Make linux compatible, add behavior-only session processing and add optional video background for tracking processing #19
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- Updated `acqID.m` to include support for 'digitalin.dat' files in folder listing. - Modified `concatenateDats.m` to handle behavior-only sessions, reading metadata from `info.rhd` or `settings.xml`, and skipping LFP, Kilosort, and SleepScore processing. - Enhanced `fillMissingDats.m` to use `digitalin.dat` as a reference for behavior-only sessions, adjusting channel calculations accordingly. - Updated `preprocessSession.m` to incorporate behavior-only mode, skipping XML file requirements and adjusting session metadata creation. - Improved `read_Intan_RHD2000_file_bz.m` for cross-platform file discovery and handling multiple `.rhd` files. - Introduced `sessionTemplate_behaviorOnly.m` to create minimal session metadata for behavior-only recordings, including detection of digital and analog channels.
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Pull Request Overview
This PR adds behavior-only session processing capabilities and enhances video background support for tracking data visualization. The main purpose is to enable processing of behavioral recordings that don't contain electrophysiology data (no amplifier.dat files) while also improving the manual tracking error detection workflow.
Key changes:
- Added behavior-only mode that skips electrophysiology processing and uses
digitalin.datfiles as reference instead ofamplifier.dat - Enhanced manual tracker jump detection with optional video frame overlay for easier visual identification of tracking errors
- Improved cross-platform file handling and video processing with better error handling and ffmpeg fallback support
Reviewed Changes
Copilot reviewed 9 out of 10 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| sessionTemplate_behaviorOnly.m | New template for creating minimal session metadata for behavior-only recordings |
| read_Intan_RHD2000_file_bz.m | Enhanced cross-platform file discovery and multi-file handling |
| preprocessSession.m | Added behavior-only mode support with conditional processing |
| fillMissingDats.m | Updated to use digitalin.dat as reference for behavior-only sessions |
| concatenateDats.m | Modified to handle behavior-only sessions with metadata from info.rhd/settings.xml |
| acqID.m | Added digitalin.dat support in folder listing |
| process_and_sync_dlc.m | Improved video frame rate extraction and TTL channel selection |
| manual_trackerjumps.m | Added video overlay functionality for tracking visualization |
| general_behavior_file.m | Added video overlay parameter and fixed file path separators |
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Co-authored-by: Copilot <[email protected]>
kushaangupta
changed the title
Co-authored-by: Copilot <[email protected]>
Member
|
Can you format all with MBeautifier? |
…penephys format processing errors
Collaborator
Author
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This works fine now for Ephys Intan/Openephys sessions |
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Pull Request Overview
Copilot reviewed 9 out of 10 changed files in this pull request and generated 7 comments.
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preprocessSession.mto incorporate behavior-only mode, skipping XML file requirements and adjusting session metadata creation (noamplifier.dat, no spike sorting).sessionTemplate_behaviorOnly.mto create minimal session metadata for behavior-only recordings, including detection of digital and analog channels.acqID.mto include support for 'digitalin.dat' files in folder listing.concatenateDats.mto handle behavior-only sessions, reading metadata frominfo.rhdorsettings.xml, and skipping LFP, Kilosort, and SleepScore processing.fillMissingDats.mto usedigitalin.datas a reference for behavior-only sessions, adjusting channel calculations accordingly.read_Intan_RHD2000_file_bz.mfor cross-platform file discovery and handling multiple.rhdfiles.