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-rw-r--r--src/python/gudhi/simplex_tree.pyx78
1 files changed, 58 insertions, 20 deletions
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index dfb1d985..d7991417 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -285,6 +285,22 @@ cdef class SimplexTree:
ct.append((v, filtered_simplex.second))
return ct
+ def get_boundaries(self, simplex):
+ """This function returns a generator with the boundaries of a given N-simplex.
+ If you do not need the filtration values, the boundary can also be obtained as
+ :code:`itertools.combinations(simplex,len(simplex)-1)`.
+
+ :param simplex: The N-simplex, represented by a list of vertex.
+ :type simplex: list of int.
+ :returns: The (simplices of the) boundary of a simplex
+ :rtype: generator with tuples(simplex, filtration)
+ """
+ cdef pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] it = self.get_ptr().get_boundary_iterators(simplex)
+
+ while it.first != it.second:
+ yield self.get_ptr().get_simplex_and_filtration(dereference(it.first))
+ preincrement(it.first)
+
def remove_maximal_simplex(self, simplex):
"""This function removes a given maximal N-simplex from the simplicial
complex.
@@ -328,7 +344,7 @@ cdef class SimplexTree:
return self.get_ptr().prune_above_filtration(filtration)
def expansion(self, max_dim):
- """Expands the Simplex_tree containing only its one skeleton
+ """Expands the simplex tree containing only its one skeleton
until dimension max_dim.
The expanded simplicial complex until dimension :math:`d`
@@ -338,7 +354,7 @@ cdef class SimplexTree:
The filtration value assigned to a simplex is the maximal filtration
value of one of its edges.
- The Simplex_tree must contain no simplex of dimension bigger than
+ The simplex tree must contain no simplex of dimension bigger than
1 when calling the method.
:param max_dim: The maximal dimension.
@@ -358,38 +374,54 @@ cdef class SimplexTree:
"""
return self.get_ptr().make_filtration_non_decreasing()
+ def reset_filtration(self, filtration, min_dim = 0):
+ """This function resets the filtration value of all the simplices of dimension at least min_dim. Resets all the
+ simplex tree when `min_dim = 0`.
+ `reset_filtration` may break the filtration property with `min_dim > 0`, and it is the user's responsibility to
+ make it a valid filtration (using a large enough `filt_value`, or calling `make_filtration_non_decreasing`
+ afterwards for instance).
+
+ :param filtration: New threshold value.
+ :type filtration: float.
+ :param min_dim: The minimal dimension. Default value is 0.
+ :type min_dim: int.
+ """
+ self.get_ptr().reset_filtration(filtration, min_dim)
+
def extend_filtration(self):
- """ Extend filtration for computing extended persistence. This function only uses the
- filtration values at the 0-dimensional simplices, and computes the extended persistence
- diagram induced by the lower-star filtration computed with these values.
+ """ Extend filtration for computing extended persistence. This function only uses the filtration values at the
+ 0-dimensional simplices, and computes the extended persistence diagram induced by the lower-star filtration
+ computed with these values.
.. note::
- Note that after calling this function, the filtration
- values are actually modified within the Simplex_tree.
- The function :func:`extended_persistence`
- retrieves the original values.
+ Note that after calling this function, the filtration values are actually modified within the simplex tree.
+ The function :func:`extended_persistence` retrieves the original values.
.. note::
- Note that this code creates an extra vertex internally, so you should make sure that
- the Simplex_tree does not contain a vertex with the largest possible value (i.e., 4294967295).
+ Note that this code creates an extra vertex internally, so you should make sure that the simplex tree does
+ not contain a vertex with the largest possible value (i.e., 4294967295).
+
+ This `notebook <https://github.com/GUDHI/TDA-tutorial/blob/master/Tuto-GUDHI-extended-persistence.ipynb>`_
+ explains how to compute an extension of persistence called extended persistence.
"""
self.get_ptr().compute_extended_filtration()
def extended_persistence(self, homology_coeff_field=11, min_persistence=0):
- """This function retrieves good values for extended persistence, and separate the diagrams
- into the Ordinary, Relative, Extended+ and Extended- subdiagrams.
+ """This function retrieves good values for extended persistence, and separate the diagrams into the Ordinary,
+ Relative, Extended+ and Extended- subdiagrams.
- :param homology_coeff_field: The homology coefficient field. Must be a
- prime number. Default value is 11.
+ :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11.
:type homology_coeff_field: int
- :param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the persistence diagram point coordinates) to take into
- account (strictly greater than min_persistence). Default value is
- 0.0.
- Sets min_persistence to -1.0 to see all values.
+ :param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the
+ persistence diagram point coordinates) to take into account (strictly greater than min_persistence).
+ Default value is 0.0. Sets min_persistence to -1.0 to see all values.
:type min_persistence: float
- :returns: A list of four persistence diagrams in the format described in :func:`persistence`. The first one is Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-. See https://link.springer.com/article/10.1007/s10208-008-9027-z and/or section 2.2 in https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes.
+ :returns: A list of four persistence diagrams in the format described in :func:`persistence`. The first one is
+ Ordinary, the second one is Relative, the third one is Extended+ and the fourth one is Extended-.
+ See https://link.springer.com/article/10.1007/s10208-008-9027-z and/or section 2.2 in
+ https://link.springer.com/article/10.1007/s10208-017-9370-z for a description of these subtypes.
.. note::
@@ -400,6 +432,9 @@ cdef class SimplexTree:
The coordinates of the persistence diagram points might be a little different than the
original filtration values due to the internal transformation (scaling to [-2,-1]) that is
performed on these values during the computation of extended persistence.
+
+ This `notebook <https://github.com/GUDHI/TDA-tutorial/blob/master/Tuto-GUDHI-extended-persistence.ipynb>`_
+ explains how to compute an extension of persistence called extended persistence.
"""
cdef vector[pair[int, pair[double, double]]] persistence_result
if self.pcohptr != NULL:
@@ -592,6 +627,9 @@ cdef class SimplexTree:
:param nb_iterations: The number of edge collapse iterations to perform. Default is 1.
:type nb_iterations: int
+
+ :note: collapse_edges method requires `Eigen <installation.html#eigen>`_ >= 3.1.0 and an exception is thrown
+ if this method is not available.
"""
# Backup old pointer
cdef Simplex_tree_interface_full_featured* ptr = self.get_ptr()