Release 1.5.10

Snapshot before major changes into version 2.0

New neuronal mass models

• Add Zerlaut model
• Add model Reduced Wong-Wang with Excitatory and Inhibitory Coupled Populations

Bug fixing and dependencies upgrade

• Upgrade to allenSDK 0.16
• Bug fixes in: FCD analyzer, Phase Plane
• 2 new Epileptor model variants ([Saggioetal_2017] Fast–Slow Bursters in the Unfolding of a High Codimension Singularity and the Ultra-slow Transitions of Classes

Packaging and Improvements in Visualizers

This release mostly affects tvb-framework, but few changes transcended also towards tvb-library (minor changes).

• Add Structural Connectivity and Pearson Correlation Edge Bundle Viewers (circular viewers)
• Replace MPLH5 Visualizers(PSE Continous, Wavelet, Fourier, Topographic, Pearson, Complex Coherence) with new ones based on D3.JS
• Packages distributed with Pypi (tvb-library and tvb-framework)
• Bug Fixes

License change from GPL v2 into GPL v3

• Update license of TVB from GPL v2 into GPL v3
• Expose in TVB_Distribution the Allen Connectivity creator
• New and improved PSE discreet viewer
• Bug fixes

[TVB-2111] - Error in the loading of PSE data now
[TVB-2137] - Create backend Python controller method for Explore
[TVB-2167] - PSE Discreet should be automatically refreshed, when operations are still in work
[TVB-2169] - Fix "Save Image" for the new PSE Viewer
[TVB-2170] - Integrate Colors Legend
[TVB-2171] - Needs to place results in the right area of canvas.
[TVB-2172] - replace the blacked out circles of incomplete results with a def svg of a cross x
[TVB-2173] - add clip paths
[TVB-2174] - scale circle radius based on zoom
[TVB-2175] - clean up contour tool
[TVB-2177] - brainstorm alternate data structure for the PSE results
[TVB-2180] - Construct API for new datastructure and experiment with function contents
[TVB-2181] - save button for filter is broken
[TVB-2182] - reintegrate the filter button
[TVB-2183] - NodeInfo made available using result coordinates
[TVB-2184] - fix contour save button
[TVB-2185] - Resolve step value issues
[TVB-2186] - create a way to have code for incoming data merge only executed once.
[TVB-2196] - Ipython is not correctly distributed after recent build machine redo
[TVB-2198] - PSE discreet no longer works for DataType ranges
[TVB-2153] - PSE viewer not loading in simulator panel
[TVB-2188] - Isocline viewer doesn't show in the simulator panel
[TVB-2190] - Fix SurfaceGainMatrix to RegionGainMatrix transformation
[TVB-2191] - UTF-8 locale not understood
[TVB-2203] - EEG monitor with reference doesn't work
[TVB-2217] - Contributor setup is incompatible with import tvb.simulator.lab
[TVB-2218] - Mistake in parameter labels for ZetterbergJansen class
[TVB-2228] - Fix TVB build on Mac
[TVB-2229] - If AllenCreator adapter becomes deprecated, it is still shown in GUI
[TVB-2233] - Phase plane does not show up in GUI
[TVB-2234] - Allen Creator with default throws KeyError
[TVB-2235] - Phase Plane is not working (Internal Server Error)
[TVB-2236] - Error in TS Viewer D3
[TVB-2083] - Convert discrete pse view to d3
[TVB-1932] - When importing a connectivity do not always throw exception when negative weights
[TVB-2165] - Finish Allen Connectivity Builder integration with TVB_Distribution
[TVB-2176] - brainstorm new structure for PSE data
[TVB-2194] - Redo TVB Mac Build machine
[TVB-2206] - Surface Viewers do not have Color scheme legend
[TVB-2207] - Integrate latest release of BCT (Version 2017-15-01)
[TVB-2221] - Integrate 2 mouse Connectivities in tvb-data and TVB_Distribution
[TVB-2222] - Change license text
[TVB-2225] - Fix TVB Build on Windows
[TVB-2230] - Change TVB License into GPLv3
[TVB-2231] - Finalize release 1.5.1
[TVB-1616] - Refactor DataTypes diamond-like inheritance
[TVB-2189] - Add stylistic changes to the discrete viewer where necessary.
[TVB-2214] - Improve ProjectionMatrices load from files
[TVB-2226] - Debug and identify performance bottlenecks in the PSE D3

New functionality related to simulation and visualizers

• New: export simulation configuration as JSON and reuse in web or console
• Volumetric Viewers extended and improved (more datatypes can be visualized in volume - e.g. TimeSeriesRegion; better performance)
• Color Scheme: allow to trim near-mean values in a color scheme
• New: tracts visualizer, FCD analyzer
• Refactored internal API for Adapters, with the purpose of simplifying console usage
• Allen SDK Creator added
• Reduced Wong-Wang default parameters updated to reflect usage in Hansen et al 2015
• Coefficients for the Stefanescu-Jirsa 3D model have been corrected
• ~5x accelerations for several models (Epileptor, Generic 2D Oscillator, Jansen-Rit, Reduced Wong-Wang)
• Epileptor state variables names updated to those used publications, (y0->x1, y1->y1, y2->z, y3->x2, y4->y2, y5->g)
• Models: new variables of interest for monitoring physiological signals e.g. LFP.
• Variable order integrators now available which can improve accuracy and execution speed for many cases.
• Conduction delays and coupling are now more efficient, especially for large and/or sparse connectivities.
• Comprehensive review to library logging, turn on useful debug info with log_debug(True).