edu.stanford.math.plex4.autogen.homology

Class IntPersistentHomology<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.IntSparseFormalSum<U>>

edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm<U>

edu.stanford.math.plex4.autogen.homology.IntPersistentHomology<U>

Direct Known Subclasses:

IntAbsoluteHomology, IntRelativeHomology

public abstract class IntPersistentHomology<U>
extends IntPersistenceAlgorithm<U>

This class defines the functionality for a persistence algorithm with underlying field type being int 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.

int 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.IntPersistenceAlgorithm

basisComparator, chainModule, field, filteredComparator, maxDimension, minDimension

Constructor Summary

Constructors

Constructor and Description
IntPersistentHomology(edu.stanford.math.primitivelib.autogen.algebraic.IntAbstractField 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.IntSparseFormalSum<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.IntSparseFormalSum<U>>	getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>> RV_pair, AbstractFilteredStream<U> stream)
protected AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<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.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<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.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>> RV_pair, AbstractFilteredStream<U> stream, boolean absolute)

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

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

IntPersistentHomology

public IntPersistentHomology(edu.stanford.math.primitivelib.autogen.algebraic.IntAbstractField 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 int

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.IntSparseFormalSum<U>> computeAnnotatedIntervalsImpl(AbstractFilteredStream<U> stream)

Description copied from class: IntPersistenceAlgorithm

This function provides the implementation of computeAnnotatedIntervals.

Specified by:

computeAnnotatedIntervalsImpl in class IntPersistenceAlgorithm<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: IntPersistenceAlgorithm

This function provides the implementation of computeIntervals.

Specified by:

computeIntervalsImpl in class IntPersistenceAlgorithm<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.IntSparseFormalSum<U>> getAnnotatedIntervals(edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<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.IntSparseFormalSum<U>>,gnu.trove.THashMap<U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>> RV_pair,
                                                AbstractFilteredStream<U> stream)

getAnnotatedIntervals

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