[WIP] Add dipole contribution visualization - #1178
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- Changed _OutputWidgetHandler.emit() to append new messages to the end - This ensures errors and new log messages appear at the bottom where they're more visible - Fixes issue where errors could be hidden when appearing at the top of log window Fixes: GUI error visibility issue
- Enhanced Optimizer class to accept custom callable loss functions - Added validation for custom objective function signatures - Implemented three predefined custom loss functions: * _spectral_power_loss: for matching power spectral densities * _phase_coherence_loss: for optimizing rhythmic coherence * _custom_rmse_with_weights: for time-weighted RMSE optimization - Added comprehensive example showing usage of custom loss functions - Added test suite for custom loss function validation and functionality - Updated exports in __init__.py to include new loss functions This addresses the need for custom loss functions suitable for Poisson drives and steady-state oscillations where traditional RMSE is not appropriate. Fixes: Custom loss function feature request
- Created new dipole_contributions.py module with analysis and visualization functions - Added plot_dipole_contributions() to visualize UP vs DOWN dipole components - Added analyze_dipole_contributions() to analyze component contributions - Enhanced Dipole class with plot_contributions() and analyze_contributions() methods - Identifies components that contribute to UP (positive) vs DOWN (negative) deflections: * L2 pyramidal cells and proximal drives UP components (red) * L5 pyramidal cells and distal drives DOWN components (blue) * Tonic biases based on amplitude polarity - Comprehensive example script showing usage and interpretation - Full test suite ensuring functionality and edge cases - Updated exports in __init__.py This addresses Stephanie's request for visualization showing what components contribute to dipole flow 'up' versus 'down' throughout the simulation, similar to figure C in issue jonescompneurolab#966. Features: - Time-series visualization of component contributions - Color-coded UP (red) vs DOWN (blue) components - Overlay of total dipole signal - Analysis of drive locations, layer contributions, and biases - Educational annotations and interpretive guidance
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Thank you for your contribution Arnav and apologies for the late response. Your PR is very interesting and possibly relevant to other ongoing work that we are doing ourselves. We will try to respond in greater detail to your proposed changes as soon as we can. In the meantime, if you have any figures displaying some of the functionality, it would be great if you could post it here. Thanks! |
asoplata
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Problem
Stephanie requested a visualization that shows what components (drives, channels, etc.) contribute to dipole flow "up" versus "down" throughout the simulation, similar to figure C in issue #966.
Solution
Implemented comprehensive dipole contribution analysis and visualization tools:
New Features
plot_dipole_contributions(): Time-series visualization of UP vs DOWN componentsanalyze_dipole_contributions(): Quantitative analysis of contributionsplot_contributions()andanalyze_contributions()methodsComponent Classification
Key Benefits
Files Added
dipole_contributions.pymodule with analysis functionsUsage