CohomologyPersistence class

The Python cohomology computation illustrates the use of CohomologyPersistence.

class CohomologyPersistence
__init__(prime = 11)

Initializes CohomologyPersistence with the given prime; from this point on all the computation will be performed with coefficients in \mathbb{Z}/prime \mathbb{Z}.

add(boundary, birth[, store = True][, image = True][, coefficients =[]])

Adds a simplex with the given boundary to the complex, i.e. K_{i+1} = K_i \cup \sigma and boundary = \partial \sigma. If a new class is born as a result of the addition, birth is stored with it for future reference.

If store is False and a class is born, it will not be stored in CohomologyPersistence. This avoids wasting space on the classes of the dimension equal to the maximum-dimensional simplices of the complex since such classes will never die.

The image parameter allows one to work with a case of a space L \subseteq K where the filtration of K induces a filtration of L. In this case, one may want to compute image persistence (i.e. the persistence of the sequences of the images given by the inclusion of L in K). image indicates whether the simplex added belongs to L or not.

If given, coefficients is a list parallel to boundary that provides coefficients for the corresponding boundary elements. If empty, it is assumed to be (-1)^i.

Returns:a triple (i, d, ccl). The first element is the index i. It is the internal representation of the newly added simplex, and should be used later when constructing the boundaries of its cofaces. In other words, boundary must consist of these indices. The second element d is the death element. It is None if a birth occurred, otherwise it contains the value passed as birth to add() when the class that just died was born. The third element ccl returns the dying cocycle (iterable over instances of CHSNode), in case of a death. It’s empty if a birth occurs.
__iter__()

Iterator over the live cocycles stored in CohomologyPersistence. The returned elements are of the type Cocycle below.

class Cocycle
birth

The birth value associated with the cocycle. It is passed to CohomologyPersistence in method add().

__iter__()

Iterator over the individual nodes (simplices) of the cocycle, each of type CHSNode.

class CHSNode
si

The index of the simplex, of type CHSimplexIndex.

coefficient

Coefficient in \mathbb{Z}/prime \mathbb{Z} associated with the simplex.

class CHSimplexIndex
order

The count associated with the simplex when it is inserted into CohomologyPersistence.

Adaptor

StaticCohomologyPersistence provides a wrapper around class CohomologyPersistence that’s compatible with StaticPersistence. See the documentation of the latter class for details.

class StaticCohomologyPersistence
__init__(filtration, prime = 2)

Initializes StaticCohomologyPersistence with the given Filtration. prime is passed straight to the wrapped CohomologyPersistence class.

pair_simplices()

Pairs simplices using CohomologyPersistence class.

__call__(i)

Given a node in the internal representation, the method returns its integer offset from the beginning of the filtration.

make_simplex_map(filtration)

Creates an auxilliary map from the nodes to the simplices:

smap = persistence.make_simplex_map(filtration)
for i in persistence:
    if i.unpaired(): print smap[i]
__iter__()

Iterator over the nodes (representing individual simplices). See APNode.

__len__()

Returns the number of nodes (i.e. the number of simplices).

class APNode

The following methods behave the same way as they do in SPNode.

sign()
pair()
unpaired()

The only crucial distinction in the behavior comes with the attribute cocycle.

cocycle

If the simplex is positive, this attribute stores a cocycle it created (recorded at the time of its death). The 1-dimensional cocycles can be used with the circular.smooth() function to turn them into circle-valued maps.

for i in persistence:
    if i.sign(): print i.cocycle
class ImagePersistence

This class is another wrapper around CohomologyPersistence that can compute image persistence induced by inclusion of a subcomplex. Its interface is the same as StaticCohomologyPersistence above, except for the constructor:

__init__(filtration, subcomplex)

subcomplex is a function called with every simplex. It should return True if the simplex belong to the subcomplex; False otherwise.

Circular coordinates

circular.smooth(filtration, cocycle)

Returns a map from the vertices of the simplicial complex filtration to a circle [-.5, .5], where the opposite ends of the interval are identified.