int main(){
int N = 10;
int D = 5;
int K = 4;
int rand_seed = 2;
double* X = gen_matrix(N,D);
// Build ball tree on data set
VpTree<DataPoint, euclidean_distance>* tree = new VpTree<DataPoint, euclidean_distance>();
vector<DataPoint> obj_X(N, DataPoint(D, -1, X));
std::srand((unsigned int) rand_seed);
for(int n = 0; n < N; n++) obj_X[n] = DataPoint(D, n, X + n * D);
std::random_shuffle(obj_X.begin(), obj_X.end());
pd(obj_X);
cout << "size:" << obj_X.size() << endl;
// cout << "1:" << obj_X[1] << endl;
tree->create(obj_X);
vector<DataPoint> indices;
vector<double> distances;
for(int n = 0; n < N; n++) {
// Find nearest neighbors
indices.clear();
distances.clear();
tree->search(obj_X[n], K + 1, &indices, &distances);
std::cout << n << std::endl;
pv(indices);
pv(distances);
}
free(X);
delete tree;
}
void TSNE<NDims>::computeGaussianPerplexity(double* X, unsigned int N, int D, int K) {
if(perplexity > K) Rprintf("Perplexity should be lower than K!\n");
// Allocate the memory we need
setupApproximateMemory(N, K);
// Build ball tree on data set
VpTree<DataPoint, T>* tree = new VpTree<DataPoint, T>();
vector<DataPoint> obj_X(N, DataPoint(D, -1, X));
for(unsigned int n = 0; n < N; n++) obj_X[n] = DataPoint(D, n, X + n * D);
tree->create(obj_X);
// Loop over all points to find nearest neighbors
if (verbose) Rprintf("Building tree...\n");
int steps_completed = 0;
#pragma omp parallel for schedule(guided) num_threads(num_threads)
for(unsigned int n = 0; n < N; n++) {
vector<DataPoint> indices;
vector<double> distances;
indices.reserve(K+1);
distances.reserve(K+1);
// Find nearest neighbors
tree->search(obj_X[n], K + 1, &indices, &distances);
double * cur_P = val_P.data() + row_P[n];
computeProbabilities(perplexity, K, distances.data()+1, cur_P); // +1 to avoid self.
unsigned int * cur_col_P = col_P.data() + row_P[n];
for (int m=0; m<K; ++m) {
cur_col_P[m] = indices[m+1].index(); // +1 to avoid self.
}
#pragma omp atomic
++steps_completed;
if (verbose) {
if(steps_completed % 10000 == 0) Rprintf(" - point %d of %d\n", steps_completed, N);
}
}
// Clean up memory
obj_X.clear();
delete tree;
}
void testVpTree2()
{
VpTree<Point<int>, int, EuclideanDistance<Point<int> >::DistanceIncremental> tree;
int N = 1500000;
for(int i = 0; i < N; ++i)
{
tree.insert(Point<int>(GlobalRNG.next(), GlobalRNG.next()), i);
}
int M = 15000;
for(int i = 0; i < M; ++i)
{
assert(tree.nearestNeighbor(Point<int>(GlobalRNG.next(), GlobalRNG.next())));
int k = 100;
assert(tree.kNN(Point<int>(GlobalRNG.next(), GlobalRNG.next()), k).getSize() == k);
}
}
void testVpTree()
{
VpTree<Point<int>,int, EuclideanDistance<Point<int> >::DistanceIncremental> tree;
int N = 5;
for(int i = 0; i < N; ++i)
{
tree.insert(Point<int>(i, i), i);
}
for(int i = 0; i < N; ++i)
{
int* result = tree.find(Point<int>(i, i));
if(result) DEBUG(*result);
assert(result && *result == i);
}
Vector<VpTree<Point<int>,int, EuclideanDistance<Point<int> >::DistanceIncremental>::NodeType*> result2 = tree.distanceQuery(Point<int>(0, 4), sqrt(10));
for(int i = 0; i < result2.getSize(); ++i)
{
DEBUG(result2[i]->key[0]);
DEBUG(result2[i]->key[1]);
}
}
KNNGraph_FixedK_MST::KNNGraph_FixedK_MST(std::shared_ptr<gsl::Matrix> data, PropertyList property_list)
: data_(data), property_list_(property_list) {
if (property_list_[KNNGRAPH_FIXED_K_NUMBER] == 0.0) property_list_[KNNGRAPH_FIXED_K_NUMBER] = 30.0;
if (property_list_[KNNGRAPH_FIXED_K_WITH_MST_EDGE_POOL_DEPTH] == 0.0)
property_list_[KNNGRAPH_FIXED_K_WITH_MST_EDGE_POOL_DEPTH] = property_list_[KNNGRAPH_FIXED_K_NUMBER] + 100;
if (property_list_[KNNGRAPH_GRAPH_BACKEND] == KNNGRAPH_GRAPH_BACKEND_ADJACENCYLIST) {
knngraph_ = std::make_shared<GraphUtils::AdjacencyList>(data_->rows());
} else if (property_list_[KNNGRAPH_GRAPH_BACKEND] == KNNGRAPH_GRAPH_BACKEND_BOOST) {
knngraph_ = std::make_shared<GraphUtils::BoostAdjacencyList>(data_->rows());
} else {
throw std::invalid_argument("Invalid KNNGRAPH_GRAPH_BACKEND value.");
}
kIndex FIXED_K = static_cast<Index>(property_list_[KNNGRAPH_FIXED_K_NUMBER]);
kIndex MST_EDGE_POOL_DEPTH = static_cast<Index>(property_list_[KNNGRAPH_FIXED_K_WITH_MST_EDGE_POOL_DEPTH]);
LOGI("Constructing kNN graph with FixedK_MST.")
VpTree<PixelView, SquaredDistance> vptree;
LOGI("Create PixelView array.");
auto pixel_views = CreatePixelViewsFromMatrix(*data_);
LOGI("Creating VpTree for the current data matrix.")
vptree.create(pixel_views);
LOGI("VpTree created. Now creating kNN graph.")
UnionFind uf(data_->rows());
std::vector<UndirectedEdge> unused_edges;
for (Index n = 0; n < data_->rows(); ++n) {
PixelView current_pixel = pixel_views[n];
std::vector<PixelView> results;
std::vector<Scalar> distance_squares;
vptree.search(current_pixel, MST_EDGE_POOL_DEPTH, &results, &distance_squares);
for (Index j = 0; j < MST_EDGE_POOL_DEPTH; ++j) {
if (j < FIXED_K) {
knngraph_->Connect(current_pixel.index, results[j].index, std::sqrt(distance_squares[j]));
uf.Connect(current_pixel.index, results[j].index);
} else {
unused_edges.push_back(UndirectedEdge(current_pixel.index, results[j].index, std::sqrt(distance_squares[j])));
}
}
}
LOGI("kNN graph without MST has " << uf.count() << " connected parts.")
if (uf.count() != 1) {
LOGI("Start augmenting MST.")
std::sort(std::begin(unused_edges), std::end(unused_edges), [](UndirectedEdge a, UndirectedEdge b) {
return a.weight < b.weight;
});
Index augment_count = 0;
for (auto edge : unused_edges) {
Index old_count = uf.count();
uf.Connect(edge.index_a, edge.index_b);
if (uf.count() < old_count) {
knngraph_->Connect(edge.index_a, edge.index_b, edge.weight);
augment_count++;
}
if (uf.count() == 1) break;
}
LOGI(augment_count << " edges augmented.")
if (uf.count() != 1) {
throw std::invalid_argument(
"MST Augmentation failed -- need to increase KNNGRAPH_FIXED_K_WITH_MST_EDGE_POOL_DEPTH");
}
}
// Compute input similarities with a fixed perplexity using ball trees (this function allocates memory another function should free)
void TSNE::computeGaussianPerplexity(double* X, int N, int D, int** _row_P, int** _col_P, double** _val_P, double perplexity, int K) {
if(perplexity > K) printf("Perplexity should be lower than K!\n");
// Allocate the memory we need
*_row_P = (int*) malloc((N + 1) * sizeof(int));
*_col_P = (int*) calloc(N * K, sizeof(int));
*_val_P = (double*) calloc(N * K, sizeof(double));
if(*_row_P == NULL || *_col_P == NULL || *_val_P == NULL) { cout<<"Memory allocation failed!\n"; }
int* row_P = *_row_P;
int* col_P = *_col_P;
double* val_P = *_val_P;
double* cur_P = (double*) malloc((N - 1) * sizeof(double));
if(cur_P == NULL) { cout<<"Memory allocation failed!\n"; }
row_P[0] = 0;
for(int n = 0; n < N; n++) row_P[n + 1] = row_P[n] + K;
// Build ball tree on data set
VpTree<DataPoint, euclidean_distance>* tree = new VpTree<DataPoint, euclidean_distance>();
vector<DataPoint> obj_X(N, DataPoint(D, -1, X));
for(int n = 0; n < N; n++) obj_X[n] = DataPoint(D, n, X + n * D);
tree->create(obj_X);
// Loop over all points to find nearest neighbors
printf("Building tree...\n");
vector<DataPoint> indices;
vector<double> distances;
for(int n = 0; n < N; n++) {
if(n % 10000 == 0) printf(" - point %d of %d\n", n, N);
// Find nearest neighbors
indices.clear();
distances.clear();
tree->search(obj_X[n], K + 1, &indices, &distances);
// Initialize some variables for binary search
bool found = false;
double beta = 1.0;
double min_beta = -DBL_MAX;
double max_beta = DBL_MAX;
double tol = 1e-5;
// Iterate until we found a good perplexity
int iter = 0; double sum_P;
while(!found && iter < 200) {
// Compute Gaussian kernel row
for(int m = 0; m < K; m++) cur_P[m] = exp(-beta * distances[m + 1]);
// Compute entropy of current row
sum_P = DBL_MIN;
for(int m = 0; m < K; m++) sum_P += cur_P[m];
double H = .0;
for(int m = 0; m < K; m++) H += beta * (distances[m + 1] * cur_P[m]);
H = (H / sum_P) + log(sum_P);
// Evaluate whether the entropy is within the tolerance level
double Hdiff = H - log(perplexity);
if(Hdiff < tol && -Hdiff < tol) {
found = true;
}
else {
if(Hdiff > 0) {
min_beta = beta;
if(max_beta == DBL_MAX || max_beta == -DBL_MAX)
beta *= 2.0;
else
beta = (beta + max_beta) / 2.0;
}
else {
max_beta = beta;
if(min_beta == -DBL_MAX || min_beta == DBL_MAX)
beta /= 2.0;
else
beta = (beta + min_beta) / 2.0;
}
}
// Update iteration counter
iter++;
}
// Row-normalize current row of P and store in matrix
for(int m = 0; m < K; m++) cur_P[m] /= sum_P;
for(int m = 0; m < K; m++) {
col_P[row_P[n] + m] = indices[m + 1].index();
val_P[row_P[n] + m] = cur_P[m];
}
}
// Clean up memory
obj_X.clear();
free(cur_P);
delete tree;
}
int _tmain(int argc, _TCHAR* argv[]) {
#else
int main(int argc, char **argv) {
#endif
if(argc != 2 && argc != 3) {
fprintf(stderr, "Usage: sc <img1>\n");
return 1;
}
int spSize = 5;
if(argc == 3) {
sscanf(argv[2], "%d", &spSize);
}
ImageFile imgFile (argv[1]);
if(!imgFile.Load()) {
fprintf(stderr, "Error loading file: %s\n", argv[1]);
return 1;
}
FasTC::Image<> *img = imgFile.GetImage();
const int kWidth = img->GetWidth();
const int kHeight = img->GetHeight();
const int nPixels = kWidth * kHeight;
const uint32 pixelBufSz = nPixels * sizeof(FasTC::Pixel);
FasTC::Pixel *pixels = new FasTC::Pixel[pixelBufSz];
memcpy(pixels, img->GetPixels(), pixelBufSz);
uint32 *rawPixels = new uint32[kWidth * kHeight];
for(int i = 0; i < nPixels; i++) {
// Pixels are stored as little endian ARGB, so we want ABGR
pixels[i].Shuffle(0x6C); // 01 10 11 00
rawPixels[i] = pixels[i].Pack();
}
int *labels = new int[nPixels];
int numLabels;
SLIC slic;
slic.PerformSLICO_ForGivenStepSize(
rawPixels,
kWidth,
kHeight,
labels,
numLabels,
spSize, 1.0);
std::unordered_map<uint32, Region> regions;
CollectPixels(kWidth, kHeight, pixels, labels, regions);
std::cout << "Num regions: " << regions.size() << std::endl;
for(auto &r : regions) {
r.second.Compress();
r.second.Reconstruct();
}
for(int i = 0; i < nPixels; i++) {
pixels[i] = regions[labels[i]].GetNextPixel();
pixels[i].Shuffle(0x6C);
}
std::vector<Partition<4, 4> > partitions;
EnumerateBPTC(partitions);
std::cout << partitions.size() << " 4x4 BPTC partitions" << std::endl;
VpTree<Partition<4, 4>, Partition<4, 4>::Distance> vptree;
vptree.create(partitions);
// Just to test, find the partition close to half 0 half 1..
Partition<4, 4> test;
for(uint32 i = 0; i < 16; i++) {
if(i < 8) {
test[i] = 0;
} else {
test[i] = 1;
}
}
vector<Partition<4, 4> > closest;
vptree.search(test, 1, &closest, NULL);
std::cout << closest[0].GetIndex() << std::endl;
BPTCC::CompressionSettings settings;
settings.m_NumSimulatedAnnealingSteps = 0;
settings.m_ShapeSelectionFn = ChosePresegmentedShape<4, 4>;
SelectionInfo info(vptree, labels, kWidth, kHeight);
settings.m_ShapeSelectionUserData = &info;
uint8 *outBuf = new uint8[kWidth * kHeight];
FasTC::CompressionJob cj(
FasTC::eCompressionFormat_BPTC,
reinterpret_cast<const uint8 *>(pixels),
outBuf,
static_cast<uint32>(kWidth),
static_cast<uint32>(kHeight));
StopWatch sw;
sw.Start();
BPTCC::Compress(cj, settings);
sw.Stop();
std::cout << "Compression time: " << sw.TimeInMilliseconds() << "ms" << std::endl;
CompressedImage ci(kWidth, kHeight, FasTC::eCompressionFormat_BPTC, outBuf);
FasTC::Image<> outImg(kWidth, kHeight, pixels);
std::cout << "PSNR: " << outImg.ComputePSNR(&ci) << "db" << std::endl;
ImageFile outImgFile("out.png", eFileFormat_PNG, outImg);
outImgFile.Write();
delete [] labels;
delete [] rawPixels;
delete [] pixels;
return 0;
}
// Compute input similarities with a fixed perplexity using ball trees (this function allocates memory another function should free)
void TSNE::computeGaussianPerplexity(double* X, int N, int D, unsigned int** _row_P, unsigned int** _col_P, double** _val_P,
double perplexity, int K, float gpu_mem, int verbose) {
float start;
float end;
if (perplexity > K) printf("Perplexity should be lower than K!\n");
// Allocate the memory we need
*_row_P = (unsigned int*)malloc((N + 1) * sizeof(unsigned int));
*_col_P = (unsigned int*)calloc(N * K, sizeof(unsigned int));
*_val_P = (double*)calloc(N * K, sizeof(double));
if (*_row_P == NULL || *_col_P == NULL || *_val_P == NULL) { printf("Memory allocation failed!\n"); exit(1); }
unsigned int* row_P = *_row_P;
unsigned int* col_P = *_col_P;
double* val_P = *_val_P;
double* cur_P = (double*)malloc((N - 1) * sizeof(double));
if (cur_P == NULL) { printf("Memory allocation failed!\n"); exit(1); }
row_P[0] = 0;
for (int n = 0; n < N; n++) row_P[n + 1] = row_P[n] + (unsigned int)K;
// Build ball tree on data set
VpTree<DataPoint, euclidean_distance>* tree = new VpTree<DataPoint, euclidean_distance>();
vector<DataPoint> obj_X(N, DataPoint(D, -1, X));
for (int n = 0; n < N; n++) obj_X[n] = DataPoint(D, n, X + n * D);
tree->create(obj_X);
//If using gpu then calculate and save all euclidean distances and use those to search the tree
EuclideanDistances* all_distances = new EuclideanDistances();
if (gpu_mem > 0){
if (gpu_mem > 1){
printf("Requested GPU memory needs to be between 0 and 1 (of total available memory). Setting it to 0.8.");
gpu_mem = 0.8;
}
start = clock();
computeSquaredEuclideanDistanceOnGpu(X, X, all_distances, N, D, gpu_mem, verbose);
tree->set_all_euclidean_distances(*all_distances);
end = clock();
if(verbose > 1) printf("Time spend in calculating all distances in GPU: %f\n", float(end - start) / CLOCKS_PER_SEC);
}
else{
if (verbose > 0) printf("Using CPU to calculate distances during tree search\n");
}
// Loop over all points to find nearest neighbors
if (verbose > 0) printf("Building tree...\n");
vector<DataPoint> indices;
vector<double> distances;
start = clock();
for (int n = 0; n < N; n++) {
if (n % 10000 == 0 && verbose > 1) printf(" - Building tree and finding perplexities, point %d of %d\n", n, N);
// Find nearest neighbors
indices.clear();
distances.clear();
tree->search(obj_X[n], K + 1, &indices, &distances);
// Initialize some variables for binary search
bool found = false;
double beta = 1.0;
double min_beta = -DBL_MAX;
double max_beta = DBL_MAX;
double tol = 1e-5;
// Iterate until we found a good perplexity
int iter = 0; double sum_P;
while (!found && iter < 200) {
// Compute Gaussian kernel row
for (int m = 0; m < K; m++) cur_P[m] = exp(-beta * distances[m + 1]);
// Compute entropy of current row
sum_P = DBL_MIN;
for (int m = 0; m < K; m++) sum_P += cur_P[m];
double H = .0;
for (int m = 0; m < K; m++) H += beta * (distances[m + 1] * cur_P[m]);
H = (H / sum_P) + log(sum_P);
// Evaluate whether the entropy is within the tolerance level
double Hdiff = H - log(perplexity);
if (Hdiff < tol && -Hdiff < tol) {
found = true;
}
else {
if (Hdiff > 0) {
min_beta = beta;
if (max_beta == DBL_MAX || max_beta == -DBL_MAX)
beta *= 2.0;
else
beta = (beta + max_beta) / 2.0;
}
else {
max_beta = beta;
if (min_beta == -DBL_MAX || min_beta == DBL_MAX)
beta /= 2.0;
else
beta = (beta + min_beta) / 2.0;
}
}
// Update iteration counter
iter++;
}
// Row-normalize current row of P and store in matrix
for (unsigned int m = 0; m < K; m++) cur_P[m] /= sum_P;
for (unsigned int m = 0; m < K; m++) {
col_P[row_P[n] + m] = (unsigned int)indices[m + 1].index();
val_P[row_P[n] + m] = cur_P[m];
}
distances.clear();
indices.clear();
}
end = clock();
if (verbose > 1) printf("Time spend in building tree and finding perplexities: %f\n", float(end - start) / CLOCKS_PER_SEC);
// Clean up memory
obj_X.clear();
free(cur_P);
delete tree;
delete all_distances;
}