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

Add memoized_result + update calcium imaging utility functions #121

Merged
merged 113 commits into from
Aug 9, 2024
Merged

Add memoized_result + update calcium imaging utility functions #121

merged 113 commits into from
Aug 9, 2024

Conversation

kushalbakshi
Copy link
Collaborator

This PR adds/updates the following:

  • memorized_result decorator (Dev memoized results #102)
  • caiman_loader.py and run_caiman.py to process the latest version of CaImAn
  • prairie_view_loader.py to handle single page and multi page .ome.tif files
  • New documentation to describe / explain the new and updated features
  • Latest GHA used across DataJoint Elements

Thinh Nguyen and others added 30 commits August 16, 2023 18:33
support loading multiple caiman results for multi-plane
da03b82
Merge branch 'main' into multi-plane-caiman
9d365bf
new caiman loader - handles multi-plane results
9bf69ff
improve non-rigid motion correction loading
05d7c35
added routine to combine single-page tiffs into one bigtiff
b050265
run_caimain - more robust
512e5af
add caiman_compatible mode
7d6ea0e
minor cleanup, version bump
55e5a5c
Update caiman_loader.py
cb08034
@kushalbakshi
Fix regex error
85078fd
bugfix
7b815ff
@kushalbakshi
Resolve TypeError: Add .stem()
0bf78ed
@kushalbakshi
Debug FileNotFoundError at output_dir
706df04
Merge pull request datajoint#2 from kushalbakshi/multi-plane-caiman
5a99468 
Bugfixes from testing
@kushalbakshi
Raise exception to debug summary image dimensions
df0d9b8
@kushalbakshi
Revert previous commit
13e6e94
Merge branch 'main' into multi-plane-caiman
b76429d
@kushalbakshi
Merge pull request datajoint#88 from ttngu207/multi-plane-caiman
a2cf2b2 
Multi plane caiman
@kushalbakshi
Update CHANGELOG for datajoint#88
20188ad
add validation argument to dandi upload
697e804
@kushalbakshi
Merge branch 'multi-plane-caiman' of https://github.com/kushalbakshi/…
3b4b61c 
…element-interface into multi-plane-caiman
@kushalbakshi
Check for z_fields in 2nd cycle of acqusition
7e5be44
Merge pull request datajoint#89 from kushalbakshi/multi-plane-caiman
20d5418 
Check for z_fields in 2nd cycle `.xml` file
@ttngu207
passing as argument to fit_file
b374a41
@kushalbakshi
Merge pull request datajoint#90 from ttngu207/multi-plane-caiman
7e26b82 
passing `indices` as argument to `fit_file`
@kushalbakshi
Fix typo indicies -> indices
a558909
@sidhulyalkar
Merge pull request datajoint#91 from kushalbakshi/multi-plane-caiman
f14366d 
Fix typo indicies -> indices
@kushalbakshi
Update params -> parameters
23e14b4
@sidhulyalkar
Merge pull request datajoint#92 from kushalbakshi/multi-plane-caiman
a562033 
Update params -> parameters
@kushalbakshi
Set indices=None in fit_file() + comments for clarity
fff8aba
ttngu207 and others added 27 commits June 26, 2024 11:30
@ttngu207
Merge branch 'staging' of https://github.com/datajoint/element-interface
c189c48 
 into staging
@ttngu207
Merge branch 'staging' into dev_prairieview_multipagetif
bc548de
@ttngu207
update: deprecate "caiman_compatible" argument
dbec434
@kushalbakshi
Merge pull request datajoint#114 from ttngu207/dev_prairieview_multip…
eff0d7b 
…agetif

update: deprecate "caiman_compatible" argument
@ttngu207
fix: additional safeguard to close the file and delete the tffl object
315c19a
@ttngu207
Merge branch 'staging' of https://github.com/datajoint/element-interface
02962d3 
 into dev_prairieview_multipagetif
@kushalbakshi
Merge pull request datajoint#115 from ttngu207/dev_prairieview_multip…
e025b29 
…agetif

fix: additional safeguard to close the file and delete the tffl object
@ttngu207
feat: add use_cuda for caiman
f3aea53
@kushalbakshi
Merge branch 'staging' of https://github.com/datajoint/element-interface
288ae92 
 into staging
@kushalbakshi
Merge pull request datajoint#116 from ttngu207/dev_use_cuda_flag
86f1f85 
feat: add `use_cuda` for caiman
@ttngu207
Merge branch 'dev_memoized_results' into staging
e9e17f3
@ttngu207
Merge remote-tracking branch 'upstream/dev_memoized_results' into sta…
436412d 
…ging
@ttngu207
Merge branch 'staging' of https://github.com/datajoint/element-interface
4df8a08 
 into staging
@ttngu207
Merge remote-tracking branch 'upstream/main' into staging
e2cfc6a
@ttngu207
feat: set gb_per_file and write multiple bigtiff
b525c8c
@ttngu207
chore: add warning with gb_per_file for is_multipage tiff
dc98ebc
@ttngu207
Merge pull request datajoint#117 from ttngu207/dev_write_multiple_big…
ebb6adc 
…tiff

feat: set `gb_per_file` and write multiple bigtiff
@ttngu207
fix: remove old tif files if overwrite=True
e38352e
@ttngu207
fix: incorrect dimension ordering for single-plane caimain loading
0b3b306
@kushalbakshi
Merge pull request datajoint#118 from ttngu207/dev_write_multiple_big…
57a8158 
…tiff

fix: incorrect dimension ordering for single-plane caimain loading
@ttngu207
feat(run_caiman): use output_dir for CAIMAN_TEMP
eb5254d
@kushalbakshi
Merge pull request datajoint#119 from ttngu207/dev_write_multiple_big…
19a0d27 
…tiff

feat(run_caiman): use `output_dir` for `CAIMAN_TEMP`
@kushalbakshi
Merge branch 'staging' of https://github.com/datajoint/element-interface
f633cd8 
 into staging
@kushalbakshi
Update docs, GHA, version, CHANGELOG
686bed6
@kushalbakshi
Apply black formatting
bcd6386
@kushalbakshi
Remove notebooks from GHA checks
76c27b0
@kushalbakshi
Fix version + CHANGELOG
d7b6211
@ttngu207 ttngu207 merged commit 046487b into datajoint:main Aug 9, 2024
5 of 7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ttngu207 ttngu207 ttngu207 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.
4 participants
@kushalbakshi @ttngu207 @sidhulyalkar @JaerongA