Info message when running BrainGlobe Registration plugin with no atlas installed #46

saarah815 · 2024-08-05T22:04:31Z

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Description

What is this PR

Bug fix
Addition of a new feature
Other

Why is this PR needed?

If user has no atlases installed, this widget informs user that they need to install atlas(es) before they are able to use BrainGlobe Registration plugin.

What does this PR do?

If no atlases installed:
- Info message in terminal: "No atlas installed. Please download atlas(es) from https://github.com/brainglobe/brainglobe-atlasapi"
- Message box appears in Napari GUI with same message

References

Please reference any existing issues/PRs that relate to this PR.

Issue #15

How has this PR been tested?

Please explain how any new code has been tested, and how you have ensured that no existing functionality has changed.

No atlases downloaded - info messages appear as expected
Atlases downloaded - info messages do not appear (as expected)
Deleted all atlases - info messages appear as expected

Is this a breaking change?

If this PR breaks any existing functionality, please explain how and why.

N/A

Does this PR require an update to the documentation?

If any features have changed, or have been added. Please explain how the documentation has been updated (and link to the associated PR). See here for details.

N/A

Checklist:

The code has been tested locally
Tests have been added to cover all new functionality (unit & integration)
The documentation has been updated to reflect any changes
The code has been formatted with pre-commit

codecov · 2024-08-06T09:50:14Z

Codecov Report

Attention: Patch coverage is 88.88889% with 1 line in your changes missing coverage. Please review.

Project coverage is 82.98%. Comparing base (538cdd2) to head (62b095a).
Report is 1 commits behind head on dev.

Files	Patch %	Lines
brainglobe_registration/utils/utils.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev      #46      +/-   ##
==========================================
+ Coverage   82.91%   82.98%   +0.07%     
==========================================
  Files           8        8              
  Lines         515      523       +8     
==========================================
+ Hits          427      434       +7     
- Misses         88       89       +1

☔ View full report in Codecov by Sentry.
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IgorTatarnikov

This is fantastic! I've added a few comments for you to address, but nothing major.

brainglobe_registration/registration_widget.py

IgorTatarnikov · 2024-08-06T10:32:20Z

I just noticed that we have the display_info convenience function in brainglobe-utils.qtpy.dialog that takes care of the Qt internals. This can simplify the code even further, you can import it and just call display_info with the corresponding title and message if no atlases are installed!

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

IgorTatarnikov

Last set of changes I promise! I'll mark it as approved, you can make the final changes and then I'll merge it in!

brainglobe_registration/utils/utils.py

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

for more information, see https://pre-commit.ci

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

for more information, see https://pre-commit.ci

saarah815 · 2024-08-06T17:12:43Z

Last set of changes I promise! I'll mark it as approved, you can make the final changes and then I'll merge it in!

Perfect, thank you!

IgorTatarnikov

That should fix the surprise appearance of parent_widget

brainglobe_registration/utils/utils.py

brainglobe_registration/registration_widget.py

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

for more information, see https://pre-commit.ci

* Moving from tabs to a dropdown style widget (#25) * Fixed contents margins * Added brainglobe-utils as dependency * Added min dependency version for brainglobe-utils * Add option to scale sample image (#26) * 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 * Allow free rotation of the atlas (#36) * 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]> * Cleaned up a few things * Mark 'Advanced Settings' as optional (#48) * Info message when running BrainGlobe Registration plugin with no atlas 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> * Clean up widget (#51) * Cleaned up rogue widget duplication * Added parent to parameters_tab * Fix slow plugin loading (#54) * Filter Images (#52) * 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> * Communicate napari layer deletions appropriately to the plugin (#49) * 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> --------- 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]> Co-authored-by: saarah815 <[email protected]>

saarah815 added 2 commits August 5, 2024 16:37

added error when no atlas found

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added error when no atlas found

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IgorTatarnikov self-requested a review August 6, 2024 09:41

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saarah815 and others added 3 commits August 6, 2024 11:35

Update brainglobe_registration/registration_widget.py

d65ecf8

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

Update brainglobe_registration/registration_widget.py

2b29d3a

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

changes to info message

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IgorTatarnikov approved these changes Aug 6, 2024

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saarah815 and others added 7 commits August 6, 2024 18:09

Update brainglobe_registration/utils/utils.py

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

Update brainglobe_registration/utils/utils.py

4275ad9

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

Update brainglobe_registration/utils/utils.py

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Update brainglobe_registration/utils/utils.py

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

Update brainglobe_registration/utils/utils.py

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saarah815 and others added 7 commits August 6, 2024 20:08

Update brainglobe_registration/utils/utils.py

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Update brainglobe_registration/utils/utils.py

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Update brainglobe_registration/registration_widget.py

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parent_widget

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parent_widget

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parent_widget

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IgorTatarnikov approved these changes Aug 7, 2024

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IgorTatarnikov merged commit ce8bdc5 into brainglobe:dev Aug 7, 2024
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IgorTatarnikov mentioned this pull request Aug 16, 2024

Update main wtih dev changes #55

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IgorTatarnikov mentioned this pull request Aug 16, 2024

[BUG] Plugin crash when no brainglobe atlases available #15

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Info message when running BrainGlobe Registration plugin with no atlas installed #46

Info message when running BrainGlobe Registration plugin with no atlas installed #46

saarah815 commented Aug 5, 2024

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Info message when running BrainGlobe Registration plugin with no atlas installed #46

Info message when running BrainGlobe Registration plugin with no atlas installed #46

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saarah815 commented Aug 5, 2024

Description

References

How has this PR been tested?

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

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