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Final updates #18

Merged
merged 27 commits into from
Sep 3, 2024
Merged

Final updates #18

merged 27 commits into from
Sep 3, 2024

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weiglszonja
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Final updates for the Vu 2024 conversion

Fixes

  • for dual-wavelength excitation when both channels imaging data is in the same .CXD file, the sampling frequency should be halved
  • fix inconsistency for values in "included" column (they should all be coded as boolean values)
  • add 415 nm to fiber photometry response series metadata
  • remove FilePathType, FolderPathType

Improvements

  • Update README.md and conversion notes
  • Use strict requirements and try conversion from fresh virtual environment following the steps in the readme
  • For better readability have a separate convert all sessions script for single-, and dual-wavelength sessions
  • Update tutorial

@weiglszonja
fix sampling frequency for dual-wavelength sessions
4074e2d
@weiglszonja
force boolean type for "included" ROIs
d4faa06
@weiglszonja
fix fiber photometry metadata for 415nm
93bddaa
@weiglszonja
fix for inconsistent naming of avi files
5a8647f
@weiglszonja
add 415nm to fiber photometry name suffices
31825ee
@weiglszonja
add 'video1' and 'video2' to TTL rules
d29dbd1
@weiglszonja
update README.md
86495b0
@weiglszonja
to align the timestamps of the second imaging data use the starting t…
2c89b66 
…ime of the second behavior data for dual wavelength sessions
@weiglszonja
add aligned_starting_time optional argument to the convert session sc…
f0e897e 
…ript
@weiglszonja
propagate aligned_starting_time to NWBConverter
84ba110
@weiglszonja
remove unused imports
f956773
@weiglszonja
update conversion notes
e855961
@weiglszonja
remove FilePathType from bioformats_utils.py
8dcf144
@weiglszonja
remove FilePathType from cxdimagingextractor.py
ed272f0
@weiglszonja
remove FilePathType from cxdimaginginterface.py
878f536
@weiglszonja
remove FilePathType from tiffimaginginterface.py
b9f8f92
@weiglszonja
remove FilePathType from vu2024_behaviorinterface.py
1a95ba7
@weiglszonja
remove FilePathType from vu2024_fiberphotometryinterface.py
974ad8f
@weiglszonja
remove FilePathType from vu2024_segmentationinterface.py
7c6b526
@weiglszonja
remove FilePathType from utils
2f39507
@weiglszonja
strict requirements.txt
4eaba8d
@weiglszonja
add excitation_mode optional argument to conditionally update the des…
40a7139 
…cription for the imaging data
@weiglszonja
update notes
bbda8c2
@weiglszonja
add convert all sessions
fce23f8
@weiglszonja
remove older version of convert all sessions
6b385ff
@weiglszonja
add nwb mapping to notes
b6a7574
@weiglszonja
update tutorial
cde61c6
@weiglszonja weiglszonja self-assigned this Sep 3, 2024
alessandratrapani
alessandratrapani approved these changes Sep 3, 2024
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@alessandratrapani alessandratrapani left a comment

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Looks good!

@weiglszonja weiglszonja merged commit 3c53055 into main Sep 3, 2024
1 check failed
@weiglszonja weiglszonja deleted the final_updates branch September 3, 2024 14:27
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@alessandratrapani alessandratrapani alessandratrapani approved these changes

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@weiglszonja @alessandratrapani