annotate audioDB.cpp @ 153:00928c833187 powertable

dump/restore support for the power table.
author mas01cr
date Wed, 31 Oct 2007 18:22:23 +0000
parents b1cbd2b78a18
children 97f704a32bf2
rev   line source
mas01cr@0 1 #include "audioDB.h"
mas01cr@0 2
mas01cr@105 3 #if defined(O2_DEBUG)
mas01cr@104 4 void sigterm_action(int signal, siginfo_t *info, void *context) {
mas01cr@104 5 exit(128+signal);
mas01cr@104 6 }
mas01cr@104 7
mas01cr@104 8 void sighup_action(int signal, siginfo_t *info, void *context) {
mas01cr@104 9 // FIXME: reread any configuration files
mas01cr@104 10 }
mas01cr@105 11 #endif
mas01cr@0 12
mas01cr@32 13 void audioDB::error(const char* a, const char* b, const char *sysFunc) {
mas01cr@77 14 if(isServer) {
mas01cr@81 15 /* FIXME: I think this is leaky -- we never delete err. actually
mas01cr@81 16 deleting it is tricky, though; it gets placed into some
mas01cr@81 17 soap-internal struct with uncertain extent... -- CSR,
mas01cr@81 18 2007-10-01 */
mas01cr@77 19 char *err = new char[256]; /* FIXME: overflows */
mas01cr@77 20 snprintf(err, 255, "%s: %s\n%s", a, b, sysFunc ? strerror(errno) : "");
mas01cr@77 21 /* FIXME: actually we could usefully do with a properly structured
mas01cr@77 22 type, so that we can throw separate faultstring and details.
mas01cr@77 23 -- CSR, 2007-10-01 */
mas01cr@77 24 throw(err);
mas01cr@77 25 } else {
mas01cr@77 26 cerr << a << ": " << b << endl;
mas01cr@77 27 if (sysFunc) {
mas01cr@77 28 perror(sysFunc);
mas01cr@77 29 }
mas01cr@77 30 exit(1);
mas01cr@32 31 }
mas01cr@0 32 }
mas01cr@0 33
mas01cr@76 34 audioDB::audioDB(const unsigned argc, char* const argv[]): O2_AUDIODB_INITIALIZERS
mas01cr@76 35 {
mas01cr@0 36 if(processArgs(argc, argv)<0){
mas01cr@0 37 printf("No command found.\n");
mas01cr@0 38 cmdline_parser_print_version ();
mas01cr@0 39 if (strlen(gengetopt_args_info_purpose) > 0)
mas01cr@0 40 printf("%s\n", gengetopt_args_info_purpose);
mas01cr@0 41 printf("%s\n", gengetopt_args_info_usage);
mas01cr@0 42 printf("%s\n", gengetopt_args_info_help[1]);
mas01cr@0 43 printf("%s\n", gengetopt_args_info_help[2]);
mas01cr@0 44 printf("%s\n", gengetopt_args_info_help[0]);
mas01cr@0 45 exit(1);
mas01cr@0 46 }
mas01cr@77 47
mas01cr@0 48 if(O2_ACTION(COM_SERVER))
mas01cr@0 49 startServer();
mas01cr@0 50
mas01cr@0 51 else if(O2_ACTION(COM_CREATE))
mas01cr@0 52 create(dbName);
mas01cr@0 53
mas01cr@0 54 else if(O2_ACTION(COM_INSERT))
mas01cr@0 55 insert(dbName, inFile);
mas01cr@0 56
mas01cr@0 57 else if(O2_ACTION(COM_BATCHINSERT))
mas01cr@0 58 batchinsert(dbName, inFile);
mas01cr@0 59
mas01cr@0 60 else if(O2_ACTION(COM_QUERY))
mas01cr@0 61 if(isClient)
mas01cr@0 62 ws_query(dbName, inFile, (char*)hostport);
mas01cr@0 63 else
mas01cr@76 64 query(dbName, inFile);
mas01cr@0 65
mas01cr@0 66 else if(O2_ACTION(COM_STATUS))
mas01cr@0 67 if(isClient)
mas01cr@0 68 ws_status(dbName,(char*)hostport);
mas01cr@0 69 else
mas01cr@0 70 status(dbName);
mas01cr@0 71
mas01cr@0 72 else if(O2_ACTION(COM_L2NORM))
mas01cr@0 73 l2norm(dbName);
mas01cr@0 74
mas01cr@146 75 else if(O2_ACTION(COM_POWER))
mas01cr@146 76 power_flag(dbName);
mas01cr@146 77
mas01cr@0 78 else if(O2_ACTION(COM_DUMP))
mas01cr@0 79 dump(dbName);
mas01cr@0 80
mas01cr@0 81 else
mas01cr@0 82 error("Unrecognized command",command);
mas01cr@0 83 }
mas01cr@0 84
mas01cr@133 85 audioDB::audioDB(const unsigned argc, char* const argv[], adb__queryResponse *adbQueryResponse): O2_AUDIODB_INITIALIZERS
mas01cr@76 86 {
mas01cr@97 87 try {
mas01cr@97 88 processArgs(argc, argv);
mas01cr@97 89 isServer = 1; // FIXME: Hack
mas01cr@97 90 assert(O2_ACTION(COM_QUERY));
mas01cr@133 91 query(dbName, inFile, adbQueryResponse);
mas01cr@97 92 } catch(char *err) {
mas01cr@97 93 cleanup();
mas01cr@97 94 throw(err);
mas01cr@97 95 }
mas01cr@76 96 }
mas01cr@76 97
mas01cr@133 98 audioDB::audioDB(const unsigned argc, char* const argv[], adb__statusResponse *adbStatusResponse): O2_AUDIODB_INITIALIZERS
mas01cr@76 99 {
mas01cr@97 100 try {
mas01cr@97 101 processArgs(argc, argv);
mas01cr@97 102 isServer = 1; // FIXME: Hack
mas01cr@97 103 assert(O2_ACTION(COM_STATUS));
mas01cr@133 104 status(dbName, adbStatusResponse);
mas01cr@97 105 } catch(char *err) {
mas01cr@97 106 cleanup();
mas01cr@97 107 throw(err);
mas01cr@97 108 }
mas01cr@76 109 }
mas01cr@76 110
mas01cr@97 111 void audioDB::cleanup() {
mas01cr@122 112 cmdline_parser_free(&args_info);
mas01cr@0 113 if(indata)
mas01cr@0 114 munmap(indata,statbuf.st_size);
mas01cr@0 115 if(db)
mas01cr@128 116 munmap(db,dbH->dbSize);
mas01cr@0 117 if(dbfid>0)
mas01cr@0 118 close(dbfid);
mas01cr@0 119 if(infid>0)
mas01cr@0 120 close(infid);
mas01cr@0 121 if(dbH)
mas01cr@0 122 delete dbH;
mas01cr@0 123 }
mas01cr@0 124
mas01cr@97 125 audioDB::~audioDB(){
mas01cr@97 126 cleanup();
mas01cr@97 127 }
mas01cr@97 128
mas01cr@0 129 int audioDB::processArgs(const unsigned argc, char* const argv[]){
mas01cr@0 130
mas01cr@0 131 if(argc<2){
mas01cr@0 132 cmdline_parser_print_version ();
mas01cr@0 133 if (strlen(gengetopt_args_info_purpose) > 0)
mas01cr@0 134 printf("%s\n", gengetopt_args_info_purpose);
mas01cr@0 135 printf("%s\n", gengetopt_args_info_usage);
mas01cr@0 136 printf("%s\n", gengetopt_args_info_help[1]);
mas01cr@0 137 printf("%s\n", gengetopt_args_info_help[2]);
mas01cr@0 138 printf("%s\n", gengetopt_args_info_help[0]);
mas01cr@0 139 exit(0);
mas01cr@0 140 }
mas01cr@0 141
mas01cr@0 142 if (cmdline_parser (argc, argv, &args_info) != 0)
mas01cr@0 143 exit(1) ;
mas01cr@0 144
mas01cr@0 145 if(args_info.help_given){
mas01cr@0 146 cmdline_parser_print_help();
mas01cr@0 147 exit(0);
mas01cr@0 148 }
mas01cr@0 149
mas01cr@0 150 if(args_info.verbosity_given){
mas01cr@0 151 verbosity=args_info.verbosity_arg;
mas01cr@0 152 if(verbosity<0 || verbosity>10){
mas01cr@0 153 cerr << "Warning: verbosity out of range, setting to 1" << endl;
mas01cr@0 154 verbosity=1;
mas01cr@0 155 }
mas01cr@0 156 }
mas01cr@0 157
mas01cr@129 158 if(args_info.size_given) {
mas01cr@140 159 if (args_info.size_arg < 50 || args_info.size_arg > 4000) {
mas01cr@129 160 error("Size out of range", "");
mas01cr@129 161 }
mas01cr@129 162 size = args_info.size_arg * 1000000;
mas01cr@129 163 }
mas01cr@129 164
mas01mc@17 165 if(args_info.radius_given){
mas01mc@17 166 radius=args_info.radius_arg;
mas01mc@17 167 if(radius<=0 || radius>1000000000){
mas01cr@77 168 error("radius out of range");
mas01mc@17 169 }
mas01mc@17 170 else
mas01cr@60 171 if(verbosity>3) {
mas01mc@17 172 cerr << "Setting radius to " << radius << endl;
mas01cr@60 173 }
mas01mc@17 174 }
mas01mc@17 175
mas01cr@0 176 if(args_info.SERVER_given){
mas01cr@0 177 command=COM_SERVER;
mas01cr@0 178 port=args_info.SERVER_arg;
mas01cr@0 179 if(port<100 || port > 100000)
mas01cr@0 180 error("port out of range");
mas01cr@0 181 isServer=1;
mas01cr@105 182 #if defined(O2_DEBUG)
mas01cr@104 183 struct sigaction sa;
mas01cr@104 184 sa.sa_sigaction = sigterm_action;
mas01cr@104 185 sa.sa_flags = SA_SIGINFO | SA_RESTART | SA_NODEFER;
mas01cr@104 186 sigaction(SIGTERM, &sa, NULL);
mas01cr@104 187 sa.sa_sigaction = sighup_action;
mas01cr@104 188 sa.sa_flags = SA_SIGINFO | SA_RESTART | SA_NODEFER;
mas01cr@104 189 sigaction(SIGHUP, &sa, NULL);
mas01cr@105 190 #endif
mas01cr@0 191 return 0;
mas01cr@0 192 }
mas01cr@0 193
mas01cr@0 194 // No return on client command, find database command
mas01cr@105 195 if(args_info.client_given){
mas01cr@105 196 command=COM_CLIENT;
mas01cr@105 197 hostport=args_info.client_arg;
mas01cr@105 198 isClient=1;
mas01cr@105 199 }
mas01cr@0 200
mas01cr@105 201 if(args_info.NEW_given){
mas01cr@105 202 command=COM_CREATE;
mas01cr@105 203 dbName=args_info.database_arg;
mas01cr@105 204 return 0;
mas01cr@105 205 }
mas01cr@0 206
mas01cr@105 207 if(args_info.STATUS_given){
mas01cr@105 208 command=COM_STATUS;
mas01cr@105 209 dbName=args_info.database_arg;
mas01cr@105 210 return 0;
mas01cr@105 211 }
mas01cr@0 212
mas01cr@105 213 if(args_info.DUMP_given){
mas01cr@105 214 command=COM_DUMP;
mas01cr@105 215 dbName=args_info.database_arg;
mas01cr@131 216 output = args_info.output_arg;
mas01cr@105 217 return 0;
mas01cr@105 218 }
mas01cr@0 219
mas01cr@105 220 if(args_info.L2NORM_given){
mas01cr@105 221 command=COM_L2NORM;
mas01cr@105 222 dbName=args_info.database_arg;
mas01cr@105 223 return 0;
mas01cr@105 224 }
mas01cr@0 225
mas01cr@146 226 if(args_info.POWER_given){
mas01cr@146 227 command=COM_POWER;
mas01cr@146 228 dbName=args_info.database_arg;
mas01cr@146 229 return 0;
mas01cr@146 230 }
mas01cr@146 231
mas01cr@105 232 if(args_info.INSERT_given){
mas01cr@105 233 command=COM_INSERT;
mas01cr@105 234 dbName=args_info.database_arg;
mas01cr@105 235 inFile=args_info.features_arg;
mas01cr@105 236 if(args_info.key_given)
mas01cr@105 237 key=args_info.key_arg;
mas01cr@105 238 if(args_info.times_given){
mas01cr@105 239 timesFileName=args_info.times_arg;
mas01cr@105 240 if(strlen(timesFileName)>0){
mas01cr@105 241 if(!(timesFile = new ifstream(timesFileName,ios::in)))
mas01cr@105 242 error("Could not open times file for reading", timesFileName);
mas01cr@105 243 usingTimes=1;
mas01cr@105 244 }
mas01cr@105 245 }
mas01cr@144 246 if (args_info.power_given) {
mas01cr@144 247 powerFileName = args_info.power_arg;
mas01cr@144 248 if (strlen(powerFileName) > 0) {
mas01cr@144 249 if (!(powerfd = open(powerFileName, O_RDONLY))) {
mas01cr@144 250 error("Could not open power file for reading", powerFileName, "open");
mas01cr@144 251 }
mas01cr@144 252 usingPower = 1;
mas01cr@144 253 }
mas01cr@144 254 }
mas01cr@105 255 return 0;
mas01cr@105 256 }
mas01cr@105 257
mas01cr@105 258 if(args_info.BATCHINSERT_given){
mas01cr@105 259 command=COM_BATCHINSERT;
mas01cr@105 260 dbName=args_info.database_arg;
mas01cr@105 261 inFile=args_info.featureList_arg;
mas01cr@105 262 if(args_info.keyList_given)
mas01cr@105 263 key=args_info.keyList_arg; // INCONSISTENT NO CHECK
mas01cr@0 264
mas01cr@105 265 /* TO DO: REPLACE WITH
mas01cr@0 266 if(args_info.keyList_given){
mas01mc@18 267 trackFileName=args_info.keyList_arg;
mas01mc@18 268 if(strlen(trackFileName)>0 && !(trackFile = new ifstream(trackFileName,ios::in)))
mas01mc@18 269 error("Could not open keyList file for reading",trackFileName);
mas01cr@0 270 }
mas01cr@0 271 AND UPDATE BATCHINSERT()
mas01cr@105 272 */
mas01cr@105 273
mas01cr@105 274 if(args_info.timesList_given){
mas01cr@105 275 timesFileName=args_info.timesList_arg;
mas01cr@105 276 if(strlen(timesFileName)>0){
mas01cr@105 277 if(!(timesFile = new ifstream(timesFileName,ios::in)))
mas01cr@105 278 error("Could not open timesList file for reading", timesFileName);
mas01cr@105 279 usingTimes=1;
mas01cr@105 280 }
mas01cr@105 281 }
mas01cr@145 282 if(args_info.powerList_given){
mas01cr@145 283 powerFileName=args_info.powerList_arg;
mas01cr@145 284 if(strlen(powerFileName)>0){
mas01cr@145 285 if(!(powerFile = new ifstream(powerFileName,ios::in)))
mas01cr@145 286 error("Could not open powerList file for reading", powerFileName);
mas01cr@145 287 usingPower=1;
mas01cr@145 288 }
mas01cr@145 289 }
mas01cr@105 290 return 0;
mas01cr@105 291 }
mas01cr@105 292
mas01cr@105 293 // Query command and arguments
mas01cr@105 294 if(args_info.QUERY_given){
mas01cr@105 295 command=COM_QUERY;
mas01cr@105 296 dbName=args_info.database_arg;
mas01cr@105 297 inFile=args_info.features_arg;
mas01cr@105 298
mas01cr@105 299 if(args_info.keyList_given){
mas01cr@105 300 trackFileName=args_info.keyList_arg;
mas01cr@105 301 if(strlen(trackFileName)>0 && !(trackFile = new ifstream(trackFileName,ios::in)))
mas01cr@105 302 error("Could not open keyList file for reading",trackFileName);
mas01cr@105 303 }
mas01cr@105 304
mas01cr@105 305 if(args_info.times_given){
mas01cr@105 306 timesFileName=args_info.times_arg;
mas01cr@105 307 if(strlen(timesFileName)>0){
mas01cr@105 308 if(!(timesFile = new ifstream(timesFileName,ios::in)))
mas01cr@105 309 error("Could not open times file for reading", timesFileName);
mas01cr@105 310 usingTimes=1;
mas01cr@105 311 }
mas01cr@105 312 }
mas01cr@147 313
mas01cr@147 314 if(args_info.power_given){
mas01cr@147 315 powerFileName=args_info.power_arg;
mas01cr@147 316 if(strlen(powerFileName)>0){
mas01cr@147 317 if (!(powerfd = open(powerFileName, O_RDONLY))) {
mas01cr@147 318 error("Could not open power file for reading", powerFileName, "open");
mas01cr@147 319 }
mas01cr@147 320 usingPower = 1;
mas01cr@147 321 }
mas01cr@147 322 }
mas01cr@105 323
mas01cr@105 324 // query type
mas01cr@105 325 if(strncmp(args_info.QUERY_arg, "track", MAXSTR)==0)
mas01cr@105 326 queryType=O2_TRACK_QUERY;
mas01cr@105 327 else if(strncmp(args_info.QUERY_arg, "point", MAXSTR)==0)
mas01cr@105 328 queryType=O2_POINT_QUERY;
mas01cr@105 329 else if(strncmp(args_info.QUERY_arg, "sequence", MAXSTR)==0)
mas01cr@105 330 queryType=O2_SEQUENCE_QUERY;
mas01cr@105 331 else
mas01cr@105 332 error("unsupported query type",args_info.QUERY_arg);
mas01cr@105 333
mas01cr@105 334 if(!args_info.exhaustive_flag){
mas01cr@105 335 queryPoint = args_info.qpoint_arg;
mas01cr@105 336 usingQueryPoint=1;
mas01cr@105 337 if(queryPoint<0 || queryPoint >10000)
mas01cr@105 338 error("queryPoint out of range: 0 <= queryPoint <= 10000");
mas01cr@105 339 }
mas01cr@105 340
mas01cr@105 341 pointNN = args_info.pointnn_arg;
mas01cr@105 342 if(pointNN < 1 || pointNN > 1000) {
mas01cr@105 343 error("pointNN out of range: 1 <= pointNN <= 1000");
mas01cr@105 344 }
mas01cr@105 345 trackNN = args_info.resultlength_arg;
mas01cr@105 346 if(trackNN < 1 || trackNN > 1000) {
mas01cr@105 347 error("resultlength out of range: 1 <= resultlength <= 1000");
mas01cr@105 348 }
mas01cr@105 349 sequenceLength = args_info.sequencelength_arg;
mas01cr@105 350 if(sequenceLength < 1 || sequenceLength > 1000) {
mas01cr@105 351 error("seqlen out of range: 1 <= seqlen <= 1000");
mas01cr@105 352 }
mas01cr@105 353 sequenceHop = args_info.sequencehop_arg;
mas01cr@105 354 if(sequenceHop < 1 || sequenceHop > 1000) {
mas01cr@105 355 error("seqhop out of range: 1 <= seqhop <= 1000");
mas01cr@105 356 }
mas01cr@147 357
mas01cr@147 358 if (args_info.absolute_threshold_given) {
mas01cr@147 359 if (args_info.absolute_threshold_arg >= 0) {
mas01cr@147 360 error("absolute threshold out of range: should be negative");
mas01cr@147 361 }
mas01cr@147 362 use_absolute_threshold = true;
mas01cr@147 363 absolute_threshold = args_info.absolute_threshold_arg;
mas01cr@147 364 }
mas01cr@147 365 if (args_info.relative_threshold_given) {
mas01cr@147 366 use_relative_threshold = true;
mas01cr@147 367 relative_threshold = args_info.relative_threshold_arg;
mas01cr@147 368 }
mas01cr@105 369 return 0;
mas01cr@105 370 }
mas01cr@105 371 return -1; // no command found
mas01cr@0 372 }
mas01cr@0 373
mas01cr@30 374 void audioDB::get_lock(int fd, bool exclusive) {
mas01cr@30 375 struct flock lock;
mas01cr@30 376 int status;
mas01cr@30 377
mas01cr@30 378 lock.l_type = exclusive ? F_WRLCK : F_RDLCK;
mas01cr@30 379 lock.l_whence = SEEK_SET;
mas01cr@30 380 lock.l_start = 0;
mas01cr@30 381 lock.l_len = 0; /* "the whole file" */
mas01cr@30 382
mas01cr@30 383 retry:
mas01cr@30 384 do {
mas01cr@30 385 status = fcntl(fd, F_SETLKW, &lock);
mas01cr@30 386 } while (status != 0 && errno == EINTR);
mas01cr@30 387
mas01cr@30 388 if (status) {
mas01cr@30 389 if (errno == EAGAIN) {
mas01cr@30 390 sleep(1);
mas01cr@30 391 goto retry;
mas01cr@30 392 } else {
mas01cr@32 393 error("fcntl lock error", "", "fcntl");
mas01cr@30 394 }
mas01cr@30 395 }
mas01cr@30 396 }
mas01cr@30 397
mas01cr@30 398 void audioDB::release_lock(int fd) {
mas01cr@30 399 struct flock lock;
mas01cr@30 400 int status;
mas01cr@30 401
mas01cr@30 402 lock.l_type = F_UNLCK;
mas01cr@30 403 lock.l_whence = SEEK_SET;
mas01cr@30 404 lock.l_start = 0;
mas01cr@30 405 lock.l_len = 0;
mas01cr@30 406
mas01cr@30 407 status = fcntl(fd, F_SETLKW, &lock);
mas01cr@30 408
mas01cr@30 409 if (status)
mas01cr@32 410 error("fcntl unlock error", "", "fcntl");
mas01cr@30 411 }
mas01cr@30 412
mas01cr@120 413 /* Make a new database.
mas01cr@120 414
mas01cr@120 415 The database consists of:
mas01cr@120 416
mas01cr@120 417 * a header (see dbTableHeader struct definition);
mas01cr@120 418 * keyTable: list of keys of tracks;
mas01cr@120 419 * trackTable: Maps implicit feature index to a feature vector
mas01cr@120 420 matrix (sizes of tracks)
mas01cr@120 421 * featureTable: Lots of doubles;
mas01cr@120 422 * timesTable: time points for each feature vector;
mas01cr@120 423 * l2normTable: squared l2norms for each feature vector.
mas01cr@120 424 */
mas01cr@0 425 void audioDB::create(const char* dbName){
mas01cr@31 426 if ((dbfid = open (dbName, O_RDWR|O_CREAT|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0)
mas01cr@32 427 error("Can't create database file", dbName, "open");
mas01cr@30 428 get_lock(dbfid, 1);
mas01cr@0 429
mas01cr@0 430 // go to the location corresponding to the last byte
mas01cr@129 431 if (lseek (dbfid, size - 1, SEEK_SET) == -1)
mas01cr@32 432 error("lseek error in db file", "", "lseek");
mas01cr@0 433
mas01cr@0 434 // write a dummy byte at the last location
mas01cr@0 435 if (write (dbfid, "", 1) != 1)
mas01cr@32 436 error("write error", "", "write");
mas01cr@0 437
mas01cr@0 438 // mmap the output file
mas01cr@60 439 if(verbosity) {
mas01cr@0 440 cerr << "header size:" << O2_HEADERSIZE << endl;
mas01cr@60 441 }
mas01cr@129 442 if ((db = (char*) mmap(0, size, PROT_READ | PROT_WRITE,
mas01cr@0 443 MAP_SHARED, dbfid, 0)) == (caddr_t) -1)
mas01cr@32 444 error("mmap error for creating database", "", "mmap");
mas01cr@0 445
mas01cr@0 446 dbH = new dbTableHeaderT();
mas01cr@0 447 assert(dbH);
mas01cr@0 448
mas01cr@140 449 unsigned int maxfiles = (unsigned int) rint((double) O2_MAXFILES * (double) size / (double) O2_DEFAULTDBSIZE);
mas01cr@140 450
mas01cr@0 451 // Initialize header
mas01cr@108 452 dbH->magic = O2_MAGIC;
mas01cr@108 453 dbH->version = O2_FORMAT_VERSION;
mas01cr@108 454 dbH->numFiles = 0;
mas01cr@108 455 dbH->dim = 0;
mas01cr@108 456 dbH->flags = 0;
mas01cr@108 457 dbH->length = 0;
mas01cr@108 458 dbH->fileTableOffset = ALIGN_UP(O2_HEADERSIZE, 8);
mas01cr@140 459 dbH->trackTableOffset = ALIGN_UP(dbH->fileTableOffset + O2_FILETABLESIZE*maxfiles, 8);
mas01cr@140 460 dbH->dataOffset = ALIGN_UP(dbH->trackTableOffset + O2_TRACKTABLESIZE*maxfiles, 8);
mas01cr@140 461 dbH->l2normTableOffset = ALIGN_DOWN(size - maxfiles*O2_MEANNUMVECTORS*sizeof(double), 8);
mas01cr@140 462 dbH->timesTableOffset = ALIGN_DOWN(dbH->l2normTableOffset - maxfiles*O2_MEANNUMVECTORS*sizeof(double), 8);
mas01cr@142 463 dbH->powerTableOffset = ALIGN_DOWN(dbH->timesTableOffset - maxfiles*O2_MEANNUMVECTORS*sizeof(double), 8);
mas01cr@129 464 dbH->dbSize = size;
mas01cr@0 465
mas01cr@0 466 memcpy (db, dbH, O2_HEADERSIZE);
mas01cr@60 467 if(verbosity) {
mas01cr@0 468 cerr << COM_CREATE << " " << dbName << endl;
mas01cr@60 469 }
mas01cr@0 470 }
mas01cr@0 471
mas01cr@0 472
mas01cr@0 473 void audioDB::drop(){
mas01cr@108 474 // FIXME: drop something? Should we even allow this?
mas01cr@0 475 }
mas01cr@0 476
mas01cr@120 477 void audioDB::initDBHeader(const char* dbName, bool forWrite) {
mas01cr@106 478 if ((dbfid = open(dbName, forWrite ? O_RDWR : O_RDONLY)) < 0) {
mas01cr@32 479 error("Can't open database file", dbName, "open");
mas01cr@106 480 }
mas01cr@120 481
mas01cr@30 482 get_lock(dbfid, forWrite);
mas01cr@0 483 // Get the database header info
mas01cr@0 484 dbH = new dbTableHeaderT();
mas01cr@0 485 assert(dbH);
mas01cr@0 486
mas01cr@106 487 if(read(dbfid, (char *) dbH, O2_HEADERSIZE) != O2_HEADERSIZE) {
mas01cr@106 488 error("error reading db header", dbName, "read");
mas01cr@106 489 }
mas01cr@0 490
mas01cr@108 491 if(dbH->magic == O2_OLD_MAGIC) {
mas01cr@108 492 // FIXME: if anyone ever complains, write the program to convert
mas01cr@108 493 // from the old audioDB format to the new...
mas01cr@108 494 error("database file has old O2 header", dbName);
mas01cr@108 495 }
mas01cr@0 496
mas01cr@106 497 if(dbH->magic != O2_MAGIC) {
mas01cr@106 498 cerr << "expected: " << O2_MAGIC << ", got: " << dbH->magic << endl;
mas01cr@108 499 error("database file has incorrect header", dbName);
mas01cr@108 500 }
mas01cr@108 501
mas01cr@108 502 if(dbH->version != O2_FORMAT_VERSION) {
mas01cr@108 503 error("database file has incorect version", dbName);
mas01cr@0 504 }
mas01cr@0 505
mas01cr@128 506 // FIXME: when changing file format version, remove this workaround.
mas01cr@128 507 if(dbH->dbSize == 0) {
mas01cr@128 508 dbH->dbSize = O2_DEFAULTDBSIZE;
mas01cr@128 509 }
mas01cr@128 510
mas01cr@120 511 // mmap the database file
mas01cr@128 512 if ((db = (char*) mmap(0, dbH->dbSize, PROT_READ | (forWrite ? PROT_WRITE : 0),
mas01cr@120 513 MAP_SHARED, dbfid, 0)) == (caddr_t) -1)
mas01cr@120 514 error("mmap error for initting tables of database", "", "mmap");
mas01cr@120 515
mas01cr@120 516 // Make some handy tables with correct types
mas01cr@120 517 fileTable = (char *) (db + dbH->fileTableOffset);
mas01cr@120 518 trackTable = (unsigned *) (db + dbH->trackTableOffset);
mas01cr@120 519 dataBuf = (double *) (db + dbH->dataOffset);
mas01cr@120 520 l2normTable = (double *) (db + dbH->l2normTableOffset);
mas01cr@120 521 timesTable = (double *) (db + dbH->timesTableOffset);
mas01cr@142 522 powerTable = (double *) (db + dbH->powerTableOffset);
mas01cr@120 523 }
mas01cr@120 524
mas01cr@120 525 void audioDB::initTables(const char* dbName, bool forWrite, const char* inFile = 0) {
mas01cr@120 526
mas01cr@120 527 initDBHeader(dbName, forWrite);
mas01cr@120 528
mas01cr@120 529 // open the input file
mas01cr@120 530 if (inFile && (infid = open(inFile, O_RDONLY)) < 0) {
mas01cr@120 531 error("can't open input file for reading", inFile, "open");
mas01cr@120 532 }
mas01cr@120 533 // find size of input file
mas01cr@120 534 if (inFile && fstat(infid, &statbuf) < 0) {
mas01cr@120 535 error("fstat error finding size of input", inFile, "fstat");
mas01cr@120 536 }
mas01cr@0 537 if(inFile)
mas01cr@106 538 if(dbH->dim == 0 && dbH->length == 0) // empty database
mas01cr@106 539 // initialize with input dimensionality
mas01cr@106 540 read(infid, &dbH->dim, sizeof(unsigned));
mas01cr@0 541 else {
mas01cr@0 542 unsigned test;
mas01cr@106 543 read(infid, &test, sizeof(unsigned));
mas01cr@106 544 if(dbH->dim != test) {
mas01cr@106 545 cerr << "error: expected dimension: " << dbH->dim << ", got : " << test <<endl;
mas01cr@0 546 error("feature dimensions do not match database table dimensions");
mas01cr@0 547 }
mas01cr@0 548 }
mas01cr@0 549
mas01cr@0 550 // mmap the input file
mas01cr@0 551 if (inFile && (indata = (char*)mmap (0, statbuf.st_size, PROT_READ, MAP_SHARED, infid, 0))
mas01cr@0 552 == (caddr_t) -1)
mas01cr@106 553 error("mmap error for input", inFile, "mmap");
mas01cr@0 554 }
mas01cr@0 555
mas01cr@0 556 void audioDB::insert(const char* dbName, const char* inFile){
mas01cr@0 557
mas01cr@27 558 initTables(dbName, 1, inFile);
mas01cr@0 559
mas01cr@0 560 if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01cr@0 561 error("Must use timestamps with timestamped database","use --times");
mas01cr@0 562
mas01cr@146 563 if(!usingPower && (dbH->flags & O2_FLAG_POWER))
mas01cr@146 564 error("Must use power with power-enabled database", dbName);
mas01cr@146 565
mas01cr@0 566 // Check that there is room for at least 1 more file
mas01cr@0 567 if((char*)timesTable<((char*)dataBuf+dbH->length+statbuf.st_size-sizeof(int)))
mas01cr@0 568 error("No more room in database","insert failed: reason database is full.");
mas01cr@0 569
mas01cr@0 570 if(!key)
mas01cr@0 571 key=inFile;
mas01cr@0 572 // Linear scan of filenames check for pre-existing feature
mas01cr@0 573 unsigned alreadyInserted=0;
mas01cr@0 574 for(unsigned k=0; k<dbH->numFiles; k++)
mas01cr@0 575 if(strncmp(fileTable + k*O2_FILETABLESIZE, key, strlen(key))==0){
mas01cr@0 576 alreadyInserted=1;
mas01cr@0 577 break;
mas01cr@0 578 }
mas01cr@0 579
mas01cr@0 580 if(alreadyInserted){
mas01cr@60 581 if(verbosity) {
mas01cr@0 582 cerr << "Warning: key already exists in database, ignoring: " <<inFile << endl;
mas01cr@60 583 }
mas01cr@0 584 return;
mas01cr@0 585 }
mas01cr@0 586
mas01mc@18 587 // Make a track index table of features to file indexes
mas01cr@0 588 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01cr@0 589 if(!numVectors){
mas01cr@60 590 if(verbosity) {
mas01cr@0 591 cerr << "Warning: ignoring zero-length feature vector file:" << key << endl;
mas01cr@60 592 }
mas01cr@0 593 // CLEAN UP
mas01cr@0 594 munmap(indata,statbuf.st_size);
mas01cr@128 595 munmap(db,dbH->dbSize);
mas01cr@0 596 close(infid);
mas01cr@0 597 return;
mas01cr@0 598 }
mas01cr@0 599
mas01cr@0 600 strncpy(fileTable + dbH->numFiles*O2_FILETABLESIZE, key, strlen(key));
mas01cr@0 601
mas01cr@0 602 unsigned insertoffset = dbH->length;// Store current state
mas01cr@0 603
mas01cr@0 604 // Check times status and insert times from file
mas01cr@0 605 unsigned timesoffset=insertoffset/(dbH->dim*sizeof(double));
mas01cr@0 606 double* timesdata=timesTable+timesoffset;
mas01cr@0 607 assert(timesdata+numVectors<l2normTable);
mas01cr@0 608 insertTimeStamps(numVectors, timesFile, timesdata);
mas01cr@0 609
mas01cr@144 610 double *powerdata = powerTable + timesoffset;
mas01cr@144 611 insertPowerData(numVectors, powerfd, powerdata);
mas01cr@144 612
mas01cr@0 613 // Increment file count
mas01cr@0 614 dbH->numFiles++;
mas01cr@0 615
mas01cr@0 616 // Update Header information
mas01cr@0 617 dbH->length+=(statbuf.st_size-sizeof(int));
mas01cr@0 618
mas01cr@0 619 // Copy the header back to the database
mas01cr@0 620 memcpy (db, dbH, sizeof(dbTableHeaderT));
mas01cr@0 621
mas01mc@18 622 // Update track to file index map
mas01mc@18 623 //memcpy (db+trackTableOffset+(dbH->numFiles-1)*sizeof(unsigned), &numVectors, sizeof(unsigned));
mas01mc@18 624 memcpy (trackTable+dbH->numFiles-1, &numVectors, sizeof(unsigned));
mas01cr@0 625
mas01cr@0 626 // Update the feature database
mas01cr@108 627 memcpy (db+dbH->dataOffset+insertoffset, indata+sizeof(int), statbuf.st_size-sizeof(int));
mas01cr@0 628
mas01cr@0 629 // Norm the vectors on input if the database is already L2 normed
mas01cr@0 630 if(dbH->flags & O2_FLAG_L2NORM)
mas01cr@108 631 unitNormAndInsertL2((double*)(db+dbH->dataOffset+insertoffset), dbH->dim, numVectors, 1); // append
mas01cr@0 632
mas01cr@0 633 // Report status
mas01cr@0 634 status(dbName);
mas01cr@60 635 if(verbosity) {
mas01cr@0 636 cerr << COM_INSERT << " " << dbName << " " << numVectors << " vectors "
mas01cr@0 637 << (statbuf.st_size-sizeof(int)) << " bytes." << endl;
mas01cr@60 638 }
mas01cr@0 639
mas01cr@0 640 // CLEAN UP
mas01cr@0 641 munmap(indata,statbuf.st_size);
mas01cr@0 642 close(infid);
mas01cr@0 643 }
mas01cr@0 644
mas01cr@0 645 void audioDB::insertTimeStamps(unsigned numVectors, ifstream* timesFile, double* timesdata){
mas01cr@0 646 unsigned numtimes=0;
mas01cr@0 647 if(usingTimes){
mas01cr@0 648 if(!(dbH->flags & O2_FLAG_TIMES) && !dbH->numFiles)
mas01cr@0 649 dbH->flags=dbH->flags|O2_FLAG_TIMES;
mas01cr@0 650 else if(!(dbH->flags&O2_FLAG_TIMES)){
mas01cr@0 651 cerr << "Warning: timestamp file used with non time-stamped database: ignoring timestamps" << endl;
mas01cr@0 652 usingTimes=0;
mas01cr@0 653 }
mas01cr@0 654
mas01cr@0 655 if(!timesFile->is_open()){
mas01cr@0 656 if(dbH->flags & O2_FLAG_TIMES){
mas01cr@0 657 munmap(indata,statbuf.st_size);
mas01cr@128 658 munmap(db,dbH->dbSize);
mas01cr@0 659 error("problem opening times file on timestamped database",timesFileName);
mas01cr@0 660 }
mas01cr@0 661 else{
mas01cr@0 662 cerr << "Warning: problem opening times file. But non-timestamped database, so ignoring times file." << endl;
mas01cr@0 663 usingTimes=0;
mas01cr@0 664 }
mas01cr@0 665 }
mas01cr@0 666
mas01cr@0 667 // Process time file
mas01cr@0 668 if(usingTimes){
mas01cr@0 669 do{
mas01cr@0 670 *timesFile>>*timesdata++;
mas01cr@0 671 if(timesFile->eof())
mas01cr@0 672 break;
mas01cr@0 673 numtimes++;
mas01cr@0 674 }while(!timesFile->eof() && numtimes<numVectors);
mas01cr@0 675 if(!timesFile->eof()){
mas01cr@0 676 double dummy;
mas01cr@0 677 do{
mas01cr@0 678 *timesFile>>dummy;
mas01cr@0 679 if(timesFile->eof())
mas01cr@0 680 break;
mas01cr@0 681 numtimes++;
mas01cr@0 682 }while(!timesFile->eof());
mas01cr@0 683 }
mas01cr@0 684 if(numtimes<numVectors || numtimes>numVectors+2){
mas01cr@0 685 munmap(indata,statbuf.st_size);
mas01cr@128 686 munmap(db,dbH->dbSize);
mas01cr@0 687 close(infid);
mas01cr@0 688 cerr << "expected " << numVectors << " found " << numtimes << endl;
mas01cr@0 689 error("Times file is incorrect length for features file",inFile);
mas01cr@0 690 }
mas01cr@60 691 if(verbosity>2) {
mas01cr@0 692 cerr << "numtimes: " << numtimes << endl;
mas01cr@60 693 }
mas01cr@0 694 }
mas01cr@0 695 }
mas01cr@0 696 }
mas01cr@0 697
mas01cr@144 698 void audioDB::insertPowerData(unsigned numVectors, int powerfd, double *powerdata) {
mas01cr@144 699 if (usingPower) {
mas01cr@146 700 if (!(dbH->flags & O2_FLAG_POWER)) {
mas01cr@146 701 error("Cannot insert power data on non-power DB", dbName);
mas01cr@146 702 }
mas01cr@146 703
mas01cr@144 704 int one;
mas01cr@144 705 unsigned int count;
mas01cr@144 706
mas01cr@144 707 count = read(powerfd, &one, sizeof(unsigned int));
mas01cr@144 708 if (count != sizeof(unsigned int)) {
mas01cr@144 709 error("powerfd read failed", "int", "read");
mas01cr@144 710 }
mas01cr@144 711 if (one != 1) {
mas01cr@144 712 error("dimensionality of power file not 1", powerFileName);
mas01cr@144 713 }
mas01cr@144 714
mas01cr@144 715 // FIXME: should check that the powerfile is the right size for
mas01cr@144 716 // this. -- CSR, 2007-10-30
mas01cr@144 717 count = read(powerfd, powerdata, numVectors * sizeof(double));
mas01cr@144 718 if (count != numVectors * sizeof(double)) {
mas01cr@144 719 error("powerfd read failed", "double", "read");
mas01cr@144 720 }
mas01cr@144 721 }
mas01cr@144 722 }
mas01cr@144 723
mas01cr@120 724 void audioDB::batchinsert(const char* dbName, const char* inFile) {
mas01cr@0 725
mas01cr@120 726 initDBHeader(dbName, true);
mas01cr@0 727
mas01cr@0 728 if(!key)
mas01cr@0 729 key=inFile;
mas01cr@0 730 ifstream *filesIn = 0;
mas01cr@0 731 ifstream *keysIn = 0;
mas01cr@0 732 ifstream* thisTimesFile = 0;
mas01cr@145 733 int thispowerfd = 0;
mas01cr@0 734
mas01cr@0 735 if(!(filesIn = new ifstream(inFile)))
mas01cr@0 736 error("Could not open batch in file", inFile);
mas01cr@0 737 if(key && key!=inFile)
mas01cr@0 738 if(!(keysIn = new ifstream(key)))
mas01cr@0 739 error("Could not open batch key file",key);
mas01cr@0 740
mas01cr@0 741 if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01cr@0 742 error("Must use timestamps with timestamped database","use --times");
mas01cr@0 743
mas01cr@146 744 if(!usingPower && (dbH->flags & O2_FLAG_POWER))
mas01cr@146 745 error("Must use power with power-enabled database", dbName);
mas01cr@146 746
mas01cr@0 747 unsigned totalVectors=0;
mas01cr@0 748 char *thisKey = new char[MAXSTR];
mas01cr@0 749 char *thisFile = new char[MAXSTR];
mas01cr@0 750 char *thisTimesFileName = new char[MAXSTR];
mas01cr@145 751 char *thisPowerFileName = new char[MAXSTR];
mas01cr@120 752
mas01cr@0 753 do{
mas01cr@0 754 filesIn->getline(thisFile,MAXSTR);
mas01cr@0 755 if(key && key!=inFile)
mas01cr@0 756 keysIn->getline(thisKey,MAXSTR);
mas01cr@0 757 else
mas01cr@0 758 thisKey = thisFile;
mas01cr@0 759 if(usingTimes)
mas01cr@0 760 timesFile->getline(thisTimesFileName,MAXSTR);
mas01cr@145 761 if(usingPower)
mas01cr@145 762 powerFile->getline(thisPowerFileName, MAXSTR);
mas01cr@0 763
mas01cr@0 764 if(filesIn->eof())
mas01cr@0 765 break;
mas01cr@0 766
mas01cr@0 767 // open the input file
mas01cr@0 768 if (thisFile && (infid = open (thisFile, O_RDONLY)) < 0)
mas01cr@32 769 error("can't open feature file for reading", thisFile, "open");
mas01cr@0 770
mas01cr@0 771 // find size of input file
mas01cr@0 772 if (thisFile && fstat (infid,&statbuf) < 0)
mas01cr@32 773 error("fstat error finding size of input", "", "fstat");
mas01cr@0 774
mas01cr@0 775 // Check that there is room for at least 1 more file
mas01cr@0 776 if((char*)timesTable<((char*)dataBuf+(dbH->length+statbuf.st_size-sizeof(int))))
mas01cr@0 777 error("No more room in database","insert failed: reason database is full.");
mas01cr@0 778
mas01cr@0 779 if(thisFile)
mas01cr@0 780 if(dbH->dim==0 && dbH->length==0) // empty database
mas01cr@0 781 read(infid,&dbH->dim,sizeof(unsigned)); // initialize with input dimensionality
mas01cr@0 782 else {
mas01cr@0 783 unsigned test;
mas01cr@0 784 read(infid,&test,sizeof(unsigned));
mas01cr@0 785 if(dbH->dim!=test){
mas01cr@0 786 cerr << "error: expected dimension: " << dbH->dim << ", got :" << test <<endl;
mas01cr@0 787 error("feature dimensions do not match database table dimensions");
mas01cr@0 788 }
mas01cr@0 789 }
mas01cr@0 790
mas01cr@0 791 // mmap the input file
mas01cr@0 792 if (thisFile && (indata = (char*)mmap (0, statbuf.st_size, PROT_READ, MAP_SHARED, infid, 0))
mas01cr@0 793 == (caddr_t) -1)
mas01cr@32 794 error("mmap error for input", "", "mmap");
mas01cr@0 795
mas01cr@0 796
mas01cr@0 797 // Linear scan of filenames check for pre-existing feature
mas01cr@0 798 unsigned alreadyInserted=0;
mas01cr@0 799
mas01cr@0 800 for(unsigned k=0; k<dbH->numFiles; k++)
mas01cr@0 801 if(strncmp(fileTable + k*O2_FILETABLESIZE, thisKey, strlen(thisKey))==0){
mas01cr@0 802 alreadyInserted=1;
mas01cr@0 803 break;
mas01cr@0 804 }
mas01cr@0 805
mas01cr@0 806 if(alreadyInserted){
mas01cr@60 807 if(verbosity) {
mas01cr@0 808 cerr << "Warning: key already exists in database:" << thisKey << endl;
mas01cr@60 809 }
mas01cr@0 810 }
mas01cr@0 811 else{
mas01cr@0 812
mas01mc@18 813 // Make a track index table of features to file indexes
mas01cr@0 814 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01cr@0 815 if(!numVectors){
mas01cr@60 816 if(verbosity) {
mas01cr@0 817 cerr << "Warning: ignoring zero-length feature vector file:" << thisKey << endl;
mas01cr@60 818 }
mas01cr@0 819 }
mas01cr@145 820 else{
mas01cr@0 821 if(usingTimes){
mas01cr@0 822 if(timesFile->eof())
mas01cr@0 823 error("not enough timestamp files in timesList");
mas01cr@0 824 thisTimesFile=new ifstream(thisTimesFileName,ios::in);
mas01cr@0 825 if(!thisTimesFile->is_open())
mas01cr@0 826 error("Cannot open timestamp file",thisTimesFileName);
mas01cr@0 827 unsigned insertoffset=dbH->length;
mas01cr@0 828 unsigned timesoffset=insertoffset/(dbH->dim*sizeof(double));
mas01cr@0 829 double* timesdata=timesTable+timesoffset;
mas01cr@0 830 assert(timesdata+numVectors<l2normTable);
mas01cr@0 831 insertTimeStamps(numVectors,thisTimesFile,timesdata);
mas01cr@0 832 if(thisTimesFile)
mas01cr@0 833 delete thisTimesFile;
mas01cr@0 834 }
mas01cr@145 835
mas01cr@145 836 if (usingPower) {
mas01cr@145 837 if(powerFile->eof()) {
mas01cr@145 838 error("not enough power files in powerList", powerFileName);
mas01cr@145 839 }
mas01cr@145 840 thispowerfd = open(thisPowerFileName, O_RDONLY);
mas01cr@145 841 if (thispowerfd < 0) {
mas01cr@145 842 error("failed to open power file", thisPowerFileName);
mas01cr@145 843 }
mas01cr@145 844 unsigned insertoffset = dbH->length;
mas01cr@145 845 unsigned poweroffset = insertoffset / (dbH->dim * sizeof(double));
mas01cr@145 846 double *powerdata = powerTable + poweroffset;
mas01cr@145 847 insertPowerData(numVectors, thispowerfd, powerdata);
mas01cr@145 848 if (0 < thispowerfd) {
mas01cr@145 849 close(thispowerfd);
mas01cr@145 850 }
mas01cr@145 851 }
mas01cr@0 852 strncpy(fileTable + dbH->numFiles*O2_FILETABLESIZE, thisKey, strlen(thisKey));
mas01cr@0 853
mas01cr@0 854 unsigned insertoffset = dbH->length;// Store current state
mas01cr@0 855
mas01cr@0 856 // Increment file count
mas01cr@0 857 dbH->numFiles++;
mas01cr@0 858
mas01cr@0 859 // Update Header information
mas01cr@0 860 dbH->length+=(statbuf.st_size-sizeof(int));
mas01cr@0 861 // Copy the header back to the database
mas01cr@0 862 memcpy (db, dbH, sizeof(dbTableHeaderT));
mas01cr@0 863
mas01mc@18 864 // Update track to file index map
mas01mc@18 865 //memcpy (db+trackTableOffset+(dbH->numFiles-1)*sizeof(unsigned), &numVectors, sizeof(unsigned));
mas01mc@18 866 memcpy (trackTable+dbH->numFiles-1, &numVectors, sizeof(unsigned));
mas01cr@0 867
mas01cr@0 868 // Update the feature database
mas01cr@108 869 memcpy (db+dbH->dataOffset+insertoffset, indata+sizeof(int), statbuf.st_size-sizeof(int));
mas01cr@0 870
mas01cr@0 871 // Norm the vectors on input if the database is already L2 normed
mas01cr@0 872 if(dbH->flags & O2_FLAG_L2NORM)
mas01cr@108 873 unitNormAndInsertL2((double*)(db+dbH->dataOffset+insertoffset), dbH->dim, numVectors, 1); // append
mas01cr@0 874
mas01cr@0 875 totalVectors+=numVectors;
mas01cr@0 876 }
mas01cr@0 877 }
mas01cr@0 878 // CLEAN UP
mas01cr@0 879 munmap(indata,statbuf.st_size);
mas01cr@0 880 close(infid);
mas01cr@0 881 }while(!filesIn->eof());
mas01mc@12 882
mas01cr@60 883 if(verbosity) {
mas01cr@0 884 cerr << COM_BATCHINSERT << " " << dbName << " " << totalVectors << " vectors "
mas01cr@0 885 << totalVectors*dbH->dim*sizeof(double) << " bytes." << endl;
mas01cr@60 886 }
mas01cr@0 887
mas01cr@0 888 // Report status
mas01cr@0 889 status(dbName);
mas01cr@0 890 }
mas01cr@0 891
mas01cr@76 892 // FIXME: this can't propagate the sequence length argument (used for
mas01cr@76 893 // dudCount). See adb__status() definition for the other half of
mas01cr@76 894 // this. -- CSR, 2007-10-01
mas01cr@0 895 void audioDB::ws_status(const char*dbName, char* hostport){
mas01cr@0 896 struct soap soap;
mas01cr@133 897 adb__statusResponse adbStatusResponse;
mas01cr@0 898
mas01cr@0 899 // Query an existing adb database
mas01cr@0 900 soap_init(&soap);
mas01cr@133 901 if(soap_call_adb__status(&soap,hostport,NULL,(char*)dbName,adbStatusResponse)==SOAP_OK) {
mas01cr@133 902 cout << "numFiles = " << adbStatusResponse.result.numFiles << endl;
mas01cr@133 903 cout << "dim = " << adbStatusResponse.result.dim << endl;
mas01cr@133 904 cout << "length = " << adbStatusResponse.result.length << endl;
mas01cr@133 905 cout << "dudCount = " << adbStatusResponse.result.dudCount << endl;
mas01cr@133 906 cout << "nullCount = " << adbStatusResponse.result.nullCount << endl;
mas01cr@133 907 cout << "flags = " << adbStatusResponse.result.flags << endl;
mas01cr@76 908 } else {
mas01cr@0 909 soap_print_fault(&soap,stderr);
mas01cr@76 910 }
mas01cr@0 911
mas01cr@0 912 soap_destroy(&soap);
mas01cr@0 913 soap_end(&soap);
mas01cr@0 914 soap_done(&soap);
mas01cr@0 915 }
mas01cr@0 916
mas01mc@18 917 void audioDB::ws_query(const char*dbName, const char *trackKey, const char* hostport){
mas01cr@0 918 struct soap soap;
mas01cr@133 919 adb__queryResponse adbQueryResponse;
mas01cr@0 920
mas01cr@0 921 soap_init(&soap);
mas01cr@0 922 if(soap_call_adb__query(&soap,hostport,NULL,
mas01mc@18 923 (char*)dbName,(char*)trackKey,(char*)trackFileName,(char*)timesFileName,
mas01cr@133 924 queryType, queryPoint, pointNN, trackNN, sequenceLength, adbQueryResponse)==SOAP_OK){
mas01cr@133 925 //std::cerr << "result list length:" << adbQueryResponse.result.__sizeRlist << std::endl;
mas01cr@133 926 for(int i=0; i<adbQueryResponse.result.__sizeRlist; i++)
mas01cr@133 927 std::cout << adbQueryResponse.result.Rlist[i] << " " << adbQueryResponse.result.Dist[i]
mas01cr@133 928 << " " << adbQueryResponse.result.Qpos[i] << " " << adbQueryResponse.result.Spos[i] << std::endl;
mas01cr@0 929 }
mas01cr@0 930 else
mas01cr@0 931 soap_print_fault(&soap,stderr);
mas01cr@0 932
mas01cr@0 933 soap_destroy(&soap);
mas01cr@0 934 soap_end(&soap);
mas01cr@0 935 soap_done(&soap);
mas01cr@0 936
mas01cr@0 937 }
mas01cr@0 938
mas01cr@0 939
mas01cr@133 940 void audioDB::status(const char* dbName, adb__statusResponse *adbStatusResponse){
mas01cr@0 941 if(!dbH)
mas01cr@27 942 initTables(dbName, 0, 0);
mas01cr@0 943
mas01cr@0 944 unsigned dudCount=0;
mas01cr@0 945 unsigned nullCount=0;
mas01cr@0 946 for(unsigned k=0; k<dbH->numFiles; k++){
mas01mc@18 947 if(trackTable[k]<sequenceLength){
mas01cr@0 948 dudCount++;
mas01mc@18 949 if(!trackTable[k])
mas01cr@76 950 nullCount++;
mas01cr@0 951 }
mas01cr@0 952 }
mas01cr@76 953
mas01cr@133 954 if(adbStatusResponse == 0) {
mas01cr@76 955
mas01cr@76 956 // Update Header information
mas01cr@76 957 cout << "num files:" << dbH->numFiles << endl;
mas01cr@76 958 cout << "data dim:" << dbH->dim <<endl;
mas01cr@76 959 if(dbH->dim>0){
mas01cr@76 960 cout << "total vectors:" << dbH->length/(sizeof(double)*dbH->dim)<<endl;
mas01cr@108 961 cout << "vectors available:" << (dbH->timesTableOffset-(dbH->dataOffset+dbH->length))/(sizeof(double)*dbH->dim) << endl;
mas01cr@76 962 }
mas01cr@108 963 cout << "total bytes:" << dbH->length << " (" << (100.0*dbH->length)/(dbH->timesTableOffset-dbH->dataOffset) << "%)" << endl;
mas01cr@108 964 cout << "bytes available:" << dbH->timesTableOffset-(dbH->dataOffset+dbH->length) << " (" <<
mas01cr@108 965 (100.0*(dbH->timesTableOffset-(dbH->dataOffset+dbH->length)))/(dbH->timesTableOffset-dbH->dataOffset) << "%)" << endl;
mas01cr@76 966 cout << "flags:" << dbH->flags << endl;
mas01cr@76 967
mas01cr@76 968 cout << "null count: " << nullCount << " small sequence count " << dudCount-nullCount << endl;
mas01cr@76 969 } else {
mas01cr@133 970 adbStatusResponse->result.numFiles = dbH->numFiles;
mas01cr@133 971 adbStatusResponse->result.dim = dbH->dim;
mas01cr@133 972 adbStatusResponse->result.length = dbH->length;
mas01cr@133 973 adbStatusResponse->result.dudCount = dudCount;
mas01cr@133 974 adbStatusResponse->result.nullCount = nullCount;
mas01cr@133 975 adbStatusResponse->result.flags = dbH->flags;
mas01cr@76 976 }
mas01cr@0 977 }
mas01cr@0 978
mas01cr@0 979 void audioDB::dump(const char* dbName){
mas01cr@131 980 if(!dbH) {
mas01cr@27 981 initTables(dbName, 0, 0);
mas01mc@17 982 }
mas01cr@0 983
mas01cr@131 984 if((mkdir(output, S_IRWXU|S_IRWXG|S_IRWXO)) < 0) {
mas01cr@131 985 error("error making output directory", output, "mkdir");
mas01cr@131 986 }
mas01cr@131 987
mas01cr@131 988 char *cwd = new char[PATH_MAX];
mas01cr@131 989
mas01cr@131 990 if ((getcwd(cwd, PATH_MAX)) == 0) {
mas01cr@131 991 error("error getting working directory", "", "getcwd");
mas01cr@131 992 }
mas01cr@131 993
mas01cr@131 994 if((chdir(output)) < 0) {
mas01cr@131 995 error("error changing working directory", output, "chdir");
mas01cr@131 996 }
mas01cr@131 997
mas01cr@153 998 int fLfd, tLfd = 0, pLfd = 0, kLfd;
mas01cr@153 999 FILE *fLFile, *tLFile = 0, *pLFile = 0, *kLFile;
mas01cr@131 1000
mas01cr@131 1001 if ((fLfd = open("featureList.txt", O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@131 1002 error("error creating featureList file", "featureList.txt", "open");
mas01cr@131 1003 }
mas01cr@153 1004
mas01cr@131 1005 int times = dbH->flags & O2_FLAG_TIMES;
mas01cr@131 1006 if (times) {
mas01cr@131 1007 if ((tLfd = open("timesList.txt", O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@131 1008 error("error creating timesList file", "timesList.txt", "open");
mas01cr@131 1009 }
mas01cr@131 1010 }
mas01cr@153 1011
mas01cr@153 1012 int power = dbH->flags & O2_FLAG_POWER;
mas01cr@153 1013 if (power) {
mas01cr@153 1014 if ((pLfd = open("powerList.txt", O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@153 1015 error("error creating powerList file", "powerList.txt", "open");
mas01cr@153 1016 }
mas01cr@153 1017 }
mas01cr@153 1018
mas01cr@131 1019 if ((kLfd = open("keyList.txt", O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@131 1020 error("error creating keyList file", "keyList.txt", "open");
mas01cr@131 1021 }
mas01cr@131 1022
mas01cr@131 1023 /* can these fail? I sincerely hope not. */
mas01cr@131 1024 fLFile = fdopen(fLfd, "w");
mas01cr@131 1025 if (times) {
mas01cr@131 1026 tLFile = fdopen(tLfd, "w");
mas01cr@131 1027 }
mas01cr@153 1028 if (power) {
mas01cr@153 1029 pLFile = fdopen(pLfd, "w");
mas01cr@153 1030 }
mas01cr@131 1031 kLFile = fdopen(kLfd, "w");
mas01cr@131 1032
mas01cr@131 1033 char *fName = new char[256];
mas01cr@153 1034 int ffd, pfd;
mas01cr@131 1035 FILE *tFile;
mas01cr@131 1036 unsigned pos = 0;
mas01cr@131 1037 for(unsigned k = 0; k < dbH->numFiles; k++) {
mas01cr@131 1038 fprintf(kLFile, "%s\n", fileTable + k*O2_FILETABLESIZE);
mas01cr@131 1039 snprintf(fName, 256, "%05d.features", k);
mas01cr@131 1040 if ((ffd = open(fName, O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@131 1041 error("error creating feature file", fName, "open");
mas01cr@131 1042 }
mas01cr@131 1043 if ((write(ffd, &dbH->dim, sizeof(uint32_t))) < 0) {
mas01cr@131 1044 error("error writing dimensions", fName, "write");
mas01cr@131 1045 }
mas01cr@131 1046
mas01cr@131 1047 if ((write(ffd, dataBuf + pos * dbH->dim, trackTable[k] * dbH->dim * sizeof(double))) < 0) {
mas01cr@131 1048 error("error writing data", fName, "write");
mas01cr@131 1049 }
mas01cr@131 1050 fprintf(fLFile, "%s\n", fName);
mas01cr@131 1051 close(ffd);
mas01cr@131 1052
mas01cr@131 1053 if(times) {
mas01cr@131 1054 snprintf(fName, 256, "%05d.times", k);
mas01cr@131 1055 tFile = fopen(fName, "w");
mas01cr@131 1056 for(unsigned i = 0; i < trackTable[k]; i++) {
mas01cr@131 1057 // KLUDGE: specifying 16 digits of precision after the decimal
mas01cr@131 1058 // point is (but check this!) sufficient to uniquely identify
mas01cr@131 1059 // doubles; however, that will cause ugliness, as that's
mas01cr@131 1060 // vastly too many for most values of interest. Moving to %a
mas01cr@131 1061 // here and scanf() in the timesFile reading might fix this.
mas01cr@131 1062 // -- CSR, 2007-10-19
mas01cr@131 1063 fprintf(tFile, "%.16e\n", *(timesTable + pos + i));
mas01cr@131 1064 }
mas01cr@131 1065 fprintf(tLFile, "%s\n", fName);
mas01cr@131 1066 }
mas01cr@131 1067
mas01cr@153 1068 if (power) {
mas01cr@153 1069 uint32_t one = 1;
mas01cr@153 1070 snprintf(fName, 256, "%05d.power", k);
mas01cr@153 1071 if ((pfd = open(fName, O_CREAT|O_RDWR|O_EXCL, S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP|S_IROTH|S_IWOTH)) < 0) {
mas01cr@153 1072 error("error creating power file", fName, "open");
mas01cr@153 1073 }
mas01cr@153 1074 if ((write(pfd, &one, sizeof(uint32_t))) < 0) {
mas01cr@153 1075 error("error writing one", fName, "write");
mas01cr@153 1076 }
mas01cr@153 1077 if ((write(pfd, powerTable + pos, trackTable[k] * sizeof(double))) < 0) {
mas01cr@153 1078 error("error writing data", fName, "write");
mas01cr@153 1079 }
mas01cr@153 1080 fprintf(pLFile, "%s\n", fName);
mas01cr@153 1081 close(pfd);
mas01cr@153 1082 }
mas01cr@153 1083
mas01cr@131 1084 pos += trackTable[k];
mas01cr@131 1085 cout << fileTable+k*O2_FILETABLESIZE << " " << trackTable[k] << endl;
mas01cr@131 1086 }
mas01cr@131 1087
mas01cr@131 1088 FILE *scriptFile;
mas01cr@131 1089 scriptFile = fopen("restore.sh", "w");
mas01cr@131 1090 fprintf(scriptFile, "\
mas01cr@131 1091 #! /bin/sh\n\
mas01cr@131 1092 #\n\
mas01cr@131 1093 # usage: AUDIODB=/path/to/audioDB sh ./restore.sh <newdb>\n\
mas01cr@131 1094 \n\
mas01cr@131 1095 if [ -z \"${AUDIODB}\" ]; then echo set AUDIODB variable; exit 1; fi\n\
mas01cr@131 1096 if [ -z \"$1\" ]; then echo usage: $0 newdb; exit 1; fi\n\n\
mas01cr@131 1097 \"${AUDIODB}\" -d \"$1\" -N --size=%d\n", dbH->dbSize / 1000000);
mas01cr@131 1098 if(dbH->flags & O2_FLAG_L2NORM) {
mas01cr@131 1099 fprintf(scriptFile, "\"${AUDIODB}\" -d \"$1\" -L\n");
mas01cr@131 1100 }
mas01cr@153 1101 if(power) {
mas01cr@153 1102 fprintf(scriptFile, "\"${AUDIODB}\" -d \"$1\" -P\n");
mas01cr@153 1103 }
mas01cr@131 1104 fprintf(scriptFile, "\"${AUDIODB}\" -d \"$1\" -B -F featureList.txt -K keyList.txt");
mas01cr@131 1105 if(times) {
mas01cr@131 1106 fprintf(scriptFile, " -T timesList.txt");
mas01cr@131 1107 }
mas01cr@153 1108 if(power) {
mas01cr@153 1109 fprintf(scriptFile, " -W powerList.txt");
mas01cr@153 1110 }
mas01cr@131 1111 fprintf(scriptFile, "\n");
mas01cr@131 1112 fclose(scriptFile);
mas01cr@131 1113
mas01cr@131 1114 if((chdir(cwd)) < 0) {
mas01cr@131 1115 error("error changing working directory", cwd, "chdir");
mas01cr@131 1116 }
mas01cr@131 1117
mas01cr@131 1118 fclose(fLFile);
mas01cr@131 1119 if(times) {
mas01cr@131 1120 fclose(tLFile);
mas01cr@131 1121 }
mas01cr@153 1122 if(power) {
mas01cr@153 1123 fclose(pLFile);
mas01cr@153 1124 }
mas01cr@131 1125 fclose(kLFile);
mas01cr@131 1126 delete[] fName;
mas01cr@131 1127
mas01cr@0 1128 status(dbName);
mas01cr@0 1129 }
mas01cr@0 1130
mas01cr@0 1131 void audioDB::l2norm(const char* dbName){
mas01cr@50 1132 initTables(dbName, true, 0);
mas01cr@0 1133 if(dbH->length>0){
mas01cr@0 1134 unsigned numVectors = dbH->length/(sizeof(double)*dbH->dim);
mas01cr@0 1135 unitNormAndInsertL2(dataBuf, dbH->dim, numVectors, 0); // No append
mas01cr@0 1136 }
mas01cr@0 1137 // Update database flags
mas01cr@0 1138 dbH->flags = dbH->flags|O2_FLAG_L2NORM;
mas01cr@0 1139 memcpy (db, dbH, O2_HEADERSIZE);
mas01cr@0 1140 }
mas01cr@146 1141
mas01cr@146 1142 void audioDB::power_flag(const char *dbName) {
mas01cr@146 1143 initTables(dbName, true, 0);
mas01cr@146 1144 if (dbH->length > 0) {
mas01cr@146 1145 error("cannot turn on power storage for non-empty database", dbName);
mas01cr@146 1146 }
mas01cr@146 1147 dbH->flags |= O2_FLAG_POWER;
mas01cr@146 1148 memcpy(db, dbH, O2_HEADERSIZE);
mas01cr@146 1149 }
mas01cr@0 1150
mas01cr@147 1151 bool audioDB::powers_acceptable(double p1, double p2) {
mas01cr@147 1152 if (use_absolute_threshold) {
mas01cr@147 1153 if ((p1 < absolute_threshold) || (p2 < absolute_threshold)) {
mas01cr@147 1154 return false;
mas01cr@147 1155 }
mas01cr@147 1156 }
mas01cr@147 1157 if (use_relative_threshold) {
mas01cr@147 1158 if (fabs(p1-p2) > fabs(relative_threshold)) {
mas01cr@147 1159 return false;
mas01cr@147 1160 }
mas01cr@147 1161 }
mas01cr@147 1162 return true;
mas01cr@147 1163 }
mas01cr@147 1164
mas01cr@0 1165
mas01cr@133 1166 void audioDB::query(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse){
mas01cr@0 1167 switch(queryType){
mas01cr@105 1168 case O2_POINT_QUERY:
mas01cr@133 1169 pointQuery(dbName, inFile, adbQueryResponse);
mas01cr@0 1170 break;
mas01cr@105 1171 case O2_SEQUENCE_QUERY:
mas01mc@17 1172 if(radius==0)
mas01cr@133 1173 trackSequenceQueryNN(dbName, inFile, adbQueryResponse);
mas01mc@17 1174 else
mas01cr@133 1175 trackSequenceQueryRad(dbName, inFile, adbQueryResponse);
mas01cr@0 1176 break;
mas01cr@105 1177 case O2_TRACK_QUERY:
mas01cr@133 1178 trackPointQuery(dbName, inFile, adbQueryResponse);
mas01cr@0 1179 break;
mas01cr@0 1180 default:
mas01cr@0 1181 error("unrecognized queryType in query()");
mas01cr@0 1182
mas01cr@0 1183 }
mas01cr@0 1184 }
mas01cr@0 1185
mas01cr@0 1186 //return ordinal position of key in keyTable
mas01cr@0 1187 unsigned audioDB::getKeyPos(char* key){
mas01cr@0 1188 for(unsigned k=0; k<dbH->numFiles; k++)
mas01cr@0 1189 if(strncmp(fileTable + k*O2_FILETABLESIZE, key, strlen(key))==0)
mas01cr@0 1190 return k;
mas01cr@0 1191 error("Key not found",key);
mas01cr@0 1192 return O2_ERR_KEYNOTFOUND;
mas01cr@0 1193 }
mas01cr@0 1194
mas01cr@0 1195 // Basic point query engine
mas01cr@133 1196 void audioDB::pointQuery(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse){
mas01cr@0 1197
mas01cr@27 1198 initTables(dbName, 0, inFile);
mas01cr@0 1199
mas01cr@0 1200 // For each input vector, find the closest pointNN matching output vectors and report
mas01cr@0 1201 // we use stdout in this stub version
mas01cr@0 1202 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01cr@0 1203
mas01cr@0 1204 double* query = (double*)(indata+sizeof(int));
mas01cr@0 1205 double* data = dataBuf;
mas01cr@0 1206 double* queryCopy = 0;
mas01cr@0 1207
mas01cr@0 1208 if( dbH->flags & O2_FLAG_L2NORM ){
mas01cr@0 1209 // Make a copy of the query
mas01cr@0 1210 queryCopy = new double[numVectors*dbH->dim];
mas01cr@0 1211 qNorm = new double[numVectors];
mas01cr@0 1212 assert(queryCopy&&qNorm);
mas01cr@0 1213 memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double));
mas01cr@0 1214 unitNorm(queryCopy, dbH->dim, numVectors, qNorm);
mas01cr@0 1215 query = queryCopy;
mas01cr@0 1216 }
mas01cr@0 1217
mas01cr@0 1218 // Make temporary dynamic memory for results
mas01cr@0 1219 assert(pointNN>0 && pointNN<=O2_MAXNN);
mas01cr@0 1220 double distances[pointNN];
mas01cr@0 1221 unsigned qIndexes[pointNN];
mas01cr@0 1222 unsigned sIndexes[pointNN];
mas01cr@0 1223 for(unsigned k=0; k<pointNN; k++){
mas01cr@62 1224 distances[k]=-DBL_MAX;
mas01cr@0 1225 qIndexes[k]=~0;
mas01cr@0 1226 sIndexes[k]=~0;
mas01cr@0 1227 }
mas01cr@0 1228
mas01cr@0 1229 unsigned j=numVectors;
mas01cr@0 1230 unsigned k,l,n;
mas01cr@0 1231 double thisDist;
mas01cr@0 1232
mas01cr@0 1233 unsigned totalVecs=dbH->length/(dbH->dim*sizeof(double));
mas01cr@0 1234 double meanQdur = 0;
mas01cr@0 1235 double* timesdata = 0;
mas01cr@0 1236 double* dbdurs = 0;
mas01cr@0 1237
mas01cr@0 1238 if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1239 cerr << "warning: ignoring query timestamps for non-timestamped database" << endl;
mas01cr@0 1240 usingTimes=0;
mas01cr@0 1241 }
mas01cr@0 1242
mas01cr@0 1243 else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01cr@0 1244 cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl;
mas01cr@0 1245
mas01cr@0 1246 else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1247 timesdata = new double[numVectors];
mas01cr@0 1248 insertTimeStamps(numVectors, timesFile, timesdata);
mas01cr@0 1249 // Calculate durations of points
mas01cr@0 1250 for(k=0; k<numVectors-1; k++){
mas01cr@0 1251 timesdata[k]=timesdata[k+1]-timesdata[k];
mas01cr@0 1252 meanQdur+=timesdata[k];
mas01cr@0 1253 }
mas01cr@0 1254 meanQdur/=k;
mas01cr@0 1255 // Individual exhaustive timepoint durations
mas01cr@0 1256 dbdurs = new double[totalVecs];
mas01cr@0 1257 for(k=0; k<totalVecs-1; k++)
mas01cr@0 1258 dbdurs[k]=timesTable[k+1]-timesTable[k];
mas01cr@0 1259 j--; // decrement vector counter by one
mas01cr@0 1260 }
mas01cr@0 1261
mas01cr@0 1262 if(usingQueryPoint)
mas01cr@0 1263 if(queryPoint>numVectors-1)
mas01cr@0 1264 error("queryPoint > numVectors in query");
mas01cr@0 1265 else{
mas01cr@60 1266 if(verbosity>1) {
mas01cr@0 1267 cerr << "query point: " << queryPoint << endl; cerr.flush();
mas01cr@60 1268 }
mas01cr@0 1269 query=query+queryPoint*dbH->dim;
mas01cr@0 1270 numVectors=queryPoint+1;
mas01cr@0 1271 j=1;
mas01cr@0 1272 }
mas01cr@0 1273
mas01cr@0 1274 gettimeofday(&tv1, NULL);
mas01cr@0 1275 while(j--){ // query
mas01cr@0 1276 data=dataBuf;
mas01cr@0 1277 k=totalVecs; // number of database vectors
mas01cr@0 1278 while(k--){ // database
mas01cr@0 1279 thisDist=0;
mas01cr@0 1280 l=dbH->dim;
mas01cr@0 1281 double* q=query;
mas01cr@0 1282 while(l--)
mas01cr@0 1283 thisDist+=*q++**data++;
mas01cr@0 1284 if(!usingTimes ||
mas01cr@0 1285 (usingTimes
mas01cr@0 1286 && fabs(dbdurs[totalVecs-k-1]-timesdata[numVectors-j-1])<timesdata[numVectors-j-1]*timesTol)){
mas01cr@0 1287 n=pointNN;
mas01cr@0 1288 while(n--){
mas01cr@0 1289 if(thisDist>=distances[n]){
mas01cr@0 1290 if((n==0 || thisDist<=distances[n-1])){
mas01cr@0 1291 // Copy all values above up the queue
mas01cr@0 1292 for( l=pointNN-1 ; l >= n+1 ; l--){
mas01cr@0 1293 distances[l]=distances[l-1];
mas01cr@0 1294 qIndexes[l]=qIndexes[l-1];
mas01cr@0 1295 sIndexes[l]=sIndexes[l-1];
mas01cr@0 1296 }
mas01cr@0 1297 distances[n]=thisDist;
mas01cr@0 1298 qIndexes[n]=numVectors-j-1;
mas01cr@0 1299 sIndexes[n]=dbH->length/(sizeof(double)*dbH->dim)-k-1;
mas01cr@0 1300 break;
mas01cr@0 1301 }
mas01cr@0 1302 }
mas01cr@0 1303 else
mas01cr@0 1304 break;
mas01cr@0 1305 }
mas01cr@0 1306 }
mas01cr@0 1307 }
mas01cr@0 1308 // Move query pointer to next query point
mas01cr@0 1309 query+=dbH->dim;
mas01cr@0 1310 }
mas01cr@0 1311
mas01cr@0 1312 gettimeofday(&tv2, NULL);
mas01cr@60 1313 if(verbosity>1) {
mas01cr@0 1314 cerr << endl << " elapsed time:" << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl;
mas01cr@60 1315 }
mas01cr@0 1316
mas01cr@133 1317 if(adbQueryResponse==0){
mas01cr@0 1318 // Output answer
mas01cr@0 1319 // Loop over nearest neighbours
mas01cr@0 1320 for(k=0; k < pointNN; k++){
mas01cr@0 1321 // Scan for key
mas01mc@18 1322 unsigned cumTrack=0;
mas01cr@0 1323 for(l=0 ; l<dbH->numFiles; l++){
mas01mc@18 1324 cumTrack+=trackTable[l];
mas01mc@18 1325 if(sIndexes[k]<cumTrack){
mas01cr@0 1326 cout << fileTable+l*O2_FILETABLESIZE << " " << distances[k] << " " << qIndexes[k] << " "
mas01mc@18 1327 << sIndexes[k]+trackTable[l]-cumTrack << endl;
mas01cr@0 1328 break;
mas01cr@0 1329 }
mas01cr@0 1330 }
mas01cr@0 1331 }
mas01cr@0 1332 }
mas01cr@0 1333 else{ // Process Web Services Query
mas01cr@89 1334 int listLen;
mas01cr@89 1335 for(k = 0; k < pointNN; k++) {
mas01cr@89 1336 if(distances[k] == -DBL_MAX)
mas01cr@89 1337 break;
mas01cr@89 1338 }
mas01cr@89 1339 listLen = k;
mas01cr@89 1340
mas01cr@133 1341 adbQueryResponse->result.__sizeRlist=listLen;
mas01cr@133 1342 adbQueryResponse->result.__sizeDist=listLen;
mas01cr@133 1343 adbQueryResponse->result.__sizeQpos=listLen;
mas01cr@133 1344 adbQueryResponse->result.__sizeSpos=listLen;
mas01cr@133 1345 adbQueryResponse->result.Rlist= new char*[listLen];
mas01cr@133 1346 adbQueryResponse->result.Dist = new double[listLen];
mas01cr@133 1347 adbQueryResponse->result.Qpos = new unsigned int[listLen];
mas01cr@133 1348 adbQueryResponse->result.Spos = new unsigned int[listLen];
mas01cr@133 1349 for(k=0; k<(unsigned)adbQueryResponse->result.__sizeRlist; k++){
mas01cr@133 1350 adbQueryResponse->result.Rlist[k]=new char[O2_MAXFILESTR];
mas01cr@133 1351 adbQueryResponse->result.Dist[k]=distances[k];
mas01cr@133 1352 adbQueryResponse->result.Qpos[k]=qIndexes[k];
mas01mc@18 1353 unsigned cumTrack=0;
mas01cr@0 1354 for(l=0 ; l<dbH->numFiles; l++){
mas01mc@18 1355 cumTrack+=trackTable[l];
mas01mc@18 1356 if(sIndexes[k]<cumTrack){
mas01cr@133 1357 sprintf(adbQueryResponse->result.Rlist[k], "%s", fileTable+l*O2_FILETABLESIZE);
mas01cr@0 1358 break;
mas01cr@0 1359 }
mas01cr@0 1360 }
mas01cr@133 1361 adbQueryResponse->result.Spos[k]=sIndexes[k]+trackTable[l]-cumTrack;
mas01cr@0 1362 }
mas01cr@0 1363 }
mas01cr@0 1364
mas01cr@0 1365 // Clean up
mas01cr@0 1366 if(queryCopy)
mas01cr@0 1367 delete queryCopy;
mas01cr@0 1368 if(qNorm)
mas01cr@0 1369 delete qNorm;
mas01cr@0 1370 if(timesdata)
mas01cr@0 1371 delete timesdata;
mas01cr@0 1372 if(dbdurs)
mas01cr@0 1373 delete dbdurs;
mas01cr@0 1374 }
mas01cr@0 1375
mas01mc@18 1376 // trackPointQuery
mas01mc@18 1377 // return the trackNN closest tracks to the query track
mas01mc@18 1378 // uses average of pointNN points per track
mas01cr@133 1379 void audioDB::trackPointQuery(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse){
mas01cr@27 1380 initTables(dbName, 0, inFile);
mas01cr@0 1381
mas01cr@0 1382 // For each input vector, find the closest pointNN matching output vectors and report
mas01cr@0 1383 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01cr@0 1384 double* query = (double*)(indata+sizeof(int));
mas01cr@0 1385 double* data = dataBuf;
mas01cr@0 1386 double* queryCopy = 0;
mas01cr@0 1387
mas01cr@0 1388 if( dbH->flags & O2_FLAG_L2NORM ){
mas01cr@0 1389 // Make a copy of the query
mas01cr@0 1390 queryCopy = new double[numVectors*dbH->dim];
mas01cr@0 1391 qNorm = new double[numVectors];
mas01cr@0 1392 assert(queryCopy&&qNorm);
mas01cr@0 1393 memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double));
mas01cr@0 1394 unitNorm(queryCopy, dbH->dim, numVectors, qNorm);
mas01cr@0 1395 query = queryCopy;
mas01cr@0 1396 }
mas01cr@0 1397
mas01cr@0 1398 assert(pointNN>0 && pointNN<=O2_MAXNN);
mas01mc@18 1399 assert(trackNN>0 && trackNN<=O2_MAXNN);
mas01cr@0 1400
mas01cr@0 1401 // Make temporary dynamic memory for results
mas01mc@18 1402 double trackDistances[trackNN];
mas01mc@18 1403 unsigned trackIDs[trackNN];
mas01mc@18 1404 unsigned trackQIndexes[trackNN];
mas01mc@18 1405 unsigned trackSIndexes[trackNN];
mas01cr@0 1406
mas01cr@0 1407 double distances[pointNN];
mas01cr@0 1408 unsigned qIndexes[pointNN];
mas01cr@0 1409 unsigned sIndexes[pointNN];
mas01cr@0 1410
mas01cr@0 1411 unsigned j=numVectors; // number of query points
mas01mc@18 1412 unsigned k,l,n, track, trackOffset=0, processedTracks=0;
mas01cr@0 1413 double thisDist;
mas01cr@0 1414
mas01cr@0 1415 for(k=0; k<pointNN; k++){
mas01cr@66 1416 distances[k]=-DBL_MAX;
mas01cr@0 1417 qIndexes[k]=~0;
mas01cr@0 1418 sIndexes[k]=~0;
mas01cr@0 1419 }
mas01cr@0 1420
mas01mc@18 1421 for(k=0; k<trackNN; k++){
mas01cr@66 1422 trackDistances[k]=-DBL_MAX;
mas01mc@18 1423 trackQIndexes[k]=~0;
mas01mc@18 1424 trackSIndexes[k]=~0;
mas01mc@18 1425 trackIDs[k]=~0;
mas01cr@0 1426 }
mas01cr@0 1427
mas01cr@0 1428 double meanQdur = 0;
mas01cr@0 1429 double* timesdata = 0;
mas01cr@0 1430 double* meanDBdur = 0;
mas01cr@0 1431
mas01cr@0 1432 if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1433 cerr << "warning: ignoring query timestamps for non-timestamped database" << endl;
mas01cr@0 1434 usingTimes=0;
mas01cr@0 1435 }
mas01cr@0 1436
mas01cr@0 1437 else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01cr@0 1438 cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl;
mas01cr@0 1439
mas01cr@0 1440 else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1441 timesdata = new double[numVectors];
mas01cr@0 1442 insertTimeStamps(numVectors, timesFile, timesdata);
mas01cr@0 1443 // Calculate durations of points
mas01cr@0 1444 for(k=0; k<numVectors-1; k++){
mas01cr@0 1445 timesdata[k]=timesdata[k+1]-timesdata[k];
mas01cr@0 1446 meanQdur+=timesdata[k];
mas01cr@0 1447 }
mas01cr@0 1448 meanQdur/=k;
mas01cr@0 1449 meanDBdur = new double[dbH->numFiles];
mas01cr@0 1450 for(k=0; k<dbH->numFiles; k++){
mas01cr@0 1451 meanDBdur[k]=0.0;
mas01mc@18 1452 for(j=0; j<trackTable[k]-1 ; j++)
mas01cr@0 1453 meanDBdur[k]+=timesTable[j+1]-timesTable[j];
mas01cr@0 1454 meanDBdur[k]/=j;
mas01cr@0 1455 }
mas01cr@0 1456 }
mas01cr@0 1457
mas01cr@0 1458 if(usingQueryPoint)
mas01cr@0 1459 if(queryPoint>numVectors-1)
mas01cr@0 1460 error("queryPoint > numVectors in query");
mas01cr@0 1461 else{
mas01cr@60 1462 if(verbosity>1) {
mas01cr@0 1463 cerr << "query point: " << queryPoint << endl; cerr.flush();
mas01cr@60 1464 }
mas01cr@0 1465 query=query+queryPoint*dbH->dim;
mas01cr@0 1466 numVectors=queryPoint+1;
mas01cr@0 1467 }
mas01cr@0 1468
mas01mc@18 1469 // build track offset table
mas01mc@18 1470 unsigned *trackOffsetTable = new unsigned[dbH->numFiles];
mas01mc@18 1471 unsigned cumTrack=0;
mas01mc@18 1472 unsigned trackIndexOffset;
mas01cr@0 1473 for(k=0; k<dbH->numFiles;k++){
mas01mc@18 1474 trackOffsetTable[k]=cumTrack;
mas01mc@18 1475 cumTrack+=trackTable[k]*dbH->dim;
mas01cr@0 1476 }
mas01cr@0 1477
mas01cr@0 1478 char nextKey[MAXSTR];
mas01cr@0 1479
mas01cr@0 1480 gettimeofday(&tv1, NULL);
mas01cr@0 1481
mas01mc@18 1482 for(processedTracks=0, track=0 ; processedTracks < dbH->numFiles ; track++, processedTracks++){
mas01mc@18 1483 if(trackFile){
mas01mc@18 1484 if(!trackFile->eof()){
mas01mc@18 1485 trackFile->getline(nextKey,MAXSTR);
mas01mc@18 1486 track=getKeyPos(nextKey);
mas01cr@0 1487 }
mas01cr@0 1488 else
mas01cr@0 1489 break;
mas01cr@0 1490 }
mas01mc@18 1491 trackOffset=trackOffsetTable[track]; // numDoubles offset
mas01mc@18 1492 trackIndexOffset=trackOffset/dbH->dim; // numVectors offset
mas01cr@60 1493 if(verbosity>7) {
mas01mc@18 1494 cerr << track << "." << trackOffset/(dbH->dim) << "." << trackTable[track] << " | ";cerr.flush();
mas01cr@60 1495 }
mas01cr@0 1496
mas01cr@0 1497 if(dbH->flags & O2_FLAG_L2NORM)
mas01cr@0 1498 usingQueryPoint?query=queryCopy+queryPoint*dbH->dim:query=queryCopy;
mas01cr@0 1499 else
mas01cr@0 1500 usingQueryPoint?query=(double*)(indata+sizeof(int))+queryPoint*dbH->dim:query=(double*)(indata+sizeof(int));
mas01cr@0 1501 if(usingQueryPoint)
mas01cr@0 1502 j=1;
mas01cr@0 1503 else
mas01cr@0 1504 j=numVectors;
mas01cr@0 1505 while(j--){
mas01mc@18 1506 k=trackTable[track]; // number of vectors in track
mas01mc@18 1507 data=dataBuf+trackOffset; // data for track
mas01cr@0 1508 while(k--){
mas01cr@0 1509 thisDist=0;
mas01cr@0 1510 l=dbH->dim;
mas01cr@0 1511 double* q=query;
mas01cr@0 1512 while(l--)
mas01cr@0 1513 thisDist+=*q++**data++;
mas01cr@0 1514 if(!usingTimes ||
mas01cr@0 1515 (usingTimes
mas01mc@18 1516 && fabs(meanDBdur[track]-meanQdur)<meanQdur*timesTol)){
mas01cr@0 1517 n=pointNN;
mas01cr@0 1518 while(n--){
mas01cr@0 1519 if(thisDist>=distances[n]){
mas01cr@0 1520 if((n==0 || thisDist<=distances[n-1])){
mas01cr@0 1521 // Copy all values above up the queue
mas01cr@0 1522 for( l=pointNN-1 ; l > n ; l--){
mas01cr@0 1523 distances[l]=distances[l-1];
mas01cr@0 1524 qIndexes[l]=qIndexes[l-1];
mas01cr@0 1525 sIndexes[l]=sIndexes[l-1];
mas01cr@0 1526 }
mas01cr@0 1527 distances[n]=thisDist;
mas01cr@0 1528 qIndexes[n]=numVectors-j-1;
mas01mc@18 1529 sIndexes[n]=trackTable[track]-k-1;
mas01cr@0 1530 break;
mas01cr@0 1531 }
mas01cr@0 1532 }
mas01cr@0 1533 else
mas01cr@0 1534 break;
mas01cr@0 1535 }
mas01cr@0 1536 }
mas01mc@18 1537 } // track
mas01cr@0 1538 // Move query pointer to next query point
mas01cr@0 1539 query+=dbH->dim;
mas01cr@0 1540 } // query
mas01mc@18 1541 // Take the average of this track's distance
mas01mc@18 1542 // Test the track distances
mas01cr@0 1543 thisDist=0;
mas01cr@66 1544 for (n = 0; n < pointNN; n++) {
mas01cr@66 1545 if (distances[n] == -DBL_MAX) break;
mas01cr@66 1546 thisDist += distances[n];
mas01cr@66 1547 }
mas01cr@66 1548 thisDist /= n;
mas01cr@66 1549
mas01mc@18 1550 n=trackNN;
mas01cr@0 1551 while(n--){
mas01mc@18 1552 if(thisDist>=trackDistances[n]){
mas01mc@18 1553 if((n==0 || thisDist<=trackDistances[n-1])){
mas01cr@0 1554 // Copy all values above up the queue
mas01cr@74 1555 for( l=trackNN-1 ; l > n ; l--){
mas01mc@18 1556 trackDistances[l]=trackDistances[l-1];
mas01mc@18 1557 trackQIndexes[l]=trackQIndexes[l-1];
mas01mc@18 1558 trackSIndexes[l]=trackSIndexes[l-1];
mas01mc@18 1559 trackIDs[l]=trackIDs[l-1];
mas01cr@0 1560 }
mas01mc@18 1561 trackDistances[n]=thisDist;
mas01mc@18 1562 trackQIndexes[n]=qIndexes[0];
mas01mc@18 1563 trackSIndexes[n]=sIndexes[0];
mas01mc@18 1564 trackIDs[n]=track;
mas01cr@0 1565 break;
mas01cr@0 1566 }
mas01cr@0 1567 }
mas01cr@0 1568 else
mas01cr@0 1569 break;
mas01cr@0 1570 }
mas01cr@0 1571 for(unsigned k=0; k<pointNN; k++){
mas01cr@66 1572 distances[k]=-DBL_MAX;
mas01cr@0 1573 qIndexes[k]=~0;
mas01cr@0 1574 sIndexes[k]=~0;
mas01cr@0 1575 }
mas01mc@18 1576 } // tracks
mas01cr@0 1577 gettimeofday(&tv2, NULL);
mas01cr@0 1578
mas01cr@60 1579 if(verbosity>1) {
mas01mc@18 1580 cerr << endl << "processed tracks :" << processedTracks
mas01cr@0 1581 << " elapsed time:" << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl;
mas01cr@60 1582 }
mas01cr@0 1583
mas01cr@133 1584 if(adbQueryResponse==0){
mas01cr@60 1585 if(verbosity>1) {
mas01cr@0 1586 cerr<<endl;
mas01cr@60 1587 }
mas01cr@0 1588 // Output answer
mas01cr@0 1589 // Loop over nearest neighbours
mas01mc@18 1590 for(k=0; k < min(trackNN,processedTracks); k++)
mas01mc@18 1591 cout << fileTable+trackIDs[k]*O2_FILETABLESIZE
mas01mc@18 1592 << " " << trackDistances[k] << " " << trackQIndexes[k] << " " << trackSIndexes[k] << endl;
mas01cr@0 1593 }
mas01cr@0 1594 else{ // Process Web Services Query
mas01mc@18 1595 int listLen = min(trackNN, processedTracks);
mas01cr@133 1596 adbQueryResponse->result.__sizeRlist=listLen;
mas01cr@133 1597 adbQueryResponse->result.__sizeDist=listLen;
mas01cr@133 1598 adbQueryResponse->result.__sizeQpos=listLen;
mas01cr@133 1599 adbQueryResponse->result.__sizeSpos=listLen;
mas01cr@133 1600 adbQueryResponse->result.Rlist= new char*[listLen];
mas01cr@133 1601 adbQueryResponse->result.Dist = new double[listLen];
mas01cr@133 1602 adbQueryResponse->result.Qpos = new unsigned int[listLen];
mas01cr@133 1603 adbQueryResponse->result.Spos = new unsigned int[listLen];
mas01cr@133 1604 for(k=0; k<(unsigned)adbQueryResponse->result.__sizeRlist; k++){
mas01cr@133 1605 adbQueryResponse->result.Rlist[k]=new char[O2_MAXFILESTR];
mas01cr@133 1606 adbQueryResponse->result.Dist[k]=trackDistances[k];
mas01cr@133 1607 adbQueryResponse->result.Qpos[k]=trackQIndexes[k];
mas01cr@133 1608 adbQueryResponse->result.Spos[k]=trackSIndexes[k];
mas01cr@133 1609 sprintf(adbQueryResponse->result.Rlist[k], "%s", fileTable+trackIDs[k]*O2_FILETABLESIZE);
mas01cr@0 1610 }
mas01cr@0 1611 }
mas01cr@0 1612
mas01cr@0 1613
mas01cr@0 1614 // Clean up
mas01mc@18 1615 if(trackOffsetTable)
mas01mc@18 1616 delete trackOffsetTable;
mas01cr@0 1617 if(queryCopy)
mas01cr@0 1618 delete queryCopy;
mas01cr@0 1619 if(qNorm)
mas01cr@0 1620 delete qNorm;
mas01cr@0 1621 if(timesdata)
mas01cr@0 1622 delete timesdata;
mas01cr@0 1623 if(meanDBdur)
mas01cr@0 1624 delete meanDBdur;
mas01cr@0 1625
mas01cr@0 1626 }
mas01cr@0 1627
mas01cr@148 1628 // This is a common pattern in sequence queries: what we are doing is
mas01cr@148 1629 // taking a window of length seqlen over a buffer of length length,
mas01cr@148 1630 // and placing the sum of the elements in that window in the first
mas01cr@148 1631 // element of the window: thus replacing all but the last seqlen
mas01cr@148 1632 // elements in the buffer the corresponding windowed sum.
mas01cr@148 1633 void audioDB::sequence_sum(double *buffer, int length, int seqlen) {
mas01cr@148 1634 double tmp1, tmp2, *ps;
mas01cr@148 1635 int j, w;
mas01cr@148 1636
mas01cr@148 1637 tmp1 = *buffer;
mas01cr@148 1638 j = 1;
mas01cr@148 1639 w = seqlen - 1;
mas01cr@148 1640 while(w--) {
mas01cr@148 1641 *buffer += buffer[j++];
mas01cr@148 1642 }
mas01cr@148 1643 ps = buffer + 1;
mas01cr@148 1644 w = length - seqlen; // +1 - 1
mas01cr@148 1645 while(w--) {
mas01cr@148 1646 tmp2 = *ps;
mas01cr@148 1647 *ps = *(ps - 1) - tmp1 + *(ps + seqlen - 1);
mas01cr@148 1648 tmp1 = tmp2;
mas01cr@148 1649 ps++;
mas01cr@148 1650 }
mas01cr@148 1651 }
mas01cr@0 1652
mas01mc@20 1653 // k nearest-neighbor (k-NN) search between query and target tracks
mas01mc@20 1654 // efficient implementation based on matched filter
mas01mc@20 1655 // assumes normed shingles
mas01mc@20 1656 // outputs distances of retrieved shingles, max retreived = pointNN shingles per per track
mas01cr@133 1657 void audioDB::trackSequenceQueryNN(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse){
mas01cr@0 1658
mas01cr@27 1659 initTables(dbName, 0, inFile);
mas01cr@0 1660
mas01cr@0 1661 // For each input vector, find the closest pointNN matching output vectors and report
mas01cr@0 1662 // we use stdout in this stub version
mas01cr@0 1663 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01cr@0 1664 double* query = (double*)(indata+sizeof(int));
mas01cr@0 1665 double* queryCopy = 0;
mas01cr@0 1666
mas01cr@0 1667 double qMeanL2;
mas01cr@0 1668 double* sMeanL2;
mas01cr@0 1669
mas01cr@0 1670 unsigned USE_THRESH=0;
mas01cr@0 1671 double SILENCE_THRESH=0;
mas01cr@0 1672 double DIFF_THRESH=0;
mas01cr@0 1673
mas01cr@0 1674 if(!(dbH->flags & O2_FLAG_L2NORM) )
mas01cr@55 1675 error("Database must be L2 normed for sequence query","use -L2NORM");
mas01cr@55 1676
mas01cr@55 1677 if(numVectors<sequenceLength)
mas01cr@55 1678 error("Query shorter than requested sequence length", "maybe use -l");
mas01cr@0 1679
mas01cr@60 1680 if(verbosity>1) {
mas01cr@0 1681 cerr << "performing norms ... "; cerr.flush();
mas01cr@60 1682 }
mas01cr@0 1683 unsigned dbVectors = dbH->length/(sizeof(double)*dbH->dim);
mas01mc@20 1684
mas01cr@0 1685 // Make a copy of the query
mas01cr@0 1686 queryCopy = new double[numVectors*dbH->dim];
mas01cr@0 1687 memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double));
mas01cr@0 1688 qNorm = new double[numVectors];
mas01cr@0 1689 sNorm = new double[dbVectors];
mas01cr@0 1690 sMeanL2=new double[dbH->numFiles];
mas01cr@0 1691 assert(qNorm&&sNorm&&queryCopy&&sMeanL2&&sequenceLength);
mas01cr@0 1692 unitNorm(queryCopy, dbH->dim, numVectors, qNorm);
mas01cr@0 1693 query = queryCopy;
mas01mc@20 1694
mas01cr@0 1695 // Make norm measurements relative to sequenceLength
mas01cr@0 1696 unsigned w = sequenceLength-1;
mas01cr@0 1697 unsigned i,j;
mas01cr@0 1698 double* ps;
mas01mc@20 1699
mas01cr@0 1700 // Copy the L2 norm values to core to avoid disk random access later on
mas01cr@0 1701 memcpy(sNorm, l2normTable, dbVectors*sizeof(double));
mas01cr@125 1702 double* qnPtr = qNorm;
mas01cr@0 1703 double* snPtr = sNorm;
mas01cr@149 1704
mas01cr@149 1705 double *sPower = 0, *qPower;
mas01cr@149 1706 double *spPtr = 0, *qpPtr = 0;
mas01cr@149 1707
mas01cr@149 1708 if (usingPower) {
mas01cr@149 1709 if (!(dbH->flags & O2_FLAG_POWER)) {
mas01cr@149 1710 error("database not power-enabled", dbName);
mas01cr@149 1711 }
mas01cr@149 1712 sPower = new double[dbVectors];
mas01cr@149 1713 spPtr = sPower;
mas01cr@149 1714 memcpy(sPower, powerTable, dbVectors * sizeof(double));
mas01cr@149 1715 }
mas01cr@149 1716
mas01cr@0 1717 for(i=0; i<dbH->numFiles; i++){
mas01cr@148 1718 if(trackTable[i]>=sequenceLength) {
mas01cr@148 1719 sequence_sum(snPtr, trackTable[i], sequenceLength);
mas01cr@149 1720 if (usingPower) {
mas01cr@149 1721 sequence_sum(spPtr, trackTable[i], sequenceLength);
mas01cr@149 1722 }
mas01cr@148 1723
mas01mc@20 1724 ps = snPtr;
mas01mc@20 1725 w=trackTable[i]-sequenceLength+1;
mas01mc@20 1726 while(w--){
mas01mc@20 1727 *ps=sqrt(*ps);
mas01mc@20 1728 ps++;
mas01mc@20 1729 }
mas01cr@149 1730
mas01cr@149 1731 if (usingPower) {
mas01cr@149 1732 ps = spPtr;
mas01cr@149 1733 w = trackTable[i] - sequenceLength + 1;
mas01cr@149 1734 while(w--) {
mas01cr@149 1735 *ps = *ps / sequenceLength;
mas01cr@149 1736 ps++;
mas01cr@149 1737 }
mas01cr@149 1738 }
mas01cr@0 1739 }
mas01cr@149 1740 snPtr += trackTable[i];
mas01cr@149 1741 if (usingPower) {
mas01cr@149 1742 spPtr += trackTable[i];
mas01cr@149 1743 }
mas01cr@0 1744 }
mas01cr@0 1745
mas01cr@0 1746 double* pn = sMeanL2;
mas01cr@0 1747 w=dbH->numFiles;
mas01cr@0 1748 while(w--)
mas01cr@0 1749 *pn++=0.0;
mas01cr@0 1750 ps=sNorm;
mas01mc@18 1751 unsigned processedTracks=0;
mas01cr@0 1752 for(i=0; i<dbH->numFiles; i++){
mas01mc@18 1753 if(trackTable[i]>sequenceLength-1){
mas01cr@57 1754 w = trackTable[i]-sequenceLength+1;
mas01cr@0 1755 pn = sMeanL2+i;
mas01mc@20 1756 *pn=0;
mas01cr@0 1757 while(w--)
mas01mc@20 1758 if(*ps>0)
mas01mc@20 1759 *pn+=*ps++;
mas01cr@57 1760 *pn/=trackTable[i]-sequenceLength+1;
mas01cr@0 1761 SILENCE_THRESH+=*pn;
mas01mc@18 1762 processedTracks++;
mas01cr@0 1763 }
mas01mc@18 1764 ps = sNorm + trackTable[i];
mas01cr@0 1765 }
mas01cr@60 1766 if(verbosity>1) {
mas01mc@18 1767 cerr << "processedTracks: " << processedTracks << endl;
mas01cr@60 1768 }
mas01mc@20 1769
mas01mc@18 1770 SILENCE_THRESH/=processedTracks;
mas01cr@0 1771 USE_THRESH=1; // Turn thresholding on
mas01mc@20 1772 DIFF_THRESH=SILENCE_THRESH; // mean shingle power
mas01mc@20 1773 SILENCE_THRESH/=5; // 20% of the mean shingle power is SILENCE
mas01cr@60 1774 if(verbosity>4) {
mas01mc@20 1775 cerr << "silence thresh: " << SILENCE_THRESH;
mas01cr@60 1776 }
mas01cr@148 1777
mas01cr@148 1778 sequence_sum(qnPtr, numVectors, sequenceLength);
mas01cr@149 1779 if (usingPower) {
mas01cr@149 1780 qPower = new double[numVectors];
mas01cr@149 1781 qpPtr = qPower;
mas01cr@149 1782 if (lseek(powerfd, sizeof(int), SEEK_SET) == (off_t) -1) {
mas01cr@149 1783 error("error seeking to data", powerFileName, "lseek");
mas01cr@149 1784 }
mas01cr@149 1785 int count = read(powerfd, qPower, numVectors * sizeof(double));
mas01cr@149 1786 if (count == -1) {
mas01cr@149 1787 error("error reading data", powerFileName, "read");
mas01cr@149 1788 }
mas01cr@149 1789 if ((unsigned) count != numVectors * sizeof(double)) {
mas01cr@149 1790 error("short read", powerFileName);
mas01cr@149 1791 }
mas01cr@149 1792
mas01cr@149 1793 sequence_sum(qpPtr, numVectors, sequenceLength);
mas01cr@149 1794 ps = qpPtr;
mas01cr@152 1795 w = numVectors - sequenceLength + 1;
mas01cr@149 1796 while(w--) {
mas01cr@149 1797 *ps = *ps / sequenceLength;
mas01cr@149 1798 ps++;
mas01cr@149 1799 }
mas01cr@149 1800 }
mas01cr@148 1801
mas01cr@125 1802 ps = qnPtr;
mas01mc@20 1803 qMeanL2 = 0;
mas01mc@20 1804 w=numVectors-sequenceLength+1;
mas01mc@20 1805 while(w--){
mas01mc@20 1806 *ps=sqrt(*ps);
mas01mc@20 1807 qMeanL2+=*ps++;
mas01cr@0 1808 }
mas01cr@0 1809 qMeanL2 /= numVectors-sequenceLength+1;
mas01mc@20 1810
mas01cr@60 1811 if(verbosity>1) {
mas01cr@60 1812 cerr << "done." << endl;
mas01cr@60 1813 }
mas01cr@0 1814
mas01cr@60 1815 if(verbosity>1) {
mas01mc@18 1816 cerr << "matching tracks..." << endl;
mas01cr@60 1817 }
mas01cr@0 1818
mas01cr@0 1819 assert(pointNN>0 && pointNN<=O2_MAXNN);
mas01mc@18 1820 assert(trackNN>0 && trackNN<=O2_MAXNN);
mas01cr@0 1821
mas01cr@0 1822 // Make temporary dynamic memory for results
mas01mc@18 1823 double trackDistances[trackNN];
mas01mc@18 1824 unsigned trackIDs[trackNN];
mas01mc@18 1825 unsigned trackQIndexes[trackNN];
mas01mc@18 1826 unsigned trackSIndexes[trackNN];
mas01cr@0 1827
mas01cr@0 1828 double distances[pointNN];
mas01cr@0 1829 unsigned qIndexes[pointNN];
mas01cr@0 1830 unsigned sIndexes[pointNN];
mas01cr@0 1831
mas01cr@0 1832
mas01mc@18 1833 unsigned k,l,m,n,track,trackOffset=0, HOP_SIZE=sequenceHop, wL=sequenceLength;
mas01cr@0 1834 double thisDist;
mas01cr@0 1835
mas01cr@0 1836 for(k=0; k<pointNN; k++){
mas01mc@20 1837 distances[k]=1.0e6;
mas01cr@0 1838 qIndexes[k]=~0;
mas01cr@0 1839 sIndexes[k]=~0;
mas01cr@0 1840 }
mas01cr@0 1841
mas01mc@18 1842 for(k=0; k<trackNN; k++){
mas01mc@20 1843 trackDistances[k]=1.0e6;
mas01mc@18 1844 trackQIndexes[k]=~0;
mas01mc@18 1845 trackSIndexes[k]=~0;
mas01mc@18 1846 trackIDs[k]=~0;
mas01cr@0 1847 }
mas01cr@0 1848
mas01cr@0 1849 // Timestamp and durations processing
mas01cr@0 1850 double meanQdur = 0;
mas01cr@0 1851 double* timesdata = 0;
mas01cr@0 1852 double* meanDBdur = 0;
mas01cr@0 1853
mas01cr@0 1854 if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1855 cerr << "warning: ignoring query timestamps for non-timestamped database" << endl;
mas01cr@0 1856 usingTimes=0;
mas01cr@0 1857 }
mas01cr@0 1858
mas01cr@0 1859 else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01cr@0 1860 cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl;
mas01cr@0 1861
mas01cr@0 1862 else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){
mas01cr@0 1863 timesdata = new double[numVectors];
mas01cr@0 1864 assert(timesdata);
mas01cr@0 1865 insertTimeStamps(numVectors, timesFile, timesdata);
mas01cr@0 1866 // Calculate durations of points
mas01cr@0 1867 for(k=0; k<numVectors-1; k++){
mas01cr@0 1868 timesdata[k]=timesdata[k+1]-timesdata[k];
mas01cr@0 1869 meanQdur+=timesdata[k];
mas01cr@0 1870 }
mas01cr@0 1871 meanQdur/=k;
mas01cr@60 1872 if(verbosity>1) {
mas01cr@0 1873 cerr << "mean query file duration: " << meanQdur << endl;
mas01cr@60 1874 }
mas01cr@0 1875 meanDBdur = new double[dbH->numFiles];
mas01cr@0 1876 assert(meanDBdur);
mas01cr@0 1877 for(k=0; k<dbH->numFiles; k++){
mas01cr@0 1878 meanDBdur[k]=0.0;
mas01mc@18 1879 for(j=0; j<trackTable[k]-1 ; j++)
mas01cr@0 1880 meanDBdur[k]+=timesTable[j+1]-timesTable[j];
mas01cr@0 1881 meanDBdur[k]/=j;
mas01cr@0 1882 }
mas01cr@0 1883 }
mas01cr@0 1884
mas01cr@0 1885 if(usingQueryPoint)
mas01cr@0 1886 if(queryPoint>numVectors || queryPoint>numVectors-wL+1)
mas01cr@0 1887 error("queryPoint > numVectors-wL+1 in query");
mas01cr@0 1888 else{
mas01cr@60 1889 if(verbosity>1) {
mas01cr@0 1890 cerr << "query point: " << queryPoint << endl; cerr.flush();
mas01cr@60 1891 }
mas01cr@0 1892 query=query+queryPoint*dbH->dim;
mas01cr@125 1893 qnPtr=qnPtr+queryPoint;
mas01cr@0 1894 numVectors=wL;
mas01cr@0 1895 }
mas01cr@0 1896
mas01mc@20 1897 double ** D = 0; // Differences query and target
mas01cr@0 1898 double ** DD = 0; // Matched filter distance
mas01cr@0 1899
mas01cr@0 1900 D = new double*[numVectors];
mas01cr@0 1901 assert(D);
mas01cr@0 1902 DD = new double*[numVectors];
mas01cr@0 1903 assert(DD);
mas01cr@0 1904
mas01cr@0 1905 gettimeofday(&tv1, NULL);
mas01mc@18 1906 processedTracks=0;
mas01mc@18 1907 unsigned successfulTracks=0;
mas01cr@0 1908
mas01cr@0 1909 double* qp;
mas01cr@0 1910 double* sp;
mas01cr@0 1911 double* dp;
mas01cr@0 1912
mas01mc@18 1913 // build track offset table
mas01mc@18 1914 unsigned *trackOffsetTable = new unsigned[dbH->numFiles];
mas01mc@18 1915 unsigned cumTrack=0;
mas01mc@18 1916 unsigned trackIndexOffset;
mas01cr@0 1917 for(k=0; k<dbH->numFiles;k++){
mas01mc@18 1918 trackOffsetTable[k]=cumTrack;
mas01mc@18 1919 cumTrack+=trackTable[k]*dbH->dim;
mas01cr@0 1920 }
mas01cr@0 1921
mas01cr@0 1922 char nextKey [MAXSTR];
mas01mc@20 1923
mas01mc@20 1924 // chi^2 statistics
mas01mc@20 1925 double sampleCount = 0;
mas01mc@20 1926 double sampleSum = 0;
mas01mc@20 1927 double logSampleSum = 0;
mas01mc@20 1928 double minSample = 1e9;
mas01mc@20 1929 double maxSample = 0;
mas01mc@20 1930
mas01mc@20 1931 // Track loop
mas01mc@18 1932 for(processedTracks=0, track=0 ; processedTracks < dbH->numFiles ; track++, processedTracks++){
mas01cr@0 1933
mas01mc@18 1934 // get trackID from file if using a control file
mas01mc@18 1935 if(trackFile){
mas01mc@18 1936 if(!trackFile->eof()){
mas01mc@18 1937 trackFile->getline(nextKey,MAXSTR);
mas01mc@18 1938 track=getKeyPos(nextKey);
mas01cr@0 1939 }
mas01cr@0 1940 else
mas01cr@0 1941 break;
mas01cr@0 1942 }
mas01mc@12 1943
mas01mc@18 1944 trackOffset=trackOffsetTable[track]; // numDoubles offset
mas01mc@18 1945 trackIndexOffset=trackOffset/dbH->dim; // numVectors offset
mas01cr@0 1946
mas01cr@57 1947 if(sequenceLength<=trackTable[track]){ // test for short sequences
mas01cr@0 1948
mas01cr@60 1949 if(verbosity>7) {
mas01mc@18 1950 cerr << track << "." << trackIndexOffset << "." << trackTable[track] << " | ";cerr.flush();
mas01cr@60 1951 }
mas01cr@0 1952
mas01mc@20 1953 // Sum products matrix
mas01cr@0 1954 for(j=0; j<numVectors;j++){
mas01mc@18 1955 D[j]=new double[trackTable[track]];
mas01cr@0 1956 assert(D[j]);
mas01cr@0 1957
mas01cr@0 1958 }
mas01cr@0 1959
mas01cr@0 1960 // Matched filter matrix
mas01cr@0 1961 for(j=0; j<numVectors;j++){
mas01mc@18 1962 DD[j]=new double[trackTable[track]];
mas01cr@0 1963 assert(DD[j]);
mas01cr@0 1964 }
mas01cr@0 1965
mas01mc@20 1966 // Dot product
mas01cr@0 1967 for(j=0; j<numVectors; j++)
mas01mc@18 1968 for(k=0; k<trackTable[track]; k++){
mas01cr@0 1969 qp=query+j*dbH->dim;
mas01mc@18 1970 sp=dataBuf+trackOffset+k*dbH->dim;
mas01cr@0 1971 DD[j][k]=0.0; // Initialize matched filter array
mas01cr@0 1972 dp=&D[j][k]; // point to correlation cell j,k
mas01cr@0 1973 *dp=0.0; // initialize correlation cell
mas01cr@0 1974 l=dbH->dim; // size of vectors
mas01cr@0 1975 while(l--)
mas01cr@0 1976 *dp+=*qp++**sp++;
mas01cr@0 1977 }
mas01cr@0 1978
mas01cr@0 1979 // Matched Filter
mas01cr@0 1980 // HOP SIZE == 1
mas01cr@0 1981 double* spd;
mas01cr@0 1982 if(HOP_SIZE==1){ // HOP_SIZE = shingleHop
mas01cr@0 1983 for(w=0; w<wL; w++)
mas01cr@0 1984 for(j=0; j<numVectors-w; j++){
mas01cr@0 1985 sp=DD[j];
mas01cr@0 1986 spd=D[j+w]+w;
mas01mc@18 1987 k=trackTable[track]-w;
mas01cr@0 1988 while(k--)
mas01cr@0 1989 *sp+++=*spd++;
mas01cr@0 1990 }
mas01cr@0 1991 }
mas01mc@20 1992
mas01cr@0 1993 else{ // HOP_SIZE != 1
mas01cr@0 1994 for(w=0; w<wL; w++)
mas01cr@0 1995 for(j=0; j<numVectors-w; j+=HOP_SIZE){
mas01cr@0 1996 sp=DD[j];
mas01cr@0 1997 spd=D[j+w]+w;
mas01mc@18 1998 for(k=0; k<trackTable[track]-w; k+=HOP_SIZE){
mas01cr@0 1999 *sp+=*spd;
mas01cr@0 2000 sp+=HOP_SIZE;
mas01cr@0 2001 spd+=HOP_SIZE;
mas01cr@0 2002 }
mas01cr@0 2003 }
mas01cr@0 2004 }
mas01cr@0 2005
mas01cr@60 2006 if(verbosity>3 && usingTimes) {
mas01mc@18 2007 cerr << "meanQdur=" << meanQdur << " meanDBdur=" << meanDBdur[track] << endl;
mas01cr@0 2008 cerr.flush();
mas01cr@0 2009 }
mas01cr@0 2010
mas01cr@0 2011 if(!usingTimes ||
mas01cr@0 2012 (usingTimes
mas01mc@18 2013 && fabs(meanDBdur[track]-meanQdur)<meanQdur*timesTol)){
mas01cr@0 2014
mas01cr@60 2015 if(verbosity>3 && usingTimes) {
mas01cr@0 2016 cerr << "within duration tolerance." << endl;
mas01cr@0 2017 cerr.flush();
mas01cr@0 2018 }
mas01cr@0 2019
mas01cr@0 2020 // Search for minimum distance by shingles (concatenated vectors)
mas01cr@53 2021 for(j=0;j<=numVectors-wL;j+=HOP_SIZE)
mas01cr@53 2022 for(k=0;k<=trackTable[track]-wL;k+=HOP_SIZE){
mas01cr@125 2023 thisDist=2-(2/(qnPtr[j]*sNorm[trackIndexOffset+k]))*DD[j][k];
mas01cr@60 2024 if(verbosity>10) {
mas01cr@125 2025 cerr << thisDist << " " << qnPtr[j] << " " << sNorm[trackIndexOffset+k] << endl;
mas01cr@60 2026 }
mas01mc@20 2027 // Gather chi^2 statistics
mas01mc@20 2028 if(thisDist<minSample)
mas01mc@20 2029 minSample=thisDist;
mas01mc@20 2030 else if(thisDist>maxSample)
mas01mc@20 2031 maxSample=thisDist;
mas01mc@20 2032 if(thisDist>1e-9){
mas01mc@20 2033 sampleCount++;
mas01mc@20 2034 sampleSum+=thisDist;
mas01mc@20 2035 logSampleSum+=log(thisDist);
mas01mc@20 2036 }
mas01mc@20 2037
mas01cr@125 2038 // diffL2 = fabs(qnPtr[j] - sNorm[trackIndexOffset+k]);
mas01cr@0 2039 // Power test
mas01cr@149 2040 if (usingPower) {
mas01cr@149 2041 if (!(powers_acceptable(qpPtr[j], sPower[trackIndexOffset + k]))) {
mas01cr@149 2042 thisDist = 1000000.0;
mas01cr@149 2043 }
mas01cr@149 2044 }
mas01cr@149 2045
mas01cr@149 2046 /*
mas01cr@0 2047 if(!USE_THRESH ||
mas01cr@0 2048 // Threshold on mean L2 of Q and S sequences
mas01cr@125 2049 (USE_THRESH && qnPtr[j]>SILENCE_THRESH && sNorm[trackIndexOffset+k]>SILENCE_THRESH &&
mas01cr@0 2050 // Are both query and target windows above mean energy?
mas01cr@125 2051 (qnPtr[j]>qMeanL2*.25 && sNorm[trackIndexOffset+k]>sMeanL2[track]*.25))) // && diffL2 < DIFF_THRESH )))
mas01mc@20 2052 thisDist=thisDist; // Computed above
mas01cr@0 2053 else
mas01mc@20 2054 thisDist=1000000.0;
mas01cr@149 2055 */
mas01mc@20 2056
mas01mc@20 2057 // k-NN match algorithm
mas01cr@58 2058 m=pointNN;
mas01mc@20 2059 while(m--){
mas01mc@20 2060 if(thisDist<=distances[m])
mas01mc@20 2061 if(m==0 || thisDist>=distances[m-1]){
mas01cr@0 2062 // Shuffle distances up the list
mas01cr@0 2063 for(l=pointNN-1; l>m; l--){
mas01cr@0 2064 distances[l]=distances[l-1];
mas01cr@0 2065 qIndexes[l]=qIndexes[l-1];
mas01cr@0 2066 sIndexes[l]=sIndexes[l-1];
mas01cr@0 2067 }
mas01cr@0 2068 distances[m]=thisDist;
mas01cr@0 2069 if(usingQueryPoint)
mas01cr@0 2070 qIndexes[m]=queryPoint;
mas01cr@0 2071 else
mas01cr@0 2072 qIndexes[m]=j;
mas01cr@0 2073 sIndexes[m]=k;
mas01cr@0 2074 break;
mas01mc@20 2075 }
mas01cr@0 2076 }
mas01cr@0 2077 }
mas01cr@0 2078 // Calculate the mean of the N-Best matches
mas01cr@0 2079 thisDist=0.0;
mas01cr@53 2080 for(m=0; m<pointNN; m++) {
mas01cr@53 2081 if (distances[m] == 1000000.0) break;
mas01mc@20 2082 thisDist+=distances[m];
mas01cr@53 2083 }
mas01cr@53 2084 thisDist/=m;
mas01cr@0 2085
mas01mc@12 2086 // Let's see the distances then...
mas01cr@60 2087 if(verbosity>3) {
mas01mc@18 2088 cerr << fileTable+track*O2_FILETABLESIZE << " " << thisDist << endl;
mas01cr@60 2089 }
mas01mc@12 2090
mas01mc@20 2091
mas01mc@18 2092 // All the track stuff goes here
mas01cr@58 2093 n=trackNN;
mas01cr@0 2094 while(n--){
mas01mc@20 2095 if(thisDist<=trackDistances[n]){
mas01mc@20 2096 if((n==0 || thisDist>=trackDistances[n-1])){
mas01cr@0 2097 // Copy all values above up the queue
mas01mc@18 2098 for( l=trackNN-1 ; l > n ; l--){
mas01mc@18 2099 trackDistances[l]=trackDistances[l-1];
mas01mc@18 2100 trackQIndexes[l]=trackQIndexes[l-1];
mas01mc@18 2101 trackSIndexes[l]=trackSIndexes[l-1];
mas01mc@18 2102 trackIDs[l]=trackIDs[l-1];
mas01cr@0 2103 }
mas01mc@18 2104 trackDistances[n]=thisDist;
mas01mc@18 2105 trackQIndexes[n]=qIndexes[0];
mas01mc@18 2106 trackSIndexes[n]=sIndexes[0];
mas01mc@18 2107 successfulTracks++;
mas01mc@18 2108 trackIDs[n]=track;
mas01cr@0 2109 break;
mas01cr@0 2110 }
mas01cr@0 2111 }
mas01cr@0 2112 else
mas01cr@0 2113 break;
mas01cr@0 2114 }
mas01cr@0 2115 } // Duration match
mas01mc@20 2116
mas01mc@18 2117 // Clean up current track
mas01cr@0 2118 if(D!=NULL){
mas01cr@0 2119 for(j=0; j<numVectors; j++)
mas01cr@0 2120 delete[] D[j];
mas01cr@0 2121 }
mas01cr@0 2122
mas01cr@0 2123 if(DD!=NULL){
mas01cr@0 2124 for(j=0; j<numVectors; j++)
mas01cr@0 2125 delete[] DD[j];
mas01cr@0 2126 }
mas01cr@0 2127 }
mas01mc@20 2128 // per-track reset array values
mas01mc@20 2129 for(unsigned k=0; k<pointNN; k++){
mas01mc@20 2130 distances[k]=1.0e6;
mas01mc@20 2131 qIndexes[k]=~0;
mas01mc@20 2132 sIndexes[k]=~0;
mas01mc@20 2133 }
mas01cr@0 2134 }
mas01cr@0 2135
mas01cr@0 2136 gettimeofday(&tv2,NULL);
mas01cr@60 2137 if(verbosity>1) {
mas01mc@18 2138 cerr << endl << "processed tracks :" << processedTracks << " matched tracks: " << successfulTracks << " elapsed time:"
mas01cr@0 2139 << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl;
mas01mc@20 2140 cerr << "sampleCount: " << sampleCount << " sampleSum: " << sampleSum << " logSampleSum: " << logSampleSum
mas01mc@20 2141 << " minSample: " << minSample << " maxSample: " << maxSample << endl;
mas01mc@20 2142 }
mas01cr@133 2143 if(adbQueryResponse==0){
mas01cr@60 2144 if(verbosity>1) {
mas01cr@0 2145 cerr<<endl;
mas01cr@60 2146 }
mas01cr@0 2147 // Output answer
mas01cr@0 2148 // Loop over nearest neighbours
mas01mc@18 2149 for(k=0; k < min(trackNN,successfulTracks); k++)
mas01mc@20 2150 cout << fileTable+trackIDs[k]*O2_FILETABLESIZE << " " << trackDistances[k] << " "
mas01mc@20 2151 << trackQIndexes[k] << " " << trackSIndexes[k] << endl;
mas01cr@0 2152 }
mas01cr@0 2153 else{ // Process Web Services Query
mas01mc@18 2154 int listLen = min(trackNN, processedTracks);
mas01cr@133 2155 adbQueryResponse->result.__sizeRlist=listLen;
mas01cr@133 2156 adbQueryResponse->result.__sizeDist=listLen;
mas01cr@133 2157 adbQueryResponse->result.__sizeQpos=listLen;
mas01cr@133 2158 adbQueryResponse->result.__sizeSpos=listLen;
mas01cr@133 2159 adbQueryResponse->result.Rlist= new char*[listLen];
mas01cr@133 2160 adbQueryResponse->result.Dist = new double[listLen];
mas01cr@133 2161 adbQueryResponse->result.Qpos = new unsigned int[listLen];
mas01cr@133 2162 adbQueryResponse->result.Spos = new unsigned int[listLen];
mas01cr@133 2163 for(k=0; k<(unsigned)adbQueryResponse->result.__sizeRlist; k++){
mas01cr@133 2164 adbQueryResponse->result.Rlist[k]=new char[O2_MAXFILESTR];
mas01cr@133 2165 adbQueryResponse->result.Dist[k]=trackDistances[k];
mas01cr@133 2166 adbQueryResponse->result.Qpos[k]=trackQIndexes[k];
mas01cr@133 2167 adbQueryResponse->result.Spos[k]=trackSIndexes[k];
mas01cr@133 2168 sprintf(adbQueryResponse->result.Rlist[k], "%s", fileTable+trackIDs[k]*O2_FILETABLESIZE);
mas01cr@0 2169 }
mas01cr@0 2170 }
mas01cr@0 2171
mas01cr@0 2172 // Clean up
mas01mc@18 2173 if(trackOffsetTable)
mas01mc@20 2174 delete[] trackOffsetTable;
mas01cr@0 2175 if(queryCopy)
mas01mc@20 2176 delete[] queryCopy;
mas01cr@121 2177 if(qNorm)
mas01cr@121 2178 delete[] qNorm;
mas01cr@121 2179 if(sNorm)
mas01cr@121 2180 delete[] sNorm;
mas01cr@121 2181 if(sMeanL2)
mas01cr@121 2182 delete[] sMeanL2;
mas01cr@0 2183 if(D)
mas01cr@0 2184 delete[] D;
mas01cr@0 2185 if(DD)
mas01cr@0 2186 delete[] DD;
mas01cr@0 2187 if(timesdata)
mas01mc@20 2188 delete[] timesdata;
mas01cr@0 2189 if(meanDBdur)
mas01mc@20 2190 delete[] meanDBdur;
mas01cr@0 2191 }
mas01cr@0 2192
mas01mc@20 2193 // Radius search between query and target tracks
mas01mc@20 2194 // efficient implementation based on matched filter
mas01mc@20 2195 // assumes normed shingles
mas01mc@20 2196 // outputs count of retrieved shingles, max retreived = one shingle per query shingle per track
mas01cr@133 2197 void audioDB::trackSequenceQueryRad(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse){
mas01mc@17 2198
mas01cr@27 2199 initTables(dbName, 0, inFile);
mas01mc@17 2200
mas01mc@17 2201 // For each input vector, find the closest pointNN matching output vectors and report
mas01mc@17 2202 // we use stdout in this stub version
mas01mc@17 2203 unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim);
mas01mc@17 2204 double* query = (double*)(indata+sizeof(int));
mas01mc@17 2205 double* queryCopy = 0;
mas01mc@17 2206
mas01mc@17 2207 double qMeanL2;
mas01mc@17 2208 double* sMeanL2;
mas01mc@17 2209
mas01mc@17 2210 unsigned USE_THRESH=0;
mas01mc@17 2211 double SILENCE_THRESH=0;
mas01mc@17 2212 double DIFF_THRESH=0;
mas01mc@17 2213
mas01mc@17 2214 if(!(dbH->flags & O2_FLAG_L2NORM) )
mas01mc@17 2215 error("Database must be L2 normed for sequence query","use -l2norm");
mas01mc@17 2216
mas01cr@60 2217 if(verbosity>1) {
mas01mc@17 2218 cerr << "performing norms ... "; cerr.flush();
mas01cr@60 2219 }
mas01mc@17 2220 unsigned dbVectors = dbH->length/(sizeof(double)*dbH->dim);
mas01mc@18 2221
mas01mc@17 2222 // Make a copy of the query
mas01mc@17 2223 queryCopy = new double[numVectors*dbH->dim];
mas01mc@17 2224 memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double));
mas01mc@17 2225 qNorm = new double[numVectors];
mas01mc@17 2226 sNorm = new double[dbVectors];
mas01mc@17 2227 sMeanL2=new double[dbH->numFiles];
mas01mc@17 2228 assert(qNorm&&sNorm&&queryCopy&&sMeanL2&&sequenceLength);
mas01mc@17 2229 unitNorm(queryCopy, dbH->dim, numVectors, qNorm);
mas01mc@17 2230 query = queryCopy;
mas01mc@18 2231
mas01mc@17 2232 // Make norm measurements relative to sequenceLength
mas01mc@17 2233 unsigned w = sequenceLength-1;
mas01mc@17 2234 unsigned i,j;
mas01mc@17 2235 double* ps;
mas01mc@18 2236
mas01mc@17 2237 // Copy the L2 norm values to core to avoid disk random access later on
mas01mc@17 2238 memcpy(sNorm, l2normTable, dbVectors*sizeof(double));
mas01mc@17 2239 double* snPtr = sNorm;
mas01cr@125 2240 double* qnPtr = qNorm;
mas01mc@17 2241 for(i=0; i<dbH->numFiles; i++){
mas01mc@18 2242 if(trackTable[i]>=sequenceLength){
mas01cr@148 2243 sequence_sum(snPtr, trackTable[i], sequenceLength);
mas01cr@148 2244
mas01mc@17 2245 ps = snPtr;
mas01mc@18 2246 w=trackTable[i]-sequenceLength+1;
mas01mc@17 2247 while(w--){
mas01mc@17 2248 *ps=sqrt(*ps);
mas01mc@17 2249 ps++;
mas01mc@17 2250 }
mas01mc@17 2251 }
mas01mc@18 2252 snPtr+=trackTable[i];
mas01mc@17 2253 }
mas01mc@17 2254
mas01mc@17 2255 double* pn = sMeanL2;
mas01mc@17 2256 w=dbH->numFiles;
mas01mc@17 2257 while(w--)
mas01mc@17 2258 *pn++=0.0;
mas01mc@17 2259 ps=sNorm;
mas01mc@18 2260 unsigned processedTracks=0;
mas01mc@17 2261 for(i=0; i<dbH->numFiles; i++){
mas01mc@18 2262 if(trackTable[i]>sequenceLength-1){
mas01cr@70 2263 w = trackTable[i]-sequenceLength+1;
mas01mc@17 2264 pn = sMeanL2+i;
mas01mc@17 2265 *pn=0;
mas01mc@17 2266 while(w--)
mas01mc@17 2267 if(*ps>0)
mas01mc@17 2268 *pn+=*ps++;
mas01cr@70 2269 *pn/=trackTable[i]-sequenceLength+1;
mas01mc@17 2270 SILENCE_THRESH+=*pn;
mas01mc@18 2271 processedTracks++;
mas01mc@17 2272 }
mas01mc@18 2273 ps = sNorm + trackTable[i];
mas01mc@17 2274 }
mas01cr@60 2275 if(verbosity>1) {
mas01mc@18 2276 cerr << "processedTracks: " << processedTracks << endl;
mas01cr@60 2277 }
mas01mc@17 2278
mas01mc@18 2279 SILENCE_THRESH/=processedTracks;
mas01mc@17 2280 USE_THRESH=1; // Turn thresholding on
mas01mc@18 2281 DIFF_THRESH=SILENCE_THRESH; // mean shingle power
mas01mc@17 2282 SILENCE_THRESH/=5; // 20% of the mean shingle power is SILENCE
mas01cr@60 2283 if(verbosity>4) {
mas01mc@17 2284 cerr << "silence thresh: " << SILENCE_THRESH;
mas01cr@60 2285 }
mas01cr@148 2286
mas01cr@148 2287 sequence_sum(qnPtr, numVectors, sequenceLength);
mas01cr@148 2288
mas01cr@125 2289 ps = qnPtr;
mas01mc@17 2290 qMeanL2 = 0;
mas01mc@17 2291 w=numVectors-sequenceLength+1;
mas01mc@17 2292 while(w--){
mas01mc@17 2293 *ps=sqrt(*ps);
mas01mc@17 2294 qMeanL2+=*ps++;
mas01mc@17 2295 }
mas01mc@17 2296 qMeanL2 /= numVectors-sequenceLength+1;
mas01mc@17 2297
mas01cr@60 2298 if(verbosity>1) {
mas01mc@17 2299 cerr << "done." << endl;
mas01cr@60 2300 }
mas01mc@17 2301
mas01cr@60 2302 if(verbosity>1) {
mas01mc@18 2303 cerr << "matching tracks..." << endl;
mas01cr@60 2304 }
mas01mc@17 2305
mas01mc@17 2306 assert(pointNN>0 && pointNN<=O2_MAXNN);
mas01mc@18 2307 assert(trackNN>0 && trackNN<=O2_MAXNN);
mas01mc@17 2308
mas01mc@17 2309 // Make temporary dynamic memory for results
mas01mc@18 2310 double trackDistances[trackNN];
mas01mc@18 2311 unsigned trackIDs[trackNN];
mas01mc@18 2312 unsigned trackQIndexes[trackNN];
mas01mc@18 2313 unsigned trackSIndexes[trackNN];
mas01mc@17 2314
mas01mc@17 2315 double distances[pointNN];
mas01mc@17 2316 unsigned qIndexes[pointNN];
mas01mc@17 2317 unsigned sIndexes[pointNN];
mas01mc@17 2318
mas01mc@17 2319
mas01cr@59 2320 unsigned k,l,n,track,trackOffset=0, HOP_SIZE=sequenceHop, wL=sequenceLength;
mas01mc@17 2321 double thisDist;
mas01mc@17 2322
mas01mc@17 2323 for(k=0; k<pointNN; k++){
mas01mc@17 2324 distances[k]=0.0;
mas01mc@17 2325 qIndexes[k]=~0;
mas01mc@17 2326 sIndexes[k]=~0;
mas01mc@17 2327 }
mas01mc@17 2328
mas01mc@18 2329 for(k=0; k<trackNN; k++){
mas01mc@18 2330 trackDistances[k]=0.0;
mas01mc@18 2331 trackQIndexes[k]=~0;
mas01mc@18 2332 trackSIndexes[k]=~0;
mas01mc@18 2333 trackIDs[k]=~0;
mas01mc@17 2334 }
mas01mc@17 2335
mas01mc@17 2336 // Timestamp and durations processing
mas01mc@17 2337 double meanQdur = 0;
mas01mc@17 2338 double* timesdata = 0;
mas01mc@17 2339 double* meanDBdur = 0;
mas01mc@17 2340
mas01mc@17 2341 if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){
mas01mc@17 2342 cerr << "warning: ignoring query timestamps for non-timestamped database" << endl;
mas01mc@17 2343 usingTimes=0;
mas01mc@17 2344 }
mas01mc@17 2345
mas01mc@17 2346 else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES))
mas01mc@17 2347 cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl;
mas01mc@17 2348
mas01mc@17 2349 else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){
mas01mc@17 2350 timesdata = new double[numVectors];
mas01mc@17 2351 assert(timesdata);
mas01mc@17 2352 insertTimeStamps(numVectors, timesFile, timesdata);
mas01mc@17 2353 // Calculate durations of points
mas01mc@17 2354 for(k=0; k<numVectors-1; k++){
mas01mc@17 2355 timesdata[k]=timesdata[k+1]-timesdata[k];
mas01mc@17 2356 meanQdur+=timesdata[k];
mas01mc@17 2357 }
mas01mc@17 2358 meanQdur/=k;
mas01cr@60 2359 if(verbosity>1) {
mas01mc@17 2360 cerr << "mean query file duration: " << meanQdur << endl;
mas01cr@60 2361 }
mas01mc@17 2362 meanDBdur = new double[dbH->numFiles];
mas01mc@17 2363 assert(meanDBdur);
mas01mc@17 2364 for(k=0; k<dbH->numFiles; k++){
mas01mc@17 2365 meanDBdur[k]=0.0;
mas01mc@18 2366 for(j=0; j<trackTable[k]-1 ; j++)
mas01mc@17 2367 meanDBdur[k]+=timesTable[j+1]-timesTable[j];
mas01mc@17 2368 meanDBdur[k]/=j;
mas01mc@17 2369 }
mas01mc@17 2370 }
mas01mc@17 2371
mas01mc@17 2372 if(usingQueryPoint)
mas01mc@17 2373 if(queryPoint>numVectors || queryPoint>numVectors-wL+1)
mas01mc@17 2374 error("queryPoint > numVectors-wL+1 in query");
mas01mc@17 2375 else{
mas01cr@60 2376 if(verbosity>1) {
mas01mc@17 2377 cerr << "query point: " << queryPoint << endl; cerr.flush();
mas01cr@60 2378 }
mas01mc@17 2379 query=query+queryPoint*dbH->dim;
mas01cr@125 2380 qnPtr=qnPtr+queryPoint;
mas01mc@17 2381 numVectors=wL;
mas01mc@17 2382 }
mas01mc@17 2383
mas01mc@17 2384 double ** D = 0; // Differences query and target
mas01mc@17 2385 double ** DD = 0; // Matched filter distance
mas01mc@17 2386
mas01mc@17 2387 D = new double*[numVectors];
mas01mc@17 2388 assert(D);
mas01mc@17 2389 DD = new double*[numVectors];
mas01mc@17 2390 assert(DD);
mas01mc@17 2391
mas01mc@17 2392 gettimeofday(&tv1, NULL);
mas01mc@18 2393 processedTracks=0;
mas01mc@18 2394 unsigned successfulTracks=0;
mas01mc@17 2395
mas01mc@17 2396 double* qp;
mas01mc@17 2397 double* sp;
mas01mc@17 2398 double* dp;
mas01mc@17 2399
mas01mc@18 2400 // build track offset table
mas01mc@18 2401 unsigned *trackOffsetTable = new unsigned[dbH->numFiles];
mas01mc@18 2402 unsigned cumTrack=0;
mas01mc@18 2403 unsigned trackIndexOffset;
mas01mc@17 2404 for(k=0; k<dbH->numFiles;k++){
mas01mc@18 2405 trackOffsetTable[k]=cumTrack;
mas01mc@18 2406 cumTrack+=trackTable[k]*dbH->dim;
mas01mc@17 2407 }
mas01mc@17 2408
mas01mc@17 2409 char nextKey [MAXSTR];
mas01mc@17 2410
mas01mc@17 2411 // chi^2 statistics
mas01mc@17 2412 double sampleCount = 0;
mas01mc@17 2413 double sampleSum = 0;
mas01mc@17 2414 double logSampleSum = 0;
mas01mc@17 2415 double minSample = 1e9;
mas01mc@17 2416 double maxSample = 0;
mas01mc@17 2417
mas01mc@17 2418 // Track loop
mas01mc@18 2419 for(processedTracks=0, track=0 ; processedTracks < dbH->numFiles ; track++, processedTracks++){
mas01mc@17 2420
mas01mc@18 2421 // get trackID from file if using a control file
mas01mc@18 2422 if(trackFile){
mas01mc@18 2423 if(!trackFile->eof()){
mas01mc@18 2424 trackFile->getline(nextKey,MAXSTR);
mas01mc@18 2425 track=getKeyPos(nextKey);
mas01mc@17 2426 }
mas01mc@17 2427 else
mas01mc@17 2428 break;
mas01mc@17 2429 }
mas01mc@17 2430
mas01mc@18 2431 trackOffset=trackOffsetTable[track]; // numDoubles offset
mas01mc@18 2432 trackIndexOffset=trackOffset/dbH->dim; // numVectors offset
mas01mc@17 2433
mas01cr@70 2434 if(sequenceLength<=trackTable[track]){ // test for short sequences
mas01mc@17 2435
mas01cr@60 2436 if(verbosity>7) {
mas01mc@18 2437 cerr << track << "." << trackIndexOffset << "." << trackTable[track] << " | ";cerr.flush();
mas01cr@60 2438 }
mas01cr@60 2439
mas01mc@17 2440 // Sum products matrix
mas01mc@17 2441 for(j=0; j<numVectors;j++){
mas01mc@18 2442 D[j]=new double[trackTable[track]];
mas01mc@17 2443 assert(D[j]);
mas01mc@17 2444
mas01mc@17 2445 }
mas01mc@17 2446
mas01mc@17 2447 // Matched filter matrix
mas01mc@17 2448 for(j=0; j<numVectors;j++){
mas01mc@18 2449 DD[j]=new double[trackTable[track]];
mas01mc@17 2450 assert(DD[j]);
mas01mc@17 2451 }
mas01mc@17 2452
mas01mc@17 2453 // Dot product
mas01mc@17 2454 for(j=0; j<numVectors; j++)
mas01mc@18 2455 for(k=0; k<trackTable[track]; k++){
mas01mc@17 2456 qp=query+j*dbH->dim;
mas01mc@18 2457 sp=dataBuf+trackOffset+k*dbH->dim;
mas01mc@17 2458 DD[j][k]=0.0; // Initialize matched filter array
mas01mc@17 2459 dp=&D[j][k]; // point to correlation cell j,k
mas01mc@17 2460 *dp=0.0; // initialize correlation cell
mas01mc@17 2461 l=dbH->dim; // size of vectors
mas01mc@17 2462 while(l--)
mas01mc@17 2463 *dp+=*qp++**sp++;
mas01mc@17 2464 }
mas01mc@17 2465
mas01mc@17 2466 // Matched Filter
mas01mc@17 2467 // HOP SIZE == 1
mas01mc@17 2468 double* spd;
mas01mc@17 2469 if(HOP_SIZE==1){ // HOP_SIZE = shingleHop
mas01mc@17 2470 for(w=0; w<wL; w++)
mas01mc@17 2471 for(j=0; j<numVectors-w; j++){
mas01mc@17 2472 sp=DD[j];
mas01mc@17 2473 spd=D[j+w]+w;
mas01mc@18 2474 k=trackTable[track]-w;
mas01mc@17 2475 while(k--)
mas01mc@17 2476 *sp+++=*spd++;
mas01mc@17 2477 }
mas01mc@17 2478 }
mas01mc@17 2479
mas01mc@17 2480 else{ // HOP_SIZE != 1
mas01mc@17 2481 for(w=0; w<wL; w++)
mas01mc@17 2482 for(j=0; j<numVectors-w; j+=HOP_SIZE){
mas01mc@17 2483 sp=DD[j];
mas01mc@17 2484 spd=D[j+w]+w;
mas01mc@18 2485 for(k=0; k<trackTable[track]-w; k+=HOP_SIZE){
mas01mc@17 2486 *sp+=*spd;
mas01mc@17 2487 sp+=HOP_SIZE;
mas01mc@17 2488 spd+=HOP_SIZE;
mas01mc@17 2489 }
mas01mc@17 2490 }
mas01mc@17 2491 }
mas01mc@17 2492
mas01cr@60 2493 if(verbosity>3 && usingTimes) {
mas01mc@18 2494 cerr << "meanQdur=" << meanQdur << " meanDBdur=" << meanDBdur[track] << endl;
mas01mc@17 2495 cerr.flush();
mas01mc@17 2496 }
mas01mc@17 2497
mas01mc@17 2498 if(!usingTimes ||
mas01mc@17 2499 (usingTimes
mas01mc@18 2500 && fabs(meanDBdur[track]-meanQdur)<meanQdur*timesTol)){
mas01mc@17 2501
mas01cr@60 2502 if(verbosity>3 && usingTimes) {
mas01mc@17 2503 cerr << "within duration tolerance." << endl;
mas01mc@17 2504 cerr.flush();
mas01mc@17 2505 }
mas01mc@17 2506
mas01mc@17 2507 // Search for minimum distance by shingles (concatenated vectors)
mas01cr@70 2508 for(j=0;j<=numVectors-wL;j+=HOP_SIZE)
mas01cr@70 2509 for(k=0;k<=trackTable[track]-wL;k+=HOP_SIZE){
mas01cr@125 2510 thisDist=2-(2/(qnPtr[j]*sNorm[trackIndexOffset+k]))*DD[j][k];
mas01cr@60 2511 if(verbosity>10) {
mas01cr@125 2512 cerr << thisDist << " " << qnPtr[j] << " " << sNorm[trackIndexOffset+k] << endl;
mas01cr@60 2513 }
mas01mc@17 2514 // Gather chi^2 statistics
mas01mc@17 2515 if(thisDist<minSample)
mas01mc@17 2516 minSample=thisDist;
mas01mc@17 2517 else if(thisDist>maxSample)
mas01mc@17 2518 maxSample=thisDist;
mas01mc@17 2519 if(thisDist>1e-9){
mas01mc@17 2520 sampleCount++;
mas01mc@17 2521 sampleSum+=thisDist;
mas01mc@17 2522 logSampleSum+=log(thisDist);
mas01mc@17 2523 }
mas01mc@17 2524
mas01cr@125 2525 // diffL2 = fabs(qnPtr[j] - sNorm[trackIndexOffset+k]);
mas01mc@17 2526 // Power test
mas01mc@17 2527 if(!USE_THRESH ||
mas01mc@17 2528 // Threshold on mean L2 of Q and S sequences
mas01cr@125 2529 (USE_THRESH && qnPtr[j]>SILENCE_THRESH && sNorm[trackIndexOffset+k]>SILENCE_THRESH &&
mas01mc@17 2530 // Are both query and target windows above mean energy?
mas01cr@125 2531 (qnPtr[j]>qMeanL2*.25 && sNorm[trackIndexOffset+k]>sMeanL2[track]*.25))) // && diffL2 < DIFF_THRESH )))
mas01mc@17 2532 thisDist=thisDist; // Computed above
mas01mc@17 2533 else
mas01mc@17 2534 thisDist=1000000.0;
mas01mc@17 2535 if(thisDist>=0 && thisDist<=radius){
mas01mc@17 2536 distances[0]++; // increment count
mas01mc@18 2537 break; // only need one track point per query point
mas01mc@17 2538 }
mas01mc@17 2539 }
mas01mc@17 2540 // How many points were below threshold ?
mas01mc@17 2541 thisDist=distances[0];
mas01mc@17 2542
mas01mc@17 2543 // Let's see the distances then...
mas01cr@60 2544 if(verbosity>3) {
mas01mc@18 2545 cerr << fileTable+track*O2_FILETABLESIZE << " " << thisDist << endl;
mas01cr@60 2546 }
mas01mc@17 2547
mas01mc@18 2548 // All the track stuff goes here
mas01mc@18 2549 n=trackNN;
mas01mc@17 2550 while(n--){
mas01mc@18 2551 if(thisDist>trackDistances[n]){
mas01mc@18 2552 if((n==0 || thisDist<=trackDistances[n-1])){
mas01mc@17 2553 // Copy all values above up the queue
mas01mc@18 2554 for( l=trackNN-1 ; l > n ; l--){
mas01mc@18 2555 trackDistances[l]=trackDistances[l-1];
mas01mc@18 2556 trackQIndexes[l]=trackQIndexes[l-1];
mas01mc@18 2557 trackSIndexes[l]=trackSIndexes[l-1];
mas01mc@18 2558 trackIDs[l]=trackIDs[l-1];
mas01mc@17 2559 }
mas01mc@18 2560 trackDistances[n]=thisDist;
mas01mc@18 2561 trackQIndexes[n]=qIndexes[0];
mas01mc@18 2562 trackSIndexes[n]=sIndexes[0];
mas01mc@18 2563 successfulTracks++;
mas01mc@18 2564 trackIDs[n]=track;
mas01mc@17 2565 break;
mas01mc@17 2566 }
mas01mc@17 2567 }
mas01mc@17 2568 else
mas01mc@17 2569 break;
mas01mc@17 2570 }
mas01mc@17 2571 } // Duration match
mas01mc@17 2572
mas01mc@18 2573 // Clean up current track
mas01mc@17 2574 if(D!=NULL){
mas01mc@17 2575 for(j=0; j<numVectors; j++)
mas01mc@17 2576 delete[] D[j];
mas01mc@17 2577 }
mas01mc@17 2578
mas01mc@17 2579 if(DD!=NULL){
mas01mc@17 2580 for(j=0; j<numVectors; j++)
mas01mc@17 2581 delete[] DD[j];
mas01mc@17 2582 }
mas01mc@17 2583 }
mas01mc@18 2584 // per-track reset array values
mas01mc@17 2585 for(unsigned k=0; k<pointNN; k++){
mas01mc@17 2586 distances[k]=0.0;
mas01mc@17 2587 qIndexes[k]=~0;
mas01mc@17 2588 sIndexes[k]=~0;
mas01mc@17 2589 }
mas01mc@17 2590 }
mas01mc@17 2591
mas01mc@17 2592 gettimeofday(&tv2,NULL);
mas01cr@60 2593 if(verbosity>1) {
mas01mc@18 2594 cerr << endl << "processed tracks :" << processedTracks << " matched tracks: " << successfulTracks << " elapsed time:"
mas01mc@17 2595 << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl;
mas01mc@17 2596 cerr << "sampleCount: " << sampleCount << " sampleSum: " << sampleSum << " logSampleSum: " << logSampleSum
mas01mc@17 2597 << " minSample: " << minSample << " maxSample: " << maxSample << endl;
mas01mc@17 2598 }
mas01mc@17 2599
mas01cr@133 2600 if(adbQueryResponse==0){
mas01cr@60 2601 if(verbosity>1) {
mas01mc@17 2602 cerr<<endl;
mas01cr@60 2603 }
mas01mc@17 2604 // Output answer
mas01mc@17 2605 // Loop over nearest neighbours
mas01mc@18 2606 for(k=0; k < min(trackNN,successfulTracks); k++)
mas01mc@18 2607 cout << fileTable+trackIDs[k]*O2_FILETABLESIZE << " " << trackDistances[k] << endl;
mas01mc@17 2608 }
mas01mc@17 2609 else{ // Process Web Services Query
mas01mc@18 2610 int listLen = min(trackNN, processedTracks);
mas01cr@133 2611 adbQueryResponse->result.__sizeRlist=listLen;
mas01cr@133 2612 adbQueryResponse->result.__sizeDist=listLen;
mas01cr@133 2613 adbQueryResponse->result.__sizeQpos=listLen;
mas01cr@133 2614 adbQueryResponse->result.__sizeSpos=listLen;
mas01cr@133 2615 adbQueryResponse->result.Rlist= new char*[listLen];
mas01cr@133 2616 adbQueryResponse->result.Dist = new double[listLen];
mas01cr@133 2617 adbQueryResponse->result.Qpos = new unsigned int[listLen];
mas01cr@133 2618 adbQueryResponse->result.Spos = new unsigned int[listLen];
mas01cr@133 2619 for(k=0; k<(unsigned)adbQueryResponse->result.__sizeRlist; k++){
mas01cr@133 2620 adbQueryResponse->result.Rlist[k]=new char[O2_MAXFILESTR];
mas01cr@133 2621 adbQueryResponse->result.Dist[k]=trackDistances[k];
mas01cr@133 2622 adbQueryResponse->result.Qpos[k]=trackQIndexes[k];
mas01cr@133 2623 adbQueryResponse->result.Spos[k]=trackSIndexes[k];
mas01cr@133 2624 sprintf(adbQueryResponse->result.Rlist[k], "%s", fileTable+trackIDs[k]*O2_FILETABLESIZE);
mas01mc@17 2625 }
mas01mc@17 2626 }
mas01mc@17 2627
mas01mc@17 2628 // Clean up
mas01mc@18 2629 if(trackOffsetTable)
mas01mc@18 2630 delete[] trackOffsetTable;
mas01mc@17 2631 if(queryCopy)
mas01mc@17 2632 delete[] queryCopy;
mas01cr@121 2633 if(qNorm)
mas01cr@121 2634 delete[] qNorm;
mas01cr@121 2635 if(sNorm)
mas01cr@121 2636 delete[] sNorm;
mas01cr@121 2637 if(sMeanL2)
mas01cr@121 2638 delete[] sMeanL2;
mas01mc@17 2639 if(D)
mas01mc@17 2640 delete[] D;
mas01mc@17 2641 if(DD)
mas01mc@17 2642 delete[] DD;
mas01mc@17 2643 if(timesdata)
mas01mc@17 2644 delete[] timesdata;
mas01mc@17 2645 if(meanDBdur)
mas01mc@17 2646 delete[] meanDBdur;
mas01mc@17 2647
mas01mc@17 2648
mas01mc@17 2649 }
mas01mc@17 2650
mas01cr@0 2651 // Unit norm block of features
mas01cr@0 2652 void audioDB::unitNorm(double* X, unsigned dim, unsigned n, double* qNorm){
mas01cr@0 2653 unsigned d;
mas01cr@59 2654 double L2, *p;
mas01cr@60 2655 if(verbosity>2) {
mas01cr@0 2656 cerr << "norming " << n << " vectors...";cerr.flush();
mas01cr@60 2657 }
mas01cr@0 2658 while(n--){
mas01cr@0 2659 p=X;
mas01cr@0 2660 L2=0.0;
mas01cr@0 2661 d=dim;
mas01cr@0 2662 while(d--){
mas01cr@0 2663 L2+=*p**p;
mas01cr@0 2664 p++;
mas01cr@0 2665 }
mas01mc@17 2666 /* L2=sqrt(L2);*/
mas01cr@0 2667 if(qNorm)
mas01cr@0 2668 *qNorm++=L2;
mas01mc@17 2669 /*
mas01cr@0 2670 oneOverL2 = 1.0/L2;
mas01cr@0 2671 d=dim;
mas01cr@0 2672 while(d--){
mas01cr@0 2673 *X*=oneOverL2;
mas01cr@0 2674 X++;
mas01mc@17 2675 */
mas01mc@17 2676 X+=dim;
mas01cr@0 2677 }
mas01cr@60 2678 if(verbosity>2) {
mas01cr@0 2679 cerr << "done..." << endl;
mas01cr@60 2680 }
mas01cr@0 2681 }
mas01cr@0 2682
mas01cr@0 2683 // Unit norm block of features
mas01cr@0 2684 void audioDB::unitNormAndInsertL2(double* X, unsigned dim, unsigned n, unsigned append=0){
mas01cr@0 2685 unsigned d;
mas01cr@59 2686 double *p;
mas01cr@0 2687 unsigned nn = n;
mas01cr@0 2688
mas01cr@0 2689 assert(l2normTable);
mas01cr@0 2690
mas01cr@0 2691 if( !append && (dbH->flags & O2_FLAG_L2NORM) )
mas01cr@0 2692 error("Database is already L2 normed", "automatic norm on insert is enabled");
mas01cr@0 2693
mas01cr@60 2694 if(verbosity>2) {
mas01cr@0 2695 cerr << "norming " << n << " vectors...";cerr.flush();
mas01cr@60 2696 }
mas01cr@0 2697
mas01cr@0 2698 double* l2buf = new double[n];
mas01cr@0 2699 double* l2ptr = l2buf;
mas01cr@0 2700 assert(l2buf);
mas01cr@0 2701 assert(X);
mas01cr@0 2702
mas01cr@0 2703 while(nn--){
mas01cr@0 2704 p=X;
mas01cr@0 2705 *l2ptr=0.0;
mas01cr@0 2706 d=dim;
mas01cr@0 2707 while(d--){
mas01cr@0 2708 *l2ptr+=*p**p;
mas01cr@0 2709 p++;
mas01cr@0 2710 }
mas01mc@17 2711 l2ptr++;
mas01mc@17 2712 /*
mas01mc@17 2713 oneOverL2 = 1.0/(*l2ptr++);
mas01mc@17 2714 d=dim;
mas01mc@17 2715 while(d--){
mas01cr@0 2716 *X*=oneOverL2;
mas01cr@0 2717 X++;
mas01mc@17 2718 }
mas01mc@17 2719 */
mas01mc@17 2720 X+=dim;
mas01cr@0 2721 }
mas01cr@0 2722 unsigned offset;
mas01cr@84 2723 if(append) {
mas01cr@84 2724 // FIXME: a hack, a very palpable hack: the vectors have already
mas01cr@84 2725 // been inserted, and dbH->length has already been updated. We
mas01cr@84 2726 // need to subtract off again the number of vectors that we've
mas01cr@84 2727 // inserted this time...
mas01cr@84 2728 offset=(dbH->length/(dbH->dim*sizeof(double)))-n; // number of vectors
mas01cr@84 2729 } else {
mas01cr@0 2730 offset=0;
mas01cr@84 2731 }
mas01cr@0 2732 memcpy(l2normTable+offset, l2buf, n*sizeof(double));
mas01cr@0 2733 if(l2buf)
mas01mc@17 2734 delete[] l2buf;
mas01cr@60 2735 if(verbosity>2) {
mas01cr@0 2736 cerr << "done..." << endl;
mas01cr@60 2737 }
mas01cr@0 2738 }
mas01cr@0 2739
mas01cr@0 2740
mas01cr@0 2741 // Start an audioDB server on the host
mas01cr@0 2742 void audioDB::startServer(){
mas01cr@0 2743 struct soap soap;
mas01cr@0 2744 int m, s; // master and slave sockets
mas01cr@0 2745 soap_init(&soap);
mas01cr@92 2746 // FIXME: largely this use of SO_REUSEADDR is to make writing (and
mas01cr@92 2747 // running) test cases more convenient, so that multiple test runs
mas01cr@92 2748 // in close succession don't fail because of a bin() error.
mas01cr@92 2749 // Investigate whether there are any potential drawbacks in this,
mas01cr@92 2750 // and also whether there's a better way to write the tests. --
mas01cr@92 2751 // CSR, 2007-10-03
mas01cr@92 2752 soap.bind_flags |= SO_REUSEADDR;
mas01cr@0 2753 m = soap_bind(&soap, NULL, port, 100);
mas01cr@0 2754 if (m < 0)
mas01cr@0 2755 soap_print_fault(&soap, stderr);
mas01cr@0 2756 else
mas01cr@0 2757 {
mas01cr@0 2758 fprintf(stderr, "Socket connection successful: master socket = %d\n", m);
mas01cr@0 2759 for (int i = 1; ; i++)
mas01cr@0 2760 {
mas01cr@0 2761 s = soap_accept(&soap);
mas01cr@0 2762 if (s < 0)
mas01cr@0 2763 {
mas01cr@0 2764 soap_print_fault(&soap, stderr);
mas01cr@0 2765 break;
mas01cr@0 2766 }
mas01cr@75 2767 fprintf(stderr, "%d: accepted connection from IP=%lu.%lu.%lu.%lu socket=%d\n", i,
mas01cr@0 2768 (soap.ip >> 24)&0xFF, (soap.ip >> 16)&0xFF, (soap.ip >> 8)&0xFF, soap.ip&0xFF, s);
mas01cr@0 2769 if (soap_serve(&soap) != SOAP_OK) // process RPC request
mas01cr@0 2770 soap_print_fault(&soap, stderr); // print error
mas01cr@0 2771 fprintf(stderr, "request served\n");
mas01cr@0 2772 soap_destroy(&soap); // clean up class instances
mas01cr@0 2773 soap_end(&soap); // clean up everything and close socket
mas01cr@0 2774 }
mas01cr@0 2775 }
mas01cr@0 2776 soap_done(&soap); // close master socket and detach environment
mas01cr@0 2777 }
mas01cr@0 2778
mas01cr@0 2779
mas01cr@0 2780 // web services
mas01cr@0 2781
mas01cr@0 2782 // SERVER SIDE
mas01cr@133 2783 int adb__status(struct soap* soap, xsd__string dbName, adb__statusResponse &adbStatusResponse){
mas01cr@21 2784 char* const argv[]={"audioDB",COM_STATUS,"-d",dbName};
mas01cr@21 2785 const unsigned argc = 4;
mas01cr@77 2786 try {
mas01cr@133 2787 audioDB(argc, argv, &adbStatusResponse);
mas01cr@77 2788 return SOAP_OK;
mas01cr@77 2789 } catch(char *err) {
mas01cr@77 2790 soap_receiver_fault(soap, err, "");
mas01cr@77 2791 return SOAP_FAULT;
mas01cr@77 2792 }
mas01cr@0 2793 }
mas01cr@0 2794
mas01cr@0 2795 // Literal translation of command line to web service
mas01cr@0 2796
mas01cr@133 2797 int adb__query(struct soap* soap, xsd__string dbName, xsd__string qKey, xsd__string keyList, xsd__string timesFileName, xsd__int qType, xsd__int qPos, xsd__int pointNN, xsd__int trackNN, xsd__int seqLen, adb__queryResponse &adbQueryResponse){
mas01cr@0 2798 char queryType[256];
mas01cr@0 2799 for(int k=0; k<256; k++)
mas01cr@0 2800 queryType[k]='\0';
mas01cr@105 2801 if(qType == O2_POINT_QUERY)
mas01cr@0 2802 strncpy(queryType, "point", strlen("point"));
mas01cr@105 2803 else if (qType == O2_SEQUENCE_QUERY)
mas01cr@0 2804 strncpy(queryType, "sequence", strlen("sequence"));
mas01cr@105 2805 else if(qType == O2_TRACK_QUERY)
mas01mc@18 2806 strncpy(queryType,"track", strlen("track"));
mas01cr@0 2807 else
mas01cr@0 2808 strncpy(queryType, "", strlen(""));
mas01cr@0 2809
mas01cr@0 2810 if(pointNN==0)
mas01cr@0 2811 pointNN=10;
mas01mc@18 2812 if(trackNN==0)
mas01mc@18 2813 trackNN=10;
mas01cr@0 2814 if(seqLen==0)
mas01cr@0 2815 seqLen=16;
mas01cr@0 2816
mas01cr@0 2817 char qPosStr[256];
mas01cr@0 2818 sprintf(qPosStr, "%d", qPos);
mas01cr@0 2819 char pointNNStr[256];
mas01cr@0 2820 sprintf(pointNNStr,"%d",pointNN);
mas01mc@18 2821 char trackNNStr[256];
mas01mc@18 2822 sprintf(trackNNStr,"%d",trackNN);
mas01cr@0 2823 char seqLenStr[256];
mas01cr@0 2824 sprintf(seqLenStr,"%d",seqLen);
mas01cr@0 2825
mas01cr@0 2826 const char* argv[] ={
mas01cr@0 2827 "./audioDB",
mas01cr@0 2828 COM_QUERY,
mas01cr@0 2829 queryType, // Need to pass a parameter
mas01cr@0 2830 COM_DATABASE,
mas01cr@0 2831 dbName,
mas01cr@0 2832 COM_FEATURES,
mas01cr@0 2833 qKey,
mas01cr@0 2834 COM_KEYLIST,
mas01cr@0 2835 keyList==0?"":keyList,
mas01cr@0 2836 COM_TIMES,
mas01cr@0 2837 timesFileName==0?"":timesFileName,
mas01cr@0 2838 COM_QPOINT,
mas01cr@0 2839 qPosStr,
mas01cr@0 2840 COM_POINTNN,
mas01cr@0 2841 pointNNStr,
mas01mc@18 2842 COM_TRACKNN,
mas01mc@18 2843 trackNNStr, // Need to pass a parameter
mas01cr@0 2844 COM_SEQLEN,
mas01cr@0 2845 seqLenStr
mas01cr@0 2846 };
mas01cr@0 2847
mas01cr@0 2848 const unsigned argc = 19;
mas01cr@79 2849 try {
mas01cr@133 2850 audioDB(argc, (char* const*)argv, &adbQueryResponse);
mas01cr@79 2851 return SOAP_OK;
mas01cr@79 2852 } catch (char *err) {
mas01cr@79 2853 soap_receiver_fault(soap, err, "");
mas01cr@79 2854 return SOAP_FAULT;
mas01cr@79 2855 }
mas01cr@0 2856 }
mas01cr@0 2857
mas01cr@0 2858 int main(const unsigned argc, char* const argv[]){
mas01cr@0 2859 audioDB(argc, argv);
mas01cr@0 2860 }
mas01cr@104 2861