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change kdTree code to choose the number of leaves #962

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merged 3 commits into from
Sep 5, 2023
Merged

change kdTree code to choose the number of leaves #962

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607a763
change kdTree code to choose the number of leaves
MohamedKISSI Aug 24, 2023
73c9fea
Use clang-format
MohamedKISSI Aug 25, 2023
24c053e
code with recommended changes
MohamedKISSI Sep 4, 2023
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130 changes: 107 additions & 23 deletions core/base/kdTree/KDTree.h
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Original file line number Diff line number Diff line change
Expand Up @@ -64,14 +64,18 @@ namespace ttk {
const int &ptNumber,
const int &dimension,
const std::vector<std::vector<dataType>> &weights = {},
const int weight_number = 1);
const int weight_number = 1,
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I'd recommend to take the habit to use references for function parameters (unless pointers are necessary), even for integers.
const int weight_number = 1 -> const int &weightNumber = 1
(also, we usually don't use underscores for names in TTK, but a camel wording)

int nodeNumber = -1);
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int &nodeNumber = -1 --> const int &nodeNumber = -1 (unless it is not read only)


void buildRecursive(dataType *data,
std::vector<int> &idx_side,
const int &ptNumber,
const int &dimension,
KDTree<dataType, Container> *parent,
KDTreeMap &correspondence_map,
const int nodeNumber,
const int maximumLevel,
int &createdNumberNode,
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same as above const (if indeed read only)

const std::vector<std::vector<dataType>> &weights = {},
const int weight_number = 1);

Expand Down Expand Up @@ -146,15 +150,67 @@ typename ttk::KDTree<dataType, Container>::KDTreeMap
const int &ptNumber,
const int &dimension,
const std::vector<std::vector<dataType>> &weights,
const int weight_number) {
const int weight_number,
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same remark as above const int &weightNumber.

int nodeNumber) {
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same remark as above const int &nodeNumber


int createdNumberNode = 1;
int idGenerator = createdNumberNode - 1;
int maximumLevel = 0;

int correspondence_map_size = 0;

if(nodeNumber == -1) {
correspondence_map_size = ptNumber;
} else {
correspondence_map_size = nodeNumber;
maximumLevel = ceil(log2(nodeNumber + 1)) - 1;
}

KDTreeMap correspondence_map(correspondence_map_size);

KDTreeMap correspondence_map(ptNumber);
// First, perform a argsort on the data
// initialize original index locations
for(int axis = 0; axis < dimension; axis++) {
coords_min_[axis] = std::numeric_limits<dataType>::lowest();
coords_max_[axis] = std::numeric_limits<dataType>::max();
dataType x_max = std::numeric_limits<dataType>::lowest();
dataType x_min = std::numeric_limits<dataType>::max();
dataType y_max = std::numeric_limits<dataType>::lowest();
dataType y_min = std::numeric_limits<dataType>::max();
dataType z_max = std::numeric_limits<dataType>::lowest();
dataType z_min = std::numeric_limits<dataType>::max();

for(int i = 0; i < ptNumber * dimension; i += dimension) {
if(x_max < data[i]) {
x_max = data[i];
}
if(x_min > data[i]) {
x_min = data[i];
}

if(y_max < data[i + 1]) {
y_max = data[i + 1];
}
if(y_min > data[i + 1]) {
y_min = data[i + 1];
}

if(dimension > 2) {
if(z_max < data[i + 2]) {
z_max = data[i + 2];
}
if(z_min > data[i + 2]) {
z_min = data[i + 2];
}
}
}

coords_min_[0] = x_min;
coords_max_[0] = x_max;
coords_min_[1] = y_min;
coords_max_[1] = y_max;
if(dimension > 2) {
coords_min_[2] = z_min;
coords_max_[2] = z_max;
}

std::vector<int> idx(ptNumber);
for(int i = 0; i < ptNumber; i++) {
idx[i] = i;
Expand All @@ -164,15 +220,21 @@ typename ttk::KDTree<dataType, Container>::KDTreeMap
return data[dimension * i1 + coords_number_]
< data[dimension * i2 + coords_number_];
});
int const median_loc = (int)(ptNumber - 1) / 2;
int const median_idx = idx[median_loc];
correspondence_map[median_idx] = this;
int median_loc = (int)(ptNumber - 1) / 2;
int median_idx = idx[median_loc];

for(int axis = 0; axis < dimension; axis++) {
coordinates_[axis] = data[dimension * median_idx + axis];
}

id_ = median_idx;
if(nodeNumber == -1) {
correspondence_map[median_idx] = this;
id_ = median_idx;
} else {
correspondence_map[idGenerator] = this;
id_ = idGenerator;
}

parent_ = nullptr;
level_ = 0;

Expand All @@ -189,7 +251,8 @@ typename ttk::KDTree<dataType, Container>::KDTreeMap
}
}

if(idx.size() > 2) {
if(((nodeNumber == -1) && (idx.size() > 2))
|| ((nodeNumber != -1) && (createdNumberNode < nodeNumber))) {
// Build left leaf
std::vector<int> idx_left(median_loc);
for(int i = 0; i < median_loc; i++) {
Expand All @@ -199,10 +262,12 @@ typename ttk::KDTree<dataType, Container>::KDTreeMap
this->left_
= std::make_unique<KDTree>(this, (coords_number_ + 1) % dimension, true);
this->left_->buildRecursive(data, idx_left, ptNumber, dimension, this,
correspondence_map, weights, weight_number);
correspondence_map, nodeNumber, maximumLevel,
createdNumberNode, weights, weight_number);
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weightNumber

}

if(idx.size() > 1) {
if(((nodeNumber == -1) && (idx.size() > 1))
|| ((nodeNumber != -1) && (createdNumberNode < nodeNumber))) {
// Build right leaf
std::vector<int> idx_right(ptNumber - median_loc - 1);
for(int i = 0; i < ptNumber - median_loc - 1; i++) {
Expand All @@ -211,7 +276,8 @@ typename ttk::KDTree<dataType, Container>::KDTreeMap
this->right_
= std::make_unique<KDTree>(this, (coords_number_ + 1) % dimension, false);
this->right_->buildRecursive(data, idx_right, ptNumber, dimension, this,
correspondence_map, weights, weight_number);
correspondence_map, nodeNumber, maximumLevel,
createdNumberNode, weights, weight_number);
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weightNumber

}

return correspondence_map;
Expand All @@ -225,23 +291,35 @@ void ttk::KDTree<dataType, Container>::buildRecursive(
const int &dimension,
KDTree<dataType, Container> *parent,
KDTreeMap &correspondence_map,
const int nodeNumber,
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const int &nodeNumber

const int maximumLevel,
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const int &maximumLevel

int &createdNumberNode,
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const int &createdNumberNode (unless not read-only)

const std::vector<std::vector<dataType>> &weights,
const int weight_number) {

createdNumberNode++;
int idGenerator = createdNumberNode - 1;

// First, perform a argsort on the data
sort(idx_side.begin(), idx_side.end(), [&](int i1, int i2) {
return data[dimension * i1 + coords_number_]
< data[dimension * i2 + coords_number_];
});
int const median_loc = (int)(idx_side.size() - 1) / 2;
int const median_idx = idx_side[median_loc];
correspondence_map[median_idx] = this;
int median_loc = (int)(idx_side.size() - 1) / 2;
int median_idx = idx_side[median_loc];

for(int axis = 0; axis < dimension; axis++) {
coordinates_[axis] = data[dimension * median_idx + axis];
}

id_ = median_idx;
if(nodeNumber == -1) {
correspondence_map[median_idx] = this;
id_ = median_idx;
} else {
correspondence_map[idGenerator] = this;
id_ = idGenerator;
}

parent_ = parent;
level_ = parent->level_ + 1;

Expand Down Expand Up @@ -278,7 +356,9 @@ void ttk::KDTree<dataType, Container>::buildRecursive(
= parent_->coordinates_[parent_->coords_number_];
}

if(idx_side.size() > 2) {
if(((nodeNumber == -1) && (idx_side.size() > 2))
|| ((nodeNumber != -1) && (level_ < maximumLevel)
&& (createdNumberNode < nodeNumber))) {
// Build left leaf
std::vector<int> idx_left(median_loc);
for(int i = 0; i < median_loc; i++) {
Expand All @@ -288,10 +368,13 @@ void ttk::KDTree<dataType, Container>::buildRecursive(
this->left_
= std::make_unique<KDTree>(this, (coords_number_ + 1) % dimension, true);
this->left_->buildRecursive(data, idx_left, ptNumber, dimension, this,
correspondence_map, weights, weight_number);
correspondence_map, nodeNumber, maximumLevel,
createdNumberNode, weights, weight_number);
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weightNumber

}

if(idx_side.size() > 1) {
if(((nodeNumber == -1) && (idx_side.size() > 1))
|| ((nodeNumber != -1) && (level_ < maximumLevel)
&& (createdNumberNode < nodeNumber))) {
// Build right leaf
std::vector<int> idx_right(idx_side.size() - median_loc - 1);
for(unsigned int i = 0; i < idx_side.size() - median_loc - 1; i++) {
Expand All @@ -300,7 +383,8 @@ void ttk::KDTree<dataType, Container>::buildRecursive(
this->right_
= std::make_unique<KDTree>(this, (coords_number_ + 1) % dimension, false);
this->right_->buildRecursive(data, idx_right, ptNumber, dimension, this,
correspondence_map, weights, weight_number);
correspondence_map, nodeNumber, maximumLevel,
createdNumberNode, weights, weight_number);
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weightNumber

}
}

Expand Down Expand Up @@ -414,4 +498,4 @@ void ttk::KDTree<dataType, Container>::recursiveGetKClosest(
k, coordinates, neighbours, costs, weight_index, power);
}
}
}
}
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