edu.stanford.math.plex4.autogen.homology

Class ObjectPersistentHomology<F,U>

java.lang.Object

edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceAlgorithm<T>

edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceBasisAlgorithm<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>

edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm<F,U>

edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology<F,U>

Direct Known Subclasses:

ObjectAbsoluteHomology, ObjectRelativeHomology

public abstract class ObjectPersistentHomology<F,U>
extends ObjectPersistenceAlgorithm<F,U>

This class defines the functionality for a persistence algorithm with underlying field type being F and underlying basis element type being U. It acts as an intermediate layer between the interface AbstractPersistenceBasisAlgorithm and the actual implementations of the persistent homology/cohomology algorithms.

F the underlying type of the coefficient field

U the underlying basis type

Author:

autogen

Field Summary

Fields inherited from class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm

basisComparator, chainModule, field, filteredComparator, maxDimension, minDimension

Constructor Summary

Constructors

Constructor and Description
ObjectPersistentHomology(edu.stanford.math.primitivelib.autogen.algebraic.ObjectAbstractField<F> field, java.util.Comparator<U> basisComparator, int minDimension, int maxDimension) This constructor initializes the object with a field and a comparator on the basis type.

Method Summary

Methods

Modifier and Type	Method and Description
protected AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>	computeAnnotatedIntervalsImpl(AbstractFilteredStream<U> stream) This function provides the implementation of computeAnnotatedIntervals.
protected BarcodeCollection<java.lang.Integer>	computeIntervalsImpl(AbstractFilteredStream<U> stream) This function provides the implementation of computeIntervals.
protected abstract AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>	getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair, AbstractFilteredStream<U> stream)
protected AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>	getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair, AbstractFilteredStream<U> stream, boolean absolute)
protected abstract BarcodeCollection<java.lang.Integer>	getIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair, AbstractFilteredStream<U> stream)
protected BarcodeCollection<java.lang.Integer>	getIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair, AbstractFilteredStream<U> stream, boolean absolute)

Methods inherited from class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm

computeAnnotatedIndexIntervals, computeIndexIntervals, getChainModule, getField, initializeFilteredComparator, low

Methods inherited from class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceBasisAlgorithm

computeAnnotatedIntervals

Methods inherited from class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceAlgorithm

computeIntervals

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ObjectPersistentHomology

public ObjectPersistentHomology(edu.stanford.math.primitivelib.autogen.algebraic.ObjectAbstractField<F> field,
                        java.util.Comparator<U> basisComparator,
                        int minDimension,
                        int maxDimension)

This constructor initializes the object with a field and a comparator on the basis type.

Parameters:

field - a field structure on the type F

basisComparator - a comparator on the basis type U

minDimension - the minimum dimension to compute

maxDimension - the maximum dimension to compute

Method Detail

computeAnnotatedIntervalsImpl

protected AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>> computeAnnotatedIntervalsImpl(AbstractFilteredStream<U> stream)

Description copied from class: ObjectPersistenceAlgorithm

This function provides the implementation of computeAnnotatedIntervals.

Specified by:

computeAnnotatedIntervalsImpl in class ObjectPersistenceAlgorithm<F,U>

Parameters:

stream - the filtered chain complex

Returns:

the augmented persistence intervals

computeIntervalsImpl

protected BarcodeCollection<java.lang.Integer> computeIntervalsImpl(AbstractFilteredStream<U> stream)

Description copied from class: ObjectPersistenceAlgorithm

This function provides the implementation of computeIntervals.

Specified by:

computeIntervalsImpl in class ObjectPersistenceAlgorithm<F,U>

Parameters:

stream - the filtered chain complex

Returns:

the persistence intervals of the given complex

getAnnotatedIntervals

protected abstract AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>> getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair,
                                                                                                                                               AbstractFilteredStream<U> stream)

getIntervals

protected abstract BarcodeCollection<java.lang.Integer> getIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair,
                                                AbstractFilteredStream<U> stream)

getAnnotatedIntervals

protected AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>> getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair,
                                                                                                                                               AbstractFilteredStream<U> stream,
                                                                                                                                               boolean absolute)

getIntervals

protected BarcodeCollection<java.lang.Integer> getIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.ObjectSparseFormalSum<F,U>>> RV_pair,
                                                AbstractFilteredStream<U> stream,
                                                boolean absolute)