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Test insertion of simplex with NaN filtration value #424

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Test insertion of simplex with NaN filtration value #424

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73c8001
Test insertion of simplex with NaN filtration value
mglisse Nov 5, 2020
52a5406
Slightler longer test
mglisse Nov 5, 2020
767f8cb
More doc.
mglisse Nov 5, 2020
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12 changes: 10 additions & 2 deletions src/Simplex_tree/include/gudhi/Simplex_tree.h
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Expand Up @@ -763,9 +763,13 @@ class Simplex_tree {
return insert_vertex_vector(copy, filtration);
}

/** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of
/** \brief Insert a N-simplex and all its subfaces, from a N-simplex represented by a range of
* Vertex_handles, in the simplicial complex.
*
* Inserting a simplex with filtration value NaN does not modify the
* filtration value of any pre-existing simplex. Pre-existing NaN may or may
* not be updated by an insertion with a real value.
*
* @param[in] Nsimplex range of Vertex_handles, representing the vertices of the new N-simplex
* @param[in] filtration the filtration value assigned to the new N-simplex.
* @return If the new simplex is inserted successfully (i.e. it was not in the
Expand Down Expand Up @@ -819,6 +823,8 @@ class Simplex_tree {
Simplex_handle simplex_one = insertion_result.first;
bool one_is_new = insertion_result.second;
if (!one_is_new) {
// In order for an insertion to handle pre-existing NaN like +Inf, we would need
// filtration(simplex_one) > filt || (isnan(filtration(simplex_one)) && ! isnan(filt))
if (filtration(simplex_one) > filt) {
assign_filtration(simplex_one, filt);
} else {
Expand Down Expand Up @@ -1352,7 +1358,8 @@ class Simplex_tree {
* filtration values.
* @return True if any filtration value was modified, false if the filtration was already non-decreasing.
*
* If a simplex has a `NaN` filtration value, it is considered lower than any other defined filtration value.
* If a simplex of dimension 1 or more has a `NaN` filtration value,
* it is considered lower than any other defined filtration value.
*/
bool make_filtration_non_decreasing() {
bool modified = false;
Expand All @@ -1379,6 +1386,7 @@ class Simplex_tree {
for (auto& simplex : boost::adaptors::reverse(sib->members())) {
// Find the maximum filtration value in the border
Boundary_simplex_range boundary = boundary_simplex_range(&simplex);
// We would need a loop using fmax to get consistent results when a vertex has NaN.
Boundary_simplex_iterator max_border = std::max_element(std::begin(boundary), std::end(boundary),
[](Simplex_handle sh1, Simplex_handle sh2) {
return filtration(sh1) < filtration(sh2);
Expand Down
14 changes: 14 additions & 0 deletions src/python/gudhi/simplex_tree.pyx
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Expand Up @@ -184,6 +184,15 @@ cdef class SimplexTree:
simplices are already present with a higher filtration value, their
filtration value is lowered.

.. note::

Inserting a simplex with filtration value `math.nan` does not
modify the filtration value of any simplex already present.
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Perhaps complete this note by adding a warning in the vein of what is done for assign_filtration() saying (e.g.) "In this particular case, the result will not be a valid filtration anymore. Callers are responsible for fixing this (using assign_filtration() or make_filtration_non_decreasing() for instance) before calling any function that relies on the filtration property, like persistence().

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I hadn't realized it, but having some NaN in the complex can have some weird effects. In particular, if I have vertex 0 with value NaN, inserting edge [0, 1] with value 42 does not change the value of vertex 0. I added some confusing text to the doc. We could change that behavior, but would need to check that it doesn't slow things down for normal operations.

However, it produces an invalid filtration, which needs to be fixed
with :meth:`make_filtration_non_decreasing` or
:meth:`assign_filtration`. Inserting simplices with real filtration
value may or may not update pre-existing NaN.
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:param simplex: The N-simplex to insert, represented by a list of
vertex.
:type simplex: list of int
Expand Down Expand Up @@ -368,6 +377,11 @@ cdef class SimplexTree:
"""This function ensures that each simplex has a higher filtration
value than its faces by increasing the filtration values.

.. note::

For this function, a value of NaN for a simplex of dimension 1 or more
is considered smaller than any other value.

:returns: True if any filtration value was modified,
False if the filtration was already non-decreasing.
:rtype: bool
Expand Down
22 changes: 22 additions & 0 deletions src/python/test/test_simplex_tree.py
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Expand Up @@ -10,6 +10,7 @@

from gudhi import SimplexTree
import pytest
import math

__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
Expand Down Expand Up @@ -399,3 +400,24 @@ def test_boundaries_iterator():

with pytest.raises(RuntimeError):
list(st.get_boundaries([6])) # (6) does not exist

# insert with NaN must not modify filtration values
# make_filtration_non_decreasing considers NaN small
def test_nan():
st = SimplexTree()
st.insert([1], 2.)
st.insert([4], 5.)
st.insert([2], -1.)
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Suggested change
st.insert([2], -1.)
st.insert([2], -1.)
st.insert([1,2], 2.)

Perhaps already add a single edge (with an admissible value) to make sure that both inserting nan and make_filtration_non_decreasing() do not play any role there

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I inserted an extra edge.

st.insert([1, 4], 6.)
st.insert([1, 2, 4], math.nan)
assert st.filtration([1]) == 2.
assert st.filtration([2]) == -1.
assert st.filtration([4]) == 5.
assert st.filtration([1, 4]) == 6.
assert math.isnan(st.filtration([2, 4]))
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Suggested change
assert math.isnan(st.filtration([2, 4]))
assert math.isnan(st.filtration([2, 4]))
assert st.filtration([4]) == 5.
assert st.filtration([2]) == -1.
assert st.filtration([1]) == 2.
assert st.filtration([1,2]) == 2.

Perhaps we may want to make sure that we did not modify any of the previous values even before calling st.make_persistence_non_decreasing().

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I thought that checking after make_persistence_non_decreasing would be sufficient (if we overwrite a value with insert, make_persistence_non_decreasing won't be able to reinvent that value), but why not, done.

st.make_filtration_non_decreasing()
assert st.filtration([1, 2, 4]) == 6.
assert st.filtration([1, 2]) == 2.
assert st.filtration([1, 4]) == 6.
assert st.filtration([2]) == -1.
assert st.filtration([4]) == 5.