Adding/implementing interfaces for continuous CMI estimators to allow all combinations of univariate/multivariate arrays to be passed for var1/var2/conditional

java/source/infodynamics/measures/continuous/ConditionalMutualInfoCalculatorMultiVariate.java

@@ -129,17 +129,8 @@ public interface ConditionalMutualInfoCalculatorMultiVariate
 			double[][] cond) throws Exception;
 
 	/**
-	 * Sets a single series from which to compute the PDF.
-	 * Cannot be called in conjunction with
-	 * {@link #startAddObservations()} / {@link #addObservations(double[][], double[][], double[][])} or
-	 * {@link #addObservations(double[][], double[][], double[][], int, int)} /
-	 * {@link #finaliseAddObservations()}.</p>
-	 * 
-	 * <p>The supplied series may be (multivariate) time-series or 
-	 * simply a set of separate observations without a time interpretation.
-	 * 
-	 * <p>This method can only be used where dimensions of all
-	 * variables have been set to 1.</p>
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimensions of all variables have been set to 1 
 	 * 
 	 * @param var1 univariate observations for variable 1
 	 * @param var2 univariate observations for variable 2
@@ -151,6 +142,90 @@ public interface ConditionalMutualInfoCalculatorMultiVariate
 	public void setObservations(double[] var1, double[] var2,
 			double[] cond) throws Exception;
 
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimensions of var2 and cond are 1 
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[][] var1, double[] var2,
+			double[] cond) throws Exception;
+
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimensions of var1 and cond are 1 
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[] var1, double[][] var2,
+			double[] cond) throws Exception;
+
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimensions of var1 and var2 are 1 
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[] var1, double[] var2,
+			double[][] cond) throws Exception;
+
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimension of cond is 1 
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[][] var1, double[][] var2,
+			double[] cond) throws Exception;
+
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimension of var2 is 1 
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[][] var1, double[] var2,
+			double[][] cond) throws Exception;
+
+	/**
+	 * As per {@link #setObservations(double[][], double[][], double[][])}
+	 * but where dimension of var1 is 1 
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void setObservations(double[] var1, double[][] var2,
+			double[][] cond) throws Exception;
+
 	/**
 	 * Sets a single series from which to compute the PDF,
 	 *  where all the various observations are valid.
@@ -248,18 +323,8 @@ public interface ConditionalMutualInfoCalculatorMultiVariate
 			double[][] cond) throws Exception;
 	
 	/**
-	 * <p>Adds a new set of observations to update the PDFs with - is
-	 * intended to be called multiple times.
-	 * Must be called after {@link #startAddObservations()}; call
-	 * {@link #finaliseAddObservations()} once all observations have
-	 * been supplied.</p>
-	 * 
-	 * <p>Note that the arrays must not be over-written by the user
-	 *  until after finaliseAddObservations() has been called
-	 *  (they are not copied by this method necessarily, but the method
-	 *  may simply hold a pointer to them).</p>
-	 * 
-	 * <p>This method can only be used where dimensions of all
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of all
 	 * variables have been set to 1.</p>
 	 * 
 	 * @param var1 univariate observations for variable 1
@@ -272,6 +337,96 @@ public interface ConditionalMutualInfoCalculatorMultiVariate
 	public void addObservations(double[] var1, double[] var2,
 			double[] cond) throws Exception;
 	
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * var2 and cond have been set to 1.</p>
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[][] var1, double[] var2,
+			double[] cond) throws Exception;
+
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * var1 and cond have been set to 1.</p>
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[] var1, double[][] var2,
+			double[] cond) throws Exception;
+
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * var1 and var2 have been set to 1.</p>
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[] var1, double[] var2,
+			double[][] cond) throws Exception;
+
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * var1 have been set to 1.</p>
+	 * 
+	 * @param var1 univariate observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[] var1, double[][] var2,
+			double[][] cond) throws Exception;
+
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * var2 have been set to 1.</p>
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 univariate observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[][] var1, double[] var2,
+			double[][] cond) throws Exception;
+
+	/**
+	 * <p>As per {@link #addObservations(double[][], double[][], double[][])}
+	 * but can only be used where dimensions of
+	 * cond have been set to 1.</p>
+	 * 
+	 * @param var1 observations for variable 1
+	 * @param var2 observations for variable 2
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @param cond univariate observations for the conditional
+	 *  Length must match <code>var1</code>, and their indices must correspond.
+	 * @throws Exception
+	 */
+	public void addObservations(double[][] var1, double[][] var2,
+			double[] cond) throws Exception;
+
 	/**
 	 * <p>Adds a new sub-series of observations to update the PDFs with - is
 	 * intended to be called multiple times.

java/source/infodynamics/measures/continuous/ConditionalMutualInfoMultiVariateCommon.java

@@ -287,8 +287,7 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 	}
 
 	@Override
-	public void setObservations(double[][] var1, double[][] var2,
-			double[][] cond) throws Exception {
+	public void setObservations(double[][] var1, double[][] var2, double[][] cond) throws Exception {
 		startAddObservations();
 		addObservations(var1, var2, cond);
 		finaliseAddObservations();
@@ -297,7 +296,8 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 
 	/**
 	 * A non-overloaded method signature for setObservations with 2D arguments, as there have been
-	 *  some problems calling overloaded versions of setObservations from jpype. 
+	 *  some problems calling overloaded versions of setObservations from python jpype.
+	 *  Resolved if one follows the AutoAnalyser generated code, but left for back compatibility.
 	 * 
 	 * @param var1
 	 * @param var2
@@ -309,8 +309,55 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 	}
 
 	@Override
-	public void setObservations(double[] var1, double[] var2,
-			double[] cond) throws Exception {
+	public void setObservations(double[] var1, double[] var2, double[] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[][] var1, double[] var2, double[] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[] var1, double[][] var2, double[] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[] var1, double[] var2, double[][] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[] var1, double[][] var2, double[][] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[][] var1, double[] var2, double[][] cond) throws Exception {
+		startAddObservations();
+		addObservations(var1, var2, cond);
+		finaliseAddObservations();
+		addedMoreThanOneObservationSet = false;
+	}
+
+	@Override
+	public void setObservations(double[][] var1, double[][] var2, double[] cond) throws Exception {
 		startAddObservations();
 		addObservations(var1, var2, cond);
 		finaliseAddObservations();
@@ -319,7 +366,8 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 
 	/**
 	 * A non-overloaded method signature for setObservations with 1D arguments, as there have been
-	 *  some problems calling overloaded versions of setObservations from jpype. 
+	 *  some problems calling overloaded versions of setObservations from python jpype.
+	 *  Resolved if one follows the AutoAnalyser generated code, but left for back compatibility.
 	 * 
 	 * @param var1
 	 * @param var2
@@ -428,6 +476,7 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 		}
 		double[][] reshapedConditional = null;
 		if (dimensionsCond == 1) {
+			// This won't execute if dimensionsCond == 0
 			reshapedConditional = MatrixUtils.reshape(cond, cond.length, 1);
 		}
 		addObservations(MatrixUtils.reshape(var1, var1.length, 1),
@@ -436,6 +485,110 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
 
 	}
 	
+	@Override
+	public void addObservations(double[][] var1, double[] var2,
+			double[] cond) throws Exception {
+		if ((dimensionsVar2 != 1) ||
+				((dimensionsCond != 1) && (dimensionsCond != 0))) {
+			throw new Exception("The number of dimensions for variables var2 and cond (having been initialised to " +
+					dimensionsVar2 + " & " +
+					dimensionsCond + ") can only be 1 (or 0 for conditional) when " +
+					"the addObservations(double[][],double[],double[]) and " + 
+					"setObservations(double[][],double[],double[]) methods are called");
+		}
+		double[][] reshapedConditional = null;
+		if (dimensionsCond == 1) {
+			// This won't execute if dimensionsCond == 0
+			reshapedConditional = MatrixUtils.reshape(cond, cond.length, 1);
+		}
+		addObservations(var1,
+						MatrixUtils.reshape(var2, var2.length, 1),
+						reshapedConditional);
+	}
+
+	@Override
+	public void addObservations(double[] var1, double[][] var2,
+			double[] cond) throws Exception {
+		if ((dimensionsVar1 != 1) ||
+				((dimensionsCond != 1) && (dimensionsCond != 0))) {
+			throw new Exception("The number of dimensions for variables var1 and cond (having been initialised to " +
+					dimensionsVar1 + " & " +
+					dimensionsCond + ") can only be 1 (or 0 for conditional) when " +
+					"the addObservations(double[],double[][],double[]) and " + 
+					"setObservations(double[],double[][],double[]) methods are called");
+		}
+		double[][] reshapedConditional = null;
+		if (dimensionsCond == 1) {
+			// This won't execute if dimensionsCond == 0
+			reshapedConditional = MatrixUtils.reshape(cond, cond.length, 1);
+		}
+		addObservations(MatrixUtils.reshape(var1, var1.length, 1),
+						var2,
+						reshapedConditional);
+	}
+
+	@Override
+	public void addObservations(double[] var1, double[] var2,
+			double[][] cond) throws Exception {
+		if ((dimensionsVar1 != 1) || (dimensionsVar2 != 1)) {
+			throw new Exception("The number of dimensions for variables var1 and var2 (having been initialised to " +
+					dimensionsVar1 + " & " +
+					dimensionsVar2 + ") can only be 1 when " +
+					"the addObservations(double[],double[],double[][]) and " + 
+					"setObservations(double[],double[],double[][]) methods are called");
+		}
+		addObservations(MatrixUtils.reshape(var1, var1.length, 1),
+						MatrixUtils.reshape(var2, var2.length, 1),
+						cond);
+	}
+
+	@Override
+	public void addObservations(double[] var1, double[][] var2,
+			double[][] cond) throws Exception {
+		if (dimensionsVar1 != 1) {
+			throw new Exception("The number of dimensions for variable var1 (having been initialised to " +
+					dimensionsVar1 + ") can only be 1 when " +
+					"the addObservations(double[],double[][],double[][]) and " + 
+					"setObservations(double[],double[][],double[][]) methods are called");
+		}
+		addObservations(MatrixUtils.reshape(var1, var1.length, 1),
+						var2,
+						cond);
+	}
+
+	@Override
+	public void addObservations(double[][] var1, double[] var2,
+			double[][] cond) throws Exception {
+		if (dimensionsVar2 != 1) {
+			throw new Exception("The number of dimensions for variable var2 (having been initialised to " +
+					dimensionsVar2 + ") can only be 1 when " +
+					"the addObservations(double[][],double[],double[][]) and " + 
+					"setObservations(double[][],double[],double[][]) methods are called");
+		}
+		addObservations(var1,
+						MatrixUtils.reshape(var2, var2.length, 1),
+						cond);
+	}
+
+	@Override
+	public void addObservations(double[][] var1, double[][] var2,
+			double[] cond) throws Exception {
+		if ((dimensionsCond != 1) && (dimensionsCond != 0)) {
+			throw new Exception("The number of dimensions for variable cond (having been initialised to " +
+					dimensionsCond + ") can only be 1 or 0 when " +
+					"the addObservations(double[][],double[][],double[]) and " + 
+					"setObservations(double[][],double[][],double[]) methods are called");
+		}
+		double[][] reshapedConditional = null;
+		if (dimensionsCond == 1) {
+			// This won't execute if dimensionsCond == 0
+			reshapedConditional = MatrixUtils.reshape(cond, cond.length, 1);
+		}
+		addObservations(var1,
+						var2,
+						reshapedConditional);
+	}
+
 	/**
 	 * A non-overloaded method signature for addObservations with 1D arguments, as there have been
 	 *  some problems calling overloaded versions of setObservations from jpype. 

java/unittests/infodynamics/measures/continuous/gaussian/ConditionalMutualInfoMultiVariateTester.java

@@ -176,7 +176,7 @@ public class ConditionalMutualInfoMultiVariateTester extends
 		ConditionalMutualInfoCalculatorMultiVariateGaussian condMiCalc =
 				new ConditionalMutualInfoCalculatorMultiVariateGaussian();
 		condMiCalc.initialise(1, 1, 0);
-		condMiCalc.setObservations(source, dest, null);	
+		condMiCalc.setObservations(source, dest, (double[][]) null);	
 		double condMi = condMiCalc.computeAverageLocalOfObservations();
 		assertEquals(mi, condMi, 0.000001);
 

java/unittests/infodynamics/measures/continuous/kraskov/ConditionalMutualInfoMultiVariateTester.java

@@ -700,7 +700,7 @@ public class ConditionalMutualInfoMultiVariateTester
 			//		EuclideanUtils.NORM_MAX_NORM_STRING);
 			condMiCalc.setProperty(MutualInfoCalculatorMultiVariateKraskov.PROP_ADD_NOISE, "0"); // Need consistency for unit tests
 			condMiCalc.initialise(var1[0].length, var2[0].length, 0);
-			condMiCalc.setObservations(var1, var2, null);
+			condMiCalc.setObservations(var1, var2, (double[][]) null);
 			// condMiCalc.setDebug(true);
 			double mi = condMiCalc.computeAverageLocalOfObservations();
 			// condMiCalc.setDebug(false);