Catching OutOfMemoryError in Discrete calculator creation for all other discrete calculators (only MI was done in the previous commit). Also simplified constructor calls (with code re-use) for conditional TE.

java/source/infodynamics/measures/discrete/BlockEntropyCalculatorDiscrete.java

@@ -106,7 +106,14 @@ public class BlockEntropyCalculatorDiscrete extends EntropyCalculatorDiscrete {
 		// Create storage for counts of observations.
 		// We're recreating stateCount, which was created in super()
 		//  however the super() didn't create it for blocksize > 1
-		stateCount = new int[MathsUtils.power(base, blocksize)];
+		try {
+			stateCount = new int[MathsUtils.power(base, blocksize)];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a Runtimexception
+			throw new RuntimeException("Requested memory for the base " +
+					base + " and k=" + blocksize+ " is too large for the JVM at this time", e);
+		}
 
 		// Create constants for tracking stateValues
 		maxShiftedValue = new int[base];

java/source/infodynamics/measures/discrete/CombinedActiveEntRateCalculatorDiscrete.java

@@ -100,9 +100,16 @@ public class CombinedActiveEntRateCalculatorDiscrete {
 		
 		if (changedSizes) {
 			// Create storage for counts of observations
-			jointCount = new int[base][MathsUtils.power(base, history)];
-			prevCount = new int[MathsUtils.power(base, history)];
-			nextCount = new int[base];
+			try {
+				jointCount = new int[base][MathsUtils.power(base, history)];
+				prevCount = new int[MathsUtils.power(base, history)];
+				nextCount = new int[base];
+			} catch (OutOfMemoryError e) {
+				// Allow any Exceptions to be thrown, but catch and wrap
+				//  Error as a Runtimexception
+				throw new RuntimeException("Requested memory for the base " +
+						base + " and k=" + history + " is too large for the JVM at this time", e);
+			}
 		} else {
 			// Just set counts to zeros without recreating the space
 			MatrixUtils.fill(jointCount, 0);

java/source/infodynamics/measures/discrete/ConditionalMutualInformationCalculatorDiscrete.java

@@ -117,10 +117,18 @@ public class ConditionalMutualInformationCalculatorDiscrete
 		this.condBase = condBase;
 		
 		// Create storage for extra counts of observations
-		firstSecondCondCount = new int[base1][base2][condBase];
-		firstCondCount = new int[base1][condBase];		
-		secondCondCount = new int[base2][condBase];
-		condCount = new int[condBase];
+		try {
+			firstSecondCondCount = new int[base1][base2][condBase];
+			firstCondCount = new int[base1][condBase];
+			secondCondCount = new int[base2][condBase];
+			condCount = new int[condBase];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as an Exception
+			throw new RuntimeException("Requested memory for the MI bases (" +
+					base1 + ", " + base2 + ", " + condBase +
+					") is too large for the JVM at this time", e);
+		}
 	}
 
 	@Override

java/source/infodynamics/measures/discrete/ConditionalTransferEntropyCalculatorDiscrete.java

@@ -185,6 +185,15 @@ public class ConditionalTransferEntropyCalculatorDiscrete
 		base_power_k = MathsUtils.power(base, k);
 		base_power_num_others = MathsUtils.power(base_others, numOtherInfoContributors);
 
+		// Relaxing this assumption so we can use this calculation as
+		//  a time-lagged conditional MI at will:
+		//if (k < 1) {
+		//	throw new RuntimeException("History k " + history + " is not >= 1 a ContextOfPastMeasureCalculator");
+		//}
+
+		// Which time step do we start taking observations from?
+		// Normally this is k (to allow k previous time steps)
+		//  but if k==0 (becoming a lagged MI), it's 1.
 		startObservationTime = Math.max(k, 1);
 
 		// check that we can convert the base tuple into an integer ok
@@ -196,10 +205,18 @@ public class ConditionalTransferEntropyCalculatorDiscrete
 		}
 
 		// Create storage for counts of observations
-		sourceDestPastOthersCount = new int[base][base][base_power_k][base_power_num_others];
-		sourcePastOthersCount = new int[base][base_power_k][base_power_num_others];
-		destPastOthersCount = new int [base][base_power_k][base_power_num_others];
-		pastOthersCount = new int[base_power_k][base_power_num_others];
+		try {
+			sourceDestPastOthersCount = new int[base][base][base_power_k][base_power_num_others];
+			sourcePastOthersCount = new int[base][base_power_k][base_power_num_others];
+			destPastOthersCount = new int [base][base_power_k][base_power_num_others];
+			pastOthersCount = new int[base_power_k][base_power_num_others];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the base " +
+					base + ", k=" + k + " num of others " + numOtherInfoContributors +
+					" with base " + base_others + ") is too large for the JVM at this time", e);
+		}
 		
 		// Create constants for tracking prevValues
 		maxShiftedValue = new int[base];
@@ -223,44 +240,7 @@ public class ConditionalTransferEntropyCalculatorDiscrete
 	public ConditionalTransferEntropyCalculatorDiscrete
 		(int base, int history, int numOtherInfoContributors) {
 
-		super(base);
-		
-		k = history;
-		base_others = base; // If unspecified, the base of the conditional variables is the same as src and tgt
-		this.numOtherInfoContributors = numOtherInfoContributors;
-		base_power_k = MathsUtils.power(base, k);
-		base_power_num_others = MathsUtils.power(base, numOtherInfoContributors);
-		
-		// Relaxing this assumption so we can use this calculation as
-		//  a time-lagged conditional MI at will:
-		//if (k < 1) {
-		//	throw new RuntimeException("History k " + history + " is not >= 1 a ContextOfPastMeasureCalculator");
-		//}
-		
-		// Which time step do we start taking observations from?
-		// Normally this is k (to allow k previous time steps)
-		//  but if k==0 (becoming a lagged MI), it's 1.
-		startObservationTime = Math.max(k, 1);
-
-		// check that we can convert the base tuple into an integer ok
-		if (k > Math.log(Integer.MAX_VALUE) / log_base) {
-			throw new RuntimeException("Base and history combination too large");
-		}
-		if (numOtherInfoContributors < 1) {
-			throw new RuntimeException("Number of other info contributors < 1 for CompleteTECalculator");
-		}
-		
-		// Create storage for counts of observations
-		sourceDestPastOthersCount = new int[base][base][base_power_k][base_power_num_others];
-		sourcePastOthersCount = new int[base][base_power_k][base_power_num_others];
-		destPastOthersCount = new int [base][base_power_k][base_power_num_others];
-		pastOthersCount = new int[base_power_k][base_power_num_others];
-		
-		// Create constants for tracking prevValues
-		maxShiftedValue = new int[base];
-		for (int v = 0; v < base; v++) {
-			maxShiftedValue[v] = v * MathsUtils.power(base, k-1);
-		}
+		this(base, history, numOtherInfoContributors, base);
 	}
 
 	@Override

java/source/infodynamics/measures/discrete/ContextOfPastMeasureCalculatorDiscrete.java

@@ -114,9 +114,16 @@ public abstract class ContextOfPastMeasureCalculatorDiscrete extends
 		noObservationStorage = dontCreateObsStorage;
 		if (!dontCreateObsStorage) {
 			// Create storage for counts of observations
-			nextPastCount = new int[base][base_power_k];
-			pastCount = new int[base_power_k];
-			nextCount = new int[base];
+			try {
+				nextPastCount = new int[base][base_power_k];
+				pastCount = new int[base_power_k];
+				nextCount = new int[base];
+			} catch (OutOfMemoryError e) {
+				// Allow any Exceptions to be thrown, but catch and wrap
+				//  Error as a RuntimeException
+				throw new RuntimeException("Requested memory for the base " +
+						base + " and k=" + k + " is too large for the JVM at this time", e);
+			}
 		}
 	}
 	

java/source/infodynamics/measures/discrete/EntropyCalculatorDiscrete.java

@@ -94,7 +94,15 @@ public class EntropyCalculatorDiscrete extends InfoMeasureCalculatorDiscrete
 		super(base);
 		
 		// Create storage for counts of observations
-		stateCount = new int[base];
+		try {
+			stateCount = new int[base];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the base (" +
+					base + ") is too large for the JVM at this time", e);
+		}
+
 	}
 	
 	@Override

java/source/infodynamics/measures/discrete/MultiInformationCalculatorDiscrete.java

@@ -80,8 +80,16 @@ public class MultiInformationCalculatorDiscrete extends InfoMeasureCalculatorDis
 		super(base);
 		this.numVars = numVars;
 		jointStates = MathsUtils.power(base, numVars);
-		jointCount = new int[jointStates];
-		marginalCounts = new int[numVars][base];
+		try {
+			jointCount = new int[jointStates];
+			marginalCounts = new int[numVars][base];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the base " +
+					base + " with " + numVars +
+					" variables is too large for the JVM at this time", e);
+		}
 	}
 
 	@Override

java/source/infodynamics/measures/discrete/MutualInformationCalculatorDiscrete.java

@@ -123,8 +123,8 @@ public class MutualInformationCalculatorDiscrete extends InfoMeasureCalculatorDi
 			jCount = new int[base2];
 		} catch (OutOfMemoryError e) {
 			// Allow any Exceptions to be thrown, but catch and wrap
-			//  Error as an Exception
-			throw new Exception("Requested memory for the MI bases (" +
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the MI bases (" +
 					base1 + ", " + base2 + ") is too large for the JVM at this time", e);
 		}
 	}

java/source/infodynamics/measures/discrete/PredictiveInformationCalculatorDiscrete.java

@@ -135,9 +135,17 @@ public class PredictiveInformationCalculatorDiscrete {
 		}
 
 		// Create storage for counts of observations
-		jointCount = new int[base_power_k][base_power_k];
-		prevCount = new int[base_power_k];
-		nextCount = new int[base_power_k];
+		try {
+			jointCount = new int[base_power_k][base_power_k];
+			prevCount = new int[base_power_k];
+			nextCount = new int[base_power_k];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the base " +
+					numDiscreteValues + " with k=" + blockLength +
+					") is too large for the JVM at this time", e);
+		}
 
 		// Create constants for tracking prevValues and nextValues
 		maxShiftedValue = new int[numDiscreteValues];

java/source/infodynamics/measures/discrete/SeparableInfoCalculatorDiscrete.java

@@ -179,9 +179,17 @@ public class SeparableInfoCalculatorDiscrete extends ContextOfPastMeasureCalcula
 		}
 		if (!dontCreateObsStorage) {
 			// Create storage for extra counts of observations
-			sourceNumValueNextPastCount = new int[numInfoContributors][base][base][base_power_k];
-			sourcesNextPastCount = new int[base_power_sources][base][base_power_k];
-			sourceNumValuePastCount = new int[numInfoContributors][base][base_power_k];
+			try {
+				sourceNumValueNextPastCount = new int[numInfoContributors][base][base][base_power_k];
+				sourcesNextPastCount = new int[base_power_sources][base][base_power_k];
+				sourceNumValuePastCount = new int[numInfoContributors][base][base_power_k];
+			} catch (OutOfMemoryError e) {
+				// Allow any Exceptions to be thrown, but catch and wrap
+				//  Error as a RuntimeException
+				throw new RuntimeException("Requested memory for the base " +
+						base + " with k=" + k + " and " + numInfoContributors +
+						" sources is too large for the JVM at this time", e);
+			}
 		}
 	}
 

java/source/infodynamics/measures/discrete/TransferEntropyCalculatorDiscrete.java

@@ -244,8 +244,16 @@ public class TransferEntropyCalculatorDiscrete extends ContextOfPastMeasureCalcu
 		}
 
 		// Create storage for extra counts of observations
-		sourceNextPastCount = new int[base_power_l][base][base_power_k];
-		sourcePastCount = new int[base_power_l][base_power_k];
+		try {
+			sourceNextPastCount = new int[base_power_l][base][base_power_k];
+			sourcePastCount = new int[base_power_l][base_power_k];
+		} catch (OutOfMemoryError e) {
+			// Allow any Exceptions to be thrown, but catch and wrap
+			//  Error as a RuntimeException
+			throw new RuntimeException("Requested memory for the base " +
+					base + ", k=" + k + ", l=" + sourceHistoryEmbedLength +
+					" is too large for the JVM at this time", e);
+		}
 		
 		// Which time step do we start taking observations from?
 		// These two integers represent the earliest next time step, in the cases where the destination