diff options
Diffstat (limited to 'src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h')
| -rw-r--r-- | src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h | 144 |
1 files changed, 80 insertions, 64 deletions
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h index 26c97872..d9c91832 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -23,20 +23,17 @@ #ifndef BITMAP_CUBICAL_COMPLEX_BASE_H_
#define BITMAP_CUBICAL_COMPLEX_BASE_H_
+#include <gudhi/counter.h>
+
#include <iostream>
#include <string>
#include <vector>
-#include <string>
#include <cstdlib>
#include <climits>
#include <fstream>
#include <algorithm>
#include <iterator>
-#include <gudhi/counter.h>
-
-using namespace std;
-
/**
* This is a class implementing a basic bitmap data structure to store cubical complexes. It implements only the most basic subroutines.
* The idea of the bitmap is the following. Our aim is to have a memory efficient data structure to store d-dimensional cubical complex C being a cubical decomposition
@@ -89,7 +86,7 @@ class Bitmap_cubical_complex_base { * cells. The most typical one is by so called lower star filtration. This function is always called by any constructor which takes the top dimensional cells. If you use such a constructor,
* then there is no need to call this function. Call it only if you are putting the filtration of the cells by your own (for instance by using topDimensionalCellsIterator).
**/
- void impose_lower_star_filtration(); //assume that top dimensional cells are already set.
+ void impose_lower_star_filtration(); // assume that top dimensional cells are already set.
/**
* Returns dimension of a complex.
@@ -109,9 +106,9 @@ class Bitmap_cubical_complex_base { * Writing to stream operator.
**/
template <typename K>
- friend ostream& operator<<(ostream & os_, const Bitmap_cubical_complex_base<K>& b_);
+ friend std::ostream& operator<<(std::ostream & os_, const Bitmap_cubical_complex_base<K>& b_);
- //ITERATORS
+ // ITERATORS
/**
* Iterator through all cells in the complex (in order they appear in the structure -- i.e. in lexicographical order).
@@ -142,7 +139,6 @@ class Bitmap_cubical_complex_base { **/
class Top_dimensional_cells_iterator : std::iterator< std::input_iterator_tag, double > {
public:
-
Top_dimensional_cells_iterator(Bitmap_cubical_complex_base& b_) : b(b_) {
for (size_t i = 0; i != b_.dimension(); ++i) {
this->counter.push_back(0);
@@ -150,7 +146,7 @@ class Bitmap_cubical_complex_base { }
Top_dimensional_cells_iterator operator++() {
- //first find first element of the counter that can be increased:
+ // first find first element of the counter that can be increased:
size_t dim = 0;
while ((dim != this->b.dimension()) && (this->counter[dim] == this->b.sizes[dim] - 1))++dim;
@@ -191,7 +187,7 @@ class Bitmap_cubical_complex_base { }
T& operator*() {
- //given the counter, compute the index in the array and return this element.
+ // given the counter, compute the index in the array and return this element.
unsigned index = 0;
for (size_t i = 0; i != this->counter.size(); ++i) {
index += (2 * this->counter[i] + 1) * this->b.multipliers[i];
@@ -209,7 +205,7 @@ class Bitmap_cubical_complex_base { void printCounter() {
for (size_t i = 0; i != this->counter.size(); ++i) {
- cout << this->counter[i] << " ";
+ std::cout << this->counter[i] << " ";
}
}
friend class Bitmap_cubical_complex_base;
@@ -255,10 +251,10 @@ class Bitmap_cubical_complex_base { for (size_t i = 0; i != sizes_.size(); ++i) {
this->sizes.push_back(sizes_[i]);
this->multipliers.push_back(multiplier);
- //multiplier *= 2*(sizes[i]+1)+1;
+ // multiplier *= 2*(sizes[i]+1)+1;
multiplier *= 2 * sizes_[i] + 1;
}
- //std::reverse( this->sizes.begin() , this->sizes.end() );
+ // std::reverse( this->sizes.begin() , this->sizes.end() );
std::vector<T> data(multiplier);
std::fill(data.begin(), data.end(), INT_MAX);
this->totalNumberOfCells = multiplier;
@@ -287,9 +283,11 @@ class Bitmap_cubical_complex_base { };
template <typename K>
-ostream& operator<<(ostream & out_, const Bitmap_cubical_complex_base<K>& b_) {
- //for ( typename bitmap<K>::all_cells_const_iterator it = b.all_cells_const_begin() ; it != b.all_cells_const_end() ; ++it )
- for (typename Bitmap_cubical_complex_base<K>::all_cells_const_iterator it = b_.all_cells_const_begin(); it != b_.all_cells_const_end(); ++it) {
+std::ostream& operator<<(std::ostream & out_, const Bitmap_cubical_complex_base<K>& b_) {
+ // for ( typename bitmap<K>::all_cells_const_iterator it = b.all_cells_const_begin() ;
+ // it != b.all_cells_const_end() ; ++it )
+ for (typename Bitmap_cubical_complex_base<K>::all_cells_const_iterator it = b_.all_cells_const_begin();
+ it != b_.all_cells_const_end(); ++it) {
out_ << *it << " ";
}
return out_;
@@ -301,7 +299,8 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(std::vector<unsigned }
template <typename T>
-Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(std::vector<unsigned> sizesInFollowingDirections_, std::vector<T> topDimensionalCells_) {
+Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(std::vector<unsigned> sizesInFollowingDirections_,
+ std::vector<T> topDimensionalCells_) {
this->set_up_containers(sizesInFollowingDirections_);
size_t numberOfTopDimensionalElements = 1;
@@ -309,8 +308,12 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(std::vector<unsigned numberOfTopDimensionalElements *= sizesInFollowingDirections_[i];
}
if (numberOfTopDimensionalElements != topDimensionalCells_.size()) {
- cerr << "Error in constructor Bitmap_cubical_complex_base( std::vector<size_t> sizesInFollowingDirections_ , std::vector<float> topDimensionalCells_ ). Number of top dimensional elements that follow from sizesInFollowingDirections vector is different than the size of topDimensionalCells vector." << endl;
- throw ("Error in constructor Bitmap_cubical_complex_base( std::vector<size_t> sizesInFollowingDirections_ , std::vector<float> topDimensionalCells_ ). Number of top dimensional elements that follow from sizesInFollowingDirections vector is different than the size of topDimensionalCells vector.");
+ std::cerr << "Error in constructor Bitmap_cubical_complex_base( std::vector<size_t> sizesInFollowingDirections_ , "
+ "std::vector<float> topDimensionalCells_ ). Number of top dimensional elements that follow from "
+ "sizesInFollowingDirections vector is different than the size of topDimensionalCells vector." << std::endl;
+ throw("Error in constructor Bitmap_cubical_complex_base( std::vector<size_t> sizesInFollowingDirections_ , "
+ "std::vector<float> topDimensionalCells_ ). Number of top dimensional elements that follow from "
+ "sizesInFollowingDirections vector is different than the size of topDimensionalCells vector.");
}
Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
@@ -325,13 +328,13 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(std::vector<unsigned template <typename T>
Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(char* perseusStyleFile_) {
bool dbg = false;
- ifstream inFiltration, inIds;
+ std::ifstream inFiltration, inIds;
inFiltration.open(perseusStyleFile_);
unsigned dimensionOfData;
inFiltration >> dimensionOfData;
if (dbg) {
- cerr << "dimensionOfData : " << dimensionOfData << endl;
+ std::cerr << "dimensionOfData : " << dimensionOfData << std::endl;
}
std::vector<unsigned> sizes;
@@ -341,7 +344,7 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(char* perseusStyleFi sizeInThisDimension = abs(sizeInThisDimension);
sizes.push_back(sizeInThisDimension);
if (dbg) {
- cerr << "sizeInThisDimension : " << sizeInThisDimension << endl;
+ std::cerr << "sizeInThisDimension : " << sizeInThisDimension << std::endl;
}
}
this->set_up_containers(sizes);
@@ -349,12 +352,14 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(char* perseusStyleFi Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
it = this->top_dimensional_cells_begin();
- //TODO -- over here we also need to read id's of cell and put them to bitmapElement structure!
+ // TODO(Pawel Dlotko): Over here we also need to read id's of cell and put them to bitmapElement structure!
while (!inFiltration.eof()) {
double filtrationLevel;
inFiltration >> filtrationLevel;
if (dbg) {
- cerr << "Cell of an index : " << it.computeIndexInBitmap() << " and dimension: " << this->get_dimension_of_a_cell(it.computeIndexInBitmap()) << " get the value : " << filtrationLevel << endl;
+ std::cerr << "Cell of an index : " << it.computeIndexInBitmap() << " and dimension: " <<
+ this->get_dimension_of_a_cell(it.computeIndexInBitmap()) << " get the value : " <<
+ filtrationLevel << std::endl;
}
*it = filtrationLevel;
++it;
@@ -366,7 +371,8 @@ Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(char* perseusStyleFi template <typename T>
std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(size_t cell_) {
bool bdg = false;
- //first of all, we need to take the list of coordinates in which the cell has nonzero length. We do it by using modified version to compute dimension of a cell:
+ // First of all, we need to take the list of coordinates in which the cell has nonzero length.
+ // We do it by using modified version to compute dimension of a cell:
std::vector< unsigned > dimensionsInWhichCellHasNonzeroLength;
unsigned dimension = 0;
size_t cell1 = cell_;
@@ -380,9 +386,9 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(siz }
if (bdg) {
- cerr << "dimensionsInWhichCellHasNonzeroLength : \n";
+ std::cerr << "dimensionsInWhichCellHasNonzeroLength : \n";
for (size_t i = 0; i != dimensionsInWhichCellHasNonzeroLength.size(); ++i) {
- cerr << dimensionsInWhichCellHasNonzeroLength[i] << endl;
+ std::cerr << dimensionsInWhichCellHasNonzeroLength[i] << std::endl;
}
getchar();
}
@@ -393,9 +399,12 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(siz boundaryElements.push_back(cell_ - multipliers[ dimensionsInWhichCellHasNonzeroLength[i] ]);
boundaryElements.push_back(cell_ + multipliers[ dimensionsInWhichCellHasNonzeroLength[i] ]);
- if (bdg) cerr << "multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " << multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << endl;
- if (bdg) cerr << "cell_ - multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " << cell_ - multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << endl;
- if (bdg) cerr << "cell_ + multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " << cell_ + multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << endl;
+ if (bdg) std::cerr << "multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " <<
+ multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << std::endl;
+ if (bdg) std::cerr << "cell_ - multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " <<
+ cell_ - multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << std::endl;
+ if (bdg) std::cerr << "cell_ + multipliers[dimensionsInWhichCellHasNonzeroLength[i]] : " <<
+ cell_ + multipliers[dimensionsInWhichCellHasNonzeroLength[i]] << std::endl;
}
return boundaryElements;
}
@@ -403,7 +412,8 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_boundary_of_a_cell(siz template <typename T>
std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell(size_t cell_) {
bool bdg = false;
- //first of all, we need to take the list of coordinates in which the cell has nonzero length. We do it by using modified version to compute dimension of a cell:
+ // First of all, we need to take the list of coordinates in which the cell has nonzero length.
+ // We do it by using modified version to compute dimension of a cell:
std::vector< unsigned > dimensionsInWhichCellHasZeroLength;
unsigned dimension = 0;
size_t cell1 = cell_;
@@ -417,16 +427,16 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell(s }
std::vector<unsigned> counter = this->compute_counter_for_given_cell(cell_);
- //reverse(counter.begin() , counter.end());
+ // reverse(counter.begin() , counter.end());
if (bdg) {
- cerr << "dimensionsInWhichCellHasZeroLength : \n";
+ std::cerr << "dimensionsInWhichCellHasZeroLength : \n";
for (size_t i = 0; i != dimensionsInWhichCellHasZeroLength.size(); ++i) {
- cerr << dimensionsInWhichCellHasZeroLength[i] << endl;
+ std::cerr << dimensionsInWhichCellHasZeroLength[i] << std::endl;
}
- cerr << "\n counter : " << endl;
+ std::cerr << "\n counter : " << std::endl;
for (size_t i = 0; i != counter.size(); ++i) {
- cerr << counter[i] << endl;
+ std::cerr << counter[i] << std::endl;
}
getchar();
}
@@ -435,27 +445,29 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell(s if (dimensionsInWhichCellHasZeroLength.size() == 0)return coboundaryElements;
for (size_t i = 0; i != dimensionsInWhichCellHasZeroLength.size(); ++i) {
if (bdg) {
- cerr << "Dimension : " << i << endl;
+ std::cerr << "Dimension : " << i << std::endl;
if (counter[dimensionsInWhichCellHasZeroLength[i]] == 0) {
- cerr << "In dimension : " << i << " we cannot substract, since we will jump out of a Bitmap_cubical_complex_base \n";
+ std::cerr << "In dimension : " << i <<
+ " we cannot substract, since we will jump out of a Bitmap_cubical_complex_base \n";
}
if (counter[dimensionsInWhichCellHasZeroLength[i]] == 2 * this->sizes[dimensionsInWhichCellHasZeroLength[i]]) {
- cerr << "In dimension : " << i << " we cannot substract, since we will jump out of a Bitmap_cubical_complex_base \n";
+ std::cerr << "In dimension : " << i <<
+ " we cannot substract, since we will jump out of a Bitmap_cubical_complex_base \n";
}
}
- if ((cell_ > multipliers[dimensionsInWhichCellHasZeroLength[i]]) && (counter[dimensionsInWhichCellHasZeroLength[i]] != 0))
- //if ( counter[dimensionsInWhichCellHasZeroLength[i]] != 0 )
- {
- if (bdg)cerr << "Subtracting : " << cell_ - multipliers[dimensionsInWhichCellHasZeroLength[i]] << endl;
+ if ((cell_ > multipliers[dimensionsInWhichCellHasZeroLength[i]]) &&
+ (counter[dimensionsInWhichCellHasZeroLength[i]] != 0)) {
+ // if ( counter[dimensionsInWhichCellHasZeroLength[i]] != 0 )
+ if (bdg)std::cerr << "Subtracting : " << cell_ - multipliers[dimensionsInWhichCellHasZeroLength[i]] << std::endl;
coboundaryElements.push_back(cell_ - multipliers[dimensionsInWhichCellHasZeroLength[i]]);
}
- if ((cell_ + multipliers[dimensionsInWhichCellHasZeroLength[i]] < this->data.size()) && (counter[dimensionsInWhichCellHasZeroLength[i]] != 2 * this->sizes[dimensionsInWhichCellHasZeroLength[i]]))
- //if ( counter[dimensionsInWhichCellHasZeroLength[i]] != 2*this->sizes[dimensionsInWhichCellHasZeroLength[i]] )
- {
+ if ((cell_ + multipliers[dimensionsInWhichCellHasZeroLength[i]] < this->data.size()) &&
+ (counter[dimensionsInWhichCellHasZeroLength[i]] != 2 * this->sizes[dimensionsInWhichCellHasZeroLength[i]])) {
+ // if ( counter[dimensionsInWhichCellHasZeroLength[i]] != 2*this->sizes[dimensionsInWhichCellHasZeroLength[i]] )
coboundaryElements.push_back(cell_ + multipliers[dimensionsInWhichCellHasZeroLength[i]]);
- if (bdg)cerr << "Adding : " << cell_ + multipliers[dimensionsInWhichCellHasZeroLength[i]] << endl;
+ if (bdg)std::cerr << "Adding : " << cell_ + multipliers[dimensionsInWhichCellHasZeroLength[i]] << std::endl;
}
}
return coboundaryElements;
@@ -464,19 +476,19 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cell(s template <typename T>
unsigned Bitmap_cubical_complex_base<T>::get_dimension_of_a_cell(size_t cell_) {
bool dbg = false;
- if (dbg)cerr << "\n\n\n Computing position o a cell of an index : " << cell_ << endl;
+ if (dbg)std::cerr << "\n\n\n Computing position o a cell of an index : " << cell_ << std::endl;
unsigned dimension = 0;
for (size_t i = this->multipliers.size(); i != 0; --i) {
unsigned position = cell_ / multipliers[i - 1];
- if (dbg)cerr << "i-1 :" << i - 1 << endl;
- if (dbg)cerr << "cell_ : " << cell_ << endl;
- if (dbg)cerr << "position : " << position << endl;
- if (dbg)cerr << "multipliers[" << i - 1 << "] = " << multipliers[i - 1] << endl;
+ if (dbg)std::cerr << "i-1 :" << i - 1 << std::endl;
+ if (dbg)std::cerr << "cell_ : " << cell_ << std::endl;
+ if (dbg)std::cerr << "position : " << position << std::endl;
+ if (dbg)std::cerr << "multipliers[" << i - 1 << "] = " << multipliers[i - 1] << std::endl;
if (dbg)getchar();
if (position % 2 == 1) {
- if (dbg)cerr << "Nonzero length in this direction \n";
+ if (dbg)std::cerr << "Nonzero length in this direction \n";
dimension++;
}
cell_ = cell_ % multipliers[i - 1];
@@ -493,11 +505,12 @@ template <typename T> void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() {
bool dbg = false;
- //this vector will be used to check which elements have already been taken care of in imposing lower star filtration:
+ // this vector will be used to check which elements have already been taken care of in imposing lower star filtration:
std::vector<bool> isThisCellConsidered(this->data.size(), false);
std::vector<size_t> indicesToConsider;
- //we assume here that we already have a filtration on the top dimensional cells and we have to extend it to lower ones.
+ // we assume here that we already have a filtration on the top dimensional cells
+ // and we have to extend it to lower ones.
typename Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
for (it = this->top_dimensional_cells_begin(); it != this->top_dimensional_cells_end(); ++it) {
indicesToConsider.push_back(it.computeIndexInBitmap());
@@ -505,9 +518,9 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() { while (indicesToConsider.size()) {
if (dbg) {
- cerr << "indicesToConsider in this iteration \n";
+ std::cerr << "indicesToConsider in this iteration \n";
for (size_t i = 0; i != indicesToConsider.size(); ++i) {
- cout << indicesToConsider[i] << " ";
+ std::cout << indicesToConsider[i] << " ";
}
getchar();
}
@@ -529,9 +542,12 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() { }
template <typename T>
-std::vector< size_t > Bitmap_cubical_complex_base<T>::generate_vector_of_shifts_for_bitmaps_with_periodic_boundary_conditions(std::vector< bool > directionsForPeriodicBCond_) {
+std::vector< size_t >
+Bitmap_cubical_complex_base<T>::generate_vector_of_shifts_for_bitmaps_with_periodic_boundary_conditions(std::vector< bool > directionsForPeriodicBCond_) {
bool dbg = false;
- if (this->sizes.size() != directionsForPeriodicBCond_.size())throw "directionsForPeriodicBCond_ vector size is different from the size of the bitmap. The program will now terminate \n";
+ if (this->sizes.size() != directionsForPeriodicBCond_.size())
+ throw ("directionsForPeriodicBCond_ vector size is different from the size of the bitmap. "
+ "The program will now terminate \n");
std::vector<int> sizes(this->sizes.size());
for (size_t i = 0; i != this->sizes.size(); ++i)sizes[i] = 2 * this->sizes[i];
@@ -544,7 +560,7 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::generate_vector_of_shifts_ size_t position;
if (!c.isFinal()) {
position = i;
- //result.push_back( i );
+ // result.push_back( i );
} else {
std::vector< bool > finals = c.directionsOfFinals();
bool jumpInPosition = false;
@@ -555,7 +571,7 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::generate_vector_of_shifts_ }
}
if (jumpInPosition == true) {
- //in this case this guy is final, so we need to find 'the opposite one'
+ // in this case this guy is final, so we need to find 'the opposite one'
position = compute_position_in_bitmap(c.findOpposite(directionsForPeriodicBCond_));
} else {
position = i;
@@ -563,8 +579,8 @@ std::vector< size_t > Bitmap_cubical_complex_base<T>::generate_vector_of_shifts_ }
result.push_back(position);
if (dbg) {
- cerr << " position : " << position << endl;
- cerr << c << endl;
+ std::cerr << " position : " << position << std::endl;
+ std::cerr << c << std::endl;
getchar();
}
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