Featuremapper

[philippjfr]

This should provide the basis to begin splitting the FeatureMapper submodule out of the core of Topographica. The FeatureMapper components will be found primarily in the top section of topo/analysis/featureresponses.py, in topo/command/analysis.py and topo/command/pylabplot.py. The code passes all tests and provides a 1.5-2x speedup over the previous measurement code.

Several issues and minor fixes that remain:

• pattern_present and measure_response have very similar use cases and duplicate a lot of code, should decide on including one or the other.
• Setting different defaults for subsets of MeasurementResponseCommands is still cumbersome (see models/lissom_oo_or.ty)
• A lot of the documentation needs to be revisited to ensure FeatureMapper classes no longer reference attributes and functionality internal to Topographica.
• Naming of some classes may need to be reconsidered.

This pull request is not meant to be merged immediately at this stage but should now be ready for an initial review and testing. Any and all feedback would be greatly appreciated.

[philippjfr]

Further issues:

• Saving snapshots fails with the following error: PicklingError: Can't pickle <type 'function'>: it's not the same object as builtin.function
• Test pattern window does not reset time properly and generates warning saying that restore_state is not a parameter.

[jbednar]

| * Saving snapshots fails with the following error: PicklingError: Can't pickle <type 'function'>: it's not the same object as builtin.function

From a recent bug report, this appears to be happening with stock Topographica, though why it doesn't cause test failures is a mystery to me.

[philippjfr]

Recent commits fix the test pattern window bug mentioned above and another bug, which would occur when training was interrupted causing any subsequent measurement to fail due to improper handling of the timer stop flag.

[jbednar]

Ok, I've gone through all the changes line by line, and apart from any issues I noted there, it looks good to me. The process in lissom_oo_or.ty is definitely something we need to fix, so let's talk about that. We should also talk about pattern_present vs. measure_response, and any remaining naming issues. And then let's merge this pull request and set up FeatureMapper!