testVoxelComplex.cpp

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#include "DGtal/base/SetFunctions.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/topology/CubicalComplexFunctions.h"
#include "DGtal/topology/CubicalComplex.h"
#include "DGtal/topology/KhalimskyCellHashFunctions.h"
#include "DGtal/topology/VoxelComplex.h"
#include "DGtal/topology/VoxelComplexFunctions.h"
#include "DGtalCatch.h"
#include <iostream>
#include <unordered_map>
 
#include "DGtal/geometry/volumes/distance/DistanceTransformation.h"
#include "DGtal/geometry/volumes/distance/ExactPredicateLpSeparableMetric.h"
#include "DGtal/geometry/volumes/distance/VoronoiMap.h"
#include "DGtal/images/SimpleThresholdForegroundPredicate.h"
#include "DGtal/kernel/BasicPointPredicates.h"
#include "DGtal/topology/NeighborhoodConfigurations.h"
#include "DGtal/topology/tables/NeighborhoodTables.h"
// #include <DGtal/io/viewers/Viewer3D.h>
 
using namespace std;
using namespace DGtal;
 
// Fixture for object from a diamond set
struct Fixture_complex_diamond {
    // type aliases
    using Point = DGtal::Z3i::Point;
    using Domain = DGtal::Z3i::Domain;
    using KSpace = DGtal::Z3i::KSpace;
 
    using FixtureDigitalTopology = DGtal::Z3i::DT26_6;
    using FixtureDigitalSet = DGtal::DigitalSetByAssociativeContainer<
        DGtal::Z3i::Domain,
        std::unordered_set<typename DGtal::Z3i::Domain::Point>>;
    using FixtureComplex = DGtal::VoxelComplex<KSpace>;
 
 
    // Constructor
    Fixture_complex_diamond() :
        complex_fixture(ks_fixture) {
            create_complex_from_set(create_set());
    }
 
    // fixture data
    FixtureComplex complex_fixture;
    KSpace ks_fixture; // needed because ConstAlias in CC constructor.
 
    // Function members
    FixtureDigitalSet create_set() {
        using namespace DGtal;
 
        // trace.beginBlock ( "Create Fixture_object_diamond" );
        Point p1(-10, -10, -10);
        Point p2(10, 10, 10);
        Domain domain(p1, p2);
        Point c(0, 0, 0);
 
        // diamond of radius 4
        FixtureDigitalSet set_fixture(domain);
        for (auto it = domain.begin(); it != domain.end(); ++it) {
            if ((*it - c).norm1() <= 3)
                set_fixture.insertNew(*it);
        }
        set_fixture.erase(c);
 
        return set_fixture;
    }
 
    FixtureComplex &create_complex_from_set(const FixtureDigitalSet &input_set) {
 
        ks_fixture.init(input_set.domain().lowerBound(),
                        input_set.domain().upperBound(), true);
        complex_fixture = FixtureComplex(ks_fixture);
        complex_fixture.construct(input_set);
        return complex_fixture;
    }
};
 
TEST_CASE_METHOD(Fixture_complex_diamond, "insertVoxel", "[insert][close]") {
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    auto s3 = vc.nbCells(3);
    auto s2 = vc.nbCells(2);
    auto s1 = vc.nbCells(1);
    auto s0 = vc.nbCells(0);
    SECTION("insertVoxel in border") {
        Point p{0, 0, 4};
        auto vc_new = vc;
        vc_new.insertVoxelPoint(p);
        auto sa3 = vc_new.nbCells(3);
        auto sa2 = vc_new.nbCells(2);
        auto sa1 = vc_new.nbCells(1);
        auto sa0 = vc_new.nbCells(0);
        auto d3 = sa3 - s3;
        CHECK(d3 == 1);
        auto d2 = sa2 - s2;
        CHECK(d2 == 5);
        auto d1 = sa1 - s1;
        CHECK(d1 == 8);
        auto d0 = sa0 - s0;
        CHECK(d0 == 4);
    }
    SECTION("insertVoxel isolated") {
        Point p{5, 0, 0};
        auto vc_new = vc;
        vc_new.insertVoxelCell(ks.uSpel(p));
        auto sa3 = vc_new.nbCells(3);
        auto sa2 = vc_new.nbCells(2);
        auto sa1 = vc_new.nbCells(1);
        auto sa0 = vc_new.nbCells(0);
        auto d3 = sa3 - s3;
        CHECK(d3 == 1);
        auto d2 = sa2 - s2;
        CHECK(d2 == 6);
        auto d1 = sa1 - s1;
        CHECK(d1 == 12);
        auto d0 = sa0 - s0;
        CHECK(d0 == 8);
    }
    SECTION("insertVoxel interior") {
        Point p{0, 2, 0};
        auto vc_new = vc;
        vc_new.insertVoxelCell(ks.uSpel(p));
        auto sa3 = vc_new.nbCells(3);
        auto sa2 = vc_new.nbCells(2);
        auto sa1 = vc_new.nbCells(1);
        auto sa0 = vc_new.nbCells(0);
        auto d3 = sa3 - s3;
        CHECK(d3 == 0);
        auto d2 = sa2 - s2;
        CHECK(d2 == 0);
        auto d1 = sa1 - s1;
        CHECK(d1 == 0);
        auto d0 = sa0 - s0;
        CHECK(d0 == 0);
    }
}
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Faces of voxel",
                 "[neighborhood][faces]") {
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    bool closed = true;
    bool no_hint = false;
    auto not_found = vc.end(3);
 
    SECTION("Voxel is in the interior of the complex.") {
        Point p{0, 0, 2};
        auto cellMapIt = vc.findCell(3, ks.uSpel(p));
        CHECK(cellMapIt != not_found);
        auto cell = cellMapIt->first;
        auto kfaces = ks.uFaces(cell);
        CAPTURE(p);
        CAPTURE(cell);
        CHECK(kfaces.size() == 26);
        auto vcBoundary_closed = vc.cellBoundary(cell, closed);
        CHECK(vcBoundary_closed.size() == 26);
        auto vcBoundary_no_hint = vc.cellBoundary(cell, no_hint);
        CHECK(vcBoundary_no_hint.size() == 26);
    }
    SECTION("Voxel is in the exterior") {
        Point p{0, 0, 5};
        auto cellMapIt = vc.findCell(3, ks.uSpel(p));
        CHECK(cellMapIt == not_found);
        auto cell = ks.uSpel(p);
        auto kfaces = ks.uFaces(cell);
        CAPTURE(p);
        CAPTURE(cell);
        CHECK(kfaces.size() == 26);
        // We know that is not closed, but checking the differences:
        auto vcBoundary_closed = vc.cellBoundary(cell, closed);
        CHECK(vcBoundary_closed.size() == 26);
        // Right method to call:
        auto vcBoundary_no_hint = vc.cellBoundary(cell, no_hint);
        CHECK(vcBoundary_no_hint.size() == 0);
    }
    SECTION("Voxel is out, but surrounded by in voxels") {
        Point p{0, 0, 0};
        auto cellMapIt = vc.findCell(3, ks.uSpel(p));
        CHECK(cellMapIt == not_found);
        auto cell = ks.uSpel(p);
        auto kfaces = ks.uFaces(cell);
        CAPTURE(p);
        CAPTURE(cell);
        CHECK(kfaces.size() == 26);
        auto vcBoundary_closed = vc.cellBoundary(cell, closed);
        CHECK(vcBoundary_closed.size() == 26);
        auto vcBoundary_no_hint = vc.cellBoundary(cell, no_hint);
        CHECK(vcBoundary_no_hint.size() == 26);
    }
    SECTION("Voxel is in the border") {
        Point p{0, 0, 3};
        auto cellMapIt = vc.findCell(3, ks.uSpel(p));
        CHECK(cellMapIt != not_found);
        auto cell = cellMapIt->first;
        auto kfaces = ks.uFaces(cell);
        CAPTURE(p);
        CAPTURE(cell);
        CHECK(kfaces.size() == 26);
        auto vcBoundary_closed = vc.cellBoundary(cell, closed);
        CHECK(vcBoundary_closed.size() == 26);
        auto vcBoundary_no_hint = vc.cellBoundary(cell, no_hint);
        CHECK(vcBoundary_no_hint.size() == 26);
    }
}
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Neighbors from Object and KSpace",
        "[neighborhood]") {
    auto &vc = complex_fixture;
    SECTION(" get neighbors from Kspace") {
        {
            Dimension dim_voxel = 3;
            auto it = vc.begin(dim_voxel);
            for (std::size_t n = 0; n < 10; ++n)
                ++it;
            auto cell = it->first;
            auto point_from_kspace_1 = cell.preCell().coordinates;
            size_t expected_num_adjacent_voxels = 12;
 
            SECTION("properNeighborhood from KSpace"
                    "does not output all adjacent voxels.") {
 
                size_t expected_kspace_neighborhood = 7;
                auto neigh_k = vc.space().uNeighborhood(cell);
                CHECK(neigh_k.size() == expected_kspace_neighborhood);
 
                auto propN_k = vc.space().uProperNeighborhood(cell);
                CHECK(propN_k.size() == expected_kspace_neighborhood - 1);
            }
 
            SECTION("Getting associated pointels and voxels from input_cell") {
                std::set<FixtureComplex::Cell> pointel_set;
                vc.pointelsFromCell(pointel_set, cell);
                std::set<FixtureComplex::Cell> voxel_set;
                for (auto &&p : pointel_set)
                    vc.spelsFromCell(voxel_set, p);
                SECTION("Gets desired full adjancency for voxels") {
                    CHECK(voxel_set.size() == expected_num_adjacent_voxels);
                }
                auto clique = vc.Kneighborhood(cell);
                CHECK(clique.nbCells(3) == expected_num_adjacent_voxels);
            }
        }
    }
}
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Test Simplicity", "[simplicity]") {
    auto &vc = complex_fixture;
    Dimension dim_voxel = 3;
    auto cit = vc.begin(dim_voxel);
    for (std::size_t n = 0; n < 10; ++n)
        ++cit;
    auto cell = cit->first;
 
    SECTION("querying voxel simplicity") {
        size_t nsimples{0};
        std::vector<FixtureComplex::Cell> non_simple_cells;
        for (auto it = vc.begin(dim_voxel); it != vc.end(dim_voxel); ++it) {
            if (vc.isSimple(it->first))
                ++nsimples;
            else
                non_simple_cells.emplace_back(it->first);
        }
 
        // Border points are simple in diamond.
        // auto border_size = vc.object().border().size();
        size_t border_size = 44;
        REQUIRE(nsimples == border_size);
    }
}
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Test table wrappers",
                 "[table][simple]") {
    auto &vc = complex_fixture;
    trace.beginBlock("loadTable");
    vc.setSimplicityTable(functions::loadTable(simplicity::tableSimple26_6));
    trace.endBlock();
    auto dim_voxel = 3;
    auto cit = vc.begin(dim_voxel);
    for (std::size_t n = 0; n < 10; ++n)
        ++cit;
    auto cell = cit->first;
 
    SECTION("querying voxel simplicity") {
        size_t nsimples{0};
        std::vector<FixtureComplex::Cell> non_simple_cells;
        for (auto it = vc.begin(dim_voxel); it != vc.end(dim_voxel); ++it) {
            if (vc.isSimple(it->first))
                ++nsimples;
            else
                non_simple_cells.emplace_back(it->first);
        }
 
        // Border points are simple in diamond.
        size_t border_size = 44;
        REQUIRE(nsimples == border_size);
    }
}
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Cliques Masks K_2", "[clique]") {
    auto &vc = complex_fixture;
    auto itc = vc.begin(3);
    for (std::size_t n = 0; n < 10; ++n)
        ++itc;
    auto cell = itc->first;
    Point p_cell = vc.space().uCoords(cell);
    auto neigh6 = vc.space().uProperNeighborhood(cell);
    REQUIRE(neigh6.size() == 6);
    KSpace::Cells cells;
    for(auto & n : neigh6)
        if(vc.belongs(n)) cells.push_back(n);
    REQUIRE(cells.size() == 2);
 
    std::vector<std::pair<bool, FixtureComplex::Clique>> cliques_p;
    bool verbose = true;
    for (auto && cell_n : cells) {
        auto cell_point = vc.space().uCoords(cell_n);
        cliques_p.emplace_back(vc.K_2(p_cell, cell_point, verbose));
        auto &is_critical = cliques_p.back().first;
        auto &k2_clique = cliques_p.back().second;
        CHECK(is_critical == true);
        CHECK(k2_clique.nbCells(3) == 2);
    }
 
    SECTION(" Check same results for different K_2 interfaces") {
        for (auto && cell_n : cells) {
            auto co_face = vc.surfelBetweenAdjacentSpels(cell_n, cell);
 
            auto cell_point = vc.space().uCoords(cell_n);
            using namespace DGtal::functions;
            CHECK(isEqual(vc.K_2(p_cell, cell_point, false).second,
                          vc.K_2(cell, cell_n, false).second) == true);
            CHECK(isEqual(vc.K_2(p_cell, cell_point, false).second,
                          vc.K_2(co_face, false).second) == true);
        } // endfor
    }     // then_interfaces
} // test
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Cliques Masks K_1", "[clique]") {
    auto &vc = complex_fixture;
    auto itc = vc.begin(3);
    for (std::size_t n = 0; n < 10; ++n)
        ++itc;
    auto cell = itc->first;
    Point p_cell = vc.space().uCoords(cell);
 
    SECTION("K_1 mask from a linel") {
        auto linel =
            vc.space().uCell(cell.preCell().coordinates + Point{0, 1, 1});
 
        using namespace DGtal::functions;
        auto k1p = vc.K_1(linel, true);
        auto &is_critical = k1p.first;
        CHECK(is_critical == true);
        auto &k1_clique = k1p.second;
        // numer of voxels in clique
        CHECK(k1_clique.nbCells(3) == 3);
    }
} // test
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Cliques Masks K_0", "[clique]") {
    auto &vc = complex_fixture;
    auto itc = vc.begin(3);
    for (std::size_t n = 0; n < 10; ++n)
        ++itc;
    auto cell = itc->first;
    Point p_cell = vc.space().uCoords(cell);
 
    SECTION("K_0 mask from a pointel") {
        auto pointel = vc.space().uPointel(p_cell);
        // auto pointel = vc.space().uPointel(Point{0,0,0});
 
        using namespace DGtal::functions;
        auto k0_mask = vc.K_0(pointel, true);
 
        auto &is_critical = k0_mask.first;
        CHECK(is_critical == false);
        auto &k0_clique = k0_mask.second;
        // numer of voxels in clique
        CHECK(k0_clique.nbCells(3) == 1);
    }
} // test
 
TEST_CASE_METHOD(Fixture_complex_diamond, "Get All Critical Cliques of diamond",
                 "[critical][clique]") {
    auto &vc = complex_fixture;
    using namespace DGtal::functions;
    SECTION(" Get all criticalCliques() ") {
        auto criticals = vc.criticalCliques();
        CHECK(criticals.size() == 4);
 
        CHECK(vc.nbCells(3) == 62);
        CHECK(criticals[3].size() == 18);
        CHECK(vc.nbCells(2) == 264);
        CHECK(criticals[2].size() == 108);
        CHECK(vc.nbCells(1) == 360);
        CHECK(criticals[1].size() == 168);
        CHECK(vc.nbCells(0) == 160);
        CHECK(criticals[0].size() == 32);
    }
}
 
 
// Fixture for complex fig 4 of Asymmetric parallel 3D thinning scheme
struct Fixture_complex_fig4 {
    // type aliases
    using Point = DGtal::Z3i::Point;
    using Domain = DGtal::Z3i::Domain;
    using KSpace = DGtal::Z3i::KSpace;
 
    using FixtureDigitalSet = DGtal::DigitalSetByAssociativeContainer<
        DGtal::Z3i::Domain,
        std::unordered_set<typename DGtal::Z3i::Domain::Point>>;
    using FixtureMap = std::unordered_map<KSpace::Cell, CubicalCellData>;
    using FixtureComplex = DGtal::VoxelComplex<KSpace, FixtureMap>;
 
    // fixture data
    FixtureComplex complex_fixture;
    KSpace ks_fixture; // needed because ConstAlias in CC constructor.
 
    // Constructor
    Fixture_complex_fig4() : complex_fixture(ks_fixture) {
        create_complex_from_set(create_set());
    }
 
    // Function members
    FixtureDigitalSet create_set() {
        using namespace DGtal;
 
        Point p1(-10, -10, -10);
        Point p2(10, 10, 10);
        Domain domain(p1, p2);
 
        // 12 voxels of fig4, centered in critical voxel
        FixtureDigitalSet fig4_set(domain);
        Point a1(0, 0, 0);
        fig4_set.insertNew(a1);
        Point a2(0, -1, 0);
        fig4_set.insertNew(a2);
        Point a3(1, -1, 0);
        fig4_set.insertNew(a3);
        Point c1(0, 1, -1);
        fig4_set.insertNew(c1);
        Point c2(1, 1, -1);
        fig4_set.insertNew(c2);
        Point c3(1, 2, -1);
        fig4_set.insertNew(c3);
        Point c4(0, 2, -1);
        fig4_set.insertNew(c4);
        Point b1(0, 2, 0);
        fig4_set.insertNew(b1);
        Point b2(-1, 3, 0);
        fig4_set.insertNew(b2);
        Point l1(1, 0, -2);
        fig4_set.insertNew(l1);
        Point l2(2, 0, -2);
        fig4_set.insertNew(l2);
        Point r1(1, 3, -2);
        fig4_set.insertNew(r1);
 
        return fig4_set;
    }
 
    FixtureComplex &create_complex_from_set(const FixtureDigitalSet &input_set) {
 
        ks_fixture.init(input_set.domain().lowerBound(),
                        input_set.domain().upperBound(), true);
        complex_fixture = FixtureComplex(ks_fixture);
        complex_fixture.construct(input_set);
        return complex_fixture;
    }
};
TEST_CASE_METHOD(Fixture_complex_fig4, "Get All Critical Cliques of fig4",
                 "[critical][clique]") {
    auto &vc = complex_fixture;
    using namespace DGtal::functions;
    SECTION(" Get all criticalCliques() ") {
        auto criticals = vc.criticalCliques(true);
        CHECK(criticals.size() == 4);
 
        CHECK(vc.nbCells(3) == 12);
        CHECK(criticals[3].size() == 1);
        CHECK(vc.nbCells(2) == 64);
        CHECK(criticals[2].size() == 3);
        CHECK(vc.nbCells(1) == 109);
        CHECK(criticals[1].size() == 2);
        CHECK(vc.nbCells(0) == 58);
        CHECK(criticals[0].size() == 6);
    }
}
 
/* zeroSurface and oneSurface */
TEST_CASE_METHOD(Fixture_complex_fig4, "zeroSurface and oneSurface",
                 "[isSurface][function]") {
    auto &vc = complex_fixture;
    using namespace DGtal::functions;
    vc.clear();
    Point c(0, 0, 0);
    {
        vc.insertCell(3, vc.space().uSpel(c));
    }
    Point r(0, 1, 0);
    {
        vc.insertCell(3, vc.space().uSpel(r));
    }
    Point l(0, -1, 0);
    {
        vc.insertCell(3, vc.space().uSpel(l));
    }
    // Init an object
    using DigitalTopology = DGtal::Z3i::DT26_6;
    using DigitalSet = DGtal::DigitalSetByAssociativeContainer<
        DGtal::Z3i::Domain,
        std::unordered_set<typename DGtal::Z3i::Domain::Point>>;
    using Object = DGtal::Object<DigitalTopology, DigitalSet>;
    DigitalTopology::ForegroundAdjacency adjF;
    DigitalTopology::BackgroundAdjacency adjB;
    auto domain = DGtal::Z3i::Domain(ks_fixture.lowerBound(), ks_fixture.upperBound());
    DigitalTopology topo(
            adjF, adjB, DGtal::DigitalTopologyProperties::JORDAN_DT);
 
    SECTION("checking zero surfaces of original set") {
        std::set<Point> zeroSurfacesCells;
        DigitalSet voxel_set(domain);
        vc.dumpVoxels(voxel_set);
        Object object(topo, voxel_set);
        for (const auto &p : voxel_set) {
            auto small_obj = object.properNeighborhood(p);
            if (isZeroSurface(small_obj))
                zeroSurfacesCells.insert(p);
        }
        CHECK(zeroSurfacesCells.size() == 1);
    }
 
    SECTION("checking one surfaces of original set") {
        Point u(-1, 0, 0);
        {
            vc.insertCell(3, vc.space().uSpel(u));
        }
        Point d(1, 0, 0);
        {
            vc.insertCell(3, vc.space().uSpel(d));
        }
 
        std::set<Point> oneSurfacesCells;
        DigitalSet voxel_set(domain);
        vc.dumpVoxels(voxel_set);
        Object object(topo, voxel_set);
 
        for (const auto &p : voxel_set) {
            auto small_obj = object.properNeighborhood(p);
            if (isOneSurface(small_obj))
                oneSurfacesCells.insert(p);
        }
        CHECK(oneSurfacesCells.size() == 1);
    }
}
 
// Fixture for complex fig 4 of Asymmetric parallel 3D thinning scheme
struct Fixture_isthmus {
    // type aliases
    using Point = DGtal::Z3i::Point;
    using Domain = DGtal::Z3i::Domain;
    using KSpace = DGtal::Z3i::KSpace;
 
    using FixtureDigitalTopology = DGtal::Z3i::DT26_6;
    using FixtureDigitalSet = DGtal::DigitalSetByAssociativeContainer<
        DGtal::Z3i::Domain,
        std::unordered_set<typename DGtal::Z3i::Domain::Point>>;
    using FixtureMap = std::unordered_map<KSpace::Cell, CubicalCellData>;
    using FixtureComplex = DGtal::VoxelComplex<KSpace, FixtureMap>;
 
    // fixture data
    FixtureComplex complex_fixture;
    FixtureDigitalSet set_fixture;
    KSpace ks_fixture; // needed because ConstAlias in CC constructor.
 
    // Constructor
    Fixture_isthmus() : complex_fixture(ks_fixture), set_fixture(create_set()) {
        create_complex_from_set(set_fixture);
    }
 
    // Function members
    FixtureDigitalSet create_set() {
        using namespace DGtal;
 
        Point p1(-10, -10, -10);
        Point p2(10, 10, 10);
        Domain domain(p1, p2);
 
        FixtureDigitalSet fig6_set(domain);
 
        Point c00(0, 0, 0);
        fig6_set.insertNew(c00);
        Point c01(-1, 0, 0);
        fig6_set.insertNew(c01);
        Point c02(-2, 0, 0);
        fig6_set.insertNew(c02);
        Point c03(-2, 0, 1);
        fig6_set.insertNew(c03);
 
        Point c10(0, 1, 0);
        fig6_set.insertNew(c10);
        Point y(-1, 1, 0);
        fig6_set.insertNew(y);
        Point c12(-2, 1, 0);
        fig6_set.insertNew(c12);
        Point c13(-2, 1, 1);
        fig6_set.insertNew(c13);
 
        Point c20(0, 2, 0);
        fig6_set.insertNew(c20);
        Point c21(-1, 2, 0);
        fig6_set.insertNew(c21);
        Point c22(-1, 2, 1);
        fig6_set.insertNew(c22);
        Point c33(-1, 2, -1);
        fig6_set.insertNew(c33);
 
        Point c30(-1, 3, 0);
        fig6_set.insertNew(c30);
        Point c31(-1, 3, 1);
        fig6_set.insertNew(c31);
 
        Point x(-1, 4, 0);
        fig6_set.insertNew(x);
 
        Point c50(-1, 5, 0);
        fig6_set.insertNew(c50);
        Point c51(-1, 5, -1);
        fig6_set.insertNew(c51);
        Point c52(-2, 5, 0);
        fig6_set.insertNew(c52);
 
        Point c60(-1, 6, 0);
        fig6_set.insertNew(c60);
        Point c61(-2, 6, 0);
        fig6_set.insertNew(c61);
        Point c62(-2, 6, -1);
        fig6_set.insertNew(c62);
 
        return fig6_set;
    }
 
    FixtureComplex &create_complex_from_set(const FixtureDigitalSet &input_set) {
 
        ks_fixture.init(input_set.domain().lowerBound(),
                        input_set.domain().upperBound(), true);
        complex_fixture = FixtureComplex(ks_fixture);
        complex_fixture.construct(input_set);
        return complex_fixture;
    }
};
 
TEST_CASE_METHOD(Fixture_isthmus, "Thin disconnected complex",
                 "[isthmus][thin][function]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    Point x(-1, 4, 0);
    set_fixture.erase(x);
    // Delete one point and reconstruct complex.
    /* obj_fixture.pointSet().erase(x); */
    vc.clear();
    vc.construct(set_fixture);
    SECTION("with skelUltimate") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectFirst<FixtureComplex>, skelUltimate<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 2);
    }
}
 
 
TEST_CASE_METHOD(Fixture_isthmus, "Check isthmus", "[isthmus][function]") {
    auto &vc = complex_fixture;
    using namespace DGtal::functions;
    auto &ks = vc.space();
    Point x(-1, 4, 0); // oneIsthmus
    Point y(-1, 1, 0); // twoIsthmus
 
    SECTION("checking one isthmus") {
        std::set<Point> isthmus;
        for (const auto &p : set_fixture) {
            if (oneIsthmus(vc, ks.uSpel(p)))
                isthmus.insert(p);
        }
        CHECK(isthmus.size() == 1);
        auto xit = isthmus.find(x);
        CHECK(*xit == x);
    }
 
    SECTION("checking 2 isthmus") {
        std::set<Point> isthmus;
        for (const auto &p : set_fixture) {
            if (twoIsthmus(vc, ks.uSpel(p)))
                isthmus.insert(p);
        }
        CHECK(isthmus.size() == 1);
        auto yit = isthmus.find(y);
        CHECK(*yit == y);
    }
 
    SECTION("checking 1 and 2 isthmus") {
        std::set<Point> isthmus;
        for (const auto &p : set_fixture) {
            if (skelIsthmus(vc, ks.uSpel(p)))
                isthmus.insert(p);
        }
        CHECK(isthmus.size() == 2);
        auto xit = isthmus.find(x);
        auto yit = isthmus.find(y);
        CHECK(xit != isthmus.end());
        CHECK(yit != isthmus.end());
    }
}
TEST_CASE_METHOD(Fixture_isthmus, "Thin complex", "[isthmus][thin][function]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    SECTION("with skelUltimate") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectFirst<FixtureComplex>, skelUltimate<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 1);
    }
    SECTION("with skelEnd") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectFirst<FixtureComplex>, skelEnd<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 5);
    }
    SECTION("with oneIsthmus") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, oneIsthmus<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 3);
    }
    SECTION("with twoIsthmus") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, twoIsthmus<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 1);
    }
    SECTION("with skelIsthmus") {
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelIsthmus<FixtureComplex>);
        CHECK(vc_new.nbCells(3) == 3);
    }
}
//
TEST_CASE_METHOD(Fixture_isthmus, "Persistence thin",
                 "[persistence][isthmus][thin][function]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    SECTION("with skelUltimate") {
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelUltimate<FixtureComplex>, 0);
        CHECK(vc_new.nbCells(3) == 1);
    }
    SECTION("with skelEnd") {
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelEnd<FixtureComplex>, 0);
        CHECK(vc_new.nbCells(3) == 5);
    }
    SECTION("with oneIsthmus") {
        // Not using LUT skel function (slow):
        //auto vc_new = persistenceAsymetricThinningScheme< FixtureComplex >(
        //    vc, selectRandom<FixtureComplex>, oneIsthmus<FixtureComplex>, 0);
        //
        // with LUT:
        auto table = *functions::loadTable(isthmusicity::tableOneIsthmus);
        auto pointToMaskMap =
            *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
        auto oneIsthmusTable =
            [&table, &pointToMaskMap](const FixtureComplex &fc,
                                      const FixtureComplex::Cell &c) {
                return skelWithTable(table, pointToMaskMap, fc, c);
            };
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, oneIsthmusTable, 0);
        CHECK(vc_new.nbCells(3) == 3);
    }
    SECTION("with twoIsthmus") {
        // Not using LUT skel function (slow):
        //auto vc_new = persistenceAsymetricThinningScheme< FixtureComplex >(
        //    vc, selectRandom<FixtureComplex>, twoIsthmus<FixtureComplex>, 0);
        //
        // with LUT:
        auto table = *functions::loadTable(isthmusicity::tableTwoIsthmus);
        auto pointToMaskMap =
            *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
        auto twoIsthmusTable =
            [&table, &pointToMaskMap](const FixtureComplex &fc,
                                      const FixtureComplex::Cell &c) {
                return skelWithTable(table, pointToMaskMap, fc, c);
            };
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, twoIsthmusTable, 0);
        CHECK(vc_new.nbCells(3) == 1);
    }
    SECTION("with skelIsthmus") {
        // Not using LUT skel function (slow):
        //auto vc_new = persistenceAsymetricThinningScheme< FixtureComplex >(
        //   vc, selectRandom<FixtureComplex>, skelIsthmus<FixtureComplex>, 0);
        //
        // with LUT:
        auto table = *functions::loadTable(isthmusicity::tableIsthmus);
        auto pointToMaskMap =
            *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
        auto isthmusTable = [&table,
                             &pointToMaskMap](const FixtureComplex &fc,
                                              const FixtureComplex::Cell &c) {
            return skelWithTable(table, pointToMaskMap, fc, c);
        };
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, isthmusTable, 0);
        CHECK(vc_new.nbCells(3) == 3);
    }
}
 
// Fixture for an X
struct Fixture_X {
    // type aliases
    using Point = DGtal::Z3i::Point;
    using Domain = DGtal::Z3i::Domain;
    using KSpace = DGtal::Z3i::KSpace;
 
    using FixtureDigitalTopology = DGtal::Z3i::DT26_6;
    using FixtureDigitalSet = DGtal::DigitalSetByAssociativeContainer<
        DGtal::Z3i::Domain,
        std::unordered_set<typename DGtal::Z3i::Domain::Point>>;
    using FixtureMap = std::unordered_map<KSpace::Cell, CubicalCellData>;
    using FixtureComplex = DGtal::VoxelComplex<KSpace>;
 
    // fixture data
    FixtureComplex complex_fixture;
    FixtureDigitalSet set_fixture;
    KSpace ks_fixture; // needed because ConstAlias in CC constructor.
 
    // Constructor
    Fixture_X() : complex_fixture(ks_fixture), set_fixture(create_set()) {
        create_complex_from_set(set_fixture);
    }
 
    // Function members
    FixtureDigitalSet create_set() {
        using namespace DGtal;
 
        Point p1(-16, -16, -16);
        Point p2(16, 16, 16);
        Domain domain(p1, p2);
 
        FixtureDigitalSet a_set(domain);
        std::vector<Point> center_set;
        center_set.reserve(9);
 
        Point c00(0, 0, 0);
        center_set.push_back(c00);
        Point c01x(-1, 0, 0);
        center_set.push_back(c01x);
        Point c10x(1, 0, 0);
        center_set.push_back(c10x);
        Point c02x(-2, 0, 0);
        center_set.push_back(c02x);
        Point c20x(2, 0, 0);
        center_set.push_back(c20x);
 
        Point c01y(0, -1, 0);
        center_set.push_back(c01y);
        Point c10y(0, 1, 0);
        center_set.push_back(c10y);
        Point c02y(0, -2, 0);
        center_set.push_back(c02y);
        Point c20y(0, 2, 0);
        center_set.push_back(c20y);
 
        Point z_pos(0, 0, 1);
        int branch_length(4);
        std::vector<Point> diagonals;
        diagonals.reserve(6);
        for (const auto &p : center_set) {
            diagonals.clear();
            for (int l = 0; l <= branch_length; ++l) {
                diagonals.push_back({l, l, 0});
                diagonals.push_back({l, -l, 0});
                diagonals.push_back({-l, l, 0});
                diagonals.push_back({-l, -l, 0});
                for (int z = -1; z <= 1; ++z)
                    for (const auto &d : diagonals)
                        a_set.insert(p + d + (z * z_pos));
            }
        }
 
                return a_set;
    }
 
    FixtureComplex &create_complex_from_set(FixtureDigitalSet &input_set) {
 
        ks_fixture.init(input_set.domain().lowerBound(),
                        input_set.domain().upperBound(), true);
        complex_fixture = FixtureComplex(ks_fixture);
        complex_fixture.construct(input_set);
        return complex_fixture;
    }
};
 
TEST_CASE_METHOD(Fixture_X, "X Thin",
                 "[x][persistence][isthmus][thin][function]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    bool verbose = true;
    SECTION(
        "persistence value of 1 is equivalent to the assymetric algorithm") {
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectFirst<FixtureComplex>, skelEnd<FixtureComplex>, 1,
            verbose);
 
        auto vc_assymetric = asymetricThinningScheme<FixtureComplex>(
            vc, selectFirst<FixtureComplex>, skelEnd<FixtureComplex>, true);
        // 10% tolerance
        CHECK(vc_assymetric.nbCells(3) ==
              Approx(vc_new.nbCells(3)).epsilon(0.1));
    }
    SECTION("persistence value: infinite is equivalent to ultimate skeleton") {
        auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelEnd<FixtureComplex>, 100,
            verbose);
        REQUIRE(vc_new.nbCells(3) == 1);
    }
}
 
TEST_CASE_METHOD(Fixture_X, "X Thin with Isthmus, and tables",
                 "[x][isthmus][thin][function][table]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    bool verbose = true;
 
    // Disabled to reduce test time
    // SECTION("Compute with skelIsthmus") {
    //     trace.beginBlock("Fixture_X skelIsthmus");
    //     auto vc_new = asymetricThinningScheme<FixtureComplex>(
    //         vc, selectRandom<FixtureComplex>, skelIsthmus<FixtureComplex>,
    //         verbose);
    //     trace.endBlock();
    // }
    SECTION("Compute with skelWithTable (isIsthmus)") {
        trace.beginBlock("Fixture_X skelIsthmus with table");
        auto table = *functions::loadTable(isthmusicity::tableIsthmus);
        auto pointToMaskMap =
            *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
        auto skelWithTableIsthmus =
            [&table, &pointToMaskMap](const FixtureComplex &fc,
                                      const FixtureComplex::Cell &c) {
                return skelWithTable(table, pointToMaskMap, fc, c);
            };
 
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelWithTableIsthmus, verbose);
 
        trace.endBlock();
    }
 
    SECTION("Compute with skelWithTable (isIsthmus) and empty Object") {
        trace.beginBlock("Fixture_X skelIsthmus with table (empty objectSet)");
        vc.setSimplicityTable(
            functions::loadTable(simplicity::tableSimple26_6));
        vc.clear();
        auto table = *functions::loadTable(isthmusicity::tableIsthmus);
        auto pointToMaskMap =
            *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
        auto skelWithTableIsthmus =
            [&table, &pointToMaskMap](const FixtureComplex &fc,
                                      const FixtureComplex::Cell &c) {
                return skelWithTable(table, pointToMaskMap, fc, c);
            };
 
        auto vc_new = asymetricThinningScheme<FixtureComplex>(
            vc, selectRandom<FixtureComplex>, skelWithTableIsthmus, verbose);
 
        trace.endBlock();
    }
}
 
TEST_CASE_METHOD(Fixture_X, "X DistanceMap", "[x][distance][thin]") {
    using namespace DGtal::functions;
    auto &vc = complex_fixture;
    auto &ks = vc.space();
    boost::ignore_unused_variable_warning(ks);
    using Predicate = Z3i::DigitalSet;
    using L3Metric = ExactPredicateLpSeparableMetric<Z3i::Space, 3>;
    using DT = DistanceTransformation<Z3i::Space, Predicate, L3Metric>;
    bool verbose = true;
    SECTION("Fixture_X Distance Map") {
        trace.beginBlock("With a Distance Map");
        L3Metric l3;
        DT dt(set_fixture.domain(), set_fixture, l3);
        // Create wrap around selectMaxValue to use the thinning.
        auto selectDistMax = [&dt](const FixtureComplex::Clique &clique) {
            return selectMaxValue<DT, FixtureComplex>(dt, clique);
        };
        SECTION("asymetricThinning"){
            auto vc_new = asymetricThinningScheme<FixtureComplex>(
                    vc, selectDistMax, skelEnd<FixtureComplex>, verbose);
        }
        SECTION("persistenceThinning"){
            auto table = *functions::loadTable(isthmusicity::tableOneIsthmus);
            auto pointToMaskMap =
                *functions::mapZeroPointNeighborhoodToConfigurationMask<Point>();
            auto oneIsthmusTable =
                [&table, &pointToMaskMap](const FixtureComplex &fc,
                        const FixtureComplex::Cell &c) {
                    return skelWithTable(table, pointToMaskMap, fc, c);
                };
            int persistence = 3;
            auto vc_new = persistenceAsymetricThinningScheme<FixtureComplex>(
                    vc, selectDistMax, oneIsthmusTable,
                    persistence, verbose);
            // SECTION( "visualize the thining" ){
            //     int argc(1);
            //     char** argv(nullptr);
            //     QApplication app(argc, argv);
            //     Viewer3D<> viewer(ks_fixture);
            //     viewer.show();
            //
            //     viewer.setFillColor(Color(200, 200, 200, 100));
            //     for ( auto it = vc_new.begin(3); it!= vc_new.end(3); ++it )
            //         viewer << it->first;
            //
            //     // All kspace voxels
            //     viewer.setFillColor(Color(40, 40, 40, 10));
            //     for ( auto it = vc.begin(3); it!= vc.end(3); ++it )
            //         viewer << it->first;
            //
            //     viewer << Viewer3D<>::updateDisplay;
            //     app.exec();
            // }
        }
 
    }
 
    trace.endBlock();
}
 
// REQUIRE(vc_new.nbCells(3) == 38);