Java Code Examples for cern.colt.matrix.DoubleMatrix2D#size()

/**
 * Returns the Frobenius norm of matrix <tt>A</tt>, which is <tt>Sqrt(Sum(A[i,j]<sup>2</sup>))</tt>.
 */
public double normF(DoubleMatrix2D A) {
	if (A.size()==0) return 0;
	return A.aggregate(hypotFunction(),cern.jet.math.Functions.identity);
}
 

/**
 * Returns the matrix's fraction of non-zero cells; <tt>A.cardinality() / A.size()</tt>.
 */
public double density(DoubleMatrix2D A) {
	return A.cardinality() / (double) A.size();
}
 

public static SparseDoubleMatrix2D checkIncestConditionParents(	DoubleMatrix2D signatureNodeIncestVector,
																DoubleMatrix2D functionNodeIncestVector,
																SparseDoubleMatrix2D signatureAdjacencyMatrix, 
																SparseDoubleMatrix2D functionAdjacencyMatrix,
																int[] signatureDepths,
																int[] functionDepths,
																int depth,
																SparseDoubleMatrix2D candidateList) {

	SparseDoubleMatrix2D signatureSelector = new SparseDoubleMatrix2D(1, signatureDepths.length);
	SparseDoubleMatrix2D functionSelector = new SparseDoubleMatrix2D(1, functionDepths.length);

	for(int i=0; i<signatureNodeIncestVector.size(); ++i) {
		if(signatureNodeIncestVector.get(0, i) == 0.0)
			continue;

		signatureSelector.assign(0.0);
		signatureSelector.set(0, i, 1.0);

		DoubleMatrix2D signatureNodeParentVector = Algebra.DEFAULT.mult(signatureSelector, Algebra.DEFAULT.transpose(signatureAdjacencyMatrix));

		// only bipartite match on incest parents
		for(int iParent = 0; iParent < signatureNodeParentVector.columns(); ++iParent) {
			if(signatureNodeParentVector.get(0, iParent) > 0 && signatureDepths[iParent] != depth) {
				signatureNodeParentVector.set(0, iParent, 0.0);
			}
		}

		int signatureIncestParentCount = signatureNodeParentVector.cardinality();

		for(int j=0; j<functionNodeIncestVector.size(); ++j) {
			if(candidateList.get(i, j) == 0.0)
				continue;

			functionSelector.assign(0.0);
			functionSelector.set(0, j, 1.0);

			DoubleMatrix2D functionNodeParentVector = Algebra.DEFAULT.mult(functionSelector, Algebra.DEFAULT.transpose(functionAdjacencyMatrix));

			// only bipartite match on incest parents
			for(int iParent = 0; iParent < functionNodeParentVector.columns(); ++iParent) {
				if(functionNodeParentVector.get(0, iParent) > 0 && functionDepths[iParent] != depth) {
					functionNodeParentVector.set(0, iParent, 0.0);
				}
			}

			int functionIncestParentCount = functionNodeParentVector.cardinality();

			// bipartite matching, if !sufficient
			if(	candidateList.get(i, j) > 0 && (signatureIncestParentCount > functionIncestParentCount ||
				!bipartiteMatchingVector(candidateList, signatureNodeParentVector, functionNodeParentVector, signatureDepths, functionDepths))) {
				// remove candidacy
				candidateList.set(i, j, 0.0);
			}
		}
	}

	return candidateList;
}
 

/**
 * Returns the Frobenius norm of matrix <tt>A</tt>, which is <tt>Sqrt(Sum(A[i,j]<sup>2</sup>))</tt>.
 */
public double normF(DoubleMatrix2D A) {
	if (A.size()==0) return 0;
	return A.aggregate(hypotFunction(),cern.jet.math.Functions.identity);
}
 

/**
 * Returns the matrix's fraction of non-zero cells; <tt>A.cardinality() / A.size()</tt>.
 */
public double density(DoubleMatrix2D A) {
	return A.cardinality() / (double) A.size();
}
 

/**
Returns a string representation of the given matrix with axis as well as rows and columns labeled.
Pass <tt>null</tt> to one or more parameters to indicate that the corresponding decoration element shall not appear in the string converted matrix.

@param matrix The matrix to format.
@param rowNames The headers of all rows (to be put to the left of the matrix).
@param columnNames The headers of all columns (to be put to above the matrix).
@param rowAxisName The label of the y-axis.
@param columnAxisName The label of the x-axis.
@param title The overall title of the matrix to be formatted.
@return the matrix converted to a string.
*/
protected String toTitleString(DoubleMatrix2D matrix, String[] rowNames, String[] columnNames, String rowAxisName, String columnAxisName, String title) {
	if (matrix.size()==0) return "Empty matrix";
	String[][] s = format(matrix);
	//String oldAlignment = this.alignment;
	//this.alignment = DECIMAL;
	align(s);
	//this.alignment = oldAlignment;
	return new cern.colt.matrix.objectalgo.Formatter().toTitleString(cern.colt.matrix.ObjectFactory2D.dense.make(s), rowNames,columnNames,rowAxisName,columnAxisName,title);
}
 

/**
Returns a string representation of the given matrix with axis as well as rows and columns labeled.
Pass <tt>null</tt> to one or more parameters to indicate that the corresponding decoration element shall not appear in the string converted matrix.

@param matrix The matrix to format.
@param rowNames The headers of all rows (to be put to the left of the matrix).
@param columnNames The headers of all columns (to be put to above the matrix).
@param rowAxisName The label of the y-axis.
@param columnAxisName The label of the x-axis.
@param title The overall title of the matrix to be formatted.
@return the matrix converted to a string.
*/
protected String toTitleString(DoubleMatrix2D matrix, String[] rowNames, String[] columnNames, String rowAxisName, String columnAxisName, String title) {
	if (matrix.size()==0) return "Empty matrix";
	String[][] s = format(matrix);
	//String oldAlignment = this.alignment;
	//this.alignment = DECIMAL;
	align(s);
	//this.alignment = oldAlignment;
	return new cern.colt.matrix.objectalgo.Formatter().toTitleString(cern.colt.matrix.ObjectFactory2D.dense.make(s), rowNames,columnNames,rowAxisName,columnAxisName,title);
}