Improved NFTsim - Paper publication

v.1.1.0 (2018-08-28)

Stable realease following acceptance and publication of the NFTsim article

New

• Enables two-sided spectrum +nf/rfft.
• Adds an adaptive default setting for sigma.
• Adds output files of config files testing white noise input.
• Adds a check that 'Nodes' is a perfect square.
• Adds a simple Sine Timeseries, two args: Amplitude; Frequency.

Changes

• Changes variable name PSD -> ASD (Amplitude Spectral Density).
• Fixes PulseSigmoid for unspecified Duration or Period.
• Uses machine representable number for Interval.
• Uses machine representable number for Deltat.
• Replaces value of Tau with the numerical value is actually used.
• Changes "nus" to "nu" in CouplingRamp.
• Changes Std to StdDev.

Fix

• Fixes problem in the frquency vector +nf/rfft.
• Shifts Fourier components to have the centre at 0.
• Normalizes by the actual length of the epochs used to calculate the FFT. This normalization preserves PSD under changes in the frequency resolution (as it should be).
• Fixes akward indexing in Coupling Ramp

Updates

• Merges branch 'master' into ref-manual-review.
• Expands reference docs.
• Updates README.md.
• Adds language tags to C++ listings.
• Adds missing math mode. Corrects section cross reference.
• Updates numerical test data following change from PSD to ASD.
• Expands explanation about ASD and PSD.
• Updates user manual after changes in input paramters for stimulus of type White.
• Improves alignment of summary output from --check all.

Other - Dev

• Updates text on how to reproduce previous results.

• Merges branch 'fix-configs-compare' of https://github.com/stuart-knock/nftsim into stuart-knock-fix-configs-compare Updates python utility for developers ... Yes, we need more python here.

• Updates configs_compare after recent changes to numerical tests.

• Reword error message to give more useful information to users. The name long_coupling is a misnomer. The mechanisms in this class would provide the support for long-range coupling, but that is not the only purpose of this class.

• Updates nf_configs to use new, dedicated, .conf files.

  • Also removes file compression, the files are intentionally
    smaller now and uncompressed text allows git to do its work.

• Adds an initial set of quick to run, small output, .conf files.

First public release

The title says it all!

Overview

NeuroField is written in C++ and implements streamlined standard methods to solve hyperbolic partial differential equations such as the damped 2D wave equation; time stepping methods to solve ordinary differential equations; and procedures for delay differential equations. Careful numerical analysis has resulted in a suite of methods that is fast, accurate, and robust.

NeuroField comes with a collection of custom made Matlab functions that allow for an easy access to the compiled code, for users without prior knowledge of C++. End-users need only to write plain text files as described in the User Manual.

Purpose

The code has been tailored to use these state equations to solve an unlimited number of user-defined continuum neural field models. The input and output files are both plain-text, so NeuroField can be easily integrated into existing workflows and analyses written in other programming languages.

This is our first public release to make the code available to the research community.

Features summary

• 2D neural fields
• Square lattice
• Rectangular lattice
• Periodic boundary conditions
• Absorbing boundary conditions
• Complex local connectivity kernels
• Arbitrary number of neural populations
• Space-dependent parameters
• Time-dependent parameters
• Synaptic plasticity
• I/O in physical units (SI)
• Parameters derived from experimental data
• Analytic test cases
• Examples from published papers
• Visualization tools
• Ancillary analysis tools

Issue Summary

We improved the ancilliary Matlab and bash scripts for benchmarks.

Update wave solver and improved dev documentation

This version is close to what the first public release will be. The solver for the Wave equation has been updated and we now have a specific reference and a one to one match between implementation and analytic derivation. For more details about the differences between the previous and current implementation, have a look at pull request #95.

Also, the code is now commented, Doxygen generated documentation is more readable for both dev and nondev types.

Update solver for dendritic dynamics

From this version on, the default solver for dendritic dynamics is 4th Runge-Kutta. While this new implementation decreases performance, it is more general and it does not make assumptions about the underlying dynamics of phi and Q.

Pull request #81 describes in more detail the differences between the now default Dendrite class and DendriteIntegral (previous version).

First month of updates and refactoring.

• Extended Makefile (with help targets for developers and generalized cross-compilation (g++ and clang))
• Increased code readability thanks to the adoption of guidelines
• Increase code readability and proper use of C++11
• Slightly better code documentation and definitely better reference manual
• Cleaner Readme file
• Additional configuration files including model with basal ganglia
• New Coupling class