Filter Images #52
Merged
Filter Images #52
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #52 +/- ##
==========================================
- Coverage 82.98% 80.96% -2.03%
==========================================
Files 8 8
Lines 523 541 +18
==========================================
+ Hits 434 438 +4
- Misses 89 103 +14 ☔ View full report in Codecov by Sentry. |
IgorTatarnikov
approved these changes
Aug 12, 2024
There was a problem hiding this comment.
Just a few tiny things to change mostly with formatting.
Great job coming up with a solution to the weird error thrown by morphology.opening. We could also utilise features of a dask array to fix this. Since the atlas is always loaded as a dask array we can call .compute() on the atlas layer before passing it to the filter_plane function. This basically does the same thing, where it forces dask to convert that plane into a plain old numpy array.
It might be worth changing to that solution since I got a warning from dask when using np.copy. Changing the approach would help safeguard us against future deprecations.
|
Sounds good, thank you! All new changes have been pushed. |
IgorTatarnikov
approved these changes
Aug 12, 2024
Co-authored-by: Igor Tatarnikov <[email protected]>
Co-authored-by: Igor Tatarnikov <[email protected]>
Co-authored-by: Igor Tatarnikov <[email protected]>
Co-authored-by: Igor Tatarnikov <[email protected]>
for more information, see https://pre-commit.ci
IgorTatarnikov
approved these changes
Aug 13, 2024
7 tasks
alessandrofelder
added a commit
that referenced
this pull request
Aug 16, 2024
* 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]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Before submitting a pull request (PR), please read the contributing guide.
Please fill out as much of this template as you can, but if you have any problems or questions, just leave a comment and we will help out :)
Description
What is this PR
Why is this PR needed?
Adds option to filter fixed and moving image before registration.
What does this PR do?
Adds checkbox in UI above 'Run' button. Filters images if ticked.
Replicates functionality of
brainreg.core.utils.preprocess.filter_plane.References
Please reference any existing issues/PRs that relate to this PR.
#50
How has this PR been tested?
Tested locally.
Is this a breaking change?
No.
Does this PR require an update to the documentation?
Checklist: