

    @IgorTatarnikov
    IgorTatarnikov committed Jul 26, 2024
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  6. Merge branch 'atlas-yaw-pitch' of https://github.com/brainglobe/bg-el… 

    …astix into atlas-yaw-pitch
    @IgorTatarnikov
    IgorTatarnikov committed Jul 26, 2024
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