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removal of child pointer + factorization of intrusive list column
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@hschreiber
hschreiber committed Sep 28, 2023
1 parent cc168c2 commit bd9234d
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Showing 26 changed files with 2,438 additions and 1,484 deletions.
31 changes: 14 additions & 17 deletions src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@ namespace persistence_matrix {

template<class Master_matrix>
class Base_matrix
: public Master_matrix::Base_swap_option, protected Master_matrix::Matrix_row_access_option
: public Master_matrix::template Base_swap_option<Base_matrix<Master_matrix> >,
protected Master_matrix::Matrix_row_access_option
{
public:
using index = typename Master_matrix::index;
Expand Down Expand Up @@ -73,8 +74,8 @@ class Base_matrix

Base_matrix& operator=(const Base_matrix& other);
friend void swap(Base_matrix& matrix1, Base_matrix& matrix2){
swap(static_cast<typename Master_matrix::Base_swap_option&>(matrix1),
static_cast<typename Master_matrix::Base_swap_option&>(matrix2));
swap(static_cast<typename Master_matrix::template Base_swap_option<Base_matrix<Master_matrix> >&>(matrix1),
static_cast<typename Master_matrix::template Base_swap_option<Base_matrix<Master_matrix> >&>(matrix2));
matrix1.matrix_.swap(matrix2.matrix_);
std::swap(matrix1.nextInsertIndex_, matrix2.nextInsertIndex_);

Expand Down Expand Up @@ -102,7 +103,7 @@ class Base_matrix
void print(); //for debug

private:
using swap_opt = typename Master_matrix::Base_swap_option;
using swap_opt = typename Master_matrix::template Base_swap_option<Base_matrix<Master_matrix> >;
using ra_opt = typename Master_matrix::Matrix_row_access_option;
using matrix_type = typename Master_matrix::column_container_type;
using cell_rep_type = typename std::conditional<
Expand All @@ -111,6 +112,8 @@ class Base_matrix
std::pair<index,Field_element_type>
>::type;

friend swap_opt; //direct access to matrix_ to avoid row reorder.

matrix_type matrix_;
index nextInsertIndex_;

Expand All @@ -119,15 +122,15 @@ class Base_matrix

template<class Master_matrix>
inline Base_matrix<Master_matrix>::Base_matrix()
: swap_opt(matrix_),
: swap_opt(),
ra_opt(),
nextInsertIndex_(0)
{}

template<class Master_matrix>
template<class Container_type>
inline Base_matrix<Master_matrix>::Base_matrix(const std::vector<Container_type> &columns)
: swap_opt(matrix_, columns.size()),
: swap_opt(columns.size()),
ra_opt(columns.size()), //not ideal if max row index is much smaller than max column index, does that happen often?
matrix_(!Master_matrix::Option_list::has_removable_columns && Master_matrix::Option_list::has_row_access ? 0 : columns.size()),
nextInsertIndex_(columns.size())
Expand All @@ -154,7 +157,7 @@ inline Base_matrix<Master_matrix>::Base_matrix(const std::vector<Container_type>

template<class Master_matrix>
inline Base_matrix<Master_matrix>::Base_matrix(unsigned int numberOfColumns)
: swap_opt(matrix_, numberOfColumns),
: swap_opt(numberOfColumns),
ra_opt(numberOfColumns),
matrix_(!Master_matrix::Option_list::has_removable_columns && Master_matrix::Option_list::has_row_access ? 0 : numberOfColumns),
nextInsertIndex_(0)
Expand All @@ -165,13 +168,10 @@ inline Base_matrix<Master_matrix>::Base_matrix(unsigned int numberOfColumns)

template<class Master_matrix>
inline Base_matrix<Master_matrix>::Base_matrix(const Base_matrix &matrixToCopy)
: swap_opt(matrixToCopy),
ra_opt(matrixToCopy),
: swap_opt(static_cast<const swap_opt&>(matrixToCopy)),
ra_opt(static_cast<const ra_opt&>(matrixToCopy)),
nextInsertIndex_(matrixToCopy.nextInsertIndex_)
{
if constexpr (Master_matrix::Option_list::has_column_and_row_swaps)
swap_opt::matrix_ = &matrix_;

if constexpr (Master_matrix::Option_list::has_row_access){
matrix_.reserve(matrixToCopy.matrix_.size());
if constexpr (Master_matrix::Option_list::has_removable_columns){
Expand All @@ -191,14 +191,11 @@ inline Base_matrix<Master_matrix>::Base_matrix(const Base_matrix &matrixToCopy)

template<class Master_matrix>
inline Base_matrix<Master_matrix>::Base_matrix(Base_matrix &&other) noexcept
: swap_opt(std::move(other)),
ra_opt(std::move(other)),
: swap_opt(std::move(static_cast<swap_opt&>(other))),
ra_opt(std::move(static_cast<ra_opt&>(other))),
matrix_(std::move(other.matrix_)),
nextInsertIndex_(std::exchange(other.nextInsertIndex_, 0))
{
if constexpr (Master_matrix::Option_list::has_column_and_row_swaps)
swap_opt::matrix_ = &matrix_;

if constexpr (Master_matrix::Option_list::has_row_access){
if constexpr (Master_matrix::Option_list::has_removable_columns){
for (auto& p : matrix_){
Expand Down
5 changes: 5 additions & 0 deletions src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_row_access.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,11 @@
namespace Gudhi {
namespace persistence_matrix {

struct Dummy_matrix_row_access{
Dummy_matrix_row_access(){};
Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfColumns){};
};

template<typename Row_type, typename Row_container_type, bool has_removable_rows, typename index>
class Base_matrix_row_access
{
Expand Down
25 changes: 9 additions & 16 deletions ...Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h
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Original file line number Diff line number Diff line change
Expand Up @@ -48,34 +48,27 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
Column_type(const Container_type& nonZeroRowIndices)
: Base(nonZeroRowIndices)
{}
template<class Container_type>
Column_type(const Container_type& nonZeroRowIndices, dimension_type dimension)
: Base(nonZeroRowIndices, dimension)
{}
template<class Row_container_type>
Column_type(index columnIndex, Row_container_type &rowContainer)
: Base(columnIndex, rowContainer)
{}
template<class Container_type, class Row_container_type>
Column_type(index columnIndex, const Container_type& nonZeroRowIndices, Row_container_type &rowContainer)
: Base(columnIndex, nonZeroRowIndices, rowContainer)
{}
template<class Container_type>
Column_type(const Container_type& nonZeroRowIndices, dimension_type dimension)
: Base(nonZeroRowIndices, dimension)
{}
template<class Container_type, class Row_container_type>
Column_type(index columnIndex, const Container_type& nonZeroRowIndices, dimension_type dimension, Row_container_type &rowContainer)
: Base(columnIndex, nonZeroRowIndices, dimension, rowContainer)
{}
Column_type(const Column_type& column)
: Base(static_cast<const Base&>(column))
{}
Column_type(const Column_type& column, index columnIndex)
: Base(static_cast<const Base&>(column), columnIndex)
{}
template<class Row_container_type>
Column_type(const Column_type& column, index columnIndex, Row_container_type &rowContainer)
: Base(static_cast<const Base&>(column), columnIndex, rowContainer)
{}
Column_type(Column_type&& column) noexcept
: Base(std::move(static_cast<Base&&>(column)))
: Base(std::move(static_cast<Base&>(column)))
{}

index get_rep() const{
Expand All @@ -88,7 +81,7 @@ class Base_matrix_with_column_compression : protected Master_matrix::Matrix_row_
struct Hasher {
size_t operator()(const Column_type& c) const
{
return std::hash<Base>()(c);
return std::hash<Base>()(static_cast<Base>(c));
}
};

Expand Down Expand Up @@ -216,7 +209,7 @@ inline Base_matrix_with_column_compression<Master_matrix>::Base_matrix_with_colu

template<class Master_matrix>
inline Base_matrix_with_column_compression<Master_matrix>::Base_matrix_with_column_compression(const Base_matrix_with_column_compression &matrixToCopy)
: ra_opt(matrixToCopy),
: ra_opt(static_cast<const ra_opt&>(matrixToCopy)),
columnClasses_(matrixToCopy.columnClasses_),
repToColumn_(matrixToCopy.repToColumn_.size(), nullptr),
nextColumnIndex_(0)
Expand All @@ -237,7 +230,7 @@ inline Base_matrix_with_column_compression<Master_matrix>::Base_matrix_with_colu

template<class Master_matrix>
inline Base_matrix_with_column_compression<Master_matrix>::Base_matrix_with_column_compression(Base_matrix_with_column_compression &&other) noexcept
: ra_opt(std::move(other)),
: ra_opt(std::move(static_cast<ra_opt&>(other))),
columnToRep_(std::move(other.columnToRep_)),
columnClasses_(std::move(other.columnClasses_)),
repToColumn_(std::move(other.repToColumn_)),
Expand Down Expand Up @@ -512,7 +505,7 @@ inline void Base_matrix_with_column_compression<Master_matrix>::_insert_column(i
return;
}

repToColumn_[columnIndex]->set_rep(columnIndex);
col.set_rep(columnIndex);
auto res = columnToRep_.insert(col);
if (res.first->get_rep() != columnIndex){
_insert_double_column(columnIndex, res.first);
Expand Down
50 changes: 28 additions & 22 deletions src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,15 @@
namespace Gudhi {
namespace persistence_matrix {

struct Dummy_base_pairing{
Dummy_base_pairing& operator=([[maybe_unused]] Dummy_base_pairing other){return *this;}
friend void swap([[maybe_unused]] Dummy_base_pairing& d1, [[maybe_unused]] Dummy_base_pairing& d2){}

Dummy_base_pairing(){}
Dummy_base_pairing([[maybe_unused]] const Dummy_base_pairing& matrixToCopy){}
Dummy_base_pairing([[maybe_unused]] Dummy_base_pairing&& other) noexcept{}
};

template<class Master_matrix>
class Base_pairing
{
Expand All @@ -27,7 +36,7 @@ class Base_pairing
using dimension_type = typename Master_matrix::dimension_type;
using Bar = typename Master_matrix::Bar;

Base_pairing(matrix_type& matrix, dimension_type& maxDim);
Base_pairing();
Base_pairing(const Base_pairing& matrixToCopy);
Base_pairing(Base_pairing&& other) noexcept;

Expand All @@ -43,36 +52,34 @@ class Base_pairing
protected:
using column_type = typename Master_matrix::Column_type;
using dictionnary_type = typename Master_matrix::bar_dictionnary_type;
using base_matrix = typename Master_matrix::Boundary_matrix_type;

matrix_type* matrix_;
dimension_type* maxDim_;
barcode_type barcode_;
dictionnary_type indexToBar_;
bool isReduced_;

void _reduce();
void _remove_maximal(index columnIndex);

constexpr base_matrix* _matrix() { return static_cast<base_matrix*>(this); }
constexpr const base_matrix* _matrix() const { return static_cast<const base_matrix*>(this); }
};

template<class Master_matrix>
inline Base_pairing<Master_matrix>::Base_pairing(matrix_type &matrix, dimension_type &maxDim)
: matrix_(&matrix), maxDim_(&maxDim), isReduced_(false)
inline Base_pairing<Master_matrix>::Base_pairing()
: isReduced_(false)
{}

template<class Master_matrix>
inline Base_pairing<Master_matrix>::Base_pairing(const Base_pairing &matrixToCopy)
: matrix_(matrixToCopy.matrix_),
maxDim_(matrixToCopy.maxDim_),
barcode_(matrixToCopy.barcode_),
: barcode_(matrixToCopy.barcode_),
indexToBar_(matrixToCopy.indexToBar_),
isReduced_(matrixToCopy.isReduced_)
{}

template<class Master_matrix>
inline Base_pairing<Master_matrix>::Base_pairing(Base_pairing<Master_matrix> &&other) noexcept
: matrix_(other.matrix_),
maxDim_(other.maxDim_),
barcode_(std::move(other.barcode_)),
: barcode_(std::move(other.barcode_)),
indexToBar_(std::move(other.indexToBar_)),
isReduced_(std::move(other.isReduced_))
{}
Expand All @@ -89,20 +96,19 @@ template<class Master_matrix>
inline void Base_pairing<Master_matrix>::_reduce()
{
std::unordered_map<index, index> pivotsToColumn;
auto& matrix = *matrix_;

for (int d = *maxDim_; d > 0; d--){
for (unsigned int i = 0; i < matrix_->size(); i++){
if (!(matrix.at(i).is_empty()) && matrix.at(i).get_dimension() == d)
for (int d = _matrix()->get_max_dimension(); d > 0; d--){
for (unsigned int i = 0; i < _matrix()->get_number_of_columns(); i++){
auto& curr = _matrix()->get_column(i);
if (!(curr.is_empty()) && curr.get_dimension() == d)
{
column_type &curr = matrix.at(i);
int pivot = curr.get_pivot();

while (pivot != -1 && pivotsToColumn.find(pivot) != pivotsToColumn.end()){
if constexpr (Master_matrix::Option_list::is_z2){
curr += matrix.at(pivotsToColumn.at(pivot));
curr += _matrix()->get_column(pivotsToColumn.at(pivot));
} else {
column_type &toadd = matrix.at(pivotsToColumn.at(pivot));
column_type &toadd = _matrix()->get_column(pivotsToColumn.at(pivot));
typename Master_matrix::Field_type coef = curr.get_pivot_value();
coef = coef.get_inverse();
coef *= (Master_matrix::Field_type::get_characteristic() - static_cast<unsigned int>(toadd.get_pivot_value()));
Expand All @@ -114,17 +120,17 @@ inline void Base_pairing<Master_matrix>::_reduce()

if (pivot != -1){
pivotsToColumn.emplace(pivot, i);
matrix.at(pivot).clear();
_matrix()->get_column(pivot).clear();
barcode_.push_back(Bar(d - 1, pivot, i));
} else {
matrix.at(i).clear();
curr.clear();
barcode_.push_back(Bar(d, i, -1));
}
}
}
}
for (unsigned int i = 0; i < matrix_->size(); i++){
if (matrix.at(i).get_dimension() == 0 && pivotsToColumn.find(i) == pivotsToColumn.end()){
for (unsigned int i = 0; i < _matrix()->get_number_of_columns(); i++){
if (_matrix()->get_column(i).get_dimension() == 0 && pivotsToColumn.find(i) == pivotsToColumn.end()){
barcode_.push_back(Bar(0, i, -1));
}
}
Expand Down
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