simulator/doc/todo.txt - Githubissues

[Issue migrated from SourceForge | ID: 3031712 | Submitted by 'tbekolay'] [http://sourceforge.net/support/tracker.php?aid=3031712]

This is just a todo.txt from the simulator/doc directory. Putting it here so that I can remove it from the SVN repository, as it makes more sense to have it in the bug tracker than mixed in with the code.

We should go over this list, take anything that still needs to be done and make separate feature requests / bugs for them, and then close this.

TODO (release):

DONE (Sunday) make scope test network
DONE (Monday) python keyword "that"; python dictionary of networks
DONE (Tuesday) make console names legal python names
DONE change cursor colour in script console
DONE (Tuesday) clean up script editor window
DONE (Tuesday) UI event on add/remove projection/node in network
DONE (Tuesday) memory leak in spike raster? (see email from shu early feb)
DONE make visiblymutable listeners transient
DONE support name changes in network members
DONE support change of function input dimension
DONE support noise parameter changes
DONE fix bug where config window doesn't close
DONE add exit & remove exception in script editor on (File->close)
DONE make transform configurable for Decoded Termination
DONE help popup
DONE improve code completion (particularly static methods and constructors)
DONE persist command history
move configuration UI code to simulator-ui
plot popups from config using UI code; matlab exports of matrices and vectors
hide config params as needed
remove util configuration/configurable
(wait for Shu to do accelerators) ctrl shortcut keys for save, open, new
DONE do we need a way to create top-level UI objects from scripts?
change package names to nengo
use config matrix editor throughout
DONE add new icons
move to sourceforge
tutorials
review Izhikevich spike generator and make list of default settings (e.g. custom, adapting, bursting)

TODO:

expand help in python
custom popups (e.g. plot function)
fix icons
map class names (eg Impl -> default implementation)
configuration: for private classes, look for method declaration on public interfaces (eg NoiseFactory); see http://forums.bea.com/thread.jspa?threadID=600004396
do something about units in relationship between synapticintegrator output and spikegenerator input
clean up musculoskeletal code
DONE events for Shu
DONE clean up config UI code
DONE constructor args not appearing for LTISystem (eg NoiseImplDF)
DONE make config initialization and factory for UI
DONE clean up configuration-related code in API
DONE fix SingleValuedProperty

TODO OLD:

NO unify linear terminations at SynapticIntegrator and NEFEnsemble levels
DONE spike-based learning
DONE revisit LinearSynapticIntegrator (particularly network timestep-period cycles with rate input)
DONE learning at neuron level
DONE RK45 integrator
DONE documentation wrappers
DONE UI flag for plots
DONE metadata for networks
DONE use cases for Shu
DONE allow decoding of arbitrary outputs in NEFEnsembleImpl and DecodedOrigin
DONE document and implement NEFEnsembleFactory, remove old EnsembleFactory
DONE fix bug in LIFSpikeGenerator
DONE model activities and direct simulation
DONE review model
DONE clean up reference model
DONE exception model
DONE make everything serializable
NO (not sure this is supported by matlab interface) switch to generics as appropriate
DONE impls for simple classes
DONE tests for simple classes
DONE SpikeGenerator and Probeable-based Origins
DONE LinearExponentialTermination
DONE basic plotting
DONE CompositeNeuron (or SpikingNeuron or DefaultSpikingNeuron)
DONE fix LIF impl
DONE write DefaultEnsemble (expandable?)
DONE write DefaultNEFEnsemble
DONE write encoder factories: even, random, function-based, axis-clustered (use tanh)
DONE function generator
DONE (in NEFEnsembleImpl) write constant-rate decoder factory
DONE write and use diagonal linear system
DONE write LocalSimulator
DONE file serialization of Networks (add serializable Node interface)
DONE function interpreter
DONE change package names
DONE matlab interface
DONE ensemble factory
DONE improved plotting
DONE scale linear system output
DONE clean up termination properties (tauPSC maybe not universal)
DONE decoding plots

TODO LATER:

SequentialQuadraticApproximator (to support constraints)
DensityCostApproximator (for greater accuracy with greater cost; user specifies baseline number of samples at uniform density)
TODO: OriginWrapper to perform functions on values (eg unit conversion) (should model some biological process -- not a valid way to get function outputs of ensembles)
clean up LinearSynapticIntegrator
NEURON interface
Izhikevich SpikeGenerator (any CONSTANT_RATE parameter ranges?)
Poisson and exponential PDFs (see references in Deak, 1977)
Hopfield temporal coding
Associative memory network
TD learning
DistributedSimulator
user interface
DONE adapting LIF SpikeGenerator
DONE Conductance delays
DONE STDP
DONE negative weights
DONE write simulation-based decoder factory
DONE standard ensemble plots
DONE Poisson process SpikeGenerator
DONE Hodgkin-Huxley SpikeGenerator
NO script facade

NOTES:

If Eclipse tasks list doesn't populate, delete the project, remove .classpath and .project, and make new project
The matlab-java interface prefers to convert an nX1 matrix to a 1-d array rather than a 2-d array, so if a class has methods of the same name but one with float[] arg and the other with float[][] arg, there doesn't seem to be a way call the latter with a float[n][1]. No remaining cases of this in nengo presently, Possible future case if MU.clone() is implemented for vectors as well as matrices.
Plotting: JFreeChart produces nice graphs and supports a variety of export formats, but doesn't support 3D plots. JMathPlot does support 3D, but doesn't seem to support export at all, and needs JDK 1.5 (although the latter could probably be changed with little work). Will use JFreeChart for now. 3D plots would be handy, but the need would probably will arise during non-standard analytical work, where it might be better to export to Matlab or some other plotting package anyway. We don't have to support every plotting possibility here.
have had problems with simulator-ui not building; this fixes it (from http://forum.java.sun.com/thread.jspa?threadID=688073&messageID=4019106) -Right Click Project you are working on from Package Explorer -Go to Properties -Go to Java Build Path from the right tree structure -Go to Libraries Tab -Choose Add Library Button -Select JRE System Library -Hit Next, the Radio button will prompt the Workspace default JRE, and let it be that way -Hit Finish

nengo / nengo-1.4

simulator/doc/todo.txt #99