// Function that runs the Barnes-Hut implementation of t-SNE
int main() {
// Define some variables
int origN, N, D, no_dims, *landmarks;
double perc_landmarks;
double perplexity, theta, *data;
int rand_seed = -1;
TSNE* tsne = new TSNE();
// Read the parameters and the dataset
if(tsne->load_data(&data, &origN, &D, &no_dims, &theta, &perplexity, &rand_seed)) {
// Make dummy landmarks
N = origN;
int* landmarks = (int*) malloc(N * sizeof(int));
if(landmarks == NULL) { printf("Memory allocation failed!\n"); exit(1); }
for(int n = 0; n < N; n++) landmarks[n] = n;
// Now fire up the SNE implementation
double* Y = (double*) malloc(N * no_dims * sizeof(double));
double* costs = (double*) calloc(N, sizeof(double));
if(Y == NULL || costs == NULL) { printf("Memory allocation failed!\n"); exit(1); }
tsne->run(data, N, D, Y, no_dims, perplexity, theta, rand_seed, false);
// Save the results
tsne->save_data(Y, landmarks, costs, N, no_dims);
// Clean up the memory
free(data); data = NULL;
free(Y); Y = NULL;
free(costs); costs = NULL;
free(landmarks); landmarks = NULL;
}
delete(tsne);
}
// Function that runs the Barnes-Hut implementation of t-SNE
int main(int argc, char** argv) {
int metrics = 0;
if (argc > 1) {
if (!strcmp(argv[1], "1")) metrics = 1;
}
// Define some variables
int origN, N, D, no_dims = 2, *landmarks;
double perc_landmarks;
double perplexity, theta, *data;
TSNE* tsne = new TSNE();
// Read the parameters and the dataset
if(tsne->load_data(&data, &origN, &D, &theta, &perplexity)) {
// Make dummy landmarks
N = origN;
int* landmarks = (int*) malloc(N * sizeof(int));
if(landmarks == NULL) { printf("Memory allocation failed!\n"); exit(1); }
for(int n = 0; n < N; n++) landmarks[n] = n;
// Now fire up the SNE implementation
double* Y = (double*) malloc(N * no_dims * sizeof(double));
double* costs = (double*) calloc(N, sizeof(double));
if(Y == NULL || costs == NULL) { printf("Memory allocation failed!\n"); exit(1); }
double (*metric_func) (const DataPoint&, const DataPoint&);
switch (metrics) {
case 1: metric_func = log_cosine_distance; printf("Using %s As Distance Metrics.\n", "Log-Cosine-Similarity"); break;
default: metric_func = euclidean_distance; printf("Using %s As Distance Metrics.\n", "Euclidean-Distance"); break;
}
tsne->run(data, N, D, Y, no_dims, perplexity, theta, metric_func);
// Save the results
tsne->save_data(Y, landmarks, costs, N, no_dims);
// Clean up the memory
free(data); data = NULL;
free(Y); Y = NULL;
free(costs); costs = NULL;
free(landmarks); landmarks = NULL;
}
delete(tsne);
}
// Function that runs the Barnes-Hut implementation of t-SNE
int main() {
// Define some variables
int origN, N, D, no_dims, iterations, *landmarks;
double perc_landmarks;
double perplexity, theta, eta, *data;
float gpu_mem;
int verbose;
int rand_seed = -1;
int seed = 0;
TSNE* tsne = new TSNE();
time_t start = clock();
// Read the parameters and the dataset
if (tsne->load_data(&data, &origN, &D, &no_dims, &theta, &perplexity, &eta, &iterations, &seed, &gpu_mem, &verbose, &rand_seed)) {
// Set random seed
if (rand_seed >= 0) {
if (verbose > 0) printf("Using random seed: %d\n", rand_seed);
srand((unsigned int)rand_seed);
}
else {
if (verbose > 0) printf("Using current time as random seed...\n");
srand(time(NULL));
}
// Make dummy landmarks
N = origN;
int* landmarks = (int*)malloc(N * sizeof(int));
if (landmarks == NULL) { printf("Memory allocation failed!\n"); exit(1); }
for (int n = 0; n < N; n++) landmarks[n] = n;
// Now fire up the SNE implementation
double* Y = (double*)malloc(N * no_dims * sizeof(double));
double* costs = (double*)calloc(N, sizeof(double));
if (Y == NULL || costs == NULL) { printf("Memory allocation failed!\n"); exit(1); }
tsne->zeroMean(data, N, D);
tsne->normalize(data, N, D);
if (seed == 0){
seed = origN;
}
tsne->runWithCenterOfMass(data, Y, origN, seed, D, no_dims, perplexity, theta, eta, iterations, gpu_mem, verbose);
// Save the results
tsne->save_data(Y, landmarks, costs, N, no_dims, verbose);
// Clean up the memory
free(data); data = NULL;
free(Y); Y = NULL;
free(costs); costs = NULL;
free(landmarks); landmarks = NULL;
}
delete(tsne);
time_t end = clock();
if (verbose > 0) printf("T-sne required %f seconds (%f minutes) to run\n", float(end - start) / CLOCKS_PER_SEC, float(end - start) / (60 * CLOCKS_PER_SEC));
}
void TsneProjector::Project(vector<vector<float>>& values, vector<vector<float>>& proj_values) {
int N = values[0].size();
int D = values.size();
int no_dims = 2;
double perplexity = 30;
if (perplexity > values[0].size() / 5) perplexity = values[0].size() / 5;
double theta = 0.5;
int rand_seed = 12345;
bool skip_random_init = false;
proj_values.resize(no_dims);
for (int i = 0; i < no_dims; ++i)
proj_values[i].resize(N);
vector<double> X, Y;
X.resize(N * D);
Y.resize(no_dims * N);
int accu_count = 0;
for (int i = 0; i < N; ++i) {
for (int j = 0; j < D; ++j) {
X[accu_count] = values[j][i];
accu_count++;
}
}
TSNE sne;
sne.run(X.data(), N, D, Y.data(), no_dims, perplexity, theta, rand_seed, skip_random_init);
accu_count = 0;
for (int i = 0; i < N; ++i) {
for (int j = 0; j < no_dims; ++j) {
proj_values[j][i] = Y[accu_count] * 1000;
accu_count++;
}
}
}
// Function that runs the Barnes-Hut implementation of t-SNE
// [[Rcpp::export]]
Rcpp::List Rtsne_cpp(NumericMatrix X, int no_dims_in, double perplexity_in, double theta_in, bool verbose, int max_iter, bool distance_precomputed, NumericMatrix Y_in, bool init) {
int origN, N, D, no_dims = no_dims_in;
double *data;
TSNE* tsne = new TSNE();
double perplexity = perplexity_in;
double theta = theta_in;
origN = X.nrow();
D = X.ncol();
data = (double*) calloc(D * origN, sizeof(double));
if(data == NULL) { Rcpp::stop("Memory allocation failed!\n"); }
for (int i = 0; i < origN; i++){
for (int j = 0; j < D; j++){
data[i*D+j] = X(i,j);
}
}
// Make dummy landmarks
N = origN;
if (verbose) Rprintf("Read the %i x %i data matrix successfully!\n", N, D);
int* landmarks = (int*) malloc(N * sizeof(int));
if(landmarks == NULL) { Rcpp::stop("Memory allocation failed!\n"); }
for(int n = 0; n < N; n++) landmarks[n] = n;
double* Y = (double*) malloc(N * no_dims * sizeof(double));
double* costs = (double*) calloc(N, sizeof(double));
double* itercosts = (double*) calloc((int)(ceil(max_iter/50.0)), sizeof(double));
if(Y == NULL || costs == NULL) { Rcpp::stop("Memory allocation failed!\n"); }
// Initialize solution (randomly)
if (init) {
for (int i = 0; i < N; i++){
for (int j = 0; j < no_dims; j++){
Y[i*no_dims+j] = Y_in(i,j);
}
}
if (verbose) Rprintf("Using user supplied starting positions\n");
}
// Run tsne
tsne->run(data, N, D, Y, no_dims, perplexity, theta, verbose, max_iter, costs, distance_precomputed, itercosts, init);
// Save the results
Rcpp::NumericMatrix Yr(N, no_dims);
for (int i = 0; i < N; i++){
for (int j = 0; j < no_dims; j++){
Yr(i,j) = Y[i*no_dims+j];
}
}
Rcpp::NumericVector costsr(N);
for (int i = 0; i < N; i++){
costsr(i) = costs[i];
}
Rcpp::NumericVector itercostsr((int)(ceil(max_iter/50.0)));
for (int i = 0; i < (int)(ceil(max_iter/50.0)); i++) {
itercostsr(i) = itercosts[i];
}
free(data); data = NULL;
free(Y); Y = NULL;
free(costs); costs = NULL;
free(landmarks); landmarks = NULL;
delete(tsne);
Rcpp::List output = Rcpp::List::create(Rcpp::_["theta"]=theta, Rcpp::_["perplexity"]=perplexity, Rcpp::_["N"]=N,Rcpp::_["origD"]=D,Rcpp::_["Y"]=Yr, Rcpp::_["costs"]=costsr, Rcpp::_["itercosts"]=itercostsr);
return output;
}