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Merge pull request GUDHI#1129 from VincentRouvreau/compute_persistenc…
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…e_limit_test

Fix Betti numbers on isolated zero simplices segfault and test it
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@VincentRouvreau
VincentRouvreau authored Sep 12, 2024
2 parents 2a89fd5 + e21cafa commit 4b327a9
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5 changes: 4 additions & 1 deletion src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ namespace persistent_cohomology {
/** \brief Computes the persistent cohomology of a filtered complex.
*
* \ingroup persistent_cohomology
*
*
* The computation is implemented with a Compressed Annotation Matrix
* (CAM)\cite DBLP:conf/esa/BoissonnatDM13,
* and is adapted to the computation of Multi-Field Persistent Homology (MF)
Expand Down Expand Up @@ -166,6 +166,9 @@ class Persistent_cohomology {
* Assumes that the filtration provided by the simplicial complex is
* valid. Undefined behavior otherwise. */
void compute_persistent_cohomology(Filtration_value min_interval_length = 0) {
if (dim_max_ <= 0)
return; // --------->>

interval_length_policy.set_length(min_interval_length);
Simplex_key idx_fil = -1;
std::vector<Simplex_key> vertices; // so we can check the connected components at the end
Expand Down
156 changes: 142 additions & 14 deletions src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -77,11 +77,11 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )

// Print the result. The format is, on each line: 2 dim 0 inf
// where 2 represents the field, dim the dimension of the feature.
// 2 0 0 inf
// 2 0 0 inf
// 2 1 0 inf
// 2 0 0 inf
// 2 0 0 inf
// 2 1 0 inf
// means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.

std::clog << "BETTI NUMBERS" << std::endl;

BOOST_CHECK(pcoh.betti_number(0) == 2);
Expand All @@ -95,13 +95,13 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
BOOST_CHECK(bns[2] == 0);

std::clog << "GET PERSISTENT PAIRS" << std::endl;

// Custom sort and output persistence
cmp_intervals_by_dim_then_length<Mini_simplex_tree> cmp(&st);
auto persistent_pairs = pcoh.get_persistent_pairs();

std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);

BOOST_CHECK(persistent_pairs.size() == 3);
// persistent_pairs[0] = 2 1 0 inf
BOOST_CHECK(st.dimension(get<0>(persistent_pairs[0])) == 1);
Expand Down Expand Up @@ -192,7 +192,7 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
BOOST_CHECK(bns[0] == 2);
BOOST_CHECK(bns[1] == 1);
BOOST_CHECK(bns[2] == 0);

// Check the persistent Betti numbers in [4., 10.] are b0=2, b1=1 and b2=0.
BOOST_CHECK(pcoh.persistent_betti_number(0, 4., 10.) == 2);
BOOST_CHECK(pcoh.persistent_betti_number(1, 4., 10.) == 1);
Expand All @@ -218,7 +218,7 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
BOOST_CHECK(bns[0] == 2);
BOOST_CHECK(bns[1] == 1);
BOOST_CHECK(bns[2] == 0);

// Check the persistent Betti numbers in [2.1, 100000.] are b0=2, b1=0 and b2=0.
bns = pcoh.persistent_betti_numbers(2.1, 100000.);
BOOST_CHECK(bns[0] == 2);
Expand All @@ -230,19 +230,19 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
BOOST_CHECK(bns[0] == 1);
BOOST_CHECK(bns[1] == 0);
BOOST_CHECK(bns[2] == 0);

// Check the persistent Betti numbers in [.1, 10000000.] are b0=0, b1=0 and b2=0.
bns = pcoh.persistent_betti_numbers(.1, 10000000.);
BOOST_CHECK(bns[0] == 0);
BOOST_CHECK(bns[1] == 0);
BOOST_CHECK(bns[2] == 0);

// Custom sort and output persistence
cmp_intervals_by_dim_then_length<Simplex_tree> cmp(&st);
auto persistent_pairs = pcoh.get_persistent_pairs();

std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);

BOOST_CHECK(persistent_pairs.size() == 3);
// persistent_pairs[0] = 2 1 4 inf
BOOST_CHECK(st.dimension(get<0>(persistent_pairs[0])) == 1);
Expand Down Expand Up @@ -284,13 +284,141 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2);
std::clog << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl;
BOOST_CHECK(intervals_in_dimension_2.size() == 0);
}

BOOST_AUTO_TEST_CASE( betti_numbers_empty_simplex_tree )
{
std::clog << "EMPTY COMPLEX" << std::endl;
Simplex_tree empty;
empty.initialize_filtration();
St_persistence pcoh_empty(empty, false);
pcoh_empty.init_coefficients(2);
pcoh_empty.compute_persistent_cohomology();
std::clog << "pcoh_empty.betti_numbers().size() = " << pcoh_empty.betti_numbers().size() << std::endl;
BOOST_CHECK(pcoh_empty.betti_numbers().size() == 0);
BOOST_CHECK(pcoh_empty.persistent_betti_numbers(0,1).size() == 0);
std::clog << "pcoh_empty.betti_number(0) = " << pcoh_empty.betti_number(0) << std::endl;
BOOST_CHECK(pcoh_empty.betti_number(0) == 0);
std::clog << "pcoh_empty.persistent_betti_numbers(0., 1.).size() = " << pcoh_empty.persistent_betti_numbers(0., 1.).size() << std::endl;
BOOST_CHECK(pcoh_empty.persistent_betti_numbers(0., 1.).size() == 0);
std::clog << "pcoh_empty.persistent_betti_number(0, 0., 1.) = " << pcoh_empty.persistent_betti_number(0, 0., 1.) << std::endl;
BOOST_CHECK(pcoh_empty.persistent_betti_number(0, 0., 1.) == 0);
}

BOOST_AUTO_TEST_CASE( betti_numbers_isolated_zero_simplices )
{
std::clog << "Betti numbers on isolated zero simplices" << std::endl;
Simplex_tree st;

st.insert_simplex_and_subfaces({0});
st.insert_simplex_and_subfaces({1});
st.insert_simplex_and_subfaces({2});
st.insert_simplex_and_subfaces({3});
st.insert_simplex_and_subfaces({4});

st.initialize_filtration();
{
St_persistence pcoh(st);
pcoh.init_coefficients(3);
pcoh.compute_persistent_cohomology();

// Should have no Betti numbers
auto bn = pcoh.betti_numbers();
std::clog << "bn.size() = " << bn.size() << std::endl;
BOOST_CHECK(bn.size() == 0);

std::clog << "pcoh.betti_number(0) = " << pcoh.betti_number(0) << std::endl;
BOOST_CHECK(pcoh.betti_number(0) == 0);

auto pbn = pcoh.persistent_betti_numbers(0., 1.);
std::clog << "pbn.size() = " << pbn.size() << std::endl;
BOOST_CHECK(pbn.size() == 0);

std::clog << "pcoh.persistent_betti_number(0, 0., 1.) = " << pcoh.persistent_betti_number(0, 0., 1.) << std::endl;
BOOST_CHECK(pcoh.persistent_betti_number(0, 0., 1.) == 0);
}
// Set dim_max to true
{
St_persistence pcoh(st, true);
pcoh.init_coefficients(3);
pcoh.compute_persistent_cohomology();

int num_simplices = st.num_simplices();
// Should have Betti numbers
auto bn = pcoh.betti_numbers();
std::clog << "bn.size() = " << bn.size() << std::endl;
BOOST_CHECK(bn.size() == 1);
std::clog << "bn[0] = " << bn[0] << std::endl;
BOOST_CHECK(bn[0] == num_simplices);

std::clog << "pcoh.betti_number(0) = " << pcoh.betti_number(0) << std::endl;
BOOST_CHECK(pcoh.betti_number(0) == num_simplices);

auto pbn = pcoh.persistent_betti_numbers(0., 1.);
std::clog << "pbn.size() = " << pbn.size() << std::endl;
BOOST_CHECK(pbn.size() == 1);
std::clog << "pbn[0] = " << pbn[0] << std::endl;
BOOST_CHECK(pbn[0] == num_simplices);

std::clog << "pcoh.persistent_betti_number(0, 0., 1.) = " << pcoh.persistent_betti_number(0, 0., 1.) << std::endl;
BOOST_CHECK(pcoh.persistent_betti_number(0, 0., 1.) == num_simplices);
}
}

BOOST_AUTO_TEST_CASE( betti_numbers_no_compute_persistent_cohomology )
{
std::clog << "Betti numbers when compute_persistent_cohomology is not performed" << std::endl;
Simplex_tree st;

st.insert_simplex_and_subfaces({0});
st.insert_simplex_and_subfaces({1});
st.insert_simplex_and_subfaces({2});
st.insert_simplex_and_subfaces({3});
st.insert_simplex_and_subfaces({4});

st.initialize_filtration();
{
St_persistence pcoh(st);
pcoh.init_coefficients(3);
// NO pcoh.compute_persistent_cohomology(), this is the aim of this test !

// Should have no Betti numbers
auto bn = pcoh.betti_numbers();
std::clog << "bn.size() = " << bn.size() << std::endl;
BOOST_CHECK(bn.size() == 0);

std::clog << "pcoh.betti_number(0) = " << pcoh.betti_number(0) << std::endl;
BOOST_CHECK(pcoh.betti_number(0) == 0);

auto pbn = pcoh.persistent_betti_numbers(0., 1.);
std::clog << "pbn.size() = " << pbn.size() << std::endl;
BOOST_CHECK(pbn.size() == 0);

std::clog << "pcoh.persistent_betti_number(0, 0., 1.) = " << pcoh.persistent_betti_number(0, 0., 1.) << std::endl;
BOOST_CHECK(pcoh.persistent_betti_number(0, 0., 1.) == 0);
}
// Set dim_max to true
{
St_persistence pcoh(st, true);
pcoh.init_coefficients(3);
// NO pcoh.compute_persistent_cohomology(), this is the aim of this test !

// Should have no Betti numbers
auto bn = pcoh.betti_numbers();
std::clog << "bn.size() = " << bn.size() << std::endl;
BOOST_CHECK(bn.size() == 1);
std::clog << "bn[0] = " << bn[0] << std::endl;
BOOST_CHECK(bn[0] == 0);

std::clog << "pcoh.betti_number(0) = " << pcoh.betti_number(0) << std::endl;
BOOST_CHECK(pcoh.betti_number(0) == 0);

auto pbn = pcoh.persistent_betti_numbers(0., 1.);
std::clog << "pbn.size() = " << pbn.size() << std::endl;
BOOST_CHECK(pbn.size() == 1);
std::clog << "pbn[0] = " << pbn[0] << std::endl;
BOOST_CHECK(pbn[0] == 0);

std::clog << "pcoh.persistent_betti_number(0, 0., 1.) = " << pcoh.persistent_betti_number(0, 0., 1.) << std::endl;
BOOST_CHECK(pcoh.persistent_betti_number(0, 0., 1.) == 0);
}
}

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