ioam/topographica — pull request #525 by PhilippJFR (2013-07-05 19:03:38+00:00)
Title: Featuremapper

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.