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protocols-restructuring.md

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title Documentation
layout default

Changes Made

Directory Structure

  1. Protocols Directory Configuration

    • Protocols directory location is now managed through settings
    • Location is stored in GENERAL.Protocols_Directory setting
    • System verifies directory exists during startup
    • No symbolic links or hard-coded paths
    • Single Protocols directory at root level

  2. BpodProtocols

    • Dedicated BpodProtocols/ directory for Bpod-specific protocols
    • Separates Bpodprotocols from standard BControl protocols
    • Improves clarity and maintainability

Protocol Structure Requirements

  1. Directory Organization

    • Each protocol must be in a directory named @protocolname
    • Protocol constructor file must have same name as directory
    • Old-style RPBox protocols (with _obj.m files) are excluded

  2. Required Protocol Actions

    • 'init': Initialize protocol (create windows, variables)
    • 'update': Called periodically during trials
    • 'prepare_next_trial': Prepare state machine for next trial
    • 'trial_completed': Called when trial is complete
    • 'close': Clean up when protocol is closed

  3. Automatic Variables

    • n_done_trials: Count of completed trials
    • n_started_trials: Count of started trials
    • parsed_events: Parsed events from current trial
    • latest_events: New events since last update
    • raw_events: All events from current trial

Initialization Changes

  1. Path Setup

    • Moved Protocols directory check after adding Modules to path
    • Ensures bSettings is available before use
    • Fixes "bSettings is not found" error

  2. Configuration-Based Approach

    • Removed hard-coded path checks
    • Added proper check for Protocols directory from settings
    • Uses configuration as source of truth for Protocols location
    • Provides clear error messages if directory is not found

Impact Assessment

Potential Impacts

  1. Protocol Loading

    • Verify all protocols load correctly
    • Test protocol switching
    • Check protocol inheritance
    • Verify protocol directory structure

  2. Initialization

    • Test system startup
    • Verify path setup
    • Check settings loading
    • Test protocol scanning

  3. Bpod Integration

    • Test Bpod protocol loading
    • Verify Bpod-specific features
    • Check protocol switching between Bpod and standard

Testing Required

  • Verify protocol loading in all experimental setups
  • Test protocol inheritance and dependencies
  • Validate Bpod protocol functionality
  • Check initialization sequence
  • Verify settings-based configuration
  • Test protocol directory structure
  • Verify automatic variable initialization

Next Steps

  1. Monitor protocol loading performance
  2. Gather feedback from protocol developers
  3. Update protocol development guidelines
  4. Consider additional organization improvements
  5. Document protocol development best practices

Contact

For questions about these changes, contact the system administrator.