k of
@@ -100,13 +101,6 @@ public interface ActiveInfoStorageCalculator extends EmpiricalNullDistributionCo
*/
public static final String TAU_PROP_NAME = "TAU";
- /**
- * Initialise the calculator for (re-)use, with the existing (or default) values of parameters
- * Clears any PDFs of previously supplied observations.
- *
- */
- public void initialise() throws Exception;
-
/**
* Initialise the calculator for (re-)use, with some parameters
* supplied here, and existing (or default) values of other parameters
@@ -148,23 +142,9 @@ public interface ActiveInfoStorageCalculator extends EmpiricalNullDistributionCo
* @param propertyValue value of the property
* @throws Exception for invalid property values
*/
+ @Override
public void setProperty(String propertyName, String propertyValue) throws Exception;
- /**
- * Get current property values for the calculator.
- *
- * Valid property names, and what their - * values should represent, are the same as those for - * {@link #setProperty(String, String)}
- * - *Unknown property values are responded to with a null return value.
- * - * @param propertyName name of the property - * @return current value of the property - * @throws Exception for invalid property values - */ - public String getProperty(String propertyName) throws Exception; - /** * Sets a single time-series from which to compute the PDF for the AIS. * Cannot be called in conjunction with other methods for setting/adding @@ -247,13 +227,6 @@ public interface ActiveInfoStorageCalculator extends EmpiricalNullDistributionCo */ public void addObservations(double[] observations, boolean[] valid) throws Exception; - /** - * Compute the AIS from the previously-supplied samples. - * - * @return the AIS estimate - */ - public double computeAverageLocalOfObservations() throws Exception; - /** * Compute the local AIS values for each of the * previously-supplied samples. @@ -294,37 +267,4 @@ public interface ActiveInfoStorageCalculator extends EmpiricalNullDistributionCo */ public double[] computeLocalUsingPreviousObservations(double[] newObservations) throws Exception; - /** - * Set or clear debug mode for extra debug printing to stdout - * - * @param debug new setting for debug mode (on/off) - */ - public void setDebug(boolean debug); - - /** - * Return the AIS last calculated in a call to {@link #computeAverageLocalOfObservations()} - * or {@link #computeLocalOfPreviousObservations()} after the previous - * {@link #initialise()} call. - * - * @return the last computed AIS value - */ - public double getLastAverage(); - - /** - * Get the number of samples to be used for the PDFs here - * which have been supplied by calls to - * {@link #setObservations(double[])}, {@link #addObservations(double[])} - * etc. - * - *Note that the number of samples is not equal to the length of time-series
- * supplied (since we need to accumulate the first
- * (k-1)*tau + 1
- * values of each time-series before taking a sample for AIS).
- *
No general properties are defined at the interface level here, i.e. - * there are only properties defined by child interfaces and classes.
- * - * @param propertyName name of the property - * @param propertyValue value of the property - * @throws Exception for invalid property values - */ - public void setProperty(String propertyName, String propertyValue) throws Exception; - - /** - * Get current property values for the calculator. - * - *Valid property names, and what their - * values should represent, are the same as those for - * {@link #setProperty(String, String)}
- * - *Unknown property values are responded to with a null return value.
- * - * @param propertyName name of the property - * @return current value of the property - * @throws Exception for invalid property values - */ - public String getProperty(String propertyName) throws Exception; - /** * Signal that we will add in the samples for computing the PDF * from several disjoint time-series or trials via calls to @@ -140,13 +104,6 @@ public abstract interface ChannelCalculatorCommon extends EmpiricalNullDistribut */ public boolean getAddedMoreThanOneObservationSet(); - /** - * Compute the channel measure from the previously-supplied samples. - * - * @return the estimate of the channel measure - */ - public double computeAverageLocalOfObservations() throws Exception; - /** *Computes the local values of the implemented channel measure, * for each valid observation in the previously supplied observations @@ -166,34 +123,4 @@ public abstract interface ChannelCalculatorCommon extends EmpiricalNullDistribut */ public double[] computeLocalOfPreviousObservations() throws Exception; - /** - * Set or clear debug mode for extra debug printing to stdout - * - * @param debug new setting for debug mode (on/off) - */ - public void setDebug(boolean debug); - - /** - * Return the channel measure last calculated in a call to {@link #computeAverageLocalOfObservations()} - * or {@link #computeLocalOfPreviousObservations()} after the previous - * {@link #initialise()} call. - * - * @return the last computed channel measure value - */ - public double getLastAverage(); - - /** - * Get the number of samples to be used for the PDFs here - * which have been supplied by calls to - * {@link #setObservations(double[])}, {@link #addObservations(double[])} - * etc. - * - *
Note that the number of samples may not be equal to the length of time-series - * supplied (e.g. for transfer entropy, where we need to accumulate - * a number of samples for the past history of the destination). - *
- * - * @return the number of samples to be used for the PDFs - */ - public int getNumObservations() throws Exception; } diff --git a/java/source/infodynamics/measures/continuous/ConditionalMutualInfoCalculatorMultiVariate.java b/java/source/infodynamics/measures/continuous/ConditionalMutualInfoCalculatorMultiVariate.java index f66da14..a86ce64 100755 --- a/java/source/infodynamics/measures/continuous/ConditionalMutualInfoCalculatorMultiVariate.java +++ b/java/source/infodynamics/measures/continuous/ConditionalMutualInfoCalculatorMultiVariate.java @@ -77,7 +77,7 @@ import infodynamics.utils.EmpiricalNullDistributionComputer; Theory' (John Wiley & Sons, New York, 1991)." */ public interface ConditionalMutualInfoCalculatorMultiVariate - extends EmpiricalNullDistributionComputer { + extends InfoMeasureCalculatorContinuous, EmpiricalNullDistributionComputer { /** * Initialise the calculator for (re-)use, clearing PDFs, @@ -91,35 +91,6 @@ public interface ConditionalMutualInfoCalculatorMultiVariate */ public void initialise(int var1Dimensions, int var2Dimensions, int condDimentions) throws Exception; - /** - * Set properties for the calculator. - * New property values are not guaranteed to take effect until the next call - * to an initialise method. - * - *No general properties are defined at the interface level here, i.e. - * there are only properties defined by child interfaces and classes.
- * - * @param propertyName name of the property - * @param propertyValue value of the property - * @throws Exception for invalid property values - */ - public void setProperty(String propertyName, String propertyValue) throws Exception; - - /** - * Get current property values for the calculator. - * - *Valid property names, and what their - * values should represent, are the same as those for - * {@link #setProperty(String, String)}
- * - *Unknown property values are responded to with a null return value.
- * - * @param propertyName name of the property - * @return current value of the property - * @throws Exception for invalid property values - */ - public String getProperty(String propertyName) throws Exception; - /** * Sets a single series from which to compute the PDF. * Cannot be called in conjunction with @@ -274,15 +245,6 @@ public interface ConditionalMutualInfoCalculatorMultiVariate */ public void finaliseAddObservations() throws Exception; - /** - * Compute the average conditional MI from the previously-supplied samples. - * - * @return the estimate of the conditional MI in either bits or nats - * depending on the estimator - * @throws Exception - */ - public double computeAverageLocalOfObservations() throws Exception; - /** *Computes the local values of the conditional mutual information,
* for each valid observation in the previously supplied observations
@@ -413,32 +375,11 @@ public interface ConditionalMutualInfoCalculatorMultiVariate
throws Exception;
/**
- * Set or clear debug mode for extra debug printing to stdout
- *
- * @param debug new setting for debug mode (on/off)
- */
- public void setDebug(boolean debug);
-
- /**
- * Return the conditional MI last calculated in a call to {@link #computeAverageLocalOfObservations()}
- * or {@link #computeLocalOfPreviousObservations()} after the previous
- * {@link #initialise(int, int, int)} call.
- *
- * @return the last computed conditional MI value
- */
- public double getLastAverage();
-
- /**
- * Get the number of samples to be used for the PDFs here
- * which have been supplied by calls to
- * {@link #setObservations(double[][], double[][], double[][])}, {@link #addObservations(double[][], double[][], double[][])}
- * etc.
- *
- * @return the number of samples to be used for the PDFs
* @throws Exception if the implementing class computes MI without
* explicit observations (e.g. see
* {@link infodynamics.measures.continuous.gaussian.ConditionalMutualInfoCalculatorMultiVariateGaussian})
*/
+ @Override
public int getNumObservations() throws Exception;
/**
diff --git a/java/source/infodynamics/measures/continuous/ConditionalMutualInfoMultiVariateCommon.java b/java/source/infodynamics/measures/continuous/ConditionalMutualInfoMultiVariateCommon.java
index bbb0e46..dd5460e 100755
--- a/java/source/infodynamics/measures/continuous/ConditionalMutualInfoMultiVariateCommon.java
+++ b/java/source/infodynamics/measures/continuous/ConditionalMutualInfoMultiVariateCommon.java
@@ -165,7 +165,10 @@ public abstract class ConditionalMutualInfoMultiVariateCommon implements
*/
protected double[] condStds = null;
-
+ @Override
+ public void initialise() {
+ initialise(dimensionsVar1, dimensionsVar2, dimensionsCond);
+ }
@Override
public void initialise(int var1Dimensions, int var2Dimensions, int condDimensions) {
diff --git a/java/source/infodynamics/measures/continuous/InfoMeasureCalculatorContinuous.java b/java/source/infodynamics/measures/continuous/InfoMeasureCalculatorContinuous.java
new file mode 100644
index 0000000..e2734a1
--- /dev/null
+++ b/java/source/infodynamics/measures/continuous/InfoMeasureCalculatorContinuous.java
@@ -0,0 +1,128 @@
+/*
+ * Java Information Dynamics Toolkit (JIDT)
+ * Copyright (C) 2017, Joseph T. Lizier, Ipek Oezdemir and Pedro Mediano
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see
Base interface for our information-theoretic calculators + * on continuous (double[]) data, + * providing common functionality + * for user-level measure classes.
+ * + *+ * Usage of the child classes implementing this interface is intended to follow this paradigm: + *
+ *Property names are defined by the implementing class + * (generally in their documentation). + * Unknown property values are ignored.
+ * + * @param propertyName name of the property + * @param propertyValue value of the property + * @throws Exception for invalid property values + */ + public void setProperty(String propertyName, String propertyValue) throws Exception; + + /** + * Get current property values for the calculator. + * + *Valid property names, and what their + * values should represent, are the same as those for + * {@link #setProperty(String, String)}
+ * + *Unknown property values are responded to with a null return value.
+ * + * @param propertyName name of the property + * @return current value of the property + * @throws Exception for invalid property values + */ + public String getProperty(String propertyName) throws Exception; + + /** + * Get the number of samples to be used for the PDFs here + * which have been supplied by calls to + * "setObservations", "addObservations" etc. + * + *Note that the number of samples may not be equal to the length of time-series + * supplied (e.g. for transfer entropy, where we need to accumulate + * a number of samples for the past history of the destination). + *
+ * + * @return the number of samples to be used for the PDFs + */ + public int getNumObservations() throws Exception; + + /** + * Compute the average value of the measure + * from the previously-supplied samples. + * + * @return the estimate of the measure + */ + public abstract double computeAverageLocalOfObservations() throws Exception; + + /** + * Return the measure last calculated in a call to + * {@link #computeAverageLocalOfObservations()} + * or related methods after the previous + * {@link #initialise()} call. + * + * @return the last computed measure value + */ + public double getLastAverage(); + + /** + * Set or clear debug mode for extra debug printing to stdout + * + * @param debug new setting for debug mode (on/off) + */ + public void setDebug(boolean debug); +}