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Introduce image volumes as an input for feature query #480

Merged
merged 109 commits into from
Nov 16, 2023
Merged

Introduce image volumes as an input for feature query #480

merged 109 commits into from
Nov 16, 2023

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AhmetNSimsek
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@AhmetNSimsek AhmetNSimsek commented Sep 21, 2023 •
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The primary aim of this PR is to introduce BrainStructure abstract class as a core concept that will serve as a common denominator between locations, volumes, and regions to simplify concept matching and using volumes in feature queries.

TODO:

  • e2e test: centroid = region.compute_centroids(); assert region.intersect(centroid)

dickscheid and others added 11 commits September 6, 2023 08:21
@dickscheid
remove slicing operator for building volumes of interest from Space o…
cbb2ddb 
…bjects
@dickscheid
remove setting __repr__ to name in Region
8868a78
@dickscheid
introduce NIfTI FeatureMaps as Location subclass and move assignment …
7f7da54 
…logic from AnatomicalAnchor to Region/Location classes
@dickscheid
deal more consistently with points that could not be warped
437be1f
@dickscheid
still accept Map.get_index() for multiple matches in case there is on…
654da71 
…e exact match.
@dickscheid
introduce spatialmap as a location object; simplify matching in live …
dbd1ae9 
…queries
@dickscheid
WIP: introduce LocationFilter, make Volume a LocationFilter; use Loca…
6fe6fa6 
…tionFilters for feature queries; move providers to subfolder of Volume; rename fetch_regional_map to get_regional_map; return Nifti1Image objects only on fetch
@dickscheid
first attempt to re-enable feature query by region object - still tes…
3dcf228 
…ting and needs profiling
@dickscheid
introducde SpaceWapringFailedException; remove contains implementatio…
9656765 
…n in Region
@AhmetNSimsek
fix sparsemap.fetch, small bug fixes
6da6bbc
@AhmetNSimsek
Merge branch 'main' into feat_feature_query_nifti
daeebde
@AhmetNSimsek AhmetNSimsek marked this pull request as draft September 21, 2023 16:24
dickscheid and others added 16 commits September 22, 2023 10:32
@dickscheid
_assign_image deal with updated commons.split_components api
7579ae4
@dickscheid
Region.spatial_props accept modified get_regional_map function
7bcf45e
@dickscheid
fix coordinate selection in Volume.points_inside
f20fd55 
critical error: used voxels in wapred space instead original coordinates.
@dickscheid
fix collecting coordinates for feature anchor
7a8eaee
@dickscheid
fix syntax error
c678889
@AhmetNSimsek
fix typo
c2216d8
@dickscheid
avoid redundant calls of child region maps in Region.get_regional_map
25daef2
@dickscheid
Merge branch 'feat_feature_query_nifti' of github.com:FZJ-INM1-BDA/si…
789ed99 
…ibra-python into feat_feature_query_nifti
@dickscheid
raise proper exception in volume.warp
0300d76
@AhmetNSimsek
Fix recursion error due to locationfilter.assign. Replace __contains_…
2b10a6b 
…_ with contains
@dickscheid
overwrite LocationFilter.assign() in Region to handle all cases
efa458c
@dickscheid
fix order of "in" operator
8c5ab6e
@dickscheid
remove debug output
c5c0526
@dickscheid
allow quering receptor with a nifti volume
b4b197b
@dickscheid
accept volumes for intersection computations
2fcaa0f
@dickscheid
rename LocationFilter to BrainStructure
fb73902
@AhmetNSimsek
Test: fetching a map with multiple volumes wo args and volume.merge
6a9b835
@AhmetNSimsek
Maint tests, fix volume.intersection, organize TODOs
7b7c19e
@AhmetNSimsek
get_uuid -> generate_uuid
50e4db3
@AhmetNSimsek
Add tests: check region-volume intersection, centroid containednedness
7356b80
@AhmetNSimsek
Make BigBrainIntensityProfile.location a property and refer to its an…
fff4592 
…chor
@AhmetNSimsek
Remove gifit import from volumes package
e7028b4
@AhmetNSimsek
Remove redundant tests from e2e\feature\test_get
6485f57
@AhmetNSimsek
Make Location a BrainStructure. Use this to ensure implementation of …
e4ae9e7 
…hash, eq, and repr
@AhmetNSimsek
update str and repr of core concepts
fd5301c
@AhmetNSimsek
Several bug fixes
3421cae 
-  Fix fetch cache
- fix region.fetch_cache -> getmap_cache
- Clean up get_regional_map
- Add names to volumes when extacting volumes (important for hashing)
@AhmetNSimsek
no name field bug fix volume.from_nifti
1312160
@AhmetNSimsek
further volume name adjustments for get_regional map
b6365ae
@AhmetNSimsek
Fix PointSet.intersection (rewrite)
ae02d54 
also fix bounding box import
@AhmetNSimsek
Fix Point le and ge. Use other's intersection in intersection when no…
8c9aed3 
…t clear (this is established in all others)
@AhmetNSimsek
Fix boundingbox.intersection
973d33b
@AhmetNSimsek
Remove non-convex region maps from volume tests
3aaa398
@AhmetNSimsek
fix try-except block of region assignment to locations
d3732e9
@AhmetNSimsek
Update compound feature _export
8694184
@AhmetNSimsek
Remove redundant bigbrain._choose_space and tidy bigbrain.py up
2ba1f83
@AhmetNSimsek
add/correct type hints in anchor.py
6cabaf1
@AhmetNSimsek
Use location's space for region assignment first. region.supported_sp…
f69efa8 
…aces is now a sorted list by default

Fixes issues with reproducibility.
@AhmetNSimsek AhmetNSimsek marked this pull request as ready for review November 15, 2023 14:36
@AhmetNSimsek AhmetNSimsek merged commit d182ffd into main Nov 16, 2023
18 checks passed
@AhmetNSimsek AhmetNSimsek deleted the feat_feature_query_nifti branch November 16, 2023 12:26
@AhmetNSimsek AhmetNSimsek restored the feat_feature_query_nifti branch January 26, 2024 12:22
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@AhmetNSimsek @codecov-commenter @dickscheid