Update main wtih dev changes #55
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* Fixed contents margins * Added brainglobe-utils as dependency * Added min dependency version for brainglobe-utils
* Fixed contents margins * Scaling of sample image added to adjust moving image dropdown * Added brainglobe-utils as dependency * Added error message when no images selected * Added tests for scaling * Added tests to check multiple scale_factors * Cache the moving image data to allow scaling image multiple times * Fixed tests by removing (0,0) case add guard in _on_scale_image in registration_widget.py * Fixed tests * Add docstring to _on_scale_moving_image * Replaced all curr_ variable names with current_ * Added units to pixel size selection, set max range to be 100
* Fixed contents margins * Scaling of sample image added to adjust moving image dropdown * Added brainglobe-utils as dependency * Added error message when no images selected * Atlas rotation working using scipy * Pitch, yaw, roll implemented using one affine transform * Dask loading for both the reference atlas and the rotation * Added a 'Reset Atlas' button, blocked while dask computes the rotation to avoid race conditions * Rotate atlas button also greyed out while daks processes the rotation * Use the update upload_pypi action (#29) See neuroinformatics-unit/movement#108 * Added elastix Logs directory to .gitignore * Fixed tests * Moved run_registration to be imported just as run button is clicked to avoid long boot times * Atlas rotation works again (might relate to napari 0.4.19 * Added test for atlas_rotation_signal from AdjustMovingImage view * [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 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> * 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 * 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 <[email protected]> * add codecov token (#35) * Added tests for calculate_rotated_bounding_box * Fixed docstrings for functions in utils.py * Keep track of napari layers for the atlas and atlas annotations in the napari widget class * Added tests for atlas rotation * Fixed pre-commit * Add test for reset_atlas in adjust_moving_image_view * Add caching * Update the function calls in test_adjust_moving_image_view * Apply suggestions from code review Co-authored-by: Alessandro Felder <[email protected]> * Applied suggestions from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Applied suggestions from code review --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Kimberly Meechan <[email protected]> Co-authored-by: Alessandro Felder <[email protected]>
…s installed (#46) * added error when no atlas found * added error when no atlas found * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * changes to info message * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * parent_widget * parent_widget --------- Co-authored-by: Igor Tatarnikov <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Cleaned up rogue widget duplication * Added parent to parameters_tab
* work_in_progress * filter_images * filter_images * filter_images * filter_images * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Igor Tatarnikov <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* layer_deletion * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * layer_deletion_edits * Made pytest happy * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated_layer * fixed manual vs automatic deletion * fixed manual vs automatic deletion * Refactored some old code to avoid duplication * add comments --------- Co-authored-by: Igor Tatarnikov <[email protected]> Co-authored-by: IgorTatarnikov <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
# Conflicts: # brainglobe_registration/napari.yaml
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #55 +/- ##
==========================================
+ Coverage 79.69% 81.94% +2.25%
==========================================
Files 9 9
Lines 389 587 +198
==========================================
+ Hits 310 481 +171
- Misses 79 106 +27 ☔ View full report in Codecov by Sentry. |
alessandrofelder
approved these changes
Aug 16, 2024
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Description
What is this PR
What does this PR do?
Moves dev changes into main.
References
Includes the following PRs:
#25 #26 #36 #48 #46 #51 #54 #52 #49
How has this PR been tested?
All previous tests pass.
Is this a breaking change?
No
Does this PR require an update to the documentation?
Yes, will come in a separate PR.
Checklist: