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Add multi-plane processing using CaImAn #174

Merged
merged 54 commits into from
Nov 28, 2023
Merged

Add multi-plane processing using CaImAn #174

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b70f534
handle multi-channel tiff image before running CaImAn only for ScanIm…
Aug 10, 2023
d5a0cf8
Merge remote-tracking branch 'upstream/main'
Aug 10, 2023
5d71dab
support multiplane processing with CaImAn - per-plane basis
Aug 16, 2023
53a75b8
update pipeline to support per-plane processing with caiman
Aug 23, 2023
34f2351
at Processing - generate new PerPlaneProcessingTask or confirm all P…
Aug 23, 2023
d471a04
Update setup.py
Aug 23, 2023
23e6527
bugfix
Aug 23, 2023
187522b
minor fix
Aug 24, 2023
02e87f0
Update attribute `channel=' '` -> `channel=null`
kushalbakshi Aug 24, 2023
54dbf3a
Update `aggr` function with `.proj()`
kushalbakshi Aug 24, 2023
bfc1125
Update `key_source` for `Processing`
kushalbakshi Aug 24, 2023
b7c9e05
update caiman results ingestion - use latest caiman loader
Aug 25, 2023
a0bb444
Update version.py
Aug 25, 2023
b2961f6
Revert `Processing` ker_source + fix output_dir error
kushalbakshi Aug 25, 2023
6d03f94
Update key_source logic for `Processing`
kushalbakshi Aug 25, 2023
38021f3
Fix for str AttributeError
kushalbakshi Aug 25, 2023
e6d4c5b
Fix TypeError for 'str' and 'str'
kushalbakshi Aug 25, 2023
16d4573
Debug mkdir AttributeError
kushalbakshi Aug 25, 2023
3cb8b70
Update caiman_loader keys for motion correction
kushalbakshi Aug 29, 2023
c12e7bb
Remove mask classification extraction from caiman loader
kushalbakshi Aug 29, 2023
07de08b
Merge branch 'per-plane-processing' of https://github.com/ttngu207/el…
kushalbakshi Aug 29, 2023
a499fed
Add exception to debug summary images
kushalbakshi Aug 29, 2023
9322f77
Refine summary image loading
kushalbakshi Aug 29, 2023
a57a024
Internal variable fkey -> field_key
kushalbakshi Aug 29, 2023
a645be4
Append to summary image list
kushalbakshi Aug 29, 2023
bf48a58
fix incorrect shape in summary images retrieval
Aug 29, 2023
342b86f
Manually merge changes from Thinh's branch
kushalbakshi Aug 30, 2023
e7320b3
Update element_calcium_imaging/imaging_no_curation.py
kushalbakshi Aug 30, 2023
87b180f
Merge pull request #2 from kushalbakshi/per-plane-processing
ttngu207 Aug 30, 2023
40ac3c2
Merge pull request #161 from ttngu207/per-plane-processing
kushalbakshi Sep 5, 2023
328393a
Merge branch 'main' of https://github.com/datajoint/element-calcium-i…
Sep 5, 2023
8e9178e
Merge pull request #163 from ttngu207/per-plane-processing
sidhulyalkar Sep 5, 2023
03f4b5e
update get_calcium_imaging_files parameter
sidhulyalkar Sep 6, 2023
7fd7c40
Merge branch 'main' of https://github.com/sidhulyalkar/element-calciu…
sidhulyalkar Sep 6, 2023
350deef
Merge branch 'datajoint:main' into main
ttngu207 Sep 6, 2023
e13146f
bugfix in `infer_output_dir`
Sep 6, 2023
b9a590d
Merge branch 'main' into per-plane-processing
Sep 6, 2023
7f1c596
code cleanup
Sep 6, 2023
2cf78bb
Merge pull request #165 from ttngu207/per-plane-processing
kushalbakshi Sep 6, 2023
70f2a84
Fix `PrairieViewMeta` import statements
kushalbakshi Sep 7, 2023
69831b2
Black formatting
kushalbakshi Sep 7, 2023
649fe4a
Merge pull request #166 from kushalbakshi/per-plane-processing
sidhulyalkar Sep 7, 2023
85718e5
hard set force_sktiff to true
sidhulyalkar Sep 7, 2023
4b15184
merge upstream
sidhulyalkar Sep 7, 2023
580d9ee
bump version
sidhulyalkar Sep 7, 2023
83b27a3
Merge pull request #167 from sidhulyalkar/caiman_per_plane_processing
kushalbakshi Sep 7, 2023
b30ac91
Add motion correction indicies to caiman params
kushalbakshi Oct 12, 2023
003c312
Black formatting
kushalbakshi Oct 12, 2023
d5f6a1d
Merge branch 'caiman_per_plane_processing' of https://github.com/data…
kushalbakshi Oct 16, 2023
8b33b76
Fix typo indicies -> indices
kushalbakshi Oct 16, 2023
139f5bb
Merge pull request #171 from kushalbakshi/per-plane-processing
sidhulyalkar Oct 16, 2023
c45ee5d
Revert old `slice` commit
kushalbakshi Oct 16, 2023
7651d35
Merge pull request #172 from kushalbakshi/per-plane-processing
sidhulyalkar Oct 16, 2023
b565204
Merge branch 'staging' into caiman_per_plane_processing
kushalbakshi Nov 28, 2023
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6 changes: 1 addition & 5 deletions element_calcium_imaging/imaging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -254,13 +254,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
e.g.: sub4/sess1/scan0/suite2p_0
"""
acq_software = (scan.Scan & key).fetch1("acq_software")
filetypes = dict(
ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
)

scan_dir = find_full_path(
get_imaging_root_data_dir(),
get_calcium_imaging_files(key, filetypes[acq_software])[0],
get_calcium_imaging_files(key, acq_software)[0],
).parent
root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)

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