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Merged
DavidLapous merged 3 commits into from
Jul 18, 2026
Merged

Gudhi MMA #66

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573a74f
add gudhi mma + fix make_filtration_non_decreasing + tuples for Module
hschreiber Jul 15, 2026
a1279de
added new gudhi files in pyproject.toml
hschreiber Jul 15, 2026
5d8c078
add explicit operator== for Multi_parameter_filtered_complex because …
hschreiber Jul 15, 2026
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2 changes: 1 addition & 1 deletion ext/gudhi-devel
Open in desktop
Submodule gudhi-devel updated 35 files
+67 −0 src/Multi_filtration/include/gudhi/Multi_filtration/multi_filtration_conversions.h
+3 −0 src/Multi_filtration/test/CMakeLists.txt
+94 −0 src/Multi_filtration/test/multifiltration_comp_unit_test.cpp
+1 −2 src/Multi_persistence/concept/MultiFiltrationValue.h
+1 −2 src/Multi_persistence/concept/PersistenceAlgorithm.h
+125 −39 src/Multi_persistence/include/gudhi/Multi_parameter_filtered_complex.h
+13 −19 src/Multi_persistence/include/gudhi/Multi_persistence/Box.h
+21 −34 src/Multi_persistence/include/gudhi/Multi_persistence/Line.h
+2 −2 src/Multi_persistence/include/gudhi/Multi_persistence/Module.h
+17 −32 src/Multi_persistence/include/gudhi/Multi_persistence/Multi_parameter_filtered_complex_pcoh_interface.h
+13 −25 src/Multi_persistence/include/gudhi/Multi_persistence/Persistence_interface_cohomology.h
+14 −26 src/Multi_persistence/include/gudhi/Multi_persistence/Persistence_interface_homology.h
+12 −20 src/Multi_persistence/include/gudhi/Multi_persistence/Persistence_interface_vineyard.h
+31 −62 src/Multi_persistence/include/gudhi/Multi_persistence/Point.h
+3 −6 src/Multi_persistence/include/gudhi/Multi_persistence/Summand.h
+2 −2 src/Multi_persistence/include/gudhi/Multi_persistence/summand_helpers.h
+23 −55 src/Multi_persistence/include/gudhi/Projective_cover_kernel.h
+53 −101 src/Multi_persistence/include/gudhi/Slicer.h
+16 −34 src/Multi_persistence/include/gudhi/Thread_safe_slicer.h
+3 −6 src/Multi_persistence/include/gudhi/multi_simplex_tree_helpers.h
+5 −7 src/Multi_persistence/include/gudhi/multiparameter_module_approximation.h
+51 −104 src/Multi_persistence/include/gudhi/slicer_helpers.h
+6 −22 src/Multi_persistence/test/multipersistence_batch_slice_helpers_unit_test.cpp
+6 −9 src/Multi_persistence/test/multipersistence_box_unit_test.cpp
+22 −29 src/Multi_persistence/test/multipersistence_build_slicer_helpers_unit_test.cpp
+81 −15 src/Multi_persistence/test/multipersistence_complex_unit_test.cpp
+3 −6 src/Multi_persistence/test/multipersistence_line_unit_test.cpp
+2 −19 src/Multi_persistence/test/multipersistence_mma_unit_test.cpp
+1 −1 src/Multi_persistence/test/multipersistence_module_unit_test.cpp
+10 −19 src/Multi_persistence/test/multipersistence_persistence_interface_unit_test.cpp
+4 −8 src/Multi_persistence/test/multipersistence_simplex_tree_helpers_unit_test.cpp
+29 −54 src/Multi_persistence/test/multipersistence_slicer_unit_test.cpp
+4 −4 src/Multi_persistence/test/multipersistence_summand_unit_test.cpp
+184 −0 src/python/include/python_interfaces/construction_utils.h
+3 −0 src/python/include/python_interfaces/numpy_utils.h
17 changes: 5 additions & 12 deletions multipers/_mma_nanobind.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -199,18 +199,11 @@ void bind_module_class(nb::module_& m) {
.def_prop_ro("num_parameters", &Module::get_number_of_parameters)
.def_prop_rw("box",
&Module::get_box_view,
[](Module& self, nb::object box) {
try {
if (nb::ndarray_check(box.ptr())) {
self.set_box(nb::cast<NDArray2>(box));
return;
}
self.set_box(nb::cast<std::vector<std::vector<T>>>(box));
return;
} catch (const nb::cast_error&) {
throw nb::type_error(
"Box has to be set with an array or a nested sequence of shape (2, p).");
}
[](Module& self, nb::iterable box) {
auto boxCpp =
Gudhi::python::_convert_iterable_to_cpp_type<NDArray2, std::vector<std::vector<T>>>(
box, "Box has to be set with an array or a nested sequence of shape (2, p).");
std::visit([&](auto&& val) { self.set_box(val); }, boxCpp);
})
.def("set_box",
[](Module& self, NDArray2 box) {
Expand Down
65 changes: 34 additions & 31 deletions multipers/_slicer_nanobind.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,10 @@
#include <nanobind/stl/vector.h>

#include <algorithm>
#include <cctype>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <limits>
#include <memory>
#include <optional>
#include <stdexcept>
#include <string>
Expand All @@ -28,7 +26,6 @@
#include "Persistence_slices_interface.h"
#include "ext_interface/backend_log_policy.hpp"
#include "ext_interface/nanobind_generator_basis.hpp"
#include "ext_interface/packed_multi_critical_bridge.hpp"
#include "ext_interface/nanobind_registry_helpers.hpp"
#include "ext_interface/nanobind_registry_runtime.hpp"
#include "gudhi/Multi_parameter_filtered_complex.h"
Expand All @@ -39,10 +36,9 @@
#include <python_interfaces/numpy_utils.h>
#include "multi_parameter_rank_invariant/hilbert_function.h"
#include "multi_parameter_rank_invariant/rank_invariant.h"
#include "multiparameter_module_approximation/approximation.h"
#include <gudhi/multiparameter_module_approximation.h>
#include "nanobind_array_utils.hpp"
#include "nanobind_dense_array_utils.hpp"
#include "nanobind_mma_registry_helpers.hpp"
#include "nanobind_object_utils.hpp"
#include "nanobind_slicer_serialization.hpp"

Expand Down Expand Up @@ -208,9 +204,9 @@ Wrapper& make_filtration_non_decreasing_inplace(Wrapper& self, bool safe) {
bool modified = true;
while (modified) {
modified = false;
for (size_t i = boundaries.size(); i-- > 0;) {
for (size_t i = 1; i < boundaries.size(); ++i) {
for (auto b : boundaries[i]) {
modified |= intersect_lifetimes(filtrations[b], filtrations[i]);
modified |= intersect_lifetimes(filtrations[i], filtrations[b]);
}
}
if (ordered) {
Expand Down Expand Up @@ -1676,7 +1672,7 @@ void bind_slicer_class(nb::module_& m, nb::list& available_slicers) {
nb::make_tuple(serialized_state<Wrapper, Value, Desc::is_kcritical, Desc::is_degree_rips>(self),
self.filtration_grid,
self.generator_basis,
self.minpres_degree));
self.minpres_degree));
})
.def("__reduce_ex__",
[](Wrapper& self, int) -> nb::tuple {
Expand All @@ -1686,7 +1682,7 @@ void bind_slicer_class(nb::module_& m, nb::list& available_slicers) {
nb::make_tuple(serialized_state<Wrapper, Value, Desc::is_kcritical, Desc::is_degree_rips>(self),
self.filtration_grid,
self.generator_basis,
self.minpres_degree));
self.minpres_degree));
})
.def("_serialize_state",
[](Wrapper& self) -> nb::ndarray<nb::numpy, uint8_t> {
Expand Down Expand Up @@ -1842,17 +1838,17 @@ void bind_slicer_class(nb::module_& m, nb::list& available_slicers) {
"basepoint"_a,
"direction"_a = nb::none(),
nb::rv_policy::reference_internal)
.def(
"set_slice",
[](Wrapper& self, nb::object values) -> Wrapper& {
auto c_values = cast_vector<Value>(values);
{
nb::gil_scoped_release release;
self.truc.set_slice(c_values);
}
return self;
},
nb::rv_policy::reference_internal)
// .def(
// "set_slice",
// [](Wrapper& self, nb::object values) -> Wrapper& {
// auto c_values = cast_vector<Value>(values);
// {
// nb::gil_scoped_release release;
// self.truc.set_slice(c_values);
// }
// return self;
// },
// nb::rv_policy::reference_internal)
.def(
"initialize_persistence_computation",
[](Wrapper& self, bool ignore_infinite_filtration_values) -> Wrapper& {
Expand Down Expand Up @@ -1904,15 +1900,15 @@ void bind_slicer_class(nb::module_& m, nb::list& available_slicers) {
}
return dim_barcode_to_tuple<Barcode, int>(barcode);
})
.def("get_current_filtration",
[](Wrapper& self) -> nb::ndarray<nb::numpy, Value> {
std::vector<Value> current;
{
nb::gil_scoped_release release;
current = self.truc.get_slice();
}
return owned_array<Value>(std::move(current), {current.size()});
})
// .def("get_current_filtration",
// [](Wrapper& self) -> nb::ndarray<nb::numpy, Value> {
// std::vector<Value> current;
// {
// nb::gil_scoped_release release;
// current = self.truc.get_slice();
// }
// return owned_array<Value>(std::move(current), {current.size()});
// })
.def(
"prune_above_dimension",
[](Wrapper& self, int max_dimension) -> Wrapper& {
Expand Down Expand Up @@ -2093,8 +2089,15 @@ Gudhi::multi_persistence::Module_interface<double> module_approximation_from_des
Gudhi::multi_persistence::Module<double> mod;
{
nb::gil_scoped_release release;
mod = Gudhi::multiparameter::mma::multiparameter_module_approximation(
wrapper.truc, direction, max_error, box, threshold, complete, verbose, n_jobs);
mod = Gudhi::multi_persistence::multiparameter_module_approximation(wrapper.truc,
max_error,
box.get_lower_corner(),
box.get_upper_corner(),
direction,
threshold,
complete,
verbose,
n_jobs);
}
return {std::move(mod), box};
}
Expand Down
98 changes: 45 additions & 53 deletions multipers/gudhi/Module_interface.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
#include <utility>
#include <vector>

#include <boost/type_traits/add_const.hpp> // missing in boost/range/any_range.hpp
#include <boost/range/any_range.hpp>
#include <boost/range/adaptor/type_erased.hpp>

Expand All @@ -43,6 +44,7 @@
#include <gudhi/Multi_persistence/Box.h>
#include <gudhi/Multi_persistence/utils.h>
#include <python_interfaces/numpy_utils.h>
#include <python_interfaces/construction_utils.h>

namespace Gudhi {
namespace multi_persistence {
Expand All @@ -61,7 +63,7 @@ class Module_interface {
using Summand_of_dimension_range =
boost::any_range<Summand_t, boost::forward_traversal_tag, const Summand_t &, std::ptrdiff_t>;
using Tensor1D = nanobind::ndarray<const value_type, nanobind::ndim<1>, nanobind::any_contig>;
using Tensor2D = nanobind::ndarray<const value_type, nanobind::ndim<2>>;
using Tensor2D = nanobind::ndarray<const value_type, nanobind::ndim<2> >;
template <typename IntegerType>
using IntTensor1D = nanobind::ndarray<const IntegerType, nanobind::ndim<1>, nanobind::any_contig>;
using Box_t = std::vector<T>;
Expand Down Expand Up @@ -160,7 +162,7 @@ class Module_interface {
return *this;
}

[[nodiscard]] nanobind::list get_flat_filtration_values(bool unique) const {
[[nodiscard]] nanobind::tuple get_flat_filtration_values(bool unique) const {
int numParam = module_.get_number_of_parameters();
if (numParam == get_null_value<int>()) return {}; // empty module

Expand Down Expand Up @@ -193,15 +195,14 @@ class Module_interface {
}
}

nanobind::list out;
for (auto &vals : values) {
return Gudhi::python::_build_tuple(numParam, [&](std::size_t p) {
auto &vals = values[p];
if (unique) {
std::sort(vals.begin(), vals.end());
vals.erase(std::unique(vals.begin(), vals.end()), vals.end());
}
out.append(_wrap_as_numpy_array(std::move(vals), vals.size()));
}
return out;
return _wrap_as_numpy_array(std::move(vals), vals.size());
});
}

auto get_all_dimension() const {
Expand Down Expand Up @@ -260,9 +261,8 @@ class Module_interface {
return _wrap_as_numpy_array(std::move(corners), 2, dim);
}

nanobind::list get_barcode_from_line(Tensor1D basepoint, std::optional<Tensor1D> direction, int degree) const {
nanobind::tuple get_barcode_from_line(Tensor1D basepoint, std::optional<Tensor1D> direction, int degree) const {
std::vector<std::vector<std::array<double, 2>>> barcode;
nanobind::list out;
{
nanobind::gil_scoped_release release;
Dimension dim = degree < 0 ? get_null_value<Dimension>() : static_cast<Dimension>(degree);
Expand All @@ -276,16 +276,15 @@ class Module_interface {
}
barcode = module_.get_barcode_from_line(line, dim);
}
for (auto &d : barcode) {
out.append(_wrap_as_numpy_array(std::move(d)));
}
return out;

return Gudhi::python::_build_tuple(barcode.size(),
[&](std::size_t d) { return _wrap_as_numpy_array(std::move(barcode[d])); });
}

nanobind::list get_barcode_from_lines(Tensor2D basepoints,
std::optional<Tensor2D> directions,
int degree,
bool keep_inf) const {
nanobind::tuple get_barcode_from_lines(Tensor2D basepoints,
std::optional<Tensor2D> directions,
int degree,
bool keep_inf) const {
std::vector<std::vector<std::array<double, 2>>> barcode;
std::size_t numberOfLines;
{
Expand Down Expand Up @@ -633,71 +632,64 @@ class Module_interface {
return fb;
}

static nanobind::list get_numpy_barcode_from_lines_with_inf(std::vector<std::vector<std::array<double, 2>>> &barcode,
std::size_t numberOfLines) {
nanobind::list out;
static nanobind::tuple get_numpy_barcode_from_lines_with_inf(std::vector<std::vector<std::array<double, 2>>> &barcode,
std::size_t numberOfLines) {
std::vector<std::uint64_t> splits;

if (numberOfLines == 0) {
for (auto &d : barcode) {
if (d.size() != 0) throw std::logic_error("No lines but the barcode is not empty... ?");
out.append(nanobind::make_tuple(_wrap_as_numpy_array(std::move(d), 0, 0, 2),
_wrap_as_numpy_array(std::move(splits), 0)));
}
return out;
return Gudhi::python::_build_tuple(barcode.size(), [&](std::size_t d) {
if (barcode[d].size() != 0) throw std::logic_error("No lines but the barcode is not empty... ?");
return nanobind::make_tuple(_wrap_as_numpy_array(std::move(barcode[d]), 0, 0, 2),
_wrap_as_numpy_array(std::move(splits), 0));
});
}

for (auto &d : barcode) {
if (d.size() % numberOfLines != 0)
return Gudhi::python::_build_tuple(barcode.size(), [&](std::size_t d) {
if (barcode[d].size() % numberOfLines != 0)
throw std::logic_error("Barcodes do not have consistent sizes from a line to another.");
std::size_t numberOfBars = d.size() / numberOfLines;
out.append(nanobind::make_tuple(_wrap_as_numpy_array(std::move(d), numberOfLines, numberOfBars, 2),
_wrap_as_numpy_array(std::move(splits), 0)));
}
return out;
std::size_t numberOfBars = barcode[d].size() / numberOfLines;
return nanobind::make_tuple(_wrap_as_numpy_array(std::move(barcode[d]), numberOfLines, numberOfBars, 2),
_wrap_as_numpy_array(std::move(splits), 0));
});
}

static nanobind::list get_numpy_barcode_from_lines_without_inf(
static nanobind::tuple get_numpy_barcode_from_lines_without_inf(
std::vector<std::vector<std::array<double, 2>>> &barcode,
std::size_t numberOfLines) {
nanobind::list out;

if (numberOfLines == 0) {
for (auto &d : barcode) {
if (d.size() != 0) throw std::logic_error("No lines but the barcode is not empty... ?");
return Gudhi::python::_build_tuple(barcode.size(), [&](std::size_t d) {
if (barcode[d].size() != 0) throw std::logic_error("No lines but the barcode is not empty... ?");
std::vector<std::uint64_t> splits;
out.append(
nanobind::make_tuple(_wrap_as_numpy_array(std::move(d), 0, 2), _wrap_as_numpy_array(std::move(splits), 0)));
}
return out;
return nanobind::make_tuple(_wrap_as_numpy_array(std::move(barcode[d]), 0, 2),
_wrap_as_numpy_array(std::move(splits), 0));
});
}

for (auto &d : barcode) {
if (d.size() % numberOfLines != 0)
return Gudhi::python::_build_tuple(barcode.size(), [&](std::size_t d) {
if (barcode[d].size() % numberOfLines != 0)
throw std::logic_error("Barcodes do not have consistent sizes from a line to another.");
std::vector<std::uint64_t> splits(numberOfLines - 1);
std::size_t barCount = 0;
std::size_t numberOfBars = d.size() / numberOfLines;
std::size_t numberOfBars = barcode[d].size() / numberOfLines;
std::vector<std::array<double, 2>> bars;
for (std::size_t l = 0; l < numberOfLines; ++l) {
for (std::size_t i = 0; i < numberOfBars; ++i) {
auto &b = d[i + (l * numberOfBars)];
auto &b = barcode[d][i + (l * numberOfBars)];
if (b[0] != Module<double>::T_inf) {
bars.push_back(b);
++barCount;
}
}
if (l + 1 < numberOfLines) splits[l] = barCount;
}
out.append(nanobind::make_tuple(_wrap_as_numpy_array(std::move(bars), barCount, 2),
_wrap_as_numpy_array(std::move(splits), numberOfLines - 1)));
}
return out;
return nanobind::make_tuple(_wrap_as_numpy_array(std::move(bars), barCount, 2),
_wrap_as_numpy_array(std::move(splits), numberOfLines - 1));
});
}

static nanobind::list get_numpy_barcode_from_lines(std::vector<std::vector<std::array<double, 2>>> &barcode,
std::size_t numberOfLines,
bool keepInf) {
static nanobind::tuple get_numpy_barcode_from_lines(std::vector<std::vector<std::array<double, 2>>> &barcode,
std::size_t numberOfLines,
bool keepInf) {
if (keepInf) return get_numpy_barcode_from_lines_with_inf(barcode, numberOfLines);
return get_numpy_barcode_from_lines_without_inf(barcode, numberOfLines);
}
Expand Down
2 changes: 2 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -310,6 +310,7 @@ include = [
"ext/gudhi-devel/src/Multi_persistence/include/gudhi/Thread_safe_slicer.h",
"ext/gudhi-devel/src/Multi_persistence/include/gudhi/multi_simplex_tree_helpers.h",
"ext/gudhi-devel/src/Multi_persistence/include/gudhi/slicer_helpers.h",
"ext/gudhi-devel/src/Multi_persistence/include/gudhi/multiparameter_module_approximation.h",
"ext/gudhi-devel/src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h",
"ext/gudhi-devel/src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h",
"ext/gudhi-devel/src/Persistence_matrix/include/gudhi/Matrix.h",
Expand Down Expand Up @@ -370,6 +371,7 @@ include = [
"ext/gudhi-devel/src/common/include/gudhi/reader_utils.h",
"ext/gudhi-devel/src/common/include/gudhi/simple_mdspan.h",
"ext/gudhi-devel/src/python/include/python_interfaces/numpy_utils.h",
"ext/gudhi-devel/src/python/include/python_interfaces/construction_utils.h",
"ext/hera/extern/phat/algorithms/standard_reduction.h",
"ext/hera/extern/phat/algorithms/twist_reduction.h",
"ext/hera/extern/phat/boundary_matrix.h",
Expand Down
16 changes: 12 additions & 4 deletions tests/test_slicer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,16 +96,24 @@ def test_3():
def test_make_filtration_non_decreasing_propagates_transitively():
slicer_type = mp.Slicer(return_type_only=True, dtype=np.float64)
slicer = slicer_type(
[[], [], [0, 1], [2]],
np.asarray([0, 0, 1, 2], dtype=np.int32),
np.asarray([[0, 0], [0, 0], [1, 1], [5, 5]], dtype=np.float64),
[[], [0, 2], [], [], [5], [1, 6], [2, 3]],
np.asarray([0, 1, 0, 0, 3, 2, 2], dtype=np.int32),
np.asarray(
[[0, 2, 1], [0, 2, 0], [0, 1, 2], [3, 4, 5], [6, 4, 2], [3, 4, 3], [1, 2, 4]],
dtype=np.float64,
),
)

slicer.make_filtration_non_decreasing()

got = np.asarray(slicer.get_filtrations(), dtype=np.float64)
expected = np.asarray([[5, 5], [5, 5], [5, 5], [5, 5]], dtype=np.float64)
expected = np.asarray(
[[0, 2, 1], [0, 2, 2], [0, 1, 2], [3, 4, 5], [6, 4, 5], [3, 4, 5], [3, 4, 5]],
dtype=np.float64,
)
assert np.array_equal(got, expected)


def test_rank_custom():
B = [[], [0], [0], [0], [0]]
F = [[0, 0], [2, 1], [1, 2], [3, 0], [0, 3]]
Expand Down
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