view index.cpp @ 381:9742ea0ac33d

API const correctness.

The char *path arguments to audiodb_open() and audiodb_create() should
be const; make it so.

Also arrange for the datasize, ntracks and datadim arguments to
audiodb_create() to be unsigned to match the fields in the internal
audioDB class.  Technically this is an ABI change, but since nothing is
calling this function with anything other than zero arguments yet
(correct me if I'm wrong) no-one should notice.  (If you notice, shout)

// LSH indexing
//
// Construct a persistent LSH table structure
// Store at the same location as dbName
// Naming convention:
//         dbName.lsh.${radius}.${sequenceLength}
//
//
// Author: Michael Casey
//   Date: 23 June 2008
//
// 19th August 2008 - added O2_FLAG_LARGE_ADB support

#include "audioDB.h"
#include "ReporterBase.h"


/************************* LSH point index to audioDB conversion  *****************/
Uns32T audioDB::index_to_trackID(Uns32T lshID, Uns32T nPntBits){
  assert(nPntBits);
  return lshID>>nPntBits;
}

Uns32T audioDB::index_to_trackPos(Uns32T lshID, Uns32T nPntBits){
  assert(nPntBits);
  return lshID&((1<<nPntBits)-1);
}

Uns32T audioDB::index_from_trackInfo(Uns32T trackID, Uns32T spos, Uns32T nPntBits){
  assert(nPntBits);
  return (trackID << nPntBits) | spos;
}

/************************* LSH indexing and query initialization  *****************/

char* audioDB::index_get_name(const char*dbName, double radius, Uns32T sequenceLength){
  char* indexName = new char[MAXSTR];  
  // Attempt to make new file
  if(strlen(dbName) > (MAXSTR - 32))
    error("dbName is too long for LSH index filename appendages");
  strncpy(indexName, dbName, MAXSTR);
  sprintf(indexName+strlen(dbName), ".lsh.%019.9f.%d", radius, sequenceLength);
  return indexName;
}

// return true if index exists else return false
int audioDB::index_exists(const char* dbName, double radius, Uns32T sequenceLength){
  // Test to see if file exists
  char* indexName = index_get_name(dbName, radius, sequenceLength);
  lshfid = open (indexName, O_RDONLY);
  delete[] indexName;
  close(lshfid);
  
  if(lshfid<0)
    return false;  
  else
    return true;
}

// If we are a server and have a memory-resident index, check the indexName against the resident index (using get_indexName())
// If they match, i.e. path+dbName_resident == path+dbName_requested, use
// the memory-resident index.
// Else allocate a new LSH instance and load the index from disk
LSH* audioDB::index_allocate(char* indexName, bool load_hashTables){
  LSH* gIndx=SERVER_LSH_INDEX_SINGLETON;
  if(isServer && gIndx && (strncmp(gIndx->get_indexName(), indexName, MAXSTR)==0) )
    audioDB::lsh = gIndx; // Use the global SERVER resident index
  else{
    if(audioDB::lsh)
      delete audioDB::lsh;
    audioDB::lsh = new LSH(indexName, load_hashTables);
  }
  assert(audioDB::lsh);  
  return audioDB::lsh;
}

vector<vector<float> >* audioDB::index_initialize_shingles(Uns32T sz){
  if(vv)
    delete vv;
  vv = new vector<vector<float> >(sz);
  for(Uns32T i=0 ; i < sz ; i++)
    (*vv)[i]=vector<float>(dbH->dim*sequenceLength);  // allocate shingle storage
  return vv;
}

/********************  LSH indexing audioDB database access forall s \in {S} ***********************/

// Prepare the AudioDB database for read access and allocate auxillary memory
void audioDB::index_initialize(double **snp, double **vsnp, double **spp, double **vspp, Uns32T *dvp) {
  if (!(dbH->flags & O2_FLAG_POWER)) {
    error("INDEXed database must be power-enabled", dbName);
  }

  double *snpp = 0, *sppp = 0;

  *dvp = dbH->length / (dbH->dim * sizeof(double)); // number of database vectors
  *snp = new double[*dvp];  // songs norm pointer: L2 norm table for each vector
  snpp = *snp;
  *spp = new double[*dvp]; // song powertable pointer
  sppp = *spp;

  memcpy(*snp, l2normTable, *dvp * sizeof(double));
  memcpy(*spp, powerTable, *dvp * sizeof(double));
  
  
  for(Uns32T i = 0; i < dbH->numFiles; i++){
    if(trackTable[i] >= sequenceLength) {
      sequence_sum(snpp, trackTable[i], sequenceLength);
      sequence_sqrt(snpp, trackTable[i], sequenceLength);
      
      sequence_sum(sppp, trackTable[i], sequenceLength);
      sequence_average(sppp, trackTable[i], sequenceLength);
    }
    snpp += trackTable[i];
    sppp += trackTable[i];
  }
  
  *vsnp = *snp;
  *vspp = *spp;
  
  // Move the feature vector read pointer to start of fetures in database
  lseek(dbfid, dbH->dataOffset, SEEK_SET);
}


/************************ LSH indexing ***********************************/
void audioDB::index_index_db(const char* dbName){
  char* newIndexName;
  double *fvp = 0, *sNorm = 0, *snPtr = 0, *sPower = 0, *spPtr = 0;
  Uns32T dbVectors = 0;


  printf("INDEX: initializing header\n");
  // Check if audioDB exists, initialize header and open database for read
  forWrite = false;
  initDBHeader(dbName);

  if(dbH->flags & O2_FLAG_POWER)
    usingPower = true;
  
  if(dbH->flags & O2_FLAG_TIMES)
    usingTimes = true;

  newIndexName = index_get_name(dbName, radius, sequenceLength);

  // Set unit norming flag override
  audioDB::normalizedDistance = !audioDB::no_unit_norming;

  VERB_LOG(1, "INDEX: dim %d\n", (int)dbH->dim);
  VERB_LOG(1, "INDEX: R %f\n", radius);
  VERB_LOG(1, "INDEX: seqlen %d\n", sequenceLength);
  VERB_LOG(1, "INDEX: lsh_w %f\n", lsh_param_w);
  VERB_LOG(1, "INDEX: lsh_k %d\n", lsh_param_k);
  VERB_LOG(1, "INDEX: lsh_m %d\n", lsh_param_m);
  VERB_LOG(1, "INDEX: lsh_N %d\n", lsh_param_N);
  VERB_LOG(1, "INDEX: lsh_C %d\n", lsh_param_ncols);
  VERB_LOG(1, "INDEX: lsh_b %d\n", lsh_param_b);
  VERB_LOG(1, "INDEX: normalized? %s\n", normalizedDistance?"true":"false"); 

  if((lshfid = open(newIndexName,O_RDONLY))<0){
    printf("INDEX: constructing new LSH index\n");  
    printf("INDEX: making index file %s\n", newIndexName);
    fflush(stdout);
    // Construct new LSH index
    lsh = new LSH((float)lsh_param_w, lsh_param_k,
		  lsh_param_m,
		  (Uns32T)(sequenceLength*dbH->dim),
		  lsh_param_N,
		  lsh_param_ncols,
		  (float)radius);
    assert(lsh);  

    Uns32T endTrack = lsh_param_b;
    if( endTrack > dbH->numFiles)
      endTrack = dbH->numFiles;
    // Insert up to lsh_param_b tracks
    if( ! (dbH->flags & O2_FLAG_LARGE_ADB) ){
      index_initialize(&sNorm, &snPtr, &sPower, &spPtr, &dbVectors);  
    }
    index_insert_tracks(0, endTrack, &fvp, &sNorm, &snPtr, &sPower, &spPtr);
    lsh->serialize(newIndexName, lsh_in_core?O2_SERIAL_FILEFORMAT2:O2_SERIAL_FILEFORMAT1);
    
    // Clean up
    delete lsh;
    lsh = 0;
    close(lshfid);
  }
  
  // Attempt to open LSH file
  if((lshfid = open(newIndexName,O_RDONLY))>0){
    printf("INDEX: merging with existing LSH index\n");
    fflush(stdout);
    char* mergeIndexName = newIndexName;

    // Get the lsh header info and find how many tracks are inserted already
    lsh = new LSH(mergeIndexName, false); // lshInCore=false to avoid loading hashTables here
    assert(lsh);
    Uns32T maxs = index_to_trackID(lsh->get_maxp(), lsh_n_point_bits)+1;
    delete lsh;
    lsh = 0;

    // Insert up to lsh_param_b tracks
    if(  !sNorm && !(dbH->flags & O2_FLAG_LARGE_ADB) ){
      index_initialize(&sNorm, &snPtr, &sPower, &spPtr, &dbVectors);  
    }
    // This allows for updating index after more tracks are inserted into audioDB
    for(Uns32T startTrack = maxs; startTrack < dbH->numFiles; startTrack+=lsh_param_b){

      Uns32T endTrack = startTrack + lsh_param_b;
      if( endTrack > dbH->numFiles)
	endTrack = dbH->numFiles;
      printf("Indexing track range: %d - %d\n", startTrack, endTrack);
      fflush(stdout);
      lsh = new LSH(mergeIndexName, false); // Initialize empty LSH tables
      assert(lsh);
      
      // Insert up to lsh_param_b database tracks
      index_insert_tracks(startTrack, endTrack, &fvp, &sNorm, &snPtr, &sPower, &spPtr);

      // Serialize to file (merging is performed here)
      lsh->serialize(mergeIndexName, lsh_in_core?O2_SERIAL_FILEFORMAT2:O2_SERIAL_FILEFORMAT1); // Serialize core LSH heap to disk
      delete lsh;
      lsh = 0;
    }
    
    close(lshfid);    
    printf("INDEX: done constructing LSH index.\n");  
    fflush(stdout);
    
  }
  else{
    error("Something's wrong with LSH index file");
    exit(1);
  }
    
  delete[] newIndexName;
  delete[] sNorm;
  delete[] sPower;
}


// initialize auxillary track data from filesystem
// pre-conditions:
// dbH->flags & O2_FLAG_LARGE_ADB
// feature data allocated and copied (fvp)
//
// post-conditions:
// allocated power data
// allocated l2norm data
//
void audioDB::init_track_aux_data(Uns32T trackID, double* fvp, double** sNormpp,double** snPtrp, double** sPowerp, double** spPtrp){  
  if( !(dbH->flags & O2_FLAG_LARGE_ADB) )
    error("error: init_track_large_adb required O2_FLAG_LARGE_ADB");

  // Allocate and read the power sequence
  if(trackTable[trackID]>=sequenceLength){
    
    char* prefixedString = new char[O2_MAXFILESTR];
    char* tmpStr = prefixedString;
    // Open and check dimensions of power file
    strncpy(prefixedString, powerFileNameTable+trackID*O2_FILETABLE_ENTRY_SIZE, O2_MAXFILESTR);
    prefix_name((char ** const)&prefixedString, adb_feature_root);
    if(prefixedString!=tmpStr)
      delete[] tmpStr;
    powerfd = open(prefixedString, O_RDONLY);
    if (powerfd < 0) {
      error("failed to open power file", prefixedString);
    }
    if (fstat(powerfd, &statbuf) < 0) {
      error("fstat error finding size of power file", prefixedString, "fstat");
    }
    
    if( (statbuf.st_size - sizeof(int)) / (sizeof(double)) != trackTable[trackID] )
      error("Dimension mismatch: numPowers != numVectors", prefixedString);
   
    *sPowerp = new double[trackTable[trackID]]; // Allocate memory for power values
    assert(*sPowerp);
    *spPtrp = *sPowerp;
    insertPowerData(trackTable[trackID], powerfd, *sPowerp);
    if (0 < powerfd) {
      close(powerfd);
    }
    
    sequence_sum(*sPowerp, trackTable[trackID], sequenceLength);
    sequence_average(*sPowerp, trackTable[trackID], sequenceLength);
    powerTable = 0;

    // Allocate and calculate the l2norm sequence
    *sNormpp = new double[trackTable[trackID]];
    assert(*sNormpp);
    *snPtrp = *sNormpp;
    unitNorm(fvp, dbH->dim, trackTable[trackID], *sNormpp);
    sequence_sum(*sNormpp, trackTable[trackID], sequenceLength);
    sequence_sqrt(*sNormpp, trackTable[trackID], sequenceLength);
  }
}

void audioDB::index_insert_tracks(Uns32T start_track, Uns32T end_track,
				  double** fvpp, double** sNormpp,double** snPtrp, 
				  double** sPowerp, double** spPtrp){  
  size_t nfv = 0;
  double* fvp = 0; // Keep pointer for memory allocation and free() for track data
  Uns32T trackID = 0;

  VERB_LOG(1, "indexing tracks...");

  int trackfd = dbfid;
  for(trackID = start_track ; trackID < end_track ; trackID++ ){
    if( dbH->flags & O2_FLAG_LARGE_ADB ){
      char* prefixedString = new char[O2_MAXFILESTR];
      char* tmpStr = prefixedString;
      // Open and check dimensions of feature file
      strncpy(prefixedString, featureFileNameTable+trackID*O2_FILETABLE_ENTRY_SIZE, O2_MAXFILESTR);
      prefix_name((char ** const) &prefixedString, adb_feature_root);
      if(prefixedString!=tmpStr)
	delete[] tmpStr;
      initInputFile(prefixedString, false); // nommap, file pointer at correct position
      trackfd = infid;
    }
    read_data(trackfd, trackID, &fvp, &nfv); // over-writes fvp and nfv
    *fvpp = fvp; // Protect memory allocation and free() for track data
    
    if( dbH->flags & O2_FLAG_LARGE_ADB )
      // Load power and calculate power and l2norm sequence sums
      init_track_aux_data(trackID, fvp, sNormpp, snPtrp, sPowerp, spPtrp);
    
    if(!index_insert_track(trackID, fvpp, snPtrp, spPtrp))
      break;    
    if ( dbH->flags & O2_FLAG_LARGE_ADB ){
      close(infid);
      delete[] *sNormpp;
      delete[] *sPowerp;
      *sNormpp = *sPowerp = *snPtrp = *snPtrp = 0;
    }
  } // end for(trackID = start_track ; ... )
  std::cout << "finished inserting." << endl;
}

int audioDB::index_insert_track(Uns32T trackID, double** fvpp, double** snpp, double** sppp){
  // Loop over the current input track's vectors
  Uns32T numVecs = 0;
  if (trackTable[trackID] > O2_MAXTRACKLEN) {
    if (O2_MAXTRACKLEN < sequenceLength - 1) {
      numVecs = 0;
    } else {
      numVecs = O2_MAXTRACKLEN - sequenceLength + 1;
    }
  } else {
    if (trackTable[trackID] < sequenceLength - 1) {
      numVecs = 0;
    } else {
      numVecs = trackTable[trackID] - sequenceLength + 1;
    }
  }
  
  Uns32T numVecsAboveThreshold = 0, collisionCount = 0; 
  if(numVecs){
    vv = index_initialize_shingles(numVecs);
    
    for( Uns32T pointID = 0 ; pointID < numVecs; pointID++ )
      index_make_shingle(vv, pointID, *fvpp, dbH->dim, sequenceLength);
    
    numVecsAboveThreshold = index_norm_shingles(vv, *snpp, *sppp);
    collisionCount = index_insert_shingles(vv, trackID, *sppp);
  }
  float meanCollisionCount = numVecsAboveThreshold?(float)collisionCount/numVecsAboveThreshold:0;

  /* index_norm_shingles() only goes as far as the end of the
     sequence, which is right, but the space allocated is for the
     whole track.  */

  /* But numVecs will be <trackTable[track] if trackTable[track]>O2_MAXTRACKLEN
   * So let's be certain the pointers are in the correct place
   */

  if( !(dbH->flags & O2_FLAG_LARGE_ADB) ){
    *snpp += trackTable[trackID];
    *sppp += trackTable[trackID];
    *fvpp += trackTable[trackID] * dbH->dim;
  }

  std::cout << " n=" << trackTable[trackID] << " n'=" << numVecsAboveThreshold << " E[#c]=" << lsh->get_mean_collision_rate() << " E[#p]=" << meanCollisionCount << endl;
  std::cout.flush();  
  return true;
}

Uns32T audioDB::index_insert_shingles(vector<vector<float> >* vv, Uns32T trackID, double* spp){
  Uns32T collisionCount = 0;
  cout << "[" << trackID << "]" << fileTable+trackID*O2_FILETABLE_ENTRY_SIZE;
  for( Uns32T pointID=0 ; pointID < (*vv).size(); pointID+=sequenceHop){
    if(!use_absolute_threshold || (use_absolute_threshold && (*spp >= absolute_threshold)))
      collisionCount += lsh->insert_point((*vv)[pointID], index_from_trackInfo(trackID, pointID, lsh_n_point_bits));
    spp+=sequenceHop;
    }
  return collisionCount;
}

/********************* LSH shingle construction ***************************/

// Construct shingles out of a feature matrix
// inputs:
// idx is vector index in feature matrix
// fvp is base feature matrix pointer double* [numVecs x dbH->dim]
//
// pre-conditions: 
// dbH->dim 
// sequenceLength
// idx < numVectors - sequenceLength + 1
//
// post-conditions:
// (*vv)[idx] contains a shingle with dbH->dim*sequenceLength float values

void audioDB::index_make_shingle(vector<vector<float> >* vv, Uns32T idx, double* fvp, Uns32T dim, Uns32T seqLen){
  assert(idx<(*vv).size());
  vector<float>::iterator ve = (*vv)[idx].end();
  vi=(*vv)[idx].begin();        // shingle iterator  
  // First feature vector in shingle
  if(idx==0){
    while(vi!=ve)
      *vi++ = (float)(*fvp++);
  }
  // Not first feature vector in shingle
  else{
    vector<float>::iterator ui=(*vv)[idx-1].begin() + dim; // previous shingle iterator
    // Previous seqLen-1 dim-vectors
    while(vi!=ve-dim)
      *vi++=*ui++;
    // Move data pointer to next feature vector
    fvp += ( seqLen + idx - 1 ) * dim ;
    // New d-vector
    while(vi!=ve)
      *vi++ = (float)(*fvp++);
  }
}

// norm shingles
// in-place norming, no deletions
// If using power, return number of shingles above power threshold
int audioDB::index_norm_shingles(vector<vector<float> >* vv, double* snp, double* spp){  
  int z = 0; // number of above-threshold shingles
  float l2norm;
  double power;
  float oneOverRadius = 1./(float)sqrt(radius); // Passed radius is really radius^2
  float oneOverSqrtl2NormDivRad = oneOverRadius;
  if(!spp)
    error("LSH indexing and query requires a power feature using -w or -W");
  Uns32T shingleSize = sequenceLength*dbH->dim;
  for(Uns32T a=0; a<(*vv).size(); a++){
    l2norm = (float)(*snp++);
    if(audioDB::normalizedDistance)
      oneOverSqrtl2NormDivRad = (1./l2norm)*oneOverRadius;
    
    for(Uns32T b=0; b < shingleSize ; b++)
      (*vv)[a][b]*=oneOverSqrtl2NormDivRad;

    power = *spp++;
    if(use_absolute_threshold){
      if ( power >= absolute_threshold )
	z++;
    }
    else
      z++;	
  }
  return z;
}
  

/*********************** LSH retrieval ****************************/


// return true if indexed query performed else return false
int audioDB::index_init_query(const char* dbName){

  if(!(index_exists(dbName, radius, sequenceLength)))
    return false;

  char* indexName = index_get_name(dbName, radius, sequenceLength);  

  // Test to see if file exists
  if((lshfid = open (indexName, O_RDONLY)) < 0){
    delete[] indexName;
    return false;  
  }

  lsh = index_allocate(indexName, false); // Get the header only here
  sequenceLength = lsh->get_lshHeader()->dataDim / dbH->dim; // shingleDim / vectorDim
  
  if(lsh!=SERVER_LSH_INDEX_SINGLETON){  
    if( fabs(radius - lsh->get_radius())>fabs(O2_DISTANCE_TOLERANCE))
      printf("*** Warning: adb_radius (%f) != lsh_radius (%f) ***\n", radius, lsh->get_radius());
    VERB_LOG(1,"INDEX: dim %d\n", (int)dbH->dim);
    VERB_LOG(1,"INDEX: R %f\n", lsh->get_radius());
    VERB_LOG(1,"INDEX: seqlen %d\n", sequenceLength);
    VERB_LOG(1,"INDEX: w %f\n", lsh->get_lshHeader()->get_binWidth());
    VERB_LOG(1,"INDEX: k %d\n", lsh->get_lshHeader()->get_numFuns());
    VERB_LOG(1,"INDEX: L (m*(m-1))/2 %d\n", lsh->get_lshHeader()->get_numTables());
    VERB_LOG(1,"INDEX: N %d\n", lsh->get_lshHeader()->get_numRows());
    VERB_LOG(1,"INDEX: s %d\n", index_to_trackID(lsh->get_maxp(), lsh_n_point_bits));
    VERB_LOG(1,"INDEX: Opened LSH index file %s\n", indexName);
  }

  // Check to see if we are loading hash tables into core, and do so if true
  if((lsh->get_lshHeader()->flags&O2_SERIAL_FILEFORMAT2) || lsh_in_core){
    if(SERVER_LSH_INDEX_SINGLETON)
      fprintf(stderr,"INDEX: using persistent hash tables: %s\n", lsh->get_indexName());
    else
      VERB_LOG(1,"INDEX: loading hash tables into core %s\n", (lsh->get_lshHeader()->flags&O2_SERIAL_FILEFORMAT2)?"FORMAT2":"FORMAT1");
    lsh = index_allocate(indexName, true);
  }
  
  delete[] indexName;
  return true;
}

// *Static* approximate NN point reporter callback method for lshlib
void audioDB::index_add_point_approximate(void* instancePtr, Uns32T pointID, Uns32T qpos, float dist){
  assert(instancePtr); // We need an instance for this callback
  audioDB* myself = (audioDB*) instancePtr; // Use explicit cast to recover "this" instance
  Uns32T trackID = index_to_trackID(pointID, myself->lsh_n_point_bits);
  Uns32T spos = index_to_trackPos(pointID, myself->lsh_n_point_bits);
  // Skip identity in query_from_key
  if( !myself->query_from_key || (myself->query_from_key && ( trackID != myself->query_from_key_index )) )
    myself->reporter->add_point(trackID, qpos, spos, dist);
}

// *Static* exact NN point reporter callback method for lshlib
// Maintain a queue of points to pass to query_points() for exact evaluation
void audioDB::index_add_point_exact(void* instancePtr, Uns32T pointID, Uns32T qpos, float dist){
  assert(instancePtr); // We need an instance for this callback
  audioDB* myself = (audioDB*) instancePtr; // Use explicit cast to recover "this" instance  
  Uns32T trackID = index_to_trackID(pointID, myself->lsh_n_point_bits);
  Uns32T spos = index_to_trackPos(pointID, myself->lsh_n_point_bits);
  // Skip identity in query_from_key
  if( !myself->query_from_key || (myself->query_from_key && ( trackID != myself->query_from_key_index )) )
    myself->index_insert_exact_evaluation_queue(trackID, qpos, spos);
}

void audioDB::initialize_exact_evalutation_queue(){
  if(exact_evaluation_queue)
    delete exact_evaluation_queue;
  exact_evaluation_queue = new priority_queue<PointPair, std::vector<PointPair>, std::less<PointPair> >;
}

void audioDB::index_insert_exact_evaluation_queue(Uns32T trackID, Uns32T qpos, Uns32T spos){
  PointPair p(trackID, qpos, spos);
  exact_evaluation_queue->push(p);
}

// return 0: if index does not exist
// return nqv: if index exists
int audioDB::index_query_loop(const char* dbName, Uns32T queryIndex) {
  
  unsigned int numVectors = 0;
  double *query = 0, *query_data = 0;
  double *qNorm = 0, *qnPtr = 0, *qPower = 0, *qpPtr = 0;
  double meanQdur = 0;
  void (*add_point_func)(void*,Uns32T,Uns32T,float);

  // Set the point-reporter callback based on the value of lsh_exact
  if(lsh_exact){
    initialize_exact_evalutation_queue();
    add_point_func = &index_add_point_exact;
  }
  else
    add_point_func = &index_add_point_approximate;  

  if(!index_init_query(dbName)) // sets-up LSH index structures for querying
    return 0;

  char* database = index_get_name(dbName, radius, sequenceLength);

  if(query_from_key)
    set_up_query_from_key(&query_data, &query, &qNorm, &qnPtr, &qPower, &qpPtr, &meanQdur, &numVectors, queryIndex);
  else
    set_up_query(&query_data, &query, &qNorm, &qnPtr, &qPower, &qpPtr, &meanQdur, &numVectors); // get query vectors

  VERB_LOG(1, "retrieving tracks...");
  
  assert(pointNN>0 && pointNN<=O2_MAXNN);
  assert(trackNN>0 && trackNN<=O2_MAXNN);

  gettimeofday(&tv1, NULL);   
  // query vector index
  Uns32T Nq = (numVectors>O2_MAXTRACKLEN?O2_MAXTRACKLEN:numVectors) - sequenceLength + 1;
  vv = index_initialize_shingles(Nq); // allocate memory to copy query vectors to shingles
  VERB_LOG(1, "Nq=%d", Nq);
  // Construct shingles from query features  
  for( Uns32T pointID = 0 ; pointID < Nq ; pointID++ ) 
    index_make_shingle(vv, pointID, query, dbH->dim, sequenceLength);
  
  // Normalize query vectors
  Uns32T numVecsAboveThreshold = index_norm_shingles( vv, qnPtr, qpPtr );
  VERB_LOG(1, "Nq'=%d\n", numVecsAboveThreshold);

  // Nq contains number of inspected points in query file, 
  // numVecsAboveThreshold is number of points with power >= absolute_threshold
  double* qpp = qpPtr; // Keep original qpPtr for possible exact evaluation
  if(usingQueryPoint && numVecsAboveThreshold){
    if((lsh->get_lshHeader()->flags&O2_SERIAL_FILEFORMAT2) || lsh_in_core)
      lsh->retrieve_point((*vv)[0], queryPoint, add_point_func, (void*)this);
    else
      lsh->serial_retrieve_point(database, (*vv)[0], queryPoint, add_point_func, (void*)this);
  }
  else if(numVecsAboveThreshold)
    for( Uns32T pointID = 0 ; pointID < Nq; pointID++ )
      if(!use_absolute_threshold || (use_absolute_threshold && (*qpp++ >= absolute_threshold))) {
	if((lsh->get_lshHeader()->flags&O2_SERIAL_FILEFORMAT2) || lsh_in_core) {
	  lsh->retrieve_point((*vv)[pointID], pointID, add_point_func, (void*)this);
        } else {
	  lsh->serial_retrieve_point(database, (*vv)[pointID], pointID, add_point_func, (void*)this);   
        }
      }

  if(lsh_exact)
    // Perform exact distance computation on point pairs in exact_evaluation_queue
    query_loop_points(query, qnPtr, qpPtr, meanQdur, numVectors); 
  
  gettimeofday(&tv2,NULL);
  VERB_LOG(1,"elapsed time: %ld msec\n",
           (tv2.tv_sec*1000 + tv2.tv_usec/1000) - 
           (tv1.tv_sec*1000 + tv1.tv_usec/1000))

  // Close the index file
  close(lshfid);
    
 // Clean up
  if(query_data)
    delete[] query_data;
  if(qNorm)
    delete[] qNorm;
  if(qPower)
    delete[] qPower;
  if(database)
    delete[] database;

  return Nq;
}