Mercurial > hg > audiodb
diff audioDB.cpp @ 0:9eab3e0f3068
Initial import
author | mas01cr |
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date | Fri, 20 Jul 2007 15:51:39 +0000 |
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children | 12be3560ff0f 69eb22e09772 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/audioDB.cpp Fri Jul 20 15:51:39 2007 +0000 @@ -0,0 +1,2030 @@ +/* audioDB.cpp + +audioDB version 1.0 + +A feature vector database management system for content-based retrieval. + +Usage: audioDB [OPTIONS]... + + --full-help Print help, including hidden options, and exit + -V, --version Print version and exit + -H, --help print help on audioDB usage and exit. + -v, --verbosity=detail level of detail of operational information. + (default=`1') + +Database Setup: + All database operations require a database argument. + + Database commands are UPPER CASE. Command options are lower case. + + -d, --database=filename database file required by Database commands. + -N, --NEW make a new (initially empty) database. + -S, --STATUS output database information to stdout. + -D, --DUMP output all entries: index key size. + -L, --L2NORM unit norm vectors and norm all future inserts. + +Database Insertion: + The following commands insert feature files, with optional keys and + timestamps. + + -I, --INSERT add feature vectors to an existing database. + -U, --UPDATE replace inserted vectors associated with key + with new input vectors. + -f, --features=filename binary series of vectors file {int sz:ieee + double[][sz]:eof}. + -t, --times=filename list of time points (ascii) for feature vectors. + -k, --key=identifier unique identifier associated with features. + + -B, --BATCHINSERT add feature vectors named in a --featureList + file (with optional keys in a --keyList file) + to the named database. + -F, --featureList=filename text file containing list of binary feature + vector files to process + -T, --timesList=filename text file containing list of ascii --times for + each --features file in --featureList. + -K, --keyList=filename text file containing list of unique identifiers + associated with --features. + +Database Search: + Thse commands control the retrieval behaviour. + + -Q, --QUERY=searchtype content-based search on --database using + --features as a query. Optionally restrict the + search to those segments identified in a + --keyList. (possible values="point", + "segment", "sequence") + -p, --qpoint=position ordinal position of query start point in + --features file. (default=`0') + -e, --exhaustive exhaustive search: iterate through all query + vectors in search. Overrides --qpoint. + (default=off) + -n, --pointnn=numpoints number of point nearest neighbours to use in + retrieval. (default=`10') + -R, --radius=DOUBLE radius search, returns all + points/segments/sequences inside given radius. + (default=`1.0') + -x, --expandfactor=DOUBLE time compress/expand factor of result length to + query length [1.0 .. 100.0]. (default=`1.1') + -o, --rotate rotate query vectors for rotationally invariant + search. (default=off) + -r, --resultlength=length maximum length of the result list. + (default=`10') + -l, --sequencelength=length length of sequences for sequence search. + (default=`16') + -h, --sequencehop=hop hop size of sequence window for sequence search. + (default=`1') + +Web Services: + These commands enable the database process to establish a connection via the + internet and operate as separate client and server processes. + + -s, --SERVER=port run as standalone web service on named port. + (default=`80011') + -c, --client=hostname:port run as a client using named host service. + + Copyright (C) 2007 Michael Casey, Goldsmiths, University of London + + outputs: + + key1 distance1 qpos1 spos1 + key2 distance2 qpos2 spos2 + ... + keyN distanceN qposN sposN + +*/ + +#include "audioDB.h" + +#define O2_DEBUG + + void audioDB::error(const char* a, const char* b){ + cerr << a << ":" << b << endl; + exit(1); +} + +audioDB::audioDB(const unsigned argc, char* const argv[], adb__queryResult *adbQueryResult): + dim(0), + dbName(0), + inFile(0), + key(0), + segFile(0), + segFileName(0), + timesFile(0), + timesFileName(0), + usingTimes(0), + command(0), + dbfid(0), + db(0), + dbH(0), + infid(0), + indata(0), + queryType(O2_FLAG_POINT_QUERY), + verbosity(1), + pointNN(O2_DEFAULT_POINTNN), + segNN(O2_DEFAULT_SEGNN), + segTable(0), + fileTable(0), + dataBuf(0), + l2normTable(0), + timesTable(0), + qNorm(0), + sequenceLength(16), + sequenceHop(1), + queryPoint(0), + usingQueryPoint(0), + isClient(0), + isServer(0), + port(0), + timesTol(0.1){ + + if(processArgs(argc, argv)<0){ + printf("No command found.\n"); + cmdline_parser_print_version (); + if (strlen(gengetopt_args_info_purpose) > 0) + printf("%s\n", gengetopt_args_info_purpose); + printf("%s\n", gengetopt_args_info_usage); + printf("%s\n", gengetopt_args_info_help[1]); + printf("%s\n", gengetopt_args_info_help[2]); + printf("%s\n", gengetopt_args_info_help[0]); + exit(1); + } + + if(O2_ACTION(COM_SERVER)) + startServer(); + + else if(O2_ACTION(COM_CREATE)) + create(dbName); + + else if(O2_ACTION(COM_INSERT)) + insert(dbName, inFile); + + else if(O2_ACTION(COM_BATCHINSERT)) + batchinsert(dbName, inFile); + + else if(O2_ACTION(COM_QUERY)) + if(isClient) + ws_query(dbName, inFile, (char*)hostport); + else + query(dbName, inFile, adbQueryResult); + + else if(O2_ACTION(COM_STATUS)) + if(isClient) + ws_status(dbName,(char*)hostport); + else + status(dbName); + + else if(O2_ACTION(COM_L2NORM)) + l2norm(dbName); + + else if(O2_ACTION(COM_DUMP)) + dump(dbName); + + else + error("Unrecognized command",command); +} + +audioDB::~audioDB(){ + // Clean up + if(indata) + munmap(indata,statbuf.st_size); + if(db) + munmap(db,O2_DEFAULTDBSIZE); + if(dbfid>0) + close(dbfid); + if(infid>0) + close(infid); + if(dbH) + delete dbH; +} + +int audioDB::processArgs(const unsigned argc, char* const argv[]){ + + if(argc<2){ + cmdline_parser_print_version (); + if (strlen(gengetopt_args_info_purpose) > 0) + printf("%s\n", gengetopt_args_info_purpose); + printf("%s\n", gengetopt_args_info_usage); + printf("%s\n", gengetopt_args_info_help[1]); + printf("%s\n", gengetopt_args_info_help[2]); + printf("%s\n", gengetopt_args_info_help[0]); + exit(0); + } + + if (cmdline_parser (argc, argv, &args_info) != 0) + exit(1) ; + + if(args_info.help_given){ + cmdline_parser_print_help(); + exit(0); + } + + if(args_info.verbosity_given){ + verbosity=args_info.verbosity_arg; + if(verbosity<0 || verbosity>10){ + cerr << "Warning: verbosity out of range, setting to 1" << endl; + verbosity=1; + } + } + + if(args_info.SERVER_given){ + command=COM_SERVER; + port=args_info.SERVER_arg; + if(port<100 || port > 100000) + error("port out of range"); + isServer=1; + return 0; + } + + // No return on client command, find database command + if(args_info.client_given){ + command=COM_CLIENT; + hostport=args_info.client_arg; + isClient=1; + } + + if(args_info.NEW_given){ + command=COM_CREATE; + dbName=args_info.database_arg; + return 0; + } + + if(args_info.STATUS_given){ + command=COM_STATUS; + dbName=args_info.database_arg; + return 0; + } + + if(args_info.DUMP_given){ + command=COM_DUMP; + dbName=args_info.database_arg; + return 0; + } + + if(args_info.L2NORM_given){ + command=COM_L2NORM; + dbName=args_info.database_arg; + return 0; + } + + if(args_info.INSERT_given){ + command=COM_INSERT; + dbName=args_info.database_arg; + inFile=args_info.features_arg; + if(args_info.key_given) + key=args_info.key_arg; + if(args_info.times_given){ + timesFileName=args_info.times_arg; + if(strlen(timesFileName)>0){ + if(!(timesFile = new ifstream(timesFileName,ios::in))) + error("Could not open times file for reading", timesFileName); + usingTimes=1; + } + } + return 0; + } + + if(args_info.BATCHINSERT_given){ + command=COM_BATCHINSERT; + dbName=args_info.database_arg; + inFile=args_info.featureList_arg; + if(args_info.keyList_given) + key=args_info.keyList_arg; // INCONSISTENT NO CHECK + + /* TO DO: REPLACE WITH + if(args_info.keyList_given){ + segFileName=args_info.keyList_arg; + if(strlen(segFileName)>0 && !(segFile = new ifstream(segFileName,ios::in))) + error("Could not open keyList file for reading",segFileName); + } + AND UPDATE BATCHINSERT() + */ + + if(args_info.timesList_given){ + timesFileName=args_info.timesList_arg; + if(strlen(timesFileName)>0){ + if(!(timesFile = new ifstream(timesFileName,ios::in))) + error("Could not open timesList file for reading", timesFileName); + usingTimes=1; + } + } + return 0; + } + + // Query command and arguments + if(args_info.QUERY_given){ + command=COM_QUERY; + dbName=args_info.database_arg; + inFile=args_info.features_arg; + + if(args_info.keyList_given){ + segFileName=args_info.keyList_arg; + if(strlen(segFileName)>0 && !(segFile = new ifstream(segFileName,ios::in))) + error("Could not open keyList file for reading",segFileName); + } + + if(args_info.times_given){ + timesFileName=args_info.times_arg; + if(strlen(timesFileName)>0){ + if(!(timesFile = new ifstream(timesFileName,ios::in))) + error("Could not open times file for reading", timesFileName); + usingTimes=1; + } + } + + // query type + if(strncmp(args_info.QUERY_arg, "segment", MAXSTR)==0) + queryType=O2_FLAG_SEG_QUERY; + else if(strncmp(args_info.QUERY_arg, "point", MAXSTR)==0) + queryType=O2_FLAG_POINT_QUERY; + else if(strncmp(args_info.QUERY_arg, "sequence", MAXSTR)==0) + queryType=O2_FLAG_SEQUENCE_QUERY; + else + error("unsupported query type",args_info.QUERY_arg); + + if(!args_info.exhaustive_flag){ + queryPoint = args_info.qpoint_arg; + usingQueryPoint=1; + if(queryPoint<0 || queryPoint >10000) + error("queryPoint out of range: 0 <= queryPoint <= 10000"); + } + + + pointNN=args_info.pointnn_arg; + if(pointNN<1 || pointNN >1000) + error("pointNN out of range: 1 <= pointNN <= 1000"); + + + + segNN=args_info.resultlength_arg; + if(segNN<1 || segNN >1000) + error("resultlength out of range: 1 <= resultlength <= 1000"); + + + sequenceLength=args_info.sequencelength_arg; + if(sequenceLength<1 || sequenceLength >1000) + error("seqlen out of range: 1 <= seqlen <= 1000"); + + sequenceHop=args_info.sequencehop_arg; + if(sequenceHop<1 || sequenceHop >1000) + error("seqhop out of range: 1 <= seqhop <= 1000"); + + return 0; + } + return -1; // no command found +} + +/* Make a new database + + The database consists of: + + header + --------------------------------------------------------------------------------- + | magic 4 bytes| numFiles 4 bytes | dim 4 bytes | length 4 bytes |flags 4 bytes | + --------------------------------------------------------------------------------- + + + keyTable : list of keys of segments + -------------------------------------------------------------------------- + | key 256 bytes | + -------------------------------------------------------------------------- + O2_MAXFILES*02_FILENAMELENGTH + + segTable : Maps implicit feature index to a feature vector matrix + -------------------------------------------------------------------------- + | numVectors (4 bytes) | + -------------------------------------------------------------------------- + O2_MAXFILES * 02_MEANNUMFEATURES * sizeof(INT) + + featureTable + -------------------------------------------------------------------------- + | v1 v2 v3 ... vd (double) | + -------------------------------------------------------------------------- + O2_MAXFILES * 02_MEANNUMFEATURES * DIM * sizeof(DOUBLE) + + timesTable + -------------------------------------------------------------------------- + | timestamp (double) | + -------------------------------------------------------------------------- + O2_MAXFILES * 02_MEANNUMFEATURES * sizeof(DOUBLE) + + l2normTable + -------------------------------------------------------------------------- + | nm (double) | + -------------------------------------------------------------------------- + O2_MAXFILES * 02_MEANNUMFEATURES * sizeof(DOUBLE) + +*/ + +void audioDB::create(const char* dbName){ + if ((dbfid = open (dbName, O_RDWR | O_CREAT | O_TRUNC)) < 0) + error("Can't open database file:", dbName); + + // go to the location corresponding to the last byte + if (lseek (dbfid, O2_DEFAULTDBSIZE - 1, SEEK_SET) == -1) + error("lseek error in db file"); + + // write a dummy byte at the last location + if (write (dbfid, "", 1) != 1) + error("write error"); + + // mmap the output file + if(verbosity) + cerr << "header size:" << O2_HEADERSIZE << endl; + if ((db = (char*) mmap(0, O2_DEFAULTDBSIZE, PROT_READ | PROT_WRITE, + MAP_SHARED, dbfid, 0)) == (caddr_t) -1) + error("mmap error for creating database"); + + dbH = new dbTableHeaderT(); + assert(dbH); + + // Initialize header + dbH->magic=O2_MAGIC; + dbH->numFiles=0; + dbH->length=0; + dbH->dim=0; + dbH->flags=0; //O2_FLAG_L2NORM; + + memcpy (db, dbH, O2_HEADERSIZE); + if(verbosity) + cerr << COM_CREATE << " " << dbName << endl; + +} + + +void audioDB::drop(){ + + +} + +// initTables - memory map files passed as arguments +// Precondition: database has already been created +void audioDB::initTables(const char* dbName, const char* inFile=0){ + if ((dbfid = open (dbName, O_RDWR)) < 0) + error("Can't open database file:", dbName); + + // open the input file + if (inFile && (infid = open (inFile, O_RDONLY)) < 0) + error("can't open feature file for reading", inFile); + + // find size of input file + if (inFile && fstat (infid,&statbuf) < 0) + error("fstat error finding size of input"); + + // Get the database header info + dbH = new dbTableHeaderT(); + assert(dbH); + + if(read(dbfid,(char*)dbH,sizeof(dbTableHeaderT))!=sizeof(dbTableHeaderT)) + error("error reading db header"); + + fileTableOffset = O2_HEADERSIZE; + segTableOffset = fileTableOffset + O2_FILETABLESIZE*O2_MAXFILES; + dataoffset = segTableOffset + O2_SEGTABLESIZE*O2_MAXFILES; + l2normTableOffset = O2_DEFAULTDBSIZE - O2_MAXFILES*O2_MEANNUMVECTORS*sizeof(double); + timesTableOffset = l2normTableOffset - O2_MAXFILES*O2_MEANNUMVECTORS*sizeof(double); + + if(dbH->magic!=O2_MAGIC){ + cerr << "expected: " << O2_MAGIC << ", got:" << dbH->magic << endl; + error("database file has incorrect header",dbName); + } + + if(inFile) + if(dbH->dim==0 && dbH->length==0) // empty database + read(infid,&dbH->dim,sizeof(unsigned)); // initialize with input dimensionality + else { + unsigned test; + read(infid,&test,sizeof(unsigned)); + if(dbH->dim!=test){ + cerr << "error: expected dimension: " << dbH->dim << ", got :" << test <<endl; + error("feature dimensions do not match database table dimensions"); + } + } + + // mmap the input file + if (inFile && (indata = (char*)mmap (0, statbuf.st_size, PROT_READ, MAP_SHARED, infid, 0)) + == (caddr_t) -1) + error("mmap error for input"); + + // mmap the database file + if ((db = (char*) mmap(0, O2_DEFAULTDBSIZE, PROT_READ | PROT_WRITE, + MAP_SHARED, dbfid, 0)) == (caddr_t) -1) + error("mmap error for creating database"); + + // Make some handy tables with correct types + fileTable= (char*)(db+fileTableOffset); + segTable = (unsigned*)(db+segTableOffset); + dataBuf = (double*)(db+dataoffset); + l2normTable = (double*)(db+l2normTableOffset); + timesTable = (double*)(db+timesTableOffset); + +} + +void audioDB::insert(const char* dbName, const char* inFile){ + + initTables(dbName, inFile); + + if(!usingTimes && (dbH->flags & O2_FLAG_TIMES)) + error("Must use timestamps with timestamped database","use --times"); + + // Check that there is room for at least 1 more file + if((char*)timesTable<((char*)dataBuf+dbH->length+statbuf.st_size-sizeof(int))) + error("No more room in database","insert failed: reason database is full."); + + if(!key) + key=inFile; + // Linear scan of filenames check for pre-existing feature + unsigned alreadyInserted=0; + for(unsigned k=0; k<dbH->numFiles; k++) + if(strncmp(fileTable + k*O2_FILETABLESIZE, key, strlen(key))==0){ + alreadyInserted=1; + break; + } + + if(alreadyInserted){ + if(verbosity) + cerr << "Warning: key already exists in database, ignoring: " <<inFile << endl; + return; + } + + // Make a segment index table of features to file indexes + unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim); + if(!numVectors){ + if(verbosity) + cerr << "Warning: ignoring zero-length feature vector file:" << key << endl; + // CLEAN UP + munmap(indata,statbuf.st_size); + munmap(db,O2_DEFAULTDBSIZE); + close(infid); + return; + } + + strncpy(fileTable + dbH->numFiles*O2_FILETABLESIZE, key, strlen(key)); + + unsigned insertoffset = dbH->length;// Store current state + + // Check times status and insert times from file + unsigned timesoffset=insertoffset/(dbH->dim*sizeof(double)); + double* timesdata=timesTable+timesoffset; + assert(timesdata+numVectors<l2normTable); + insertTimeStamps(numVectors, timesFile, timesdata); + + // Increment file count + dbH->numFiles++; + + // Update Header information + dbH->length+=(statbuf.st_size-sizeof(int)); + + // Copy the header back to the database + memcpy (db, dbH, sizeof(dbTableHeaderT)); + + // Update segment to file index map + //memcpy (db+segTableOffset+(dbH->numFiles-1)*sizeof(unsigned), &numVectors, sizeof(unsigned)); + memcpy (segTable+dbH->numFiles-1, &numVectors, sizeof(unsigned)); + + // Update the feature database + memcpy (db+dataoffset+insertoffset, indata+sizeof(int), statbuf.st_size-sizeof(int)); + + // Norm the vectors on input if the database is already L2 normed + if(dbH->flags & O2_FLAG_L2NORM) + unitNormAndInsertL2((double*)(db+dataoffset+insertoffset), dbH->dim, numVectors, 1); // append + + // Report status + status(dbName); + if(verbosity) + cerr << COM_INSERT << " " << dbName << " " << numVectors << " vectors " + << (statbuf.st_size-sizeof(int)) << " bytes." << endl; + + // CLEAN UP + munmap(indata,statbuf.st_size); + close(infid); +} + +void audioDB::insertTimeStamps(unsigned numVectors, ifstream* timesFile, double* timesdata){ + unsigned numtimes=0; + if(usingTimes){ + if(!(dbH->flags & O2_FLAG_TIMES) && !dbH->numFiles) + dbH->flags=dbH->flags|O2_FLAG_TIMES; + else if(!(dbH->flags&O2_FLAG_TIMES)){ + cerr << "Warning: timestamp file used with non time-stamped database: ignoring timestamps" << endl; + usingTimes=0; + } + + if(!timesFile->is_open()){ + if(dbH->flags & O2_FLAG_TIMES){ + munmap(indata,statbuf.st_size); + munmap(db,O2_DEFAULTDBSIZE); + error("problem opening times file on timestamped database",timesFileName); + } + else{ + cerr << "Warning: problem opening times file. But non-timestamped database, so ignoring times file." << endl; + usingTimes=0; + } + } + + // Process time file + if(usingTimes){ + do{ + *timesFile>>*timesdata++; + if(timesFile->eof()) + break; + numtimes++; + }while(!timesFile->eof() && numtimes<numVectors); + if(!timesFile->eof()){ + double dummy; + do{ + *timesFile>>dummy; + if(timesFile->eof()) + break; + numtimes++; + }while(!timesFile->eof()); + } + if(numtimes<numVectors || numtimes>numVectors+2){ + munmap(indata,statbuf.st_size); + munmap(db,O2_DEFAULTDBSIZE); + close(infid); + cerr << "expected " << numVectors << " found " << numtimes << endl; + error("Times file is incorrect length for features file",inFile); + } + if(verbosity>2) + cerr << "numtimes: " << numtimes << endl; + } + } +} + +void audioDB::batchinsert(const char* dbName, const char* inFile){ + + if ((dbfid = open (dbName, O_RDWR)) < 0) + error("Can't open database file:", dbName); + + if(!key) + key=inFile; + ifstream *filesIn = 0; + ifstream *keysIn = 0; + ifstream* thisTimesFile = 0; + + if(!(filesIn = new ifstream(inFile))) + error("Could not open batch in file", inFile); + if(key && key!=inFile) + if(!(keysIn = new ifstream(key))) + error("Could not open batch key file",key); + + // Get the database header info + dbH = new dbTableHeaderT(); + assert(dbH); + + if(read(dbfid,(char*)dbH,sizeof(dbTableHeaderT))!=sizeof(dbTableHeaderT)) + error("error reading db header"); + + if(!usingTimes && (dbH->flags & O2_FLAG_TIMES)) + error("Must use timestamps with timestamped database","use --times"); + + fileTableOffset = O2_HEADERSIZE; + segTableOffset = fileTableOffset + O2_FILETABLESIZE*O2_MAXFILES; + dataoffset = segTableOffset + O2_SEGTABLESIZE*O2_MAXFILES; + l2normTableOffset = O2_DEFAULTDBSIZE - O2_MAXFILES*O2_MEANNUMVECTORS*sizeof(double); + timesTableOffset = l2normTableOffset - O2_MAXFILES*O2_MEANNUMVECTORS*sizeof(double); + + if(dbH->magic!=O2_MAGIC){ + cerr << "expected:" << O2_MAGIC << ", got:" << dbH->magic << endl; + error("database file has incorrect header",dbName); + } + + + // mmap the database file + if ((db = (char*) mmap(0, O2_DEFAULTDBSIZE, PROT_READ | PROT_WRITE, + MAP_SHARED, dbfid, 0)) == (caddr_t) -1) + error("mmap error for creating database"); + + // Make some handy tables with correct types + fileTable= (char*)(db+fileTableOffset); + segTable = (unsigned*)(db+segTableOffset); + dataBuf = (double*)(db+dataoffset); + l2normTable = (double*)(db+l2normTableOffset); + timesTable = (double*)(db+timesTableOffset); + + unsigned totalVectors=0; + char *thisKey = new char[MAXSTR]; + char *thisFile = new char[MAXSTR]; + char *thisTimesFileName = new char[MAXSTR]; + + do{ + filesIn->getline(thisFile,MAXSTR); + if(key && key!=inFile) + keysIn->getline(thisKey,MAXSTR); + else + thisKey = thisFile; + if(usingTimes) + timesFile->getline(thisTimesFileName,MAXSTR); + + if(filesIn->eof()) + break; + + // open the input file + if (thisFile && (infid = open (thisFile, O_RDONLY)) < 0) + error("can't open feature file for reading", thisFile); + + // find size of input file + if (thisFile && fstat (infid,&statbuf) < 0) + error("fstat error finding size of input"); + + // Check that there is room for at least 1 more file + if((char*)timesTable<((char*)dataBuf+(dbH->length+statbuf.st_size-sizeof(int)))) + error("No more room in database","insert failed: reason database is full."); + + if(thisFile) + if(dbH->dim==0 && dbH->length==0) // empty database + read(infid,&dbH->dim,sizeof(unsigned)); // initialize with input dimensionality + else { + unsigned test; + read(infid,&test,sizeof(unsigned)); + if(dbH->dim!=test){ + cerr << "error: expected dimension: " << dbH->dim << ", got :" << test <<endl; + error("feature dimensions do not match database table dimensions"); + } + } + + // mmap the input file + if (thisFile && (indata = (char*)mmap (0, statbuf.st_size, PROT_READ, MAP_SHARED, infid, 0)) + == (caddr_t) -1) + error("mmap error for input"); + + + // Linear scan of filenames check for pre-existing feature + unsigned alreadyInserted=0; + + for(unsigned k=0; k<dbH->numFiles; k++) + if(strncmp(fileTable + k*O2_FILETABLESIZE, thisKey, strlen(thisKey))==0){ + alreadyInserted=1; + break; + } + + if(alreadyInserted){ + if(verbosity) + cerr << "Warning: key already exists in database:" << thisKey << endl; + } + else{ + + // Make a segment index table of features to file indexes + unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim); + if(!numVectors){ + if(verbosity) + cerr << "Warning: ignoring zero-length feature vector file:" << thisKey << endl; + } + else{ + if(usingTimes){ + if(timesFile->eof()) + error("not enough timestamp files in timesList"); + thisTimesFile=new ifstream(thisTimesFileName,ios::in); + if(!thisTimesFile->is_open()) + error("Cannot open timestamp file",thisTimesFileName); + unsigned insertoffset=dbH->length; + unsigned timesoffset=insertoffset/(dbH->dim*sizeof(double)); + double* timesdata=timesTable+timesoffset; + assert(timesdata+numVectors<l2normTable); + insertTimeStamps(numVectors,thisTimesFile,timesdata); + if(thisTimesFile) + delete thisTimesFile; + } + + strncpy(fileTable + dbH->numFiles*O2_FILETABLESIZE, thisKey, strlen(thisKey)); + + unsigned insertoffset = dbH->length;// Store current state + + // Increment file count + dbH->numFiles++; + + // Update Header information + dbH->length+=(statbuf.st_size-sizeof(int)); + // Copy the header back to the database + memcpy (db, dbH, sizeof(dbTableHeaderT)); + + // Update segment to file index map + //memcpy (db+segTableOffset+(dbH->numFiles-1)*sizeof(unsigned), &numVectors, sizeof(unsigned)); + memcpy (segTable+dbH->numFiles-1, &numVectors, sizeof(unsigned)); + + // Update the feature database + memcpy (db+dataoffset+insertoffset, indata+sizeof(int), statbuf.st_size-sizeof(int)); + + // Norm the vectors on input if the database is already L2 normed + if(dbH->flags & O2_FLAG_L2NORM) + unitNormAndInsertL2((double*)(db+dataoffset+insertoffset), dbH->dim, numVectors, 1); // append + + totalVectors+=numVectors; + } + } + // CLEAN UP + munmap(indata,statbuf.st_size); + close(infid); + }while(!filesIn->eof()); + + if(verbosity) + cerr << COM_BATCHINSERT << " " << dbName << " " << totalVectors << " vectors " + << totalVectors*dbH->dim*sizeof(double) << " bytes." << endl; + + // Report status + status(dbName); + +} + +void audioDB::ws_status(const char*dbName, char* hostport){ + struct soap soap; + int adbStatusResult; + + // Query an existing adb database + soap_init(&soap); + if(soap_call_adb__status(&soap,hostport,NULL,(char*)dbName,adbStatusResult)==SOAP_OK) + std::cout << "result = " << adbStatusResult << std::endl; + else + soap_print_fault(&soap,stderr); + + soap_destroy(&soap); + soap_end(&soap); + soap_done(&soap); +} + +void audioDB::ws_query(const char*dbName, const char *segKey, const char* hostport){ + struct soap soap; + adb__queryResult adbQueryResult; + + soap_init(&soap); + if(soap_call_adb__query(&soap,hostport,NULL, + (char*)dbName,(char*)segKey,(char*)segFileName,(char*)timesFileName, + queryType, queryPoint, pointNN, segNN, sequenceLength, adbQueryResult)==SOAP_OK){ + //std::cerr << "result list length:" << adbQueryResult.__sizeRlist << std::endl; + for(int i=0; i<adbQueryResult.__sizeRlist; i++) + std::cout << adbQueryResult.Rlist[i] << " " << adbQueryResult.Dist[i] + << " " << adbQueryResult.Qpos[i] << " " << adbQueryResult.Spos[i] << std::endl; + } + else + soap_print_fault(&soap,stderr); + + soap_destroy(&soap); + soap_end(&soap); + soap_done(&soap); + +} + + +void audioDB::status(const char* dbName){ + if(!dbH) + initTables(dbName, 0); + + // Update Header information + cout << "num files:" << dbH->numFiles << endl; + cout << "data dim:" << dbH->dim <<endl; + if(dbH->dim>0){ + cout << "total vectors:" << dbH->length/(sizeof(double)*dbH->dim)<<endl; + cout << "vectors available:" << (timesTableOffset-(dataoffset+dbH->length))/(sizeof(double)*dbH->dim) << endl; + } + cout << "total bytes:" << dbH->length << " (" << (100.0*dbH->length)/(timesTableOffset-dataoffset) << "%)" << endl; + cout << "bytes available:" << timesTableOffset-(dataoffset+dbH->length) << " (" << + (100.0*(timesTableOffset-(dataoffset+dbH->length)))/(timesTableOffset-dataoffset) << "%)" << endl; + cout << "flags:" << dbH->flags << endl; + + unsigned dudCount=0; + unsigned nullCount=0; + for(unsigned k=0; k<dbH->numFiles; k++){ + if(segTable[k]<sequenceLength){ + dudCount++; + if(!segTable[k]) + nullCount++; + } + } + cout << "null count: " << nullCount << " small sequence count " << dudCount-nullCount << endl; +} + + +void audioDB::dump(const char* dbName){ + if(!dbH) + initTables(dbName,0); + + for(unsigned k=0; k<dbH->numFiles; k++) + cout << fileTable+k*O2_FILETABLESIZE << " " << segTable[k] << endl; + + status(dbName); +} + +void audioDB::l2norm(const char* dbName){ + initTables(dbName,0); + if(dbH->length>0){ + unsigned numVectors = dbH->length/(sizeof(double)*dbH->dim); + unitNormAndInsertL2(dataBuf, dbH->dim, numVectors, 0); // No append + } + // Update database flags + dbH->flags = dbH->flags|O2_FLAG_L2NORM; + memcpy (db, dbH, O2_HEADERSIZE); +} + + + +void audioDB::query(const char* dbName, const char* inFile, adb__queryResult *adbQueryResult){ + switch(queryType){ + case O2_FLAG_POINT_QUERY: + pointQuery(dbName, inFile, adbQueryResult); + break; + case O2_FLAG_SEQUENCE_QUERY: + segSequenceQuery(dbName, inFile, adbQueryResult); + break; + case O2_FLAG_SEG_QUERY: + segPointQuery(dbName, inFile, adbQueryResult); + break; + default: + error("unrecognized queryType in query()"); + + } +} + +//return ordinal position of key in keyTable +unsigned audioDB::getKeyPos(char* key){ + for(unsigned k=0; k<dbH->numFiles; k++) + if(strncmp(fileTable + k*O2_FILETABLESIZE, key, strlen(key))==0) + return k; + error("Key not found",key); + return O2_ERR_KEYNOTFOUND; +} + +// Basic point query engine +void audioDB::pointQuery(const char* dbName, const char* inFile, adb__queryResult *adbQueryResult){ + + initTables(dbName, inFile); + + // For each input vector, find the closest pointNN matching output vectors and report + // we use stdout in this stub version + unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim); + + double* query = (double*)(indata+sizeof(int)); + double* data = dataBuf; + double* queryCopy = 0; + + if( dbH->flags & O2_FLAG_L2NORM ){ + // Make a copy of the query + queryCopy = new double[numVectors*dbH->dim]; + qNorm = new double[numVectors]; + assert(queryCopy&&qNorm); + memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double)); + unitNorm(queryCopy, dbH->dim, numVectors, qNorm); + query = queryCopy; + } + + // Make temporary dynamic memory for results + assert(pointNN>0 && pointNN<=O2_MAXNN); + double distances[pointNN]; + unsigned qIndexes[pointNN]; + unsigned sIndexes[pointNN]; + for(unsigned k=0; k<pointNN; k++){ + distances[k]=0.0; + qIndexes[k]=~0; + sIndexes[k]=~0; + } + + unsigned j=numVectors; + unsigned k,l,n; + double thisDist; + + unsigned totalVecs=dbH->length/(dbH->dim*sizeof(double)); + double meanQdur = 0; + double* timesdata = 0; + double* dbdurs = 0; + + if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){ + cerr << "warning: ignoring query timestamps for non-timestamped database" << endl; + usingTimes=0; + } + + else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES)) + cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl; + + else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){ + timesdata = new double[numVectors]; + insertTimeStamps(numVectors, timesFile, timesdata); + // Calculate durations of points + for(k=0; k<numVectors-1; k++){ + timesdata[k]=timesdata[k+1]-timesdata[k]; + meanQdur+=timesdata[k]; + } + meanQdur/=k; + // Individual exhaustive timepoint durations + dbdurs = new double[totalVecs]; + for(k=0; k<totalVecs-1; k++) + dbdurs[k]=timesTable[k+1]-timesTable[k]; + j--; // decrement vector counter by one + } + + if(usingQueryPoint) + if(queryPoint>numVectors-1) + error("queryPoint > numVectors in query"); + else{ + if(verbosity>1) + cerr << "query point: " << queryPoint << endl; cerr.flush(); + query=query+queryPoint*dbH->dim; + numVectors=queryPoint+1; + j=1; + } + + gettimeofday(&tv1, NULL); + while(j--){ // query + data=dataBuf; + k=totalVecs; // number of database vectors + while(k--){ // database + thisDist=0; + l=dbH->dim; + double* q=query; + while(l--) + thisDist+=*q++**data++; + if(!usingTimes || + (usingTimes + && fabs(dbdurs[totalVecs-k-1]-timesdata[numVectors-j-1])<timesdata[numVectors-j-1]*timesTol)){ + n=pointNN; + while(n--){ + if(thisDist>=distances[n]){ + if((n==0 || thisDist<=distances[n-1])){ + // Copy all values above up the queue + for( l=pointNN-1 ; l >= n+1 ; l--){ + distances[l]=distances[l-1]; + qIndexes[l]=qIndexes[l-1]; + sIndexes[l]=sIndexes[l-1]; + } + distances[n]=thisDist; + qIndexes[n]=numVectors-j-1; + sIndexes[n]=dbH->length/(sizeof(double)*dbH->dim)-k-1; + break; + } + } + else + break; + } + } + } + // Move query pointer to next query point + query+=dbH->dim; + } + + gettimeofday(&tv2, NULL); + if(verbosity>1) + cerr << endl << " elapsed time:" << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl; + + if(adbQueryResult==0){ + // Output answer + // Loop over nearest neighbours + for(k=0; k < pointNN; k++){ + // Scan for key + unsigned cumSeg=0; + for(l=0 ; l<dbH->numFiles; l++){ + cumSeg+=segTable[l]; + if(sIndexes[k]<cumSeg){ + cout << fileTable+l*O2_FILETABLESIZE << " " << distances[k] << " " << qIndexes[k] << " " + << sIndexes[k]+segTable[l]-cumSeg << endl; + break; + } + } + } + } + else{ // Process Web Services Query + int listLen = pointNN; + adbQueryResult->__sizeRlist=listLen; + adbQueryResult->__sizeDist=listLen; + adbQueryResult->__sizeQpos=listLen; + adbQueryResult->__sizeSpos=listLen; + adbQueryResult->Rlist= new char*[listLen]; + adbQueryResult->Dist = new double[listLen]; + adbQueryResult->Qpos = new int[listLen]; + adbQueryResult->Spos = new int[listLen]; + for(k=0; k<adbQueryResult->__sizeRlist; k++){ + adbQueryResult->Rlist[k]=new char[O2_MAXFILESTR]; + adbQueryResult->Dist[k]=distances[k]; + adbQueryResult->Qpos[k]=qIndexes[k]; + unsigned cumSeg=0; + for(l=0 ; l<dbH->numFiles; l++){ + cumSeg+=segTable[l]; + if(sIndexes[k]<cumSeg){ + sprintf(adbQueryResult->Rlist[k], "%s", fileTable+l*O2_FILETABLESIZE); + break; + } + } + adbQueryResult->Spos[k]=sIndexes[k]+segTable[l]-cumSeg; + } + } + + // Clean up + if(queryCopy) + delete queryCopy; + if(qNorm) + delete qNorm; + if(timesdata) + delete timesdata; + if(dbdurs) + delete dbdurs; +} + +void audioDB::sequenceQuery(const char* dbName, const char* inFile, adb__queryResult *adbQueryResult){ + +} + +// segPointQuery +// return the segNN closest segs to the query seg +// uses average of pointNN points per seg +void audioDB::segPointQuery(const char* dbName, const char* inFile, adb__queryResult *adbQueryResult){ + initTables(dbName, inFile); + + // For each input vector, find the closest pointNN matching output vectors and report + unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim); + unsigned numSegs = dbH->numFiles; + + double* query = (double*)(indata+sizeof(int)); + double* data = dataBuf; + double* queryCopy = 0; + + if( dbH->flags & O2_FLAG_L2NORM ){ + // Make a copy of the query + queryCopy = new double[numVectors*dbH->dim]; + qNorm = new double[numVectors]; + assert(queryCopy&&qNorm); + memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double)); + unitNorm(queryCopy, dbH->dim, numVectors, qNorm); + query = queryCopy; + } + + assert(pointNN>0 && pointNN<=O2_MAXNN); + assert(segNN>0 && segNN<=O2_MAXNN); + + // Make temporary dynamic memory for results + double segDistances[segNN]; + unsigned segIDs[segNN]; + unsigned segQIndexes[segNN]; + unsigned segSIndexes[segNN]; + + double distances[pointNN]; + unsigned qIndexes[pointNN]; + unsigned sIndexes[pointNN]; + + unsigned j=numVectors; // number of query points + unsigned k,l,n, seg, segOffset=0, processedSegs=0; + double thisDist; + + for(k=0; k<pointNN; k++){ + distances[k]=0.0; + qIndexes[k]=~0; + sIndexes[k]=~0; + } + + for(k=0; k<segNN; k++){ + segDistances[k]=0.0; + segQIndexes[k]=~0; + segSIndexes[k]=~0; + segIDs[k]=~0; + } + + double meanQdur = 0; + double* timesdata = 0; + double* meanDBdur = 0; + + if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){ + cerr << "warning: ignoring query timestamps for non-timestamped database" << endl; + usingTimes=0; + } + + else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES)) + cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl; + + else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){ + timesdata = new double[numVectors]; + insertTimeStamps(numVectors, timesFile, timesdata); + // Calculate durations of points + for(k=0; k<numVectors-1; k++){ + timesdata[k]=timesdata[k+1]-timesdata[k]; + meanQdur+=timesdata[k]; + } + meanQdur/=k; + meanDBdur = new double[dbH->numFiles]; + for(k=0; k<dbH->numFiles; k++){ + meanDBdur[k]=0.0; + for(j=0; j<segTable[k]-1 ; j++) + meanDBdur[k]+=timesTable[j+1]-timesTable[j]; + meanDBdur[k]/=j; + } + } + + if(usingQueryPoint) + if(queryPoint>numVectors-1) + error("queryPoint > numVectors in query"); + else{ + if(verbosity>1) + cerr << "query point: " << queryPoint << endl; cerr.flush(); + query=query+queryPoint*dbH->dim; + numVectors=queryPoint+1; + } + + // build segment offset table + unsigned *segOffsetTable = new unsigned[dbH->numFiles]; + unsigned cumSeg=0; + unsigned segIndexOffset; + for(k=0; k<dbH->numFiles;k++){ + segOffsetTable[k]=cumSeg; + cumSeg+=segTable[k]*dbH->dim; + } + + char nextKey[MAXSTR]; + + gettimeofday(&tv1, NULL); + + for(seg=0 ; seg < dbH->numFiles ; seg++, processedSegs++){ + if(segFile){ + if(!segFile->eof()){ + //*segFile>>seg; + segFile->getline(nextKey,MAXSTR); + seg=getKeyPos(nextKey); + } + else + break; + } + segOffset=segOffsetTable[seg]; // numDoubles offset + segIndexOffset=segOffset/dbH->dim; // numVectors offset + if(verbosity>7) + cerr << seg << "." << segOffset/(dbH->dim) << "." << segTable[seg] << " | ";cerr.flush(); + + if(dbH->flags & O2_FLAG_L2NORM) + usingQueryPoint?query=queryCopy+queryPoint*dbH->dim:query=queryCopy; + else + usingQueryPoint?query=(double*)(indata+sizeof(int))+queryPoint*dbH->dim:query=(double*)(indata+sizeof(int)); + if(usingQueryPoint) + j=1; + else + j=numVectors; + while(j--){ + k=segTable[seg]; // number of vectors in seg + data=dataBuf+segOffset; // data for seg + while(k--){ + thisDist=0; + l=dbH->dim; + double* q=query; + while(l--) + thisDist+=*q++**data++; + if(!usingTimes || + (usingTimes + && fabs(meanDBdur[seg]-meanQdur)<meanQdur*timesTol)){ + n=pointNN; + while(n--){ + if(thisDist>=distances[n]){ + if((n==0 || thisDist<=distances[n-1])){ + // Copy all values above up the queue + for( l=pointNN-1 ; l > n ; l--){ + distances[l]=distances[l-1]; + qIndexes[l]=qIndexes[l-1]; + sIndexes[l]=sIndexes[l-1]; + } + distances[n]=thisDist; + qIndexes[n]=numVectors-j-1; + sIndexes[n]=segTable[seg]-k-1; + break; + } + } + else + break; + } + } + } // seg + // Move query pointer to next query point + query+=dbH->dim; + } // query + // Take the average of this seg's distance + // Test the seg distances + thisDist=0; + n=pointNN; + while(n--) + thisDist+=distances[pointNN-n-1]; + thisDist/=pointNN; + n=segNN; + while(n--){ + if(thisDist>=segDistances[n]){ + if((n==0 || thisDist<=segDistances[n-1])){ + // Copy all values above up the queue + for( l=pointNN-1 ; l > n ; l--){ + segDistances[l]=segDistances[l-1]; + segQIndexes[l]=segQIndexes[l-1]; + segSIndexes[l]=segSIndexes[l-1]; + segIDs[l]=segIDs[l-1]; + } + segDistances[n]=thisDist; + segQIndexes[n]=qIndexes[0]; + segSIndexes[n]=sIndexes[0]; + segIDs[n]=seg; + break; + } + } + else + break; + } + for(unsigned k=0; k<pointNN; k++){ + distances[k]=0.0; + qIndexes[k]=~0; + sIndexes[k]=~0; + } + } // segs + gettimeofday(&tv2, NULL); + + if(verbosity>1) + cerr << endl << "processed segs :" << processedSegs + << " elapsed time:" << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl; + + if(adbQueryResult==0){ + if(verbosity>1) + cerr<<endl; + // Output answer + // Loop over nearest neighbours + for(k=0; k < min(segNN,processedSegs); k++) + cout << fileTable+segIDs[k]*O2_FILETABLESIZE + << " " << segDistances[k] << " " << segQIndexes[k] << " " << segSIndexes[k] << endl; + } + else{ // Process Web Services Query + int listLen = min(segNN, processedSegs); + adbQueryResult->__sizeRlist=listLen; + adbQueryResult->__sizeDist=listLen; + adbQueryResult->__sizeQpos=listLen; + adbQueryResult->__sizeSpos=listLen; + adbQueryResult->Rlist= new char*[listLen]; + adbQueryResult->Dist = new double[listLen]; + adbQueryResult->Qpos = new int[listLen]; + adbQueryResult->Spos = new int[listLen]; + for(k=0; k<adbQueryResult->__sizeRlist; k++){ + adbQueryResult->Rlist[k]=new char[O2_MAXFILESTR]; + adbQueryResult->Dist[k]=segDistances[k]; + adbQueryResult->Qpos[k]=segQIndexes[k]; + adbQueryResult->Spos[k]=segSIndexes[k]; + sprintf(adbQueryResult->Rlist[k], "%s", fileTable+segIDs[k]*O2_FILETABLESIZE); + } + } + + + // Clean up + if(segOffsetTable) + delete segOffsetTable; + if(queryCopy) + delete queryCopy; + if(qNorm) + delete qNorm; + if(timesdata) + delete timesdata; + if(meanDBdur) + delete meanDBdur; + +} + +void audioDB::deleteDB(const char* dbName, const char* inFile){ + +} + +// NBest matched filter distance between query and target segs +// efficient implementation +// outputs average of N minimum matched filter distances +void audioDB::segSequenceQuery(const char* dbName, const char* inFile, adb__queryResult *adbQueryResult){ + + initTables(dbName, inFile); + + // For each input vector, find the closest pointNN matching output vectors and report + // we use stdout in this stub version + unsigned numVectors = (statbuf.st_size-sizeof(int))/(sizeof(double)*dbH->dim); + unsigned numSegs = dbH->numFiles; + + double* query = (double*)(indata+sizeof(int)); + double* data = dataBuf; + double* queryCopy = 0; + + double qMeanL2; + double* sMeanL2; + + unsigned USE_THRESH=0; + double SILENCE_THRESH=0; + double DIFF_THRESH=0; + + if(!(dbH->flags & O2_FLAG_L2NORM) ) + error("Database must be L2 normed for sequence query","use -l2norm"); + + if(verbosity>1) + cerr << "performing norms ... "; cerr.flush(); + unsigned dbVectors = dbH->length/(sizeof(double)*dbH->dim); + // Make a copy of the query + queryCopy = new double[numVectors*dbH->dim]; + memcpy(queryCopy, query, numVectors*dbH->dim*sizeof(double)); + qNorm = new double[numVectors]; + sNorm = new double[dbVectors]; + sMeanL2=new double[dbH->numFiles]; + assert(qNorm&&sNorm&&queryCopy&&sMeanL2&&sequenceLength); + unitNorm(queryCopy, dbH->dim, numVectors, qNorm); + query = queryCopy; + // Make norm measurements relative to sequenceLength + unsigned w = sequenceLength-1; + unsigned i,j; + double* ps; + double tmp1,tmp2; + // Copy the L2 norm values to core to avoid disk random access later on + memcpy(sNorm, l2normTable, dbVectors*sizeof(double)); + double* snPtr = sNorm; + for(i=0; i<dbH->numFiles; i++){ + if(segTable[i]>sequenceLength){ + tmp1=*snPtr; + j=1; + w=sequenceLength-1; + while(w--) + *snPtr+=snPtr[j++]; + ps = snPtr+1; + w=segTable[i]-sequenceLength; // +1 - 1 + while(w--){ + tmp2=*ps; + *ps=*(ps-1)-tmp1+*(ps+sequenceLength); + tmp1=tmp2; + ps++; + } + } + snPtr+=segTable[i]; + } + + double* pn = sMeanL2; + w=dbH->numFiles; + while(w--) + *pn++=0.0; + ps=sNorm; + unsigned processedSegs=0; + for(i=0; i<dbH->numFiles; i++){ + if(segTable[i]>sequenceLength-1){ + w = segTable[i]-sequenceLength+1; + pn = sMeanL2+i; + while(w--) + *pn+=*ps++; + *pn/=segTable[i]-sequenceLength+1; + SILENCE_THRESH+=*pn; + processedSegs++; + } + } + if(verbosity>1) + cerr << "processedSegs: " << processedSegs << endl; + SILENCE_THRESH/=processedSegs; + USE_THRESH=1; // Turn thresholding on + DIFF_THRESH=SILENCE_THRESH/=2; // 50% of the mean shingle power + SILENCE_THRESH/=10; // 10% of the mean shingle power is SILENCE + + w=sequenceLength-1; + i=1; + tmp1=*qNorm; + while(w--) + *qNorm+=qNorm[i++]; + ps = qNorm+1; + qMeanL2 = *qNorm; + w=numVectors-sequenceLength; + while(w--){ + tmp2=*ps; + *ps=*(ps-1)-tmp1+*(ps+sequenceLength); + tmp1=tmp2; + qMeanL2+=*ps; + *ps++; + } + qMeanL2 /= numVectors-sequenceLength+1; + if(verbosity>1) + cerr << "done." << endl; + + + if(verbosity>1) + cerr << "matching segs..." << endl; + + assert(pointNN>0 && pointNN<=O2_MAXNN); + assert(segNN>0 && segNN<=O2_MAXNN); + + // Make temporary dynamic memory for results + double segDistances[segNN]; + unsigned segIDs[segNN]; + unsigned segQIndexes[segNN]; + unsigned segSIndexes[segNN]; + + double distances[pointNN]; + unsigned qIndexes[pointNN]; + unsigned sIndexes[pointNN]; + + + unsigned k,l,m,n,seg,segOffset=0, HOP_SIZE=sequenceHop, wL=sequenceLength; + double thisDist; + double oneOverWL=1.0/wL; + + for(k=0; k<pointNN; k++){ + distances[k]=0.0; + qIndexes[k]=~0; + sIndexes[k]=~0; + } + + for(k=0; k<segNN; k++){ + segDistances[k]=0.0; + segQIndexes[k]=~0; + segSIndexes[k]=~0; + segIDs[k]=~0; + } + + // Timestamp and durations processing + double meanQdur = 0; + double* timesdata = 0; + double* meanDBdur = 0; + + if(usingTimes && !(dbH->flags & O2_FLAG_TIMES)){ + cerr << "warning: ignoring query timestamps for non-timestamped database" << endl; + usingTimes=0; + } + + else if(!usingTimes && (dbH->flags & O2_FLAG_TIMES)) + cerr << "warning: no timestamps given for query. Ignoring database timestamps." << endl; + + else if(usingTimes && (dbH->flags & O2_FLAG_TIMES)){ + timesdata = new double[numVectors]; + assert(timesdata); + insertTimeStamps(numVectors, timesFile, timesdata); + // Calculate durations of points + for(k=0; k<numVectors-1; k++){ + timesdata[k]=timesdata[k+1]-timesdata[k]; + meanQdur+=timesdata[k]; + } + meanQdur/=k; + if(verbosity>1) + cerr << "mean query file duration: " << meanQdur << endl; + meanDBdur = new double[dbH->numFiles]; + assert(meanDBdur); + for(k=0; k<dbH->numFiles; k++){ + meanDBdur[k]=0.0; + for(j=0; j<segTable[k]-1 ; j++) + meanDBdur[k]+=timesTable[j+1]-timesTable[j]; + meanDBdur[k]/=j; + } + } + + if(usingQueryPoint) + if(queryPoint>numVectors || queryPoint>numVectors-wL+1) + error("queryPoint > numVectors-wL+1 in query"); + else{ + if(verbosity>1) + cerr << "query point: " << queryPoint << endl; cerr.flush(); + query=query+queryPoint*dbH->dim; + qNorm=qNorm+queryPoint; + numVectors=wL; + } + + double ** D = 0; // Cross-correlation between query and target + double ** DD = 0; // Matched filter distance + + D = new double*[numVectors]; + assert(D); + DD = new double*[numVectors]; + assert(DD); + + gettimeofday(&tv1, NULL); + processedSegs=0; + unsigned successfulSegs=0; + + double* qp; + double* sp; + double* dp; + double diffL2; + + // build segment offset table + unsigned *segOffsetTable = new unsigned[dbH->numFiles]; + unsigned cumSeg=0; + unsigned segIndexOffset; + for(k=0; k<dbH->numFiles;k++){ + segOffsetTable[k]=cumSeg; + cumSeg+=segTable[k]*dbH->dim; + } + + char nextKey [MAXSTR]; + for(seg=0 ; seg < dbH->numFiles ; seg++, processedSegs++){ + + // get segID from file if using a control file + if(segFile){ + if(!segFile->eof()){ + segFile->getline(nextKey,MAXSTR); + seg=getKeyPos(nextKey); + } + else + break; + } + segOffset=segOffsetTable[seg]; // numDoubles offset + segIndexOffset=segOffset/dbH->dim; // numVectors offset + + if(sequenceLength<segTable[seg]){ // test for short sequences + + if(verbosity>7) + cerr << seg << "." << segIndexOffset << "." << segTable[seg] << " | ";cerr.flush(); + + // Cross-correlation matrix + for(j=0; j<numVectors;j++){ + D[j]=new double[segTable[seg]]; + assert(D[j]); + + } + + // Matched filter matrix + for(j=0; j<numVectors;j++){ + DD[j]=new double[segTable[seg]]; + assert(DD[j]); + } + + // Cross Correlation + for(j=0; j<numVectors; j++) + for(k=0; k<segTable[seg]; k++){ + qp=query+j*dbH->dim; + sp=dataBuf+segOffset+k*dbH->dim; + DD[j][k]=0.0; // Initialize matched filter array + dp=&D[j][k]; // point to correlation cell j,k + *dp=0.0; // initialize correlation cell + l=dbH->dim; // size of vectors + while(l--) + *dp+=*qp++**sp++; + } + + // Matched Filter + // HOP SIZE == 1 + double* spd; + if(HOP_SIZE==1){ // HOP_SIZE = shingleHop + for(w=0; w<wL; w++) + for(j=0; j<numVectors-w; j++){ + sp=DD[j]; + spd=D[j+w]+w; + k=segTable[seg]-w; + while(k--) + *sp+++=*spd++; + } + } + else{ // HOP_SIZE != 1 + for(w=0; w<wL; w++) + for(j=0; j<numVectors-w; j+=HOP_SIZE){ + sp=DD[j]; + spd=D[j+w]+w; + for(k=0; k<segTable[seg]-w; k+=HOP_SIZE){ + *sp+=*spd; + sp+=HOP_SIZE; + spd+=HOP_SIZE; + } + } + } + + if(verbosity>3){ + cerr << "meanQdur=" << meanQdur << " meanDBdur=" << meanDBdur[seg] << endl; + cerr.flush(); + } + + if(!usingTimes || + (usingTimes + && fabs(meanDBdur[seg]-meanQdur)<meanQdur*timesTol)){ + + if(verbosity>3){ + cerr << "within duration tolerance." << endl; + cerr.flush(); + } + + // Search for minimum distance by shingles (concatenated vectors) + for(j=0;j<numVectors-wL+1;j+=HOP_SIZE) + for(k=0;k<segTable[seg]-wL+1;k+=HOP_SIZE){ + + diffL2 = fabs(qNorm[j] - sNorm[k]); + // Power test + if(!USE_THRESH || + // Threshold on mean L2 of Q and S sequences + (USE_THRESH && qNorm[j]>SILENCE_THRESH && sNorm[k]>SILENCE_THRESH && + // Are both query and target windows above mean energy? + (qNorm[j]>qMeanL2*.25 && sNorm[k]>sMeanL2[seg]*.25 && diffL2 < DIFF_THRESH ))) + thisDist=DD[j][k]*oneOverWL; + else + thisDist=0.0; + + // NBest match algorithm + for(m=0; m<pointNN; m++){ + if(thisDist>=distances[m]){ + // Shuffle distances up the list + for(l=pointNN-1; l>m; l--){ + distances[l]=distances[l-1]; + qIndexes[l]=qIndexes[l-1]; + sIndexes[l]=sIndexes[l-1]; + } + distances[m]=thisDist; + if(usingQueryPoint) + qIndexes[m]=queryPoint; + else + qIndexes[m]=j; + sIndexes[m]=k; + break; + } + } + } + // Calculate the mean of the N-Best matches + thisDist=0.0; + for(m=0; m<pointNN; m++) + thisDist+=distances[m]; + thisDist/=pointNN; + + // All the seg stuff goes here + n=segNN; + while(n--){ + if(thisDist>=segDistances[n]){ + if((n==0 || thisDist<=segDistances[n-1])){ + // Copy all values above up the queue + for( l=segNN-1 ; l > n ; l--){ + segDistances[l]=segDistances[l-1]; + segQIndexes[l]=segQIndexes[l-1]; + segSIndexes[l]=segSIndexes[l-1]; + segIDs[l]=segIDs[l-1]; + } + segDistances[n]=thisDist; + segQIndexes[n]=qIndexes[0]; + segSIndexes[n]=sIndexes[0]; + successfulSegs++; + segIDs[n]=seg; + break; + } + } + else + break; + } + } // Duration match + + // per-seg reset array values + for(unsigned k=0; k<pointNN; k++){ + distances[k]=0.0; + qIndexes[k]=~0; + sIndexes[k]=~0; + } + + // Clean up current seg + if(D!=NULL){ + for(j=0; j<numVectors; j++) + delete[] D[j]; + } + + if(DD!=NULL){ + for(j=0; j<numVectors; j++) + delete[] DD[j]; + } + } + } + + gettimeofday(&tv2,NULL); + if(verbosity>1) + cerr << endl << "processed segs :" << processedSegs << " matched segments: " << successfulSegs << " elapsed time:" + << ( tv2.tv_sec*1000 + tv2.tv_usec/1000 ) - ( tv1.tv_sec*1000+tv1.tv_usec/1000 ) << " msec" << endl; + + if(adbQueryResult==0){ + if(verbosity>1) + cerr<<endl; + // Output answer + // Loop over nearest neighbours + for(k=0; k < min(segNN,successfulSegs); k++) + cout << fileTable+segIDs[k]*O2_FILETABLESIZE << " " << segDistances[k] << " " << segQIndexes[k] << " " << segSIndexes[k] << endl; + } + else{ // Process Web Services Query + int listLen = min(segNN, processedSegs); + adbQueryResult->__sizeRlist=listLen; + adbQueryResult->__sizeDist=listLen; + adbQueryResult->__sizeQpos=listLen; + adbQueryResult->__sizeSpos=listLen; + adbQueryResult->Rlist= new char*[listLen]; + adbQueryResult->Dist = new double[listLen]; + adbQueryResult->Qpos = new int[listLen]; + adbQueryResult->Spos = new int[listLen]; + for(k=0; k<adbQueryResult->__sizeRlist; k++){ + adbQueryResult->Rlist[k]=new char[O2_MAXFILESTR]; + adbQueryResult->Dist[k]=segDistances[k]; + adbQueryResult->Qpos[k]=segQIndexes[k]; + adbQueryResult->Spos[k]=segSIndexes[k]; + sprintf(adbQueryResult->Rlist[k], "%s", fileTable+segIDs[k]*O2_FILETABLESIZE); + } + } + + + // Clean up + if(segOffsetTable) + delete segOffsetTable; + if(queryCopy) + delete queryCopy; + //if(qNorm) + //delete qNorm; + if(D) + delete[] D; + if(DD) + delete[] DD; + if(timesdata) + delete timesdata; + if(meanDBdur) + delete meanDBdur; + + +} + +void audioDB::normalize(double* X, int dim, int n){ + unsigned c = n*dim; + double minval,maxval,v,*p; + + p=X; + while(c--){ + v=*p++; + if(v<minval) + minval=v; + else if(v>maxval) + maxval=v; + } + + normalize(X, dim, n, minval, maxval); + +} + +void audioDB::normalize(double* X, int dim, int n, double minval, double maxval){ + unsigned c = n*dim; + double *p; + + + if(maxval==minval) + return; + + maxval=1.0/(maxval-minval); + c=n*dim; + p=X; + + while(c--){ + *p=(*p-minval)*maxval; + p++; + } +} + +// Unit norm block of features +void audioDB::unitNorm(double* X, unsigned dim, unsigned n, double* qNorm){ + unsigned d; + double L2, oneOverL2, *p; + if(verbosity>2) + cerr << "norming " << n << " vectors...";cerr.flush(); + while(n--){ + p=X; + L2=0.0; + d=dim; + while(d--){ + L2+=*p**p; + p++; + } + L2=sqrt(L2); + if(qNorm) + *qNorm++=L2; + oneOverL2 = 1.0/L2; + d=dim; + while(d--){ + *X*=oneOverL2; + X++; + } + } + if(verbosity>2) + cerr << "done..." << endl; +} + +// Unit norm block of features +void audioDB::unitNormAndInsertL2(double* X, unsigned dim, unsigned n, unsigned append=0){ + unsigned d; + double L2, oneOverL2, *p; + unsigned nn = n; + + assert(l2normTable); + + if( !append && (dbH->flags & O2_FLAG_L2NORM) ) + error("Database is already L2 normed", "automatic norm on insert is enabled"); + + if(verbosity>2) + cerr << "norming " << n << " vectors...";cerr.flush(); + + double* l2buf = new double[n]; + double* l2ptr = l2buf; + assert(l2buf); + assert(X); + + while(nn--){ + p=X; + *l2ptr=0.0; + d=dim; + while(d--){ + *l2ptr+=*p**p; + p++; + } + *l2ptr=sqrt(*l2ptr); + oneOverL2 = 1.0/(*l2ptr++); + d=dim; + while(d--){ + *X*=oneOverL2; + X++; + } + } + unsigned offset; + if(append) + offset=dbH->length/(dbH->dim*sizeof(double)); // number of vectors + else + offset=0; + memcpy(l2normTable+offset, l2buf, n*sizeof(double)); + if(l2buf) + delete l2buf; + if(verbosity>2) + cerr << "done..." << endl; +} + + +// Start an audioDB server on the host +void audioDB::startServer(){ + struct soap soap; + int m, s; // master and slave sockets + soap_init(&soap); + m = soap_bind(&soap, NULL, port, 100); + if (m < 0) + soap_print_fault(&soap, stderr); + else + { + fprintf(stderr, "Socket connection successful: master socket = %d\n", m); + for (int i = 1; ; i++) + { + s = soap_accept(&soap); + if (s < 0) + { + soap_print_fault(&soap, stderr); + break; + } + fprintf(stderr, "%d: accepted connection from IP=%d.%d.%d.%d socket=%d\n", i, + (soap.ip >> 24)&0xFF, (soap.ip >> 16)&0xFF, (soap.ip >> 8)&0xFF, soap.ip&0xFF, s); + if (soap_serve(&soap) != SOAP_OK) // process RPC request + soap_print_fault(&soap, stderr); // print error + fprintf(stderr, "request served\n"); + soap_destroy(&soap); // clean up class instances + soap_end(&soap); // clean up everything and close socket + } + } + soap_done(&soap); // close master socket and detach environment +} + + +// web services + +// SERVER SIDE +int adb__status(struct soap* soap, xsd__string dbName, xsd__int &adbCreateResult){ + char* const argv[]={"audioDB",COM_STATUS,dbName}; + const unsigned argc = 3; + audioDB(argc,argv); + adbCreateResult=100; + return SOAP_OK; +} + +// Literal translation of command line to web service + +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 segNN, xsd__int seqLen, adb__queryResult &adbQueryResult){ + char queryType[256]; + for(int k=0; k<256; k++) + queryType[k]='\0'; + if(qType == O2_FLAG_POINT_QUERY) + strncpy(queryType, "point", strlen("point")); + else if (qType == O2_FLAG_SEQUENCE_QUERY) + strncpy(queryType, "sequence", strlen("sequence")); + else if(qType == O2_FLAG_SEG_QUERY) + strncpy(queryType,"segment", strlen("segment")); + else + strncpy(queryType, "", strlen("")); + + if(pointNN==0) + pointNN=10; + if(segNN==0) + segNN=10; + if(seqLen==0) + seqLen=16; + + char qPosStr[256]; + sprintf(qPosStr, "%d", qPos); + char pointNNStr[256]; + sprintf(pointNNStr,"%d",pointNN); + char segNNStr[256]; + sprintf(segNNStr,"%d",segNN); + char seqLenStr[256]; + sprintf(seqLenStr,"%d",seqLen); + + const char* argv[] ={ + "./audioDB", + COM_QUERY, + queryType, // Need to pass a parameter + COM_DATABASE, + dbName, + COM_FEATURES, + qKey, + COM_KEYLIST, + keyList==0?"":keyList, + COM_TIMES, + timesFileName==0?"":timesFileName, + COM_QPOINT, + qPosStr, + COM_POINTNN, + pointNNStr, + COM_SEGNN, + segNNStr, // Need to pass a parameter + COM_SEQLEN, + seqLenStr + }; + + const unsigned argc = 19; + audioDB(argc, (char* const*)argv, &adbQueryResult); + return SOAP_OK; +} + +int main(const unsigned argc, char* const argv[]){ + audioDB(argc, argv); +} + +