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

Filter Images #52

Merged
merged 10 commits into from
Aug 13, 2024
Merged

Filter Images #52

merged 10 commits into from
Aug 13, 2024

Conversation

saarah815
Copy link
Contributor

@saarah815 saarah815 commented Aug 9, 2024 •
edited
Loading

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

  • Bug fix
  • Addition of a new feature
  • Other

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:

  • 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 Codecov
Copy link

codecov bot commented Aug 12, 2024 •
edited
Loading

Codecov Report

Attention: Patch coverage is 38.09524% with 13 lines in your changes missing coverage. Please review.

Project coverage is 80.96%. Comparing base (ce8bdc5) to head (0bac989).
Report is 2 commits behind head on dev.

Files Patch % Lines
brainglobe_registration/utils/utils.py 38.46% 8 Missing ⚠️
brainglobe_registration/registration_widget.py 37.50% 5 Missing ⚠️
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.
📢 Have feedback on the report? Share it here.

@saarah815 saarah815 marked this pull request as ready for review August 12, 2024 10:38
@saarah815 saarah815 changed the title Filter Images - Draft Filter Images Aug 12, 2024
@saarah815 saarah815 changed the title Filter Images Filter Images Aug 12, 2024
IgorTatarnikov
IgorTatarnikov approved these changes Aug 12, 2024
View reviewed changes
Copy link
Member

@IgorTatarnikov IgorTatarnikov left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

brainglobe_registration/utils/utils.py Show resolved Hide resolved
brainglobe_registration/registration_widget.py Outdated Show resolved Hide resolved
brainglobe_registration/registration_widget.py Outdated Show resolved Hide resolved
@saarah815
Copy link
Contributor Author

saarah815 commented Aug 12, 2024 •
edited
Loading

Sounds good, thank you! All new changes have been pushed.

IgorTatarnikov
IgorTatarnikov approved these changes Aug 12, 2024
View reviewed changes
Copy link
Member

@IgorTatarnikov IgorTatarnikov left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Last couple of things I noticed!

brainglobe_registration/utils/utils.py Outdated Show resolved Hide resolved
brainglobe_registration/utils/utils.py Outdated Show resolved Hide resolved
brainglobe_registration/utils/utils.py Outdated Show resolved Hide resolved
brainglobe_registration/utils/utils.py Outdated Show resolved Hide resolved
saarah815 and others added 5 commits August 13, 2024 12:11
@saarah815 @IgorTatarnikov
Update brainglobe_registration/utils/utils.py
55762fb 
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
@saarah815 @IgorTatarnikov
Update brainglobe_registration/utils/utils.py
2153af3 
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
@saarah815 @IgorTatarnikov
Update brainglobe_registration/utils/utils.py
b61b34c 
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
@saarah815 @IgorTatarnikov
Update brainglobe_registration/utils/utils.py
9a469b7 
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
0bac989 
for more information, see https://pre-commit.ci
@IgorTatarnikov IgorTatarnikov merged commit f690dea into brainglobe:dev Aug 13, 2024
11 of 13 checks passed
@IgorTatarnikov IgorTatarnikov mentioned this pull request Aug 16, 2024
Merged
7 tasks
alessandrofelder added a commit that referenced this pull request Aug 16, 2024
@IgorTatarnikov @pre-commit-ci
@K-Meech @alessandrofelder @saarah815
Update main wtih dev changes (#55)
cc23983 
* 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 <24316371+K-Meech@users.noreply.github.com>

* 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 <alessandrofelder@users.noreply.github.com>

* 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 <24316371+K-Meech@users.noreply.github.com>
Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>

* 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 <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* changes to info message

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [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 <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [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 <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [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 <61896994+IgorTatarnikov@users.noreply.github.com>
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 <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/utils/utils.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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 <61896994+IgorTatarnikov@users.noreply.github.com>

* layer_deletion_edits

* Made pytest happy

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* Update brainglobe_registration/registration_widget.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* [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 <61896994+IgorTatarnikov@users.noreply.github.com>
Co-authored-by: IgorTatarnikov <igor.tatarnikov@gmail.com>
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 <24316371+K-Meech@users.noreply.github.com>
Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Co-authored-by: saarah815 <63860766+saarah815@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@IgorTatarnikov IgorTatarnikov IgorTatarnikov approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@saarah815 @IgorTatarnikov