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.

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

[osmFISH 2/5] Implement Laplacian Filter #687

Merged
merged 3 commits into from
Oct 16, 2018
Merged

Conversation

dganguli
Copy link
Collaborator

@dganguli dganguli commented Oct 3, 2018

This filter enhances spots, and is used by the osmFISH pipeline. Under the hood, it's simply a call to scipy.ndimage.gaussian_laplace

Note that there is no test for this filter. From offline conversations, it's not clear what our testing strategy for filters are. Especially for filters that are pulled in from existing libraries, like this one. Really, what we want to test here is that the Starfish specific wrapping code works as expected.

For now, I'll rely on [osmFISH 5/5] notebook to function as the test of this filter.

@dganguli dganguli requested review from ttung and ambrosejcarr and removed request for ttung October 3, 2018 22:55
@dganguli
Copy link
Collaborator Author

dganguli commented Oct 3, 2018

FYI @simone-codeluppi

@dganguli dganguli changed the base branch from dg-detect-volume-flag to master October 3, 2018 23:12
@dganguli dganguli changed the base branch from master to dg-detect-volume-flag October 3, 2018 23:16
@ambrosejcarr ambrosejcarr force-pushed the dg-laplace-filter branch 2 times, most recently from 7fcaf6a to eda7248 Compare October 11, 2018 23:36
@ambrosejcarr
Copy link
Member

Ready for review.

@ambrosejcarr ambrosejcarr changed the base branch from dg-detect-volume-flag to master October 12, 2018 23:44
@codecov-io
Copy link

codecov-io commented Oct 13, 2018

Codecov Report

Merging #687 into master will decrease coverage by <.01%.
The diff coverage is 87.87%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #687      +/-   ##
==========================================
- Coverage   88.04%   88.04%   -0.01%     
==========================================
  Files         121      122       +1     
  Lines        4133     4166      +33     
==========================================
+ Hits         3639     3668      +29     
- Misses        494      498       +4
Impacted Files Coverage Δ
starfish/image/_filter/__init__.py 95.23% <100%> (+0.11%) ⬆️
starfish/image/_filter/laplace.py 87.5% <87.5%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d526680...225f3a0. Read the comment docs.

@ambrosejcarr ambrosejcarr merged commit 4aeab13 into master Oct 16, 2018
@ambrosejcarr ambrosejcarr deleted the dg-laplace-filter branch October 29, 2018 15:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

4 participants