Package topo

Topographica cortical map simulator package.

Topographica is designed as a collection of packages from which elements can be selected to model specific systems. For more information, see the individual subpackages:

base           - Core Topographica functions and classes
plotting       - Visualization functions and classes
analysis       - Analysis functions and classes (besides plotting)
tkgui          - Tk-based graphical user interface (GUI)
command        - High-level user commands
misc           - Various useful independent modules

The Topographica primitives library consists of a family of classes that can be used with the above functions and classes:

sheet          - Sheet classes: 2D arrays of processing units
projection     - Projection classes: connections between Sheets
pattern        - PatternGenerator classes: 2D input or weight patterns
ep             - EventProcessor classes: other simulation objects
outputfn       - Output functions, for e.g. normalization or squashing
responsefn     - Calculate the response of a Projection
learningfn     - Adjust weights for a Projection
coordmapper    - CoordinateMapperFn classes: map coords between Sheets

Each of the library directories can be extended with new classes of the appropriate type, just by adding a new .py file to that directory. E.g. new PatternGenerator classes can be added to pattern/, and will then show up in the GUI menus as potential input patterns.

$Id: __init__.py 9078 2008-09-03 01:27:06Z jbednar $

Version: $Revision: 9078 $

Submodules

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topo.analysis: Analysis tools for Topographica, other than plotting tools.
- topo.analysis.featureresponses: FeatureResponses and associated functions and classes.
- topo.analysis.vision: Vision-specific analysis functions.
topo.base: Basic files needed by all Topographica programs.
- topo.base.arrayutil: General utility functions and classes for Topographica that require numpy.
- topo.base.boundingregion: Bounding regions and bounding boxes.
- topo.base.cf: ConnectionField and associated classes.
- topo.base.functionfamily: Basic function objects.
- topo.base.parameterclasses: Moved to topo/params/__init__.py
- topo.base.patterngenerator: PatternGenerator abstract class and basic example concrete class.
- topo.base.projection: Projection and related classes.
- topo.base.sheet: Neural sheet objects and associated functions.
- topo.base.sheetcoords: Provides SheetCoordinateSystem, allowing conversion between the two coordinate systems used in Topographica.
- topo.base.sheetview: Topographica SheetView objects and its subclasses.
- topo.base.simulation: A general-purpose Simulation class for discrete events.
topo.command: A family of high-level user commands acting on the entire simulation.
- topo.command.analysis: User-level analysis commands, typically for measuring or generating SheetViews.
- topo.command.basic: High-level user-level commands controlling the entire simulation.
- topo.command.pylabplots: Line-based and matrix-based plotting commands using MatPlotLib.
topo.coordmapper: A family of function objects for transforming one set of coordinates into another.
- topo.coordmapper.basic: Functions for mapping from one 2D Cartesian coordinate system to another.
topo.ep: EventProcessor classes.
- topo.ep.basic: Basic scalar EventProcessors
topo.ipythonTk
- topo.ipythonTk.ipythonTk: This file orginally came from: http://ipython.scipy.org/moin/Cookbook/EmbeddingInGTK
- topo.ipythonTk.ipython_view: This is a modified version of source code from the Accerciser project (http://live.gnome.org/accerciser).
topo.learningfn: A family of function objects for changing a set of weights over time.
- topo.learningfn.basic: Basic learning functions.
- topo.learningfn.optimized: Learning functions (see basic.py) and projection-level learning functions (see projfn.py) written in C to optimize performance.
- topo.learningfn.projfn: Learning functions for Projections.
- topo.learningfn.som: SOM-based learning functions for CFProjections.
topo.misc: Miscellaneous functions used by Topographica files outside topo.base.
- topo.misc.commandline: Support functions for parsing command-line arguments and providing the Topographica command prompt.
- topo.misc.distribution: Distribution class
- topo.misc.filepath: Functions and classes to simplify dealing with paths.
- topo.misc.gendocs: Topographica-specific changes to the standard pydoc command.
- topo.misc.inlinec: Interface class for inline C/C++ functions.
- topo.misc.keyedlist: KeyedList sorted dictionary class.
- topo.misc.legacy: Code used to support old snapshots, and update scripts.
- topo.misc.numbergenerator: A collection of classes that, when called, generate numbers according to different distributions (e.g.
- topo.misc.patternfn
- topo.misc.playerrobot: High-level interface to the Player client libraries.
- topo.misc.robotics: Classes for using robotic or other hardware using Topographica.
- topo.misc.trace: Object classes for recording and plotting time-series data.
- topo.misc.util: General utility functions and classes.
topo.numbergen: Callable objects that generate numbers according to different distributions.
- topo.numbergen.basic: A collection of classes that, when called, generate numbers according to different distributions (e.g.
topo.outputfn: A family of function objects for transforming a matrix generated from some other function.
- topo.outputfn.basic: Simple functions operating on a matrix, potentially modifying it.
- topo.outputfn.optimized: Output functions (see basic.py) and projection-level output functions (see projfn.py) written in C to optimize performance.
- topo.outputfn.projfn: Output functions (see basic.py) that apply to a whole Projection.
topo.param: Parameters are a kind of class attribute allowing special behavior, including dynamically generated parameter values, documentation strings, constant and read-only parameters, and type or range checking at assignment time.
- topo.param.parameterized: Generic support for objects with full-featured Parameters and messaging.
- topo.param.tk: Classes linking Parameters to Tkinter.
topo.pattern: Objects capable of generating a two-dimensional array of values.
- topo.pattern.audio: Pattern generators for audio signals.
- topo.pattern.basic: Simple two-dimensional mathematical or geometrical pattern generators.
- topo.pattern.image: PatternGenerators based on bitmap images stored in files.
- topo.pattern.random: Two-dimensional pattern generators drawing from various random distributions.
- topo.pattern.rds: Random-dot stereogram patterns.
- topo.pattern.teststimuli: Composite patterns such as patches of sine gratings as used in psychophysical or physiological experiments.
topo.plotting: Topographica plotting subsystem.
- topo.plotting.bitmap: Topographica Bitmap Class.
- topo.plotting.palette: Palette class hierarchy, for constructing an RGB color out of a scalar value.
- topo.plotting.plot: Plot class.
- topo.plotting.plotfilesaver: File saving routines for plots.
- topo.plotting.plotgroup: Hierarchy of PlotGroup classes, i.e.
topo.projection: Projection classes.
- topo.projection.basic: Repository for the basic Projection types, without any special dependencies or requirements.
- topo.projection.optimized: Optimized versions of Projection classes.
topo.responsefn: A family of response functions for CFProjections.
- topo.responsefn.basic: Basic response functions.
- topo.responsefn.optimized: Response functions (see basic.py) and CFProjection response functions (see projfn.py) written in C to optimize performance.
- topo.responsefn.projfn: Projection-level response functions.
topo.sheet: Sheet classes.
- topo.sheet.basic: Neural sheet objects.
- topo.sheet.cfsom: Defines CFSOM, a sheet class that works like a Kohonen SOM extended to support topographically restricted receptive fields.
- topo.sheet.composer: A Sheet class for composing activity from different sheets into a single activity matrix.
- topo.sheet.generator: GeneratorSheet classes.
- topo.sheet.lissom: LISSOM and related sheet classes.
- topo.sheet.optimized: Inline-optimized Sheet classes
- topo.sheet.saccade: Sheets for simulating a moving eye.
- topo.sheet.slissom: The SLISSOM class.
topo.tkgui: Tk-based graphical user interface (GUI).
- topo.tkgui.editor: The GUI model editor.
- topo.tkgui.featurecurvepanel: Panels for displaying tuning curves.
- topo.tkgui.plotgrouppanel: Classes providing GUI windows for PlotGroups, allowing sets of related plots to be displayed.
- topo.tkgui.projectionpanel: PlotgroupPanels for displaying ProjectionSheet plotgroups.
- topo.tkgui.templateplotgrouppanel: class TemplatePlotGroupPanel Panel for displaying preference maps and activity plot groups.
- topo.tkgui.testpattern: The Test Pattern window allows input patterns to be previewed.
- topo.tkgui.topoconsole: TopoConsole class file.

Functions

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_mpq_pickle_support()
Allow instances of gmpy.mpq to pickle.

source code

_numpy_ufunc_pickle_support()
Allow instances of numpy.ufunc to pickle.

source code

about(display=True)
Print release and licensing information.

source code

Variables

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old_seterr_settings = {'divide': 'ignore', 'invalid': 'ignore'...

release = ''

sim = Simulation(basename_format='%(name)s_%(timestr)s', name=...

time_type_args = ()

version = ''

Variables Details

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old_seterr_settings

Value:

{'divide': 'ignore', 'invalid': 'ignore', 'over': 'ignore', 'under': 'ignore'}

sim

Value:

Simulation(basename_format='%(name)s_%(timestr)s', name=None, print_level=100, reg
ister=True, startup_commands=[], time_printing_format='%(_time)09.2f', time_type=<
built-in function mpq>, time_type_args=())