What you are getting

Release notes

• Version 2.7.2 (build 17803)

  6 changes

  Jan

  9

  2023

  Fix Tumor import and update copyright text

  • Change default param values in SigmoidalJansenRit coupling for r (the steepness of the sigmoidal transformation)and a (scaling of the coupling term) to better match the [TVB mathematics paper Sanz Leon et al, 2015]
  • Convert TumorDatasetCreator into TumorDatasetImporter
  • [TVB-3038] - SigmoidalJansenRit coupling default params
  • [TVB-3057] - Change TVB EBRAINS Tumor Dataset Adapter
  • [TVB-3058] - Adjust copyright text
  • [TVB-3059] - Release 2.7.2
  • [TVB-3029] - Find a better way to add the EBRAINS auth. token in Github Actions
  • [TVB-3054] - EditProject by member: saving description does not work in some cases

• Version 2.7.1 (build 17711)

  4 changes

  Nov

  11

  2022

  Make SiibraCreator visible in web GUI

  We reacted to a 3rd party fix by enabling previously hidden feature in TVB Web GUI to connect to EBRAINS KG through Siibra library and import from there Large Scale Connectivities or Functional Connectivities compatible with TVB Simulator

  • [TVB-3044] - new SiibraCreator failure fixed by 3rd party changes
  • [TVB-3049] - Editing/Deleting a shared project by members should not be possible (only admins)
  • [TVB-3050] - Add visual feedback to action buttons in web GUI
  • [TVB-3051] - Prepare and release version 2.7.1

• Version 2.7 (build 17682)

  40 changes

  Nov

  10

  2022

  Improvements and fixes

  • Bug fixes (e.g. Wavelet adapter, allenSDK compatibility, mutable neotraits, neocom.DirLoader)
  • BCT analyzers - switch to bctpy library
  • Siibra integration feature available in CLI - temporarily disabled from TVB-Distribution web GUI due to a KG query V3 - siibra issue
  • new BIDS monitoring module
  • add deepcopy implementation on HasTraits
  • Projects can be marked as read-only (useful for shared projects like DefaultProject on OKD EBRAINS)

  Story

  • [TVB-2951] - Integrate tvb-inversion in TVB-C

  Task

  • [TVB-2975] - Update GUI Guide on the documentation website
  • [TVB-2980] - TVB-KG integration
  • [TVB-3004] - GSOC 2022
  • [TVB-3010] - Project planning and discussions
  • [TVB-3013] - Update Jira and Confluence
  • [TVB-3032] - Test and fix new TVB_Distribution on Windows
  • [TVB-3033] - Test and fix new TVB_Distribution on Linux
  • [TVB-3034] - tvb-docs: Align new sphinx generated DOM with CSS
  • [TVB-3036] - Merge GSOC tvb-bids PR
  • [TVB-3039] - Prepare, test and do release 2.7
  • [TVB-3045] - Test before release 2.7
  • [TVB-3048] - ThirdPartyLicenses HTML is broken

  Sub-task

  • [TVB-2444] - Upgrade tvb-documentation
  • [TVB-2956] - Review code in tvb-inversion
  • [TVB-2958] - CI for tvb-inversion
  • [TVB-2966] - Run and document Benchmarks on tvb master branch against fork used for tvb-inversion (numba backend for this model)
  • [TVB-2992] - Followup new BIDS features
  • [TVB-3019] - Run simulations remotely
  • [TVB-3020] - siibra integration: analysis and API proposal
  • [TVB-3022] - Finalize "Apply Spatial Vector" page
  • [TVB-3027] - Add siibra-creator in TVB web GUI
  • [TVB-3028] - Add configuration for EBRAINS authentication token in tvb-web framework
  • [TVB-3030] - Update documentation for command line usage of siibra in TVB

  Improvement

  • [TVB-2513] - Upgrade tvb dependencies
  • [TVB-2830] - docs website: enforce HTTPS connection
  • [TVB-2878] - Copy an instance of a model or other object in TVB
  • [TVB-3006] - Integrate Sonar with tvb code
  • [TVB-3025] - Replace the current BCT modules based on Octave/Matlab with BCT-py
  • [TVB-3042] - EBRAINS token visible in web GUI after usage in a Siibra Creator

  Bug

  • [TVB-2829] - docs website: phase plane diagram for tvb.contrib.simulator.models.liley_steynross is missing
  • [TVB-2946] - Fix Wavelet adapter
  • [TVB-3017] - allenSDK is not compatible any more with TVB
  • [TVB-3023] - Neotraits mutable default behaves unexpected
  • [TVB-3026] - PhasePlaneInteractive won't show when noise.nsigma is configured
  • [TVB-3037] - Neocom: problem in h5.load(file_path, True) when non current folder
  • [TVB-3040] - Siibra creator not working with other atlas than default
  • [TVB-3041] - Model Math equations no longer visible in web GUI
  • [TVB-3043] - Siibra Creator should take token automatically when deployed in EBRAINS
  • [TVB-3046] - Reload simulation from Operations page fails in some cases

• Version 2.4.1 (build 16852)

  1 changes

  Oct

  19

  2021

  Fix Jupyter kernel for Windows and Linux distributions.

  Bug

  • [TVB-2984] - Jupyther kernel not starting from tvb Dockerfiles

• Version 2.4 (build 16845)

  33 changes

  Oct

  9

  2021

  Bug fixing, spack packaging and support encryption at export

  • Bug fixing
  • Extend encryption support to data export features
  • Improve mechanism to delete projects with links
  • Add EnumAttr to tvb-library neotraits
  • Code reviews related to tvb-storage module
  • Support Spack packaging for tvb-library, tvb-data, tvb-storage and tvb-framework

  Bug

  • [TVB-2808] - shape mismatch in SpatialAverage monitors default spatial mask
  • [TVB-2924] - Mock error using Python 3.8 environment
  • [TVB-2927] - Cannot visualize TimeSeriesSurface with BOLD ROI monitor
  • [TVB-2930] - Can't delete project containing links with Postgres
  • [TVB-2931] - Review deleting projects with links
  • [TVB-2940] - Cannot select the default mask for spatial monitor
  • [TVB-2949] - Ensure tests are copied to the final tvb-storage package
  • [TVB-2960] - Brain Activity Visualizer doesn't work for surface simulation with Bold ROI monitor
  • [TVB-2969] - BOLD ROI monitor is not working
  • [TVB-2970] - BOLD ROI monitor is not working for conn with subcortical regions
  • [TVB-2972] - Fix Tumor Dataset importer
  • [TVB-2973] - Fix tests related to REST that are failling in Jenkins

  Task

  • [TVB-2755] - Add EnumAttr in neotraits
  • [TVB-2849] - Export/Import of DatatypeGroup with related entities
  • [TVB-2879] - Review SelectField in forms
  • [TVB-2889] - Eliminate numerical runtime warnings from test suite
  • [TVB-2941] - Review importing of projects having older versions
  • [TVB-2950] - Project planning and discussions VBC
  • [TVB-2961] - Delete unnecessary code related to remove methods
  • [TVB-2968] - Surface Sim in TVB v2.* no longer has possibility to range Cortex.localcouplingstrength
  • [TVB-2971] - Limit number of launched PSE operations
  • [TVB-2974] - Testing before release 2.4
  • [TVB-2976] - Fix Jenkins builds
  • [TVB-2978] - Prepare release 2.4
  • [TVB-2979] - Replace infinite values with float max in Matrix Viewer

  Improvement

  • [TVB-2916] - Remove dependency with typing package for python>3.5
  • [TVB-2932] - Refactor storage encryption to support multi-pod deploy
  • [TVB-2933] - More functionality from exporters could move to tvb-storage
  • [TVB-2934] - Review HPC encryption exposed in the StorageInterface
  • [TVB-2945] - Keep configuration of monitors throughout simulator page
  • [TVB-2947] - Disable editing of monitored variables at simulation branch
  • [TVB-2948] - Hide the Tumor Dataset importer from importers list
  • [TVB-2964] - Provide option to generate TS file through the console interface

• Version 2.3 (build 16440)

  24 changes

  Jun

  28

  2021

  Framework optimizations, Brain Tumor dataset import button, tvb-storage module

  • Optimizations in framework: simulation run, Operations and Data structure page load
  • Start support for BIDS data: new button on Data structure page to import the Brain Tumor dataset from EBRAINS
  • Improve mechanism to cancel/delete PSE operations
  • Separate tvb-storage as a module on pypi
  • Bug fixing
  • Update documentation

  Sub-task

  • [TVB-2907] - Study BIDS specification
  • [TVB-2911] - Implement a BIDS importer for Tumor dataset
  • [TVB-2912] - Analyze API to download data from EBRAINS
  • [TVB-2942] - Review description for importers/exporters

  Bug

  • [TVB-2356] - Update Tutorial 0 on docs site
  • [TVB-2836] - Fix 'edit simulation' popup window in the simulator page
  • [TVB-2846] - SQLAlchemy raises exceptions during framework tests
  • [TVB-2867] - Models under tvb_contrib are not working
  • [TVB-2935] - Jupyter fails to start from linux distribution
  • [TVB-2943] - Cannot delete PSE simulations
  • [TVB-2944] - miss dependence : package requests

  Task

  • [TVB-2528] - Optimize run_simulation in version 2.*
  • [TVB-2868] - Update license text
  • [TVB-2900] - TVB-BIDS compatibility
  • [TVB-2909] - Fix wrongly loaded Simulator fragments when clicking Back
  • [TVB-2913] - Separate the storage handling in a different module
    
  • [TVB-2915] - Project planning and discussions VBC
  • [TVB-2936] - Remove portlets module
  • [TVB-2937] - Optimize Data Structure page
  • [TVB-2938] - Prepare release 2.3
  • [TVB-2939] - Testing before release 2.3

  Improvement

  • [TVB-2883] - Branch button should be active only if simulation is finished
  • [TVB-2908] - Ensure all operations of PSE are cancelled
  • [TVB-2923] - Optimise operations page

• Version 2.2.2 (build 16153)

  1 changes

  Apr

  28

  2021

  Bug fixing related to H5 files migration

  • Fix migration of H5 files to work in case truncated files are present
  • [TVB-2925] - Solve truncated H5 files migration related bugs

• Version 2.2.1 (build 16148)

  2 changes

  Apr

  5

  2021

  Bug fixing related to DB migration

  • Fix second startup with SQLite after migrating data from 1.5.8
  • Fix second startup with PostgreSQL with clean storage
  • [TVB-2917] - TVB with Postgres startup fails at the second attempt
  • [TVB-2921] - TVB with Sqlite and migration does not start at second attempt

• Version 2.2 (build 16145)

  306 changes

  Mar

  30

  2021

  Official TVB_Distribution with Python 3

  • Make code compatible with Python 3
  • Neotraits (splitting the aspects of: datatypes, storage, indexing, web forms)
  • Add a REST API
  • Support authentication in web with a Keycloak server
  • Added encryption mechanism for the TVB storage
  • Added encryption mechanism for uploaded data
  • Support an HPC backend to run heavy simulations with secured data
  • Change the Simulator configuration page towards a wizard structure
  • The command API has been improved and can be used individually from the web GUI now
  • Use Jinja instead of Genshi for tvb web GUI
  • CFF importer was removed
  • New export button on datatypes to allow exporting a datatype together with its references.
  • Data migration from version 1.5.8 is supported. For data generated with older versions, users should first install 1.5.8 to update their data, and then install 2.2

• Version 1.5.8 (build 8852)

  2 changes

  May

  19

  2019

  Fix Windows and Linux Distributions

  • [TVB-2465] - TVB_Distribution 1.5.6 won't start on Windows 10
  • [TVB-2466] - TVB_Distribution 1.5.6 on Linux does not run notebooks correctly

• Version 1.5.6 (build 8850)

  54 changes

  May

  16

  2019

  Bug fixing and dependencies upgrade

  • Upgrade to allenSDK 0.16
  • Upgrade to SqlAlchemy 1.1.14 and sql-migrate 0.11
  • Bug fixes in: FFT visualizer, FCD analyzer, Brain Surface visualizer, Volumetric viewer on Safari, PSE Discreet, Phase Plane
  • Publish on conda-forge (tvb-data, tvb-gdist, tvb-library)
  • Bug fixes in tvb-framework flow (start/stop/show correct version) when used from Pypi package
  • 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
  • [TVB-2320] - Upgrade to sqlalchemy 1.1.14 and migrate 0.11
  • [TVB-2360] - Finalize TVB packages on conda-forge
  • [TVB-2255] - Improve upload of NII volume mapping when auto-correct
  • [TVB-2314] - tvb-bin vs revision number on Pypi packages
  • [TVB-2316] - Restart of cherrypy from tvb-framework installed with pypi does not work
  • [TVB-2301] - Publish TVB on conda forge
  • [TVB-2315] - Wheels for gdist
  • [TVB-2318] - New packages 1.5.5 on Pypi
  • [TVB-2331] - Present TVB at SFN 2017
  • [TVB-2317] - Add start/stop/test helpers for Pypi installed TVB
  • [TVB-1074] - Extract in a table all TVB dependencies and mark the ones already on NeuroDebian
  • [TVB-2320] - Upgrade to sqlalchemy 1.1.14 and migrate 0.11
  • [TVB-2322] - Make tvb importers compatible with latest networkx version 2.0
  • [TVB-2330] - Upgrade AllenSDK dependency version
  • [TVB-2342] - Fix Mac Build after upgrade of AllenSDK, pyTables, Pillow and CherryPy
  • [TVB-2350] - pip install tvb-gdist on Linux fails
  • [TVB-2241] - octave/matlab path not automatically updated
  • [TVB-2314] - tvb-bin vs revision number on Pypi packages
  • [TVB-2321] - PSE Isocline does not correctly expand when Maximize button is pressed
  • [TVB-2324] - PSEDiscreet viewer can not work with a Group of TS (no measures)
  • [TVB-2325] - Error in FFT, when the TS sampling step is big
  • [TVB-2326] - Errors in FCD Analyzer
  • [TVB-2327] - Error in FFT Visualizer
  • [TVB-2328] - Brain surface viewer recently throws an exception
  • [TVB-2332] - Volumetric Viewer shows wrong sections on Safari
  • [TVB-2341] - PSE Discreet does not change sizes on size metric change
  • [TVB-2343] - Connectivity Measure Visualizer loads with JS error
  • [TVB-2347] - Integration of Epileptor Codim3 models is incomplete
  • [TVB-2355] - File regionMapping16k192.txt missing from TVB_Distribution
  • [TVB-2373] - Fix tvb-framework unit-tests when running in a clean env
  • [TVB-2374] - Off by 1 simulator current step
  • [TVB-2375] - tvb-framework is incompatible with latest matplotlib 2.2.0
  • [TVB-2412] - TVB Build Step 1 is incorrect after recent changes
  • [TVB-2414] - Matlab Analyzers can not be launched from recent Mac TVB_Distributions
  • [TVB-1070] - Prepare TVB packages for NeuroDebian
  • [TVB-1731] - Update some TVB dependencies
  • [TVB-2348] - TVB Node#6 in Berlin 26 feb 2018
  • [TVB-2358] - Project #2.1 Packaging TVB
  • [TVB-2359] - Project #2.3 Monitor Signals in 2D and 3D
  • [TVB-2377] - TVB Node#7 in Canada 7-8 August 2018
  • [TVB-2127] - Native launcher analysis
  • [TVB-1073] - Reorganize unit-tests
  • [TVB-2262] - New TVB VMs & scheduler
  • [TVB-2313] - Propose projects for GSOC 2018
  • [TVB-2323] - Support Ana during her workshop end of November
  • [TVB-2333] - TSV does not offer support to switch SV or Mode on complex TS signal
  • [TVB-2337] - Supervise students at GSOC 2018
  • [TVB-2338] - Write an example for Miriam
  • [TVB-2339] - Upgrade Anaconda Windowsx64 TVB Build Env
  • [TVB-2353] - After seting library profile in ipython notebook the logs from console are no longer displayed in browser
  • [TVB-2411] - Upgrade for allenSDK 0.16
  • [TVB-2319] - Topographic viewer could have ColorScheme controls
  • [TVB-2357] - Allow Connectivity.from_file to read either "centres" or"centers" files
  • [TVB-2378] - Improve the UI

• Version 1.5.3 (build 8253)

  1 changes

  May

  12

  2017

  Fixing bugs

  • [TVB-2238] - iPython Notebook fails to start on Windows and Linux

• Version 1.5.2 (build 8247)

  2 changes

  May

  11

  2017

  Fixing bugs

  • [TVB-2237] - TVB API documentation generated is missing some modules
  • [TVB-2239] - PSE metric won't run with the new numpy

• Version 1.5.1 (build 8240)

  49 changes

  May

  9

  2017

  License change from GPL v2 into GPL v3, integration of Allen Connectivity Creator

  • 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

• Version 1.5 (build 8028)

  84 changes

  Jun

  21

  2016

  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).

  Release Notes - The Virtual Brain - Version 1.5

  Sub-task

  • [TVB-1774] - Static viewer for TSVolume parcellation
  • [TVB-1775] - When TSRegion is displayed on a volume show also region labels
  • [TVB-1776] - Scaling on vertical as in TS Viewer D3
  • [TVB-1956] - Split volume viewer client in a view and a controller
  • [TVB-1958] - Improve drawing performance
  • [TVB-1959] - Simplify dependencies between timeseriesFragment and timeseriesVolume
  • [TVB-1961] - Have the possibility to show a structural anatomical background in the Volume Viewer
  • [TVB-1962] - Research on the Allen Institute available data
  • [TVB-1965] - View mapped arrays on the volume
  • [TVB-1972] - Implement version 1 of a tracts visualizer
  • [TVB-1976] - Validate DataType for streamlines
  • [TVB-1977] - Write streamlines importer
  • [TVB-1980] - Create VolumeData datatype and importer
  • [TVB-2029] - Simplify traited interface generator
  • [TVB-2032] - Identify input tree model
  • [TVB-2047] - Add button to launch Allen connectivity builder
  • [TVB-2150] - Package MATLAB toolbox with distribution
  • [TVB-2151] - Include MATLAB demo html on doc site

  Bug

  • [TVB-1856] - MATLAB demos using TVB
  • [TVB-1876] - ReducedSetFitzHughNagumo model throws shape mismatch error
  • [TVB-1944] - TutorialEvokedResponsesInTheVisualCortex is incorrect
  • [TVB-1946] - BOLD doesn't handle len(voi)>1
  • [TVB-1949] - Export of some old and complex projects is not working
  • [TVB-1951] - Github tvb-pack: tvb data failed to check out
  • [TVB-1953] - Fix RegionMappingImporterTest on Windows
  • [TVB-1964] - mseanalyseregion.ipynb is no longer up to date
  • [TVB-1983] - Region boundaries not visible in region shader based views
  • [TVB-1994] - Uploading a CFF throws CherryPy "No space left on device" errors sometimes
  • [TVB-2014] - Connectivity create (by cutting nodes) is not functioning for Connectivities with missing optional attributes (e.g. area)
  • [TVB-2028] - failure to detect matlab prevents TVB from opening
  • [TVB-2033] - Discrete stimulus has no attr _pattern
  • [TVB-2036] - MonitorTransforms default post incorrect
  • [TVB-2058] - Region indices in selections might be wrong
  • [TVB-2062] - Multiple RNGs for simulation
  • [TVB-2071] - Connectivity Cockpit: show edges from selection is no longer working
  • [TVB-2078] - Wrong mapped tables generated
  • [TVB-2092] - Non-Gen2D model + EEG gives error
  • [TVB-2101] - Incorrect analytic fwd mat for combined cortical & subcortical
  • [TVB-2121] - Review library logging
  • [TVB-2126] - Inconsistent number of samples for RK4
  • [TVB-2152] - Fix generatemodelphaseplaneimages.py
  • [TVB-2161] - Configure reshapes model parameter arrays incorrectly for numba dfuns

  New Feature

  • [TVB-764] - Implement a visualizer for current ICA analyzer (d3.js/svg)
  • [TVB-1943] - Color Scheme: trim near-mean values in a color scheme
  • [TVB-1968] - Allen connectivity builder
  • [TVB-1982] - Binary transport for numpy arrays to javascript
  • [TVB-2085] - Detail proposed PSE user interaction

  Task

  • [TVB-455] - Reuse Simulation Parameters support
  • [TVB-1769] - TSVolume
  • [TVB-1903] - Review lib docs docstrings demos
  • [TVB-1948] - Project planning and discussions
  • [TVB-1952] - Add Google Analytics for docs.thevirtualbrain.org
  • [TVB-1957] - Remove no longer needed "method_name" option when launching an operation
  • [TVB-1960] - Consider JIRA DVCS - GitHub bridge
  • [TVB-1970] - Visualize tracts in TVB
  • [TVB-1971] - Research on pipeline .TCK resulting files
  • [TVB-1986] - Basic rest state tutorial
  • [TVB-1987] - SDDEKit bindings & adapt simulator
  • [TVB-2020] - Refactor Simulator class
  • [TVB-2024] - List TVB papers on documentation site
  • [TVB-2063] - Evaluate numba package for use in simulator
  • [TVB-2069] - Create demo notebook for command UI
  • [TVB-2077] - Upgrade to Matplotlib 1.5
  • [TVB-2089] - Tvb developer setup on anaconda
  • [TVB-2095] - Verify behavior of scipy ode integrators
  • [TVB-2132] - Complete the update script(s) for release 1.5
  • [TVB-2134] - Prep a "what's new notebook/presentation" for upcoming release
  • [TVB-2144] - Test packages 1.5

  Improvement

  • [TVB-1757] - Quick text export of simulation parameters
  • [TVB-1844] - Map analysis results on anatomy
  • [TVB-1963] - Implement FCD analyzer
  • [TVB-1969] - Color Scheme not singleton
  • [TVB-1981] - Update documentation on contributor manual (part on git clone)
  • [TVB-1992] - CFF importer could support operations between fields
  • [TVB-2009] - Update BCT version form TVB distributions
  • [TVB-2025] - Algorithm vs AlgoGroup
  • [TVB-2039] - Remove monitor transforms
  • [TVB-2074] - Upgrade TVB Python & 3rd party libs
  • [TVB-2075] - Numba-based accelerations
  • [TVB-2076] - Swap history indexing algorithm
  • [TVB-2098] - Use sparse history & connectivity representation
  • [TVB-2108] - Make package of models module
  • [TVB-2131] - Sparsify coupling evaluation
  • [TVB-2154] - MATLAB incompat with Mac distribution python

• Version 1.4.1 (build 7595)

  58 changes

  Sep

  22

  2015

  Fixes for importing old projects and new Connectivity Annotations Viewer

  • New: Connectivity Ontology Annotations Importer and Viewer
  • Replace PIL library with Pillow inside the distribution
  • Fix bug on importing Default Project on Windows
  • Fix bug with left & right hemisphere labels switch in default dataset

  Sub-task

  • [TVB-1841] - Prepare TVB build machine for building the new documentation site
  • [TVB-1872] - Cleanup build logs related to documentation
  • [TVB-1885] - Create DT for mapping the data extracted from Ontology
  • [TVB-1886] - Importer for the Ontology XML
  • [TVB-1887] - View Ontology Data - First version
  • [TVB-1906] - 3D Brain viewer and selection
  • [TVB-1918] - Refactor 3rd-party-licenses introspector
  • [TVB-1921] - Some versions of Pillow seem to be incompatible with PY2APP
  • [TVB-1926] - Proposal 1
  • [TVB-1927] - Proposal 2
  • [TVB-1931] - Improve latest form of the Annotations viewer
  • [TVB-1940] - Add documentation for Annotations viewer

  Bug

  • [TVB-1745] - PIL not pip-installable, use pillow workaround
  • [TVB-1749] - Investigate why test testsigmoidaljr_coupling is failing
  • [TVB-1850] - Inconsistency in the time series viewer after branch
  • [TVB-1853] - SimulatorAdapter should only link RM and RV from current project
  • [TVB-1881] - TVB won't run simulations on the cluster from the Anaconda build
  • [TVB-1889] - Failure to import project.zips exported before release 1.4, when they contain ProjectionRegion datatypes
  • [TVB-1893] - Windows Distribution started clean won't import the default project
  • [TVB-1895] - LocalConnectivity.h5 in the DefaultProject has duplicate Surface GUID ref
  • [TVB-1896] - project_import COMMAND demo is no longer working
  • [TVB-1902] - Fix builds
  • [TVB-1907] - Investigate why is Sphinx installed in tvb-debian8 tvb-run env and not reported by the licensing tool
  • [TVB-1919] - Fix BCT test
  • [TVB-1922] - Anaconda is not reported as a dependency
  • [TVB-1923] - mplh5canvas license is not reported
  • [TVB-1925] - The new TVB Connectivity 76 has left & right hemisphere switched
  • [TVB-1929] - Import project with operations in error produces errors in the update script
  • [TVB-1930] - whitematter.displayname is not usable from tutorials
  • [TVB-1936] - Orphan tag in PDF document packed with TVB_Distribution
  • [TVB-1937] - Mac distribution does start
  • [TVB-1938] - Windows version of 1.4 doesn't ship Jon Doe Default_project

  Task

  • [TVB-1727] - Collaboration with MSc in Life Science Informatics
  • [TVB-1748] - Document how to use TVB with PostgreSQL DB
  • [TVB-1753] - Document how to install TVB from sources
  • [TVB-1857] - Step 1 in the build should separate the common parts on a single machine
  • [TVB-1877] - Project planning and discussions
  • [TVB-1878] - Move Hudson coverage build on a machine with more HDD
  • [TVB-1882] - Step 2 - for py2app
  • [TVB-1883] - Prepare one of the Anaconda build machines for running unit-tests on PostgreSQL
  • [TVB-1888] - Improve documentation of console profiles
  • [TVB-1897] - Prepare a live server for the Australia show
  • [TVB-1898] - Test the Australia demo projects
  • [TVB-1899] - Buildforconda is not removing previous version distribution ZIPs
  • [TVB-1901] - TimeSeriesRegion.hadsurfacemapping is always False after export&import
  • [TVB-1904] - Cleanup tvb_data folder
  • [TVB-1905] - Remove events.xml feature
  • [TVB-1917] - Install Octave on tvb-build-debian8
  • [TVB-1934] - Test latest distributions before a release

  Improvement

  • [TVB-1852] - Improve PhasePlane
  • [TVB-1890] - Review docs website
  • [TVB-1891] - Merge OUTSIDE/demodata and INSIDE/tvbdata
  • [TVB-1894] - Add in UserGuide -Data Structure text about node icon colouring logic
  • [TVB-1914] - Centralize code used during packaging time
  • [TVB-1915] - Create a folder for the developer resources used in TVB
  • [TVB-1916] - Retire setup_extra.py
  • [TVB-1924] - Extract RegionBoundaries in a JS reusable component
  • [TVB-1935] - Indicate better currently selected nodes when editing a Connectivity datatype

• Version 1.4 (build 7417)

  56 changes

  Jul

  16

  2015

  Improved default dataset and monitors; IPython Notebook included.

  • Default Project changed
  • S/M/EEG Monitors are making use of precomputed surface gain matrix
  • IPython Notebook is now distributed with TVB, and can be used to visualise and run demo scripts
  • Windows x64 distribution is available (based on Anaconda)
  • Speedups in running simulations and in some viewers

  Sub-task

  • [TVB-1865] - Test how a TVBDATA created with TVB winx32 can be used with the recent TVBDistribution x64
  • [TVB-1874] - EpileptorWithPermitivity to Epileptor

  Bug

  • [TVB-1041] - Noise stream is not properly given to set the initial conditions
  • [TVB-1676] - tvb-pack from GitHub is not working
  • [TVB-1708] - Face & EEG Cap missalignment
  • [TVB-1721] - DataTypeGroup entities are generated with NULL subject, and these produce failure in PSE discreet load
  • [TVB-1724] - Brain Viewer: Sections are no longer being drawn on page load
  • [TVB-1729] - Fix coupling functions
  • [TVB-1733] - Scientific unit-tests are failing when running in an env without hdf5
  • [TVB-1740] - Initial conditions are not noisy any more
  • [TVB-1744] - Create Connectivity variant is not working as expected for Inez
  • [TVB-1758] - Inability to reproduce handouts
  • [TVB-1786] - Modules not found when importing from six.move
  • [TVB-1794] - Remove old Connectivity_74 references (to fix build)
  • [TVB-1795] - Fix SimulatorTest.testsimulatorsurface
  • [TVB-1819] - Safari does not recognise NIFTI file format
  • [TVB-1828] - (GH PR) Refactor vertex mapping code
  • [TVB-1833] - DetachedInstanceError for TimeSeries created by Monitors
  • [TVB-1834] - Library Tests are no longer running on Hudson after recent changes
  • [TVB-1851] - Starting PhasePlane in an empty Project fails
  • [TVB-1866] - Problem launch ConnectivityViewer on some Connectivities
  • [TVB-1869] - Downgraded NumPy ufuncs missing methods for monitors
  • [TVB-1871] - Connectivity Viewer is broken for some connectivities (without Hemisphere info?)

  Story

  • [TVB-1771] - Prepare lead fields for TVB demo dataset

  New Feature

  • [TVB-1178] - Add IPython as the default IDE for command and library profiles

  Task

  • [TVB-1442] - Prepare a new build machine for TVB on Windows
  • [TVB-1670] - Review documentation structure
  • [TVB-1677] - Improve default region mapping
  • [TVB-1725] - Take CEpileptor out
  • [TVB-1737] - Remove "device" code bits from simulator
  • [TVB-1739] - Hudson should generate test-coverage reports
  • [TVB-1750] - Fill in unit-tests for all coupling functions
  • [TVB-1755] - Project planning and discussions
  • [TVB-1756] - Have LFP computed and displayed for simulated signals
  • [TVB-1793] - Cleanup ProjectionRegion
  • [TVB-1796] - Add CORTICAL (boolean array) to the new connectivity_192.zip
  • [TVB-1797] - LocalConnectivity creator has a wrong estimation for ram memory used
  • [TVB-1800] - S/M/EEG sensors & projection matrices
  • [TVB-1807] - Importer of Projection Matrix from npy
  • [TVB-1839] - Redo the Default Project to include the new sensors and their projections and EEGCap
  • [TVB-1840] - Test the latest packages of TVB and Release
  • [TVB-1858] - Properly align default dataset
  • [TVB-1861] - Create benchmarks for TVB 1.4
  • [TVB-1863] - Write update script for release 1.4
  • [TVB-1864] - Anaconda distribution for Linux env
  • [TVB-1867] - Prepare Console Demos for documentation site
  • [TVB-1873] - Fix mseanalyseregion
  • [TVB-1875] - Test latest packages

  Improvement

  • [TVB-1715] - In TS Volume view chunk spatial data
  • [TVB-1723] - Update Python on build machines from 2.7.7 to 2.7.9
  • [TVB-1730] - meta_path copying fails on ZMQ socket due to SixMetaPathImporter
  • [TVB-1764] - Restrict the dynamic system to the plane shown in the phase plane
  • [TVB-1772] - Implement import of Brainstorm sensors & head models
  • [TVB-1779] - Refactor s/M/EEG monitors
  • [TVB-1836] - Using a Dynamic in Burst doesn't apply integrator parameters
  • [TVB-1859] - Internal sensors should be plotted in the cortical surface, not the face surface

• Version 1.3 (build 6880)

  36 changes

  Nov

  10

  2014

  Reviewed and improved usability

  • About 40 tasks on usability, 34 improvement issues and 30 bugs fixed
  • Surface level simulations are between 2 and 8 times faster. Speedup dependent on model and simulation length.
  • Longer simulations and the Generic2dOscillator have improved the most.
  • A new Phase-Plane page
  • Changed mechanism to upload tvb-default data
  • New importers for NetworkX and MAT format
  • Allow import of Surfaces with problems (holes, pinched edges) but filter them out from simulations
  • TimeSeries Volume visualizer completed
  • Improved channel selection in visualizers
  • Static surface viewers can now display parcellation as well
  • Updates in documentation
  • [TVB-1607] - Problems in logging after recent changes
  • [TVB-1612] - Keep trajectories when axis variables change
  • [TVB-1614] - model view matrices should not be handled in drawscene
  • [TVB-1618] - Refactor related methods
  • [TVB-1623] - create ui for setting a specific time
  • [TVB-1127] - Deleting datatypes sometimes leaves trash behind
  • [TVB-1589] - Logging in library profile
  • [TVB-1596] - Problem with space reporter / User
  • [TVB-1598] - Processing time estimates have an odd format
  • [TVB-1600] - Fix phase phase plane nullclines
  • [TVB-1603] - Data structure page: the tree misses collapse/expand nodes and highlight of active node
  • [TVB-1617] - Region mapping visualizer fails to load when not launched from an overlay
  • [TVB-668] - Add information that was previous in the 'Info'-area beneath each WebGL viewer as part of the 'overlay' help-system once this is implemented.
  • [TVB-1029] - In DataType and Operation Overlay arrange the top bar with buttons to stay in fixed position
  • [TVB-1252] - Review the navigation, cursor keys and interaction with Brain Viewer viewpoint
  • [TVB-1298] - Optimize computation of inner angles of the surface triangles
  • [TVB-1412] - TVB Movies: add mechanism to pause (where not existing already) and select by time-point
  • [TVB-1457] - Add context-menu in all 3D viewers with measure points, and display at least the node label in it
  • [TVB-1590] - Refactor datatype validation
  • [TVB-1591] - BOLD monitor error message for short simulations
  • [TVB-1593] - Decrease running time for TVB builds
  • [TVB-1594] - Increase speed when opening DataType overlay
  • [TVB-1597] - Rewrite TvbProfile and TVBSettings
  • [TVB-1604] - Improve the way a Cortex objects gets populated from 'readers' in the console interface.
  • [TVB-1626] - Improve surface simulation speed
  • [TVB-1627] - improve model performance
  • [TVB-1144] - Acomodate CFF importer to support Duke Shereen's data
  • [TVB-1415] - Improve the way tagging is done in a simulation with multiple monitors
  • [TVB-1572] - Document the new phase plane page.
  • [TVB-1601] - Make a difference on the Project-Operations page between Ops Submitted and ops actually Running
  • [TVB-1605] - Add generic reader of TVB datatypes from H5 exported in the web interface
  • [TVB-1608] - Investigate strange execution time reported on a local machine
  • [TVB-1625] - After recent changes, navigation in the brain viewer is broken
  • [TVB-1629] - Split Simulator.configure() in two, to avoid memory error at launch of surface level sim
  • [TVB-1568] - Speed up Heun integrators
  • [TVB-1619] - Test latest version and small fixes for stability

• Version 1.2 (build 6195)

  27 changes

  Jun

  4

  2014

  New Documentation Site

  • New set of EEG sensors
  • UI Selection component reused on several pages in TVB
  • Improve speed on load-time for some visualizers
  • Topographic viewer - same color scheme
  • Several bug-fixes (branching a running simulation, PSE discrete refresh)
  • New scripts for the console interface

• Version 1.1.3 (build 5807)

  12 changes

  Apr

  8

  2014

  Epileptor Model

  • New visualizer for Pearson Correlation Coefficient results
  • Improvements in the TimeSeries visualizer (scaling control added)
  • Non-zeo metadata exposed for the Connectivity DataTypes

  Release Notes - The Virtual Brain - Version 1.1.3

  Sub-task

  • [TVB-1272] - Apache Redirects

  Bug

  • [TVB-1267] - TVB does not restart sometimes when started-clean from TVB_Distribution, or leaves two icons in the Mac-Bar
  • [TVB-1281] - Seeg dual view wrong signal shown on needles

  Task

  • [TVB-1047] - Update scientific methods in Connectivity datatype
  • [TVB-1256] - Improve the new JS component (Regions Selection) to take into consideration hemispheres
  • [TVB-1269] - Sprint planning and discussions
  • [TVB-1270] - Cluster: HTTPS and DomainName
  • [TVB-1271] - Move TVB-Distributions from SVN into a plain folder
  • [TVB-1274] - Add matplotlib-based visualizer for correlation coefficients
  • [TVB-1276] - Add non-zero min/max/var/mean for Connectivity.weight / tract_lengths fields
  • [TVB-1280] - A DB migration is needed for connectivity.numberofconnections

  Improvement

  • [TVB-1286] - Add automatic version number parameter also for the CSS resources, as we have for the JS resources.

• Version 1.1.2 (build 5746)

  44 changes

  Apr

  1

  2014

  Usability improvements

  • Improved images exported from TVB
  • Added whitish color schemes for exporting TVB images with better beamer compatibility.
  • Matjax issue fixed
  • New Model and Integration scheme for the Simulator
  • New static visualizers (Surface, RegionMapping)
  • New importers (OBJ - surfaces)
  • Improved existing visualizers (Brain, TimeSeries EEG)
  • New default transparent Face (for orientation)
  • New TimeSeriesMetric: Proxy Metastability

  Sub-task

  • [TVB-1260] - TimeSeriesEEG with selections should function with more than one TS input selected
  • [TVB-1261] - Structure Tree levels as User-setting are not working correct in case of the tree section from DataTypOverlay gets rendered

  Bug

  • [TVB-1120] - When computing in JS the size of the current configured burst, and one of the ranges is DataType, the message gets: "Nan"
  • [TVB-1128] - When exporting a project exclude the TEMP folder
  • [TVB-1136] - HDF5 warning message gets displayed after running the new Max x64 package
  • [TVB-1137] - Fix problem with possible script injection when working with links.
  • [TVB-1152] - flip normals of the skin_air surface
  • [TVB-1156] - Changing the visualization speed breaks the brain viewer
  • [TVB-1173] - Make the CSV importer generic
  • [TVB-1184] - After recent changes Surface Stimulus movie has a bad transparency
  • [TVB-1189] - Fix traited Range (generator of floating point ranges)
  • [TVB-1213] - Replace the link + logo for the Marseille university because it's outdated + wrong!
  • [TVB-1221] - Applying Pearson correlation coefficients to a Datatypegorup - TimeSeries launches another analyzer (from BCT)
  • [TVB-1228] - Cannot set scaling on region stimulus
  • [TVB-1240] - Configure model on the Surface level
  • [TVB-1249] - Time series visualizer fails to show up
  • [TVB-1250] - Error from BOLD monitor, equation Mixture of Gammas
  • [TVB-1254] - Create an entry point for eeg portlet preview
  • [TVB-1259] - Face OBJ importer is not automatically executed when running TVB from Distribution Mac x64

  Task

  • [TVB-1222] - Add adapter for new TimeSeriesMetric Proxy metastability
  • [TVB-1224] - Answer Robert's emails and have a skype interview with him
  • [TVB-1226] - Sprint Planning and discussions
  • [TVB-1242] - Merge SVN <--> GIT
  • [TVB-1244] - Enhance the error message when importing from .MAT files with an access key (e.g. Projection Matrix importer, but other might do as well)
  • [TVB-1245] - Integrate, scale and benchmark the new OBJ for shell transparent face
  • [TVB-1246] - Fix recent Sphinx errors at build time and wrong generated html
  • [TVB-1247] - Enhance the Upload overlay, to scale with adding of new algorithms
  • [TVB-1248] - Add a new visualizer for RegionMapping entities
  • [TVB-1258] - Test and fix small TODOs
  • [TVB-1262] - Create a small example on how to import a project in the console-interface
  • [TVB-1263] - Prepare 1.1.2 packages for the public

  Improvement

  • [TVB-1055] - Filters applied to Data structure tree are reset after uploading a file...
  • [TVB-1079] - PCA: set tabIndex on selector for components ranges (from 1 up o 49)
  • [TVB-1099] - Add column on Project -> Operations page to display JOB ID when operation was launched on the cluster.
  • [TVB-1165] - Check Delete of large data to work regardless of the data-size
  • [TVB-1206] - Validation of traited input-parameters should return nicer error messages
  • [TVB-1207] - Make nicer the error message when not enought user-space exists
  • [TVB-1220] - Avoid "white" spots in Brain Viewer from light
  • [TVB-1223] - Save Project -> Data Structure Tree levels as User Setting and reload at next page refresh
  • [TVB-1236] - Expose the wrapping semi-transparent surface displayed around sEEG as a changeable input parameter
  • [TVB-1238] - Include Connectivity-Selection web-component also in TimeSeries viewer
  • [TVB-1239] - Include Connectivity-Selection web component also in Brain Viewer
  • [TVB-1241] - Refactor the JS part of the region-selection and make it a reusable component
  • [TVB-1255] - when checking matlab version remove test mat file

• Version 1.1 (build 5250)

  11 changes

  Nov

  9

  2013

  New plugged algorithms and a new interface.

  • TVB deployed on MacOS stays as an icon in dock.
  • New Analyzer and viewer: Pearson Correlation Coefficients
  • New simulation model: LarterBreakspear
  • Add interface over HTTP using JSON, to be used from Matlab
  • Review and improvements in API documentation
  • Small bug-fixing

  Known problem:

  Chrome 30 is having a problem with MatJax, and it might happen at times that your simulator labels are not correctly rendered.https://groups.google.com/forum/#!topic/mathjax-users/CWGx1koV3SUPlease ignore the gray labels; they should have this fixed soon (Chrome / MatJax)

  Sub-task

  • [TVB-1036] - assert that the color buffer has the same length as the vertex buffer
  • [TVB-1043] - Test Larter Breakspear model and integrate it to the core models.

  Bug

  • [TVB-1017] - Brain Viewer can not display Connectivity region points
  • [TVB-1028] - 'Mutiplicative Simple' shouldn't appear on the web interface
  • [TVB-1033] - Fix Importers to accept longer file-names, or throw a proper error message
  • [TVB-1034] - Bad rendering (areas with gray unchanging color) of a TimeSeriesSurface in BrainViewer
  • [TVB-1040] - The initial conditions are conduction speed dependent
  • [TVB-1049] - Make class_diagrams.sh work again.

  Task

  • [TVB-989] - Sprint planning and discussions
  • [TVB-1064] - Attend SFN 2013 - San Diego

  Improvement

  • [TVB-1005] - New analyzer: Cross Correlation (Pearson correlation coefficient)

• Version 1.0.7 (build 5090)

  31 changes

  Sep

  2

  2013

  Export images at full resolution. Extra visualisers added. Fixed IDLE related bug on windows.

  Bug

  • [TVB-932] - Brain Visualizer scroll in movie - blocker popup does not always appear
  • [TVB-944] - Contributor's code from tvb.interfaces.... packages is not taken from the Git clone, but always from inside TVBDistribution/tvbdata
  • [TVB-962] - STOP / DELETE Burst
  • [TVB-974] - Save Image on MPLH5 tab in Connectivity Viewer produces a smaller image
  • [TVB-975] - Brain visualiser stops after first rendering, with TimeSeriesSurface
  • [TVB-976] - BOLD monitor is not working from GUI after recent changes
  • [TVB-979] - Brain portlet preview should not repeatedly read data slice from server
  • [TVB-981] - Octave / Matlab mechanism breaks for machines with versions of glibc and gfortran that are incompatible with our distribution

  Task

  • [TVB-269] - Add legend on all visualizers which have a color-scale (e.g. brain visualizer)
  • [TVB-948] - Investigate possibility to also distribute Mayavi as a dependency of TVB since some script demos need it.
  • [TVB-954] - Use Connectivity.weights and tract delays to create animated plot over time.
  • [TVB-955] - Offer brain visualizer for MEG data.
  • [TVB-956] - 3D visualizer for TimeSeriesSEEG with sEEG sensor positions displayed.
  • [TVB-967] - CLONE - Enhance the resolution of the exported PNG images from canvas.
  • [TVB-968] - Sprint Planning and Discussions
  • [TVB-969] - Test packages 1.0.6
  • [TVB-971] - Update TVB citation text
  • [TVB-972] - Create a configurable script for benchmarking TVB Simulator / Models/ Parameters
  • [TVB-977] - Merge recent changes done by Ciprian from GitHub into SVN (but not up to GitHub)
  • [TVB-983] - Merge from Ciprian's GitHub the new TVB coloring schemes
  • [TVB-984] - Test Version 1.0.7

  Improvement

  • [TVB-942] - Review and update ContributorsManual.pdf
  • [TVB-946] - Improve the message in the exception thrown when profile LIBRARY and a user launches an Importer.
  • [TVB-951] - Enhance Connectivity viewer to display edge with different weights.
  • [TVB-952] - Emphasize borders between regions for the brain region visualizer.
  • [TVB-953] - Display brian surface triangles.
  • [TVB-957] - Enhance Isocline PSE viewer to also work when NaNs are generated or some simulation failed.
  • [TVB-960] - Enhance connectivity webGL view
  • [TVB-963] - Ensure Uniform Line Endings for all TVB code files
  • [TVB-970] - Operations menu doesn't update in web pages (top left corner)
  • [TVB-982] - Hide Monitor Equations from the Temporal component of stimulus

• Version 1.0.4 (build 4760)

  7 changes

  Apr

  15

  2013

  Bug Fix in TVB-Simulator.

  • Add new monitor Stereo-EEG.
  • Fix a bug in Simulator, related to Stefanescu-Jirsa Models.

  Sub-task

  • [TVB-881] - Add tests for library.DataTypes
  • [TVB-893] - Add tests for basic.traits.

  Bug

  • [TVB-894] - Investigate current failures on Linux 64 build machine.
  • [TVB-895] - Prepare urgent release 1.0.4 for a simulator bug-fix.

  Task

  • [TVB-880] - Configure tests for Scientific-Library
  • [TVB-889] - Respond to the Pull Request of Yan - SEEG monitor added

  Improvement

  • [TVB-892] - Investigate if it's possible to take longer history from SVN when publishing on GitHub

• Version 1.0.3 (build 4730)

  41 changes

  Mar

  30

  2013

  Change TVB License. Branch a Simulation.

  Important changes:- TVB license is now GPL v2- Saving a Simulation State is possible now."Branching" a previous executed simulation, will let you avoid having transient signal.- TVB Scientific Library package is published on GitHub- BCT is available from the Large Scale Connectivity page as well- A new Connectivity importer has been added (accepting DTI Pipeline results)- Simulator Input Parameters "Variables Watched by Monitor" is not displayed as a multi-select component, instead of an array.

  Sub-task

  • [TVB-125] - Implement Streaming for TVB visualizers
  • [TVB-394] - Add possibility to choose the browser that TVB fires from the Setting page.
  • [TVB-725] - User - Manage other users: add "create new user" functionality.
  • [TVB-857] - Replace the gmail credentials we currently use to send emails from TVB with the credentials we use for the registration site.

  Bug

  • [TVB-849] - Enhance Monitor-StateVariables attribute displayed in UI.
  • [TVB-855] - A code versions updater is required for TVB, similar to what we have with file storage and database updaters.
  • [TVB-856] - Online help page is not appearing for pages with menu (Projects, Analyzers, Connectivity).
  • [TVB-863] - In Safari, the font color for disabled values in overlay windows are barely readable
  • [TVB-864] - SVG TimeSeries viewer is not working when simulation continue
  • [TVB-871] - Range UI component does not correctly fills the Step after reload
  • [TVB-874] - Continue a simulation from previous versions of TVB
  • [TVB-875] - Restore BurstConfigurations on project export/import
  • [TVB-883] - Validate String fields given by the user to not exceed DB 50 characters limit
  • [TVB-885] - Branching a group of operations throws an exception.

  New Feature

  • [TVB-396] - Persist the simulator's state in a way one can restart the operation
  • [TVB-434] - Connectivity Viewer - integrate BCT
  • [TVB-865] - Add a new Connectivity importer

  Task

  • [TVB-475] - Add tvb.core.traits.basic.Enumerate
  • [TVB-638] - GIT / SVN setup for contributors.
  • [TVB-729] - CONSOLEDEFAULT attributes are evaluated when a class is first importer (new). Because of this, if we want to change for example Connectivitydata.default = file(differentpath), the consoledefaults are still from the old reference.
  • [TVB-781] - Prepare a new VM for TVB with Python 3.
  • [TVB-851] - Split TVB_Simulator Library
  • [TVB-858] - Meetings / Discussions
  • [TVB-859] - Sprint Planning / Review
  • [TVB-860] - Prepare Contributor's work package with Git integration
  • [TVB-861] - Testing and preparing 1.0.3 release
  • [TVB-866] - Publish on GIT
  • [TVB-867] - Review TVB distribution package structure
  • [TVB-868] - Contribute to NeuroInformatics TVB article
  • [TVB-870] - Create examples for the console interface with persistence layer enabled.
  • [TVB-876] - Prepare TVB_Distribution package for Command- contributors and users
  • [TVB-877] - Prepare TVB_Distribution package for Graphical Interface contributors
  • [TVB-879] - Replace Licence text into GPL for scientific library classes.
  • [TVB-882] - Test Apache Open Meetings tool
  • [TVB-884] - Prepare TVB-Framework for Git publish

  Improvement

  • [TVB-724] - Link TAB in datatype overlay, could have buttons for projects in which a link exists, and their action will be remove-link.
  • [TVB-775] - Make it possible to only link one datatype from a datatype group to another project.
  • [TVB-796] - EEG Line viewer (when single view should expand on the entire screen.
  • [TVB-862] - Display current running version in Web-page title
  • [TVB-872] - Enable the same Title Text to appear when muse-over DataTypes tree, as it appears over Project->Operations page.
  • [TVB-878] - Improve Coverage of Unit-Tests on TVB Framework

• Version 1.0.2 (build 4480)

  31 changes

  Feb

  8

  2013

  Stable console interface. Bug fixing. Small performance and usability improvements

  The main addition of this release is a stable console interface. Aside from this there have been a number of improvements and fixes:- the fact that a Matlab installation makes BCT algorithms available in TVB is made more obvious in settings page- possibility to change between state-variable/modes in brain and time-series visualizers- two new models available: Deco-Jirsa(Mean-Field Brunel Wang) and Kuramoto Oscillator- operations are now transactional so invalid db states should not be generated- new DataTypes available: PsiTable, NerfTable, FaceSurface and CapEEG

  Sub-task

  • [TVB-535] - Integrate N-Dimension selector again.
  • [TVB-547] - Change all import operations (project or data types) to be executed transactional
  • [TVB-595] - The presence of MATLAB on a user's computer should be better supported
  • [TVB-645] - Ranges should support min/max with more than 2 decimals.
  • [TVB-699] - BurstService.remove_burst should be made transactional (otherwise, when user is not waiting enough in browser, orphan Operations/DataTypes remain.
  • [TVB-700] - Update TVB Installation document, for build machines and hard-code contributors.
  • [TVB-748] - Raise Python exception on IEEE 754 floating point exceptions that yield NaNs during simulation
  • [TVB-762] - Create CapEEG DataType. Import current SkinAir-Cut surface (open srf) in it. Use in python View-Adapter to compute sensors-to srf region-mapping and sensorstosrf positions.
  • [TVB-784] - Weird log-entries when starting TVB from Deployment package.
  • [TVB-795] - Enhance TimeSeries viewer (SVG) to support channel selection (similar to channel select in EEG viewer).
  • [TVB-818] - Do a checking for license/requirement on the *.so for Linux distributions.
  • [TVB-819] - It seems that the Windows 64 package is missing some modules after pyinstaller 2.0. Also the generated executable might have some OS dependencies which causes pythoncom errors if tested on different Windows versions.
  • [TVB-822] - Make sure all the used licenses are included for all packages. (e.g. Tcl/Tk currently does not appear on MacOSx64 or linux packages even tho they are used)
  • [TVB-829] - Verify that tvb dependencies from app.py towards tvb still cause packaging issues.
  • [TVB-830] - Cross-coherence visualizer for some input TimeSeries generates nan values that are not handled in the UI.
  • [TVB-832] - Work on the interface between TVB and BCT
  • [TVB-833] - Allow recent Measure added by Paula to be executed in the regular flow, by validating input with filters to avoid error in case of incompatibility.
  • [TVB-835] - The burst page portlet previews are not aligned properly in case the first entry from the portlets is None and the other 3 are some random portlets.
  • [TVB-836] - Import operation with not existing AlgorithmGroup
  • [TVB-838] - Set sys.path to python path
  • [TVB-840] - DB connection URL on initial config page is not modifiable
  • [TVB-844] - Create uploaders that would read and store a PsiTable / NerfTable.
  • [TVB-845] - Add icons for new DataTypes.
  • [TVB-846] - Prepare for release 1.0.2
  • [TVB-847] - EEG Monitor does not work properly with multiple inputs of different lengths.
  • [TVB-848] - Add update script to rename tables that don't have plural names like 'BURST_CONFIGURATION'.
  • [TVB-852] - Add field irrelevant to events.xml. When setting that field, the operation will be marked irrelevant.

  Bug

  • [TVB-841] - Cannot reload datatype module during console use
  • [TVB-843] - Range Control is not working correctly at times
  • [TVB-853] - Brain Visualizer portlet is not working after recent changes. JS Error: "readDataPageURL is no defined"
  • [TVB-854] - The db update scripts have problems when using meta.tables[tablename] in case tablename was not imported yet during tvb start workflow.

• Version 1.0.1 (build 4280)

  63 changes

  Dec

  18

  2012

  Performance improvement. Bug fixing

  This is a minor release but with important achievements on performance and code-cleanness:- improve performance for running a simulation on regions level with Raw monitor with a factor of 10;- improve performance on loading web pages, by making sure no duplicate JS/CSS files are loaded and some asynchronous work is done, where possible;- fix HDF5 concurrency problems by replacing the library used behind (from pyTables to H5PY);- fix MPLH5 portlets concurrency problem (when multiple of them are selected on the same page);- include IDLE python module, for preparing console-users.

  When running TVB 1.0.1 after you previously had TVB version 1.0 installed be advised that on the first login, all your datatypeswill be upgraded from TVB 1.0 pyTables format to H5PY. This might take a while depending on the amount of data you have generated.Please be patient and don't shut down TVB during this process. You also have the option to execute the tvb_clean command and dropprevious data in which case the above step is skipped.

  Sub-task

  • [TVB-339] - Based on Adapter's interface validate user received input
  • [TVB-363] - Integrate Petra's first algorithm
  • [TVB-389] - New Orleans Conference
  • [TVB-390] - On windows, it seems that the check for a free port doesn't work as needed.
  • [TVB-456] - Try to update Bzip library from 1.05 -> 1.0.6 due to security vulnerability (http://www.bzip.org/downloads.html).
  • [TVB-465] - ABCAdapter.builddisplayresult sets a wrong path when TVB is launched from Eclipse.
  • [TVB-493] - Improve the load time for each visualizer used in burst portlets for small preview launch.
  • [TVB-536] - Move ResultFigures code from FLOW code-area into PROJECT area
  • [TVB-576] - Different setup for test/development/deployment/console-use.
  • [TVB-629] - Complete test-cases for Burst/Workflow. Refactor existent BurstServiceTest and WorkflowServiceTest.
  • [TVB-640] - Traits doesn't fill defaults from current entity attributes, when called on an instance with attributes complex, but with default values on the complex attribute class.
  • [TVB-653] - Add regions multi-selection mechanism in parameter-definition as well as we have added in region-stimulus.
  • [TVB-669] - Enhance Filters displayed in UI.
  • [TVB-675] - Lots of external JavaScript ressources get requested multiple times per page
  • [TVB-726] - Merge all base*.html template into a single one. Maybe keep a different one for baseuser.
  • [TVB-730] - Review Set up Surface model page
  • [TVB-760] - Profile TVB when running with >2 < 10 users and try to enhance performance. Research in CherryPy what Threading strategy is used.
  • [TVB-766] - Review string2array method from utils.
  • [TVB-773] - Create a Windows x64 machine with real MKL libraries (using 30 days licensed package from Intel)
  • [TVB-774] - Import project structure
  • [TVB-777] - Create project operation do not work properly
  • [TVB-778] - Brain Activity with EEG lines - select node operation doesn't work
  • [TVB-779] - Import project that has some range results does not work.
  • [TVB-780] - Parameter space exploration
  • [TVB-783] - Operations in state Started
  • [TVB-785] - Increase performance with a factor of approx 20 for running a simulation from UI.Viktor's Mac: Raw monitor, length 500 - time 30 secLia's Mac - time 9 min
  • [TVB-786] - From distribution packages XSD, the relative URL is no longer valid, so no validation is done.
  • [TVB-794] - Simulation HDD estimation is wrongly computed by the framework. Simulation length doesn't seem to count.
  • [TVB-797] - Region Stimulus - 2nd step page: - add tooltip for scaling factor with short explanation;- highlight nodes which have a scaling set, by using a different style on their labels display.
  • [TVB-798] - Create unit-test trying to reproduce our problem with HDF5
  • [TVB-799] - Evaluate how much value/delay using pyTable has.
  • [TVB-800] - Model Parameters Surface: Double Gaussian equation should be removed from the available list.
  • [TVB-801] - Burst page looses focus: user-given name is lost when coming back. A burst could have at least one portlet selected by default (TimeSeries Viewer).
  • [TVB-802] - Settings - changing DB URL to postgreSQL, after the application is started is no longer working.
  • [TVB-803] - Model Parameters setting on Regions: multiple selection should be possible, select all button could be present, update default to all nodes is needed
  • [TVB-804] - TVBWindows1.0.1x32web.zip doesn't work
  • [TVB-806] - Js error displayed in console for Brain Viewer portlet.
  • [TVB-807] - Change hdf5 access python library from pytables to hdf5 in order to resolve the concurrency problems. Also do custom buffering mechanism in case of append_data since h5py performance is poor next to pytables.
  • [TVB-809] - Nan values can still be generated by launching by launching range simulations.
  • [TVB-811] - Add IDLE (Python IDE) to the distribution packages
  • [TVB-812] - Review different files positioning in TVB packages and cleanup structure.
  • [TVB-813] - Estimate and change py2app/py2exe into pyInstaller.
  • [TVB-814] - Replace all "print" occurrences in mplh5_backend with proper logging messages.
  • [TVB-815] - WebGL directional keys should rotate scene.
  • [TVB-820] - Testing and release procedures for version 1.0.1.
  • [TVB-821] - Add more filters on page View Operations. Refactor filtering classes.
  • [TVB-824] - Implement script for converting H5 files from version 1 to version 2
  • [TVB-825] - Create fileupdatemanager for generic updating from a given file storage version to current one.
  • [TVB-826] - Change H5 import, to validate File Stored version, and convert in case received version is old.
  • [TVB-827] - Validate full File Stored data on User Login
  • [TVB-828] - Validate DataType upon immediate usage
  • [TVB-831] - On introspection, if a portlet for which some workflow steps were generated si removed we should make sure all the generated workflow steps are also removed. The same logic for the removal of algorithms.
  • [TVB-834] - Operations page reports a wrong number of pages when groups exist

  Bug

  • [TVB-776] - Filters are not working for portlets (Refresh + buttons)
  • [TVB-782] - HDF5 does not support concurrent read operations
  • [TVB-805] - After recent changes an error regarding an unexisting 'FloatArray' class is thrown in the console when on the simulation page.
  • [TVB-808] - After the switch from pytables to h5py the wavelet spectogram portlet now throws a IOError when writing the results.
  • [TVB-837] - Import project with datatypes from which are missing data sets.

  Story

  • [TVB-579] - UI Design Integration & Browser related Issues
  • [TVB-642] - After SFN 2012 Improvements
  • [TVB-683] - Know Problems
  • [TVB-790] - Known Issues
  • [TVB-823] - File Storage Updates

• Version 1.0 (build 3970)

  13 changes

  Oct

  13

  2012

  SFN 2012 release

  This is a full-features release for TVB software.- You can install TVB on Mac OS (x32 or x64 architecture), Linux (x32 or x64) or Windows (x32)- TVB can be installed in 3 different configurations:* on a personal computer for single-user usage;* on a server and made accessible to an unlimited number of users through browser.The server is expected to have a decent hardware, based on the expected number of clients.Each client will need to have a compatible graphic card, and WebGL compatible browser.* or on a cluster (similar with server installation, but with parallelization support).When installed on a cluster, OAR is expected to be configured separately of TVB.- Default user is the same: admin/pass , but you can change it when TVB settings page is first displayed.- At startup, a default project will be created, containing demo-data as well (Connectivity, Cortical Surface, Projection Matrices, Sensors)- Default data is automatically filled, with every new project you create.- When filling parameters for the simulations, you can consult the manual about their meaning and the tooltips for each parameter.

  Known issues:- on Linux systems, Chrome browser has a bug when displaying select tags inside an overlay.We have one situations for this, when displaying a visualizer's top-right call-out.As this is a known bug in Chrome, we will wait for the next release to fix it. Until then we advise you to use FireFox while under Linux.

  Sub-task

  • [TVB-648] - MPLH5 visualizers do not allow interaction with their controls in browser. Blocking animation should appear when waiting for server's feedback.
  • [TVB-695] - Create build machine for Windows x64
  • [TVB-733] - General review of remaining UI quirks
  • [TVB-742] - Testing TVB
  • [TVB-765] - Prepare TVB-Booth version (DTI pipeline, Epileptor Model)
  • [TVB-767] - Burst page displays two selected bursts when changing from a 'copied' burst that finished to any other burst.
  • [TVB-768] - Uninstall PyTable from windows x32 TVB Build machine and install it without LZO and SZIP dependencies, as these 2 have license problems.
  • [TVB-769] - Validate imported connectivity from ZIP: - make sure same number of nodes are in positions, weights, tracts, orientation, areas and label vectors.
  • [TVB-771] - TVB web interface incompatibility with Linux Centos and ubuntu OS
  • [TVB-772] - Burst Bugs: Simulation parameter EEG Projection data is not submitted properly on first burst launch of a project in case you configured the simulator parameters and chose monitor but left eeg projection data hidden.

  Bug

  • [TVB-204] - Remove from StorySteps controller method readserverfile, because it slows down the process. Make the files directly accessible through CherryPy.

  Task

  • [TVB-243] - Monitor operations status:- add actions restart/stop/pause- read status (console log...)
  • [TVB-317] - Add a legend to brain visualizer.

• Version 0.9T1 (build 1883)

  0 changes

  Mar

  6

  2012

  First TVB Teaser Release.

  This is a Teaser package.- Default user is admin/pass- At startup a default project is created and a default set of input-data will exist in that project.- Simulations can be launched, with any of the models/monitors in the system.- If you have Octave or Matplotlib in the path, Brain Connectivity analizers will be visible and ready for execution.- Once you have some data in your project, you should go to the visualizers area and see them in multiple formats,or use context-menu (right-click menu) on a specific DataType (pages Project-Operations or Project-Data Structure) to see available visualizers/analyzers.

  Some of the capabilities that are currently in work are disabled from this version:- import / upload /export buttons are visible but disabled- input fields for the simulation are fixed, except for monitor, model and surface/region.