Spatial Pooling Visualization

jeffc · August 30, 2017, 3:02pm

I have been following the videos from HTM School and specifically, those associated with spatial pooling. I am attempting to reconstruct some of the visualizations. The one that I would like to be able to reconstruct is the mapping from the columns to the encoded input data. I am using the python code. However, it appears that the data members and member functions reside at the lower level .cpp routines which are referenced through a SWIG interface. Granted, I am using an earlier version of nupic but it looks like this area has not changed that much between versions.

Is there a way to access the lower level variables and pointers to objects in the .cpp files but do it within the python code?

For instance, I am working in the python debugger (pdb) and am trying to view the calculateOverlap_ data member of the SpatialPooler.

rhyolight · August 30, 2017, 4:43pm

Check out the SP docs here. They should be pretty much the same with older versions of NuPIC.

You can see how I accessed all the SP internal state from HTM School visualizations here:

github.com

htm-community/nupic-history-server/blob/master/nupic_history/sp_facade.py#L12


import multiprocessing
import time


import numpy as np


from nupic_history import SpSnapshots as SNAPS
from nupic_history.utils import compressSdr
from nupic.math import topology




class SpFacade(object):


def __init__(self, sp, ioClient, iteration=None):
  """
  A wrapper around the HTM Spatial Pooler that can save SP state to Redis for
  each compute cycle. Adds a "save=" kwarg to compute().


  :param sp: Either an instance of Spatial Pooler or a string model id
  :param ioClient: Instantiated IO client
  :param iteration: what iteration to resurrect the SP at
  """

Just look for self._sp, which is the SP instance.

scott · August 30, 2017, 4:44pm

You can call getOverlaps on the SpatialPooler (even the swigged C++ implementation). This function is defined here:

github.com

numenta/nupic.core/blob/d5f161a859c35862f9b679c077ac766cf8c2abbe/src/nupic/algorithms/SpatialPooler.hpp#L782


void getConnectedCounts(UInt connectedCounts[]) const;


/**
Print the main SP creation parameters to stdout.
 */
void printParameters() const;


/**
Returns the overlap score for each column.
 */
const vector<UInt>& getOverlaps() const;


/**
Returns the boosted overlap score for each column.
 */
const vector<Real>& getBoostedOverlaps() const;




///////////////////////////////////////////////////////////
//
// Implementation methods. all methods below this line are

And you can see some SWIG code to make sure it is wrapped properly for calling from Python here:

github.com

numenta/nupic.core/blob/d5f161a859c35862f9b679c077ac766cf8c2abbe/src/nupic/bindings/algorithms.i#L1292-L1297


PyObject* getOverlaps()
{
  const std::vector<nupic::UInt>& overlaps = self->getOverlaps();
  nupic::NumpyVectorT<nupic::UInt> npOverlaps(overlaps.size(), overlaps.data());
  return npOverlaps.forPython();
}

Also keep in mind that if you are using the Network API then you have to pull the SP algorithm class out of the region before calling this method.

jeffc · August 31, 2017, 4:41pm

Thanks, Scott and to everyone else who responded.
I guess my follow-question is more related to the version compatibility. I am running a old version (0.2.7 I believe) which does not have many of these functions that the later versions have.

Can I simply add the code above in the .i file to the existing $NUPIC/binding/algorithms.i and then make an addition to the python wrapper (algorithms_cxx.cpp)?

rhyolight · August 31, 2017, 4:55pm

Probably not. We’ve made breaking changes recently. Why can’t you upgrade?

scott · August 31, 2017, 7:10pm

It looks like 0.2.7 (of nupic.core, not sure if you meant 2.7 of nupic or nupic.core but it should be close enough) has a function for calculating overlaps for a given input:

github.com

numenta/nupic.core/blob/293a1580c94b4ea1e0df5b24bac91ea9b916da94/src/nupic/bindings/algorithms.i#L1124-L1125


def _calculateOverlap(self, inputVector):
  return self.calculateOverlap_(inputVector)

jeffc · August 31, 2017, 9:02pm

I plan to do just that.

In the interim I was hoping to see if there was something that I could do which was expedient using my existing setup rather than taking the time to upgrade.

But my intentions are to upgrade.

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Spatial Pooling Visualization

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