/**
* Called to initialize the structural anatomy with configured values and prepare the anatomical
* entities for activation.
*
* @param c
*/
public void initMatrices(final Connections c) {
SparseObjectMatrix<Column> mem = c.getMemory();
c.setMemory(mem == null ? mem = new SparseObjectMatrix<>(c.getColumnDimensions()) : mem);
c.setInputMatrix(new SparseBinaryMatrix(c.getInputDimensions()));
// Calculate numInputs and numColumns
int numInputs = c.getInputMatrix().getMaxIndex() + 1;
int numColumns = c.getMemory().getMaxIndex() + 1;
if (numColumns <= 0) {
throw new InvalidSPParamValueException("Invalid number of columns: " + numColumns);
}
if (numInputs <= 0) {
throw new InvalidSPParamValueException("Invalid number of inputs: " + numInputs);
}
c.setNumInputs(numInputs);
c.setNumColumns(numColumns);
// Fill the sparse matrix with column objects
for (int i = 0; i < numColumns; i++) {
mem.set(i, new Column(c.getCellsPerColumn(), i));
}
c.setPotentialPools(new SparseObjectMatrix<Pool>(c.getMemory().getDimensions()));
c.setConnectedMatrix(new SparseBinaryMatrix(new int[] {numColumns, numInputs}));
// Initialize state meta-management statistics
c.setOverlapDutyCycles(new double[numColumns]);
c.setActiveDutyCycles(new double[numColumns]);
c.setMinOverlapDutyCycles(new double[numColumns]);
c.setMinActiveDutyCycles(new double[numColumns]);
c.setBoostFactors(new double[numColumns]);
Arrays.fill(c.getBoostFactors(), 1);
}
/**
* Maps a column to its input bits. This method encapsulates the topology of the region. It takes
* the index of the column as an argument and determines what are the indices of the input vector
* that are located within the column's potential pool. The return value is a list containing the
* indices of the input bits. The current implementation of the base class only supports a 1
* dimensional topology of columns with a 1 dimensional topology of inputs. To extend this class
* to support 2-D topology you will need to override this method. Examples of the expected output
* of this method: * If the potentialRadius is greater than or equal to the entire input space,
* (global visibility), then this method returns an array filled with all the indices * If the
* topology is one dimensional, and the potentialRadius is 5, this method will return an array
* containing 5 consecutive values centered on the index of the column (wrapping around if
* necessary). * If the topology is two dimensional (not implemented), and the potentialRadius is
* 5, the method should return an array containing 25 '1's, where the exact indices are to be
* determined by the mapping from 1-D index to 2-D position.
*
* @param c {@link Connections} the main memory model
* @param columnIndex The index identifying a column in the permanence, potential and connectivity
* matrices.
* @param wrapAround A boolean value indicating that boundaries should be ignored.
* @return
*/
public int[] mapPotential(Connections c, int columnIndex, boolean wrapAround) {
int index = mapColumn(c, columnIndex);
TIntArrayList indices =
getNeighborsND(c, index, c.getInputMatrix(), c.getPotentialRadius(), wrapAround);
indices.add(index);
// TODO: See https://github.com/numenta/nupic.core/issues/128
indices.sort();
int[] retVal = new int[(int) Math.round(indices.size() * c.getPotentialPct())];
return ArrayUtils.sample(indices, retVal, c.getRandom());
}
/**
* The range of connectedSynapses per column, averaged for each dimension. This value is used to
* calculate the inhibition radius. This variation of the function supports arbitrary column
* dimensions.
*
* @param c the {@link Connections} (spatial pooler memory)
* @param columnIndex the current column for which to avg.
* @return
*/
public double avgConnectedSpanForColumnND(Connections c, int columnIndex) {
int[] dimensions = c.getInputDimensions();
int[] connected = c.getColumn(columnIndex).getProximalDendrite().getConnectedSynapsesSparse(c);
if (connected == null || connected.length == 0) return 0;
int[] maxCoord = new int[c.getInputDimensions().length];
int[] minCoord = new int[c.getInputDimensions().length];
Arrays.fill(maxCoord, -1);
Arrays.fill(minCoord, ArrayUtils.max(dimensions));
SparseMatrix<?> inputMatrix = c.getInputMatrix();
for (int i = 0; i < connected.length; i++) {
maxCoord = ArrayUtils.maxBetween(maxCoord, inputMatrix.computeCoordinates(connected[i]));
minCoord = ArrayUtils.minBetween(minCoord, inputMatrix.computeCoordinates(connected[i]));
}
return ArrayUtils.average(ArrayUtils.add(ArrayUtils.subtract(maxCoord, minCoord), 1));
}
/**
* Maps a column to its respective input index, keeping to the topology of the region. It takes
* the index of the column as an argument and determines what is the index of the flattened input
* vector that is to be the center of the column's potential pool. It distributes the columns over
* the inputs uniformly. The return value is an integer representing the index of the input bit.
* Examples of the expected output of this method: * If the topology is one dimensional, and the
* column index is 0, this method will return the input index 0. If the column index is 1, and
* there are 3 columns over 7 inputs, this method will return the input index 3. * If the topology
* is two dimensional, with column dimensions [3, 5] and input dimensions [7, 11], and the column
* index is 3, the method returns input index 8.
*
* @param columnIndex The index identifying a column in the permanence, potential and connectivity
* matrices.
* @return A boolean value indicating that boundaries should be ignored.
*/
public int mapColumn(Connections c, int columnIndex) {
int[] columnCoords = c.getMemory().computeCoordinates(columnIndex);
double[] colCoords = ArrayUtils.toDoubleArray(columnCoords);
double[] ratios =
ArrayUtils.divide(colCoords, ArrayUtils.toDoubleArray(c.getColumnDimensions()), 0, 0);
double[] inputCoords =
ArrayUtils.multiply(ArrayUtils.toDoubleArray(c.getInputDimensions()), ratios, 0, 0);
inputCoords =
ArrayUtils.d_add(
inputCoords,
ArrayUtils.multiply(
ArrayUtils.divide(
ArrayUtils.toDoubleArray(c.getInputDimensions()),
ArrayUtils.toDoubleArray(c.getColumnDimensions()),
0,
0),
0.5));
int[] inputCoordInts =
ArrayUtils.clip(ArrayUtils.toIntArray(inputCoords), c.getInputDimensions(), -1);
return c.getInputMatrix().computeIndex(inputCoordInts);
}