Module basic

Present the specified test patterns for the specified duration.

Given a set of input patterns (dictionary of GeneratorSheetName:PatternGenerator pairs), installs them into the specified GeneratorSheets, runs the simulation for the specified length of time, then restores the original patterns and the original simulation time. Thus this input is not considered part of the regular simulation, and is usually for testing purposes.

If a simulation is not provided, the active simulation, if one exists, is requested.

If this process is interrupted by the user, the temporary patterns may still be installed on the retina.

If overwrite_previous is true, the given inputs overwrite those previously defined.

If plastic is False, overwrites the existing values of Sheet.plastic to disable plasticity, then reenables plasticity.

Save a snapshot of the network's current state.

The snapshot is saved as a gzip-compressed Python binary pickle.

(xml snapshots are currently experimental, and will not be useful for most users.)

As this function uses Python's 'pickle' module, it is subject to the same limitations (see the pickle module's documentation) - with the notable exception of class attributes. Python does not pickle class attributes, but this function stores class attributes of any ParameterizedObject class that is declared within the topo package. See the topo.base.PicklableClassAttributes class for more information.

Save the current simulation as a Topographica script.

Generates a script that, if run, would generate a simulation with the same architecture as the one currently in memory. This can be useful when defining networks in place, so that the same general configuration can be recreated later. It also helps when comparing two similar networks generated with different scripts, so that the corresponding items can be matched rigorously.

Note that the result of this operation is usually just a starting point for further editing, because it will not usually be runnable as-is (for instance, some parameters may not have runnable representations). Even so, this is usually a good start.

Run a Topographica simulation in batch mode.

Features:

• Generates a unique, well-defined name for each 'experiment' (i.e. simulation run) based on the date, script file, and parameter settings
• Allows parameters to be varied on the command-line, to allow comparing various settings
• Saves a script capturing the simulation state periodically, to preserve parameter values from old experiments and to allow them to be reproduced exactly later
• Can perform user-specified analysis routines periodically, to monitor the simulation as it progresses.
• Stores commandline output (stdout) in the output directory

A typical use of this function is for remote execution of a large number of simulations with different parameters, often on remote machines (such as clusters).

The script_file parameter defines the .ty script we want to run in batch mode. The output_directory defines the root directory in which a unique individual directory will be created for this particular run. The optional analysis_fn can be any python function to be called at each of the simulation iterations defined in the analysis times list. This function should perform whatever analysis of the simulation you want to perform, such as plotting or calculating some statistics. The analysis_fn should avoid using any GUI functions (i.e., should not import anything from topo.tkgui), and it should save all of its results into files.

Any other optional parameters supplied will be set in the main namespace before any scripts are run. They will also be used to construct a unique topo.sim.name for the file, and they will be encoded into the simulation directory name, to make it clear how each simulation differs from the others.

default_analysis_plotgroups

Value:

['Activity', 'Orientation Preference']