feat: video acquisition support for pupillometry#5
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Ports camera recording infrastructure from the internal BrainCOGS ViRMEn fork into PureVirmen, enabling synchronized eye/pupil video capture without any DataJoint or database dependencies. Changes: - bin/engine/virmenEngine.m: add vr.preTic (before initialization) and vr.timeElapsedFirstTrial (before main loop) as stable timing anchors - extras/RigParameters.m.example: add commented video-acquisition block - sensors/camera/configureSingleCamera.m: FLIR GenTL camera setup + VideoWriter (Motion JPEG 2000) disk logger - sensors/camera/startVideoAcquisition.m: configure camera, capture vr.timeElapsedVideoStart sync timestamp, start acquisition - sensors/camera/stopVideoAcquisition.m: stop and release camera cleanly - sensors/camera/setupVideoFile.m: build output path with userid/subject/ YYYYMMDD_g# naming convention (U19-compatible) - sensors/camera/checkCameraRigParameters.m: validate required RigParameters before camera init - sensors/camera/syncBehaviorVideo.m: post-hoc frame-to-iteration alignment utility (DataJoint-free equivalent of U19 sync script) Closes #1 Assisted-by: ClaudeCode:claude-sonnet-4-6
- syncBehaviorVideo.m: replace the two O(nFrames*nIter) find loops with
single binned monotonic searches (discretize), and document the
constant-frame-rate assumption of the linspace frame-time reconstruction.
Add optional log.frameTimes override for true per-frame timestamps.
- setupVideoFile.m: use strtok to take the userid as the portion before the
FIRST underscore, matching the documented convention (strsplit{1} did the
same for the common case but the intent is now explicit).
Assisted-by: ClaudeCode:claude-opus-4.8
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Ports DataJoint-free camera recording into PureVirmen for synchronized eye/pupil video capture, plus review fixes.
What's here
sensors/camera/: FLIR GenTL camera setup + VideoWriter (Motion JPEG 2000) disk logger, start/stop, U19-compatible file naming, and a post-hoc frame↔iteration sync utility.bin/engine/virmenEngine.m: addsvr.preTicandvr.timeElapsedFirstTrialtiming anchors.extras/RigParameters.m.example: commented video-acquisition block.Review fixes applied (commit
410f1d4)syncBehaviorVideo.m: the twofind(..., 1, 'last')loops were O(nFrames × nIter) — replaced with single binned monotonic searches (discretize), so a 30-min @30fps session no longer does tens of millions of scans.linspaceover file duration, which assumes a constant frame rate / no dropped frames (FLIR cameras can drop frames). Added an optionallog.frameTimesoverride so callers with true per-frame timestamps can bypass the assumption.setupVideoFile.m: usestrtokso userid is unambiguously "the portion before the first underscore," matching the docstring.Testing
All changed files parse and pass
checkcodeunder MATLAB R2023b. The live camera path requires Image Acquisition Toolbox + FLIR Spinnaker on a Windows rig (not available on the dev machine), so the hardware path is untested here.