Revise Figure 5 code example #652
Merged
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 @@
## main #652 +/- ##
==========================================
+ Coverage 44.89% 47.99% +3.10%
==========================================
Files 71 71
Lines 7311 7296 -15
==========================================
+ Hits 3282 3502 +220
+ Misses 4029 3794 -235 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
AhmetNSimsek
requested changes
Mar 10, 2025
siibra/features/image/sections.py
Outdated
| @@ -83,6 +83,14 @@ def __repr__(self): | |||
| def section(self) -> CellbodyStainedSection: | |||
| return self._section | |||
|
|
|||
| def get_boundingbox(self): | |||
There was a problem hiding this comment.
fetch_kwargs must be passed
Comment on lines
49
to
50
| probmaps = region.parcellation.get_map("mni152", "statistical") | ||
| region_map = probmaps.get_volume(region) |
There was a problem hiding this comment.
why not
region_map = region.get_regional_map("mni152", "statistical") # this is a volume already
Comment on lines
87
to
90
| patch_locations = siibra.PointCloud( | ||
| [tuple(p.get_boundingbox().center) for p in patches], | ||
| space='bigbrain' | ||
| ) |
There was a problem hiding this comment.
patch_locations = siibra.PointCloud.union(*[p.get_boundingbox().center for p in patches])
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Outdated suggestions cannot be applied.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.
I rewrote the code example to make it closer to the manuscript figure and better understandable:
The PR should work, I tested several times, but please check it.