edu.stanford.math.plex4.homology.zigzag

Class HomologyBasisTracker<U extends PrimitiveBasisElement>

java.lang.Object

edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker<U>

Type Parameters:

U -

All Implemented Interfaces:

AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>

public class HomologyBasisTracker<U extends PrimitiveBasisElement>
extends java.lang.Object
implements AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>

This class maintains the right-filtration for performing zig-zag homology. It implements the algorithm described in the paper "Zigzag Persistent Homology and Real-valued Functions" by Gunnar Carlsson, Vin de Silva, and Dmitriy Morozov. TODO List: - cache low values for the columns to prevent re-computing

Author:

Andrew Tausz

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<java.lang.Integer>>	B
protected java.util.Comparator<U>	basisComparator
protected java.util.Set<U>	basisElements
protected java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	C
protected edu.stanford.math.primitivelib.autogen.formal_sum.IntAlgebraicFreeModule<U>	chainModule These objects performs the chain computations.
static boolean	checkConsistency
protected edu.stanford.math.primitivelib.autogen.algebraic.IntAbstractField	field This is the field over which we perform the arithmetic computations.
protected java.util.Comparator<U>	indexedComparator
protected edu.stanford.math.primitivelib.autogen.formal_sum.IntAlgebraicFreeModule<java.lang.Integer>	integerChainModule
protected java.util.Comparator<java.lang.Integer>	integerComparator
protected gnu.trove.TIntIntHashMap	internalExternalIndexMap
protected int	internalIndex
protected IntervalTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	intervalTracker
protected gnu.trove.TObjectIntHashMap<U>	objectIndexMap
protected java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	Z

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	add(U sigma)
void	add(U sigma, int externalIndex)
void	add(U sigma, java.lang.Integer index)
void	checkInvariant()
protected <X,Y> void	checkReduced(java.util.Map<X,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<Y>> map, java.util.Comparator<Y> comparator)
AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getAnnotatedBarcodes()
BarcodeCollection<java.lang.Integer>	getBarcodes()
AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getFiniteAnnotatedBarcodes()
BarcodeCollection<java.lang.Integer>	getFiniteBarcodes()
AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getInfiniteAnnotatedBarcodes()
BarcodeCollection<java.lang.Integer>	getInfiniteBarcodes()
IntervalTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getIntervalTracker()
AbstractPersistenceTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getState()
AbstractPersistenceTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>>	getStateWithoutFiniteBarcodes()
boolean	isBoundary(edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U> cycle)
protected boolean	isCycle(edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U> chain)
static void	log(java.lang.String... args)
void	remove(U sigma)
void	remove(U sigma, int externalIndex)
void	remove(U sigma, java.lang.Integer index)

Methods inherited from class java.lang.Object

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

Field Detail

field

protected final edu.stanford.math.primitivelib.autogen.algebraic.IntAbstractField field

This is the field over which we perform the arithmetic computations.

chainModule

protected final edu.stanford.math.primitivelib.autogen.formal_sum.IntAlgebraicFreeModule<U extends PrimitiveBasisElement> chainModule

These objects performs the chain computations.

integerChainModule

protected final edu.stanford.math.primitivelib.autogen.formal_sum.IntAlgebraicFreeModule<java.lang.Integer> integerChainModule

basisComparator

protected final java.util.Comparator<U extends PrimitiveBasisElement> basisComparator

integerComparator

protected final java.util.Comparator<java.lang.Integer> integerComparator

indexedComparator

protected final java.util.Comparator<U extends PrimitiveBasisElement> indexedComparator

Z

protected final java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>> Z

B

protected final java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<java.lang.Integer>> B

C

protected final java.util.Map<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>> C

internalExternalIndexMap

protected final gnu.trove.TIntIntHashMap internalExternalIndexMap

objectIndexMap

protected final gnu.trove.TObjectIntHashMap<U extends PrimitiveBasisElement> objectIndexMap

basisElements

protected final java.util.Set<U extends PrimitiveBasisElement> basisElements

internalIndex

protected int internalIndex

intervalTracker

protected final IntervalTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>> intervalTracker

checkConsistency

public static boolean checkConsistency

Constructor Detail

HomologyBasisTracker

public HomologyBasisTracker(edu.stanford.math.primitivelib.autogen.algebraic.IntAbstractField field,
                    java.util.Comparator<U> basisComparator)

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

Method Detail

log

public static void log(java.lang.String... args)

getIntervalTracker

public IntervalTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getIntervalTracker()

getFiniteAnnotatedBarcodes

public AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getFiniteAnnotatedBarcodes()

getInfiniteAnnotatedBarcodes

public AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getInfiniteAnnotatedBarcodes()

getAnnotatedBarcodes

public AnnotatedBarcodeCollection<java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getAnnotatedBarcodes()

getFiniteBarcodes

public BarcodeCollection<java.lang.Integer> getFiniteBarcodes()

getInfiniteBarcodes

public BarcodeCollection<java.lang.Integer> getInfiniteBarcodes()

getBarcodes

public BarcodeCollection<java.lang.Integer> getBarcodes()

add

public void add(U sigma)

add

public void add(U sigma,
       int externalIndex)

remove

public void remove(U sigma)

remove

public void remove(U sigma,
          int externalIndex)

checkInvariant

public void checkInvariant()

checkReduced

protected <X,Y> void checkReduced(java.util.Map<X,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<Y>> map,
                      java.util.Comparator<Y> comparator)

isCycle

protected boolean isCycle(edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U> chain)

isBoundary

public boolean isBoundary(edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U> cycle)

Specified by:

isBoundary in interface AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U extends PrimitiveBasisElement,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>>

add

public void add(U sigma,
       java.lang.Integer index)

Specified by:

add in interface AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U extends PrimitiveBasisElement,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>>

getStateWithoutFiniteBarcodes

public AbstractPersistenceTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getStateWithoutFiniteBarcodes()

getState

public AbstractPersistenceTracker<java.lang.Integer,java.lang.Integer,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U>> getState()

Specified by:

getState in interface AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U extends PrimitiveBasisElement,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>>

remove

public void remove(U sigma,
          java.lang.Integer index)

Specified by:

remove in interface AbstractHomologyTracker<java.lang.Integer,java.lang.Integer,U extends PrimitiveBasisElement,edu.stanford.math.primitivelib.autogen.formal_sum.IntSparseFormalSum<U extends PrimitiveBasisElement>>