Module Hierarchy

• 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.
  • param.external: External code required for param/tkinter interface.
  • param.parameterized: Generic support for objects with full-featured Parameters and messaging.
  • param.tk: Classes linking Parameters to Tkinter.
• topo: Topographica cortical map simulator package.
  • 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.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.pylabplot: 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.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.asizeof: and sizes of Python objects (for Python 2.2 or later [1]).
    • topo.misc.commandline: Support functions for parsing command-line arguments and providing the Topographica command prompt.
    • topo.misc.distribution: Distribution class
    • topo.misc.fixedpoint: FixedPoint objects support decimal arithmetic with a fixed number of digits (called the object's precision) after the decimal point.
    • topo.misc.gendocs: Topographica-specific changes to the standard pydoc command.
    • topo.misc.generatorsheet: GeneratorSheet: a sheet with a pattern generator.
    • topo.misc.genexamples: Commands for running the examples files in various ways.
    • 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.memuse: Functions for measuring memory usage, to allow usage to be optimized.
    • topo.misc.patternfn
    • topo.misc.picklemain: Extensions to pickle allowing items in __main__ to be saved.
    • 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.pattern: Objects capable of generating a two-dimensional array of values.
    • topo.pattern.audio: Pattern generators for audio signals.
    • topo.pattern.basic
    • 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.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.composer: A Sheet class for composing activity from different sheets into a single activity matrix.
    • 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.
  • topo.transferfn: A family of function objects for transforming a matrix generated from some other function.
    • topo.transferfn.basic: Simple functions operating on a matrix, potentially modifying it.
    • topo.transferfn.misc: Transfer functions with more complex dependencies.
    • topo.transferfn.optimized: Output functions (see basic.py) and projection-level output functions (see projfn.py) written in C to optimize performance.
    • topo.transferfn.projfn: Output functions (see basic.py) that apply to a whole Projection.