Brion  1.10.0
The Blue Brain C++ I/O library
Changelog

git master

  • 126: Add erase for map compartment reports
  • 122: Support loading of individual neurons for binary and map compartment reports
  • 121: Performance optimizations for map and binary compartment reports, fix sub target loading of map compartment reports
  • 119: Optimized brain::Circuit::loadMorphologies for slow stat'ing filesystems (GPFS)

Release 1.9.0 (09-Dec-2016)

  • 117: Changes and fixes in Brain Python module:
    • Functions that take gids now preserve the iteration order of the input in the output arrays/lists.
    • Replaced Python sets with numpy arrays in functions returning GID sets.
    • Circuit::getXYZNames functions renamed to Circuit::getXYZTypeNames.
  • 113: Support for old circuits containing only synapse center positions.
  • 110: Break PersistentMap out into keyv::Map
  • 107: Added Sphinx generated documentation of the brain python module.
  • 102: Use PersistentMap for caching synapse positions loaded from brain::Circuit
  • 94: Fixed SWC morphology parser for morphologies with soma contour. The parser was creating invalid soma sections when the first order sections where connected to arbitrary soma sample points.
  • 89: Python wrapping of brain classes.
  • 88:
    • Brain namespace enums made strongly typed.
    • Fix for brain::Section::getSamples for sections where the first point appears repeated.
  • 85: Implement brain synapses specification
  • 84: Brain synapses specification
  • 83: Add brain::Circuit::getRandomGIDs()
  • 82: Improve performance when reading synapse attributes from non-merged files
  • 81: Fix GID out-of-bounds handling for MVD3 in brain::Circuit
  • 79: Use PersistentMap for cache in brain::Circuit::loadMorphologies(); add thread safety w/ synapses cache

Release 1.8.0 (30-Jun-2016)

Release 1.7.0 (24-Mar-2016)

  • 56: Improved target parser
  • 55: Add basic provenance metadata for written HDF5 compartment reports
  • 49: Added the method brain::Circuit::getRotations
  • 46: Fixed a bug in enum to string conversions affecting morphologyConverter.
  • 45: Made targets optional.
  • 43: Add MVD3 support to brain::circuit
  • 39: Add compartment report converter tool
  • 30, 35: Added a new library, Brain, to provide higher level functions and classes. The library provides:
    • A Circuit class to get basic information from cells and targets and load morphologies at circuit level.
    • A brain::cell namspace with a Morphology class plus other related classes to access morphological data about neurons.
  • 38: Fix crash while reading more than ulimit -Sn (1024 default) morphologies
  • 37: Added support for synapse nrn_extra.h5 files.
  • 31: Fix crash while reading more than ulimit -Sn (1024 default) NEST gdf files
  • 29: New member functions in brion::BlueConfig to provide a semantic API.
  • 28: SpikeReport continues parsing files that have broken lines

Release 1.6.0 (9-Nov-2015)

  • 24: Add getURI() method in SpikeReport.
  • 22: spikeConverter can process spikes to and from stream-type SpikeReport plugins.
  • 22: SpikeReport DSO plugins in the LD_LIBRARY_PATH are loaded automatically.
  • 12: Extended brion::Synapse to also support non-merged synapse files
  • 12: Add brion::Target::parse() to resolve a given target name
  • 9: Extend SWC parser to support fork and end points and undefined section points. The Brion::SectionType enum has not been extended to include end and fork points, these types are translated into the most reasonable one based on the point ancestors.

Release 1.5.0 (7-Jul-2015)

  • Add RESTING_VOLTAGE constant.
  • Add support for binary spike reports.
  • Add support for spike writer plugin.
  • Add async IO support in brion::CompartmentReportMap.
  • brion::CompartmentReportBinary::updateMapping() more robust.
  • brion::SpikeReport API extended to support stream-based reports. A reference implementation of a stream-based spike report plugin is also provided.
  • Ensure thread-safety with non-threadsafe HDF5 library.
  • Morphology class implementation changed to support the Lunchbox plugin mechanism.
  • New morphology plugin to read SWC morphologies.
  • #3: New morphology converter tool.
  • New null compartment report for benchmarks.
  • New spike converter tool.
  • Optimized function Circuit::get for large circuits (cut down the loading time of the 3.1 M neuron circuit by 6.5 seconds in a Core i7-4930K @ 3.40GHz).
  • Replace use of iostreams by lunchbox::MemoryMap.
  • Several bugfixes and cleanups.

Release 1.4.0 (8-Oct-2014)

  • Old report readers have been adapted to be static plugins using lunchbox::IOPluginFactory.
  • New spike report reader plugin for NEST spike reports. The plugin can parse multiple report file using shell wildcards (*, ?) in the filepath provided.
  • New constructor for brion::CompartmentReport accepting an URI and the desired access mode deprecates the old read and write constructors.
  • New compartment report based on key-value stores supported by Lunchbox::PersistentMap.
  • Spike loading has been optimized (in a 12-core GPU the expected speed-up is above 4x for large files).