예제 #1
0
void
ClassAdLog::AppendLog(LogRecord *log)
{
	if (active_transaction) {
		if (active_transaction->EmptyTransaction()) {
			LogBeginTransaction *l = new LogBeginTransaction;
			active_transaction->AppendLog(l);
		}
		active_transaction->AppendLog(log);
	} else {
			//MD: using file pointer
		if (log_fp!=NULL) {
			if (log->Write(log_fp) < 0) {
				EXCEPT("write to %s failed, errno = %d", logFilename(), errno);
			}
			if( m_nondurable_level == 0 ) {
					//MD: flushing data -- using a file pointer
				if (fflush(log_fp) !=0){
					EXCEPT("flush to %s failed, errno = %d", logFilename(), errno);
				}
					//MD: syncing the data as done before
				if (condor_fsync(fileno(log_fp)) < 0) {
					EXCEPT("fsync of %s failed, errno = %d", logFilename(), errno);
				}
			}
		}
		log->Play((void *)&table);
		delete log;
	}
}
예제 #2
0
void
ClassAdLog::LogState(FILE *fp)
{
	LogRecord	*log=NULL;
	ClassAd		*ad=NULL;
	ExprTree	*expr=NULL;
	HashKey		hashval;
	MyString	key;
	const char	*attr_name = NULL;

	// This must always be the first entry in the log.
	log = new LogHistoricalSequenceNumber( historical_sequence_number, m_original_log_birthdate );
	if (log->Write(fp) < 0) {
		EXCEPT("write to %s failed, errno = %d", logFilename(), errno);
	}
	delete log;

	table.startIterations();
	while(table.iterate(ad) == 1) {
		table.getCurrentKey(hashval);
		hashval.sprint(key);
		log = new LogNewClassAd(key.Value(), ad->GetMyTypeName(), ad->GetTargetTypeName());
		if (log->Write(fp) < 0) {
			EXCEPT("write to %s failed, errno = %d", logFilename(), errno);
		}
		delete log;
			// Unchain the ad -- we just want to write out this ads exprs,
			// not all the exprs in the chained ad as well.
		AttrList *chain = dynamic_cast<AttrList*>(ad->GetChainedParentAd());
		ad->Unchain();
		ad->ResetName();
		attr_name = ad->NextNameOriginal();
		while (attr_name) {
			expr = ad->LookupExpr(attr_name);
				// This conditional used to check whether the ExprTree is
				// invisible, but no codepath sets any attributes
				// invisible for this call.
			if (expr) {
				log = new LogSetAttribute(key.Value(), attr_name,
										  ExprTreeToString(expr));
				if (log->Write(fp) < 0) {
					EXCEPT("write to %s failed, errno = %d", logFilename(),
						   errno);
				}
				delete log;
			}
			attr_name = ad->NextNameOriginal();
		}
			// ok, now that we're done writing out this ad, restore the chain
		ad->ChainToAd(chain);
	}
	if (fflush(fp) !=0){
	  EXCEPT("fflush of %s failed, errno = %d", logFilename(), errno);
	}
	if (condor_fsync(fileno(fp)) < 0) {
		EXCEPT("fsync of %s failed, errno = %d", logFilename(), errno);
	} 
}
예제 #3
0
void
ClassAdLog::FlushLog()
{
	if (log_fp!=NULL) {
		if (fflush(log_fp) !=0){
			EXCEPT("flush to %s failed, errno = %d", logFilename(), errno);
		}
	}
}
예제 #4
0
bool
ClassAdLog::SaveHistoricalLogs()
{
	if(!max_historical_logs) return true;

	MyString new_histfile;
	if(!new_histfile.sprintf("%s.%lu",logFilename(),historical_sequence_number))
	{
		dprintf(D_ALWAYS,"Aborting save of historical log: out of memory.\n");
		return false;
	}

	dprintf(D_FULLDEBUG,"About to save historical log %s\n",new_histfile.Value());

	if( hardlink_or_copy_file(logFilename(), new_histfile.Value()) < 0) {
		dprintf(D_ALWAYS,"Failed to copy %s to %s.\n",logFilename(),new_histfile.Value());
		return false;
	}

	MyString old_histfile;
	if(!old_histfile.sprintf("%s.%lu",logFilename(),historical_sequence_number - max_historical_logs))
	{
		dprintf(D_ALWAYS,"Aborting cleanup of historical logs: out of memory.\n");
		return true; // this is not a fatal error
	}

	if( unlink(old_histfile.Value()) == 0 ) {
		dprintf(D_FULLDEBUG,"Removed historical log %s.\n",old_histfile.Value());
	}
	else {
		// It's ok if the old file simply doesn't exist.
		if( errno != ENOENT ) {
			// Otherwise, it's not a fatal error, but definitely odd that
			// we failed to remove it.
			dprintf(D_ALWAYS,"WARNING: failed to remove '%s': %s\n",old_histfile.Value(),strerror(errno));
		}
		return true; // this is not a fatal error
	}
	return true;
}
예제 #5
0
void
ClassAdLog::ForceLog()
{
	// Force log changes to disk.  This involves first flushing
	// the log from memory buffers, then fsyncing to disk.
	if (log_fp!=NULL) {

		// First flush
		FlushLog();

		// Then sync
		if (condor_fsync(fileno(log_fp)) < 0) {
			EXCEPT("fsync of %s failed, errno = %d", logFilename(), errno);
		}

	}
}
예제 #6
0
// ######################################################################
bool BeoWebServer::initLogFile()
{
    // get the time of day
    time_t rawtime;
    struct tm * timeinfo;
    time ( &rawtime );
    timeinfo = localtime ( &rawtime );
    char buffer [80];
    strftime (buffer,80,
              "%Y_%m_%d__%H_%M_%S",timeinfo);
    std::string startTime(buffer);

    itsLogFolderName =
        std::string(sformat("%s%s", LOG_FOLDER, startTime.c_str()));
    LINFO("logFoldername: %s", itsLogFolderName.c_str());

    // create a log directory
    if (mkdir(itsLogFolderName.c_str(), 0777) == -1)
    {
        LFATAL("Cannot create log folder: %s", itsLogFolderName.c_str());
        return(EXIT_FAILURE);
    }

    std::string logFilename
    (sformat("%s/Log_%s.txt", itsLogFolderName.c_str(), startTime.c_str()));
    LINFO("logFilename: %s", logFilename.c_str());

    std::string cTime = std::string("Time of day: ") + startTime;
    LINFO("%s", cTime.c_str());
    cTime += std::string("\n");

    // save  in a file by appending to the file
    itsLogFilename = logFilename;
    FILE *rFile = fopen(itsLogFilename.c_str(), "at");
    if (rFile != NULL)
    {
        LDEBUG("saving result to %s", logFilename.c_str());
        fputs(cTime.c_str(), rFile);
        fclose (rFile);
    }
    else LFATAL("can't create file: %s", itsLogFilename.c_str());

    return true;
}
예제 #7
0
void
ClassAdLog::AppendLog(LogRecord *log)
{
	if (active_transaction) {
		if (active_transaction->EmptyTransaction()) {
			LogBeginTransaction *l = new LogBeginTransaction;
			active_transaction->AppendLog(l);
		}
		active_transaction->AppendLog(log);
	} else {
			//MD: using file pointer
		if (log_fp!=NULL) {
			if (log->Write(log_fp) < 0) {
				EXCEPT("write to %s failed, errno = %d", logFilename(), errno);
			}
			if( m_nondurable_level == 0 ) {
				ForceLog();  // flush and fsync
			}
		}
		log->Play((void *)&table);
		delete log;
	}
}
예제 #8
0
int main( int argc, char *argv[] )
{
//    try {

    time_t programStartTime(time(NULL) );
    boost::filesystem::path workingDir( boost::filesystem::current_path() );


    // ========== PROGRAM PARAMETERS ==========

    std::string progName( "buildrandctree" );
    std::string configFilename( "/home/raid2/moreno/Code/hClustering/config/"+progName+".cfg" );

    // program parameters
    std::string roiFilename, inputFolder, outputFolder;
    float memory( 0.5 ), maxNbDist( 1 );
    unsigned int nbLevel( 26 ), threads( 0 );
    bool keepDiscarded( false ), niftiMode( true ), debug( false );
    TC_GROWTYPE growType( TC_GROWOFF );
    size_t baseSize( 0 );

    // Declare a group of options that will be allowed only on command line
    boost::program_options::options_description genericOptions( "Generic options" );
    genericOptions.add_options()
    ( "version", "Program version" )
    ( "help,h", "Produce extended program help message" )
    ( "roi,r", boost::program_options::value< std::string >(&roiFilename), "file with the seed voxels coordinates." )
    ( "inputf,I",  boost::program_options::value< std::string >(&inputFolder), "input data folder (seed tractograms)." )
    ( "outputf,O",  boost::program_options::value< std::string >(&outputFolder), "output folder" )
    ( "maxnbdist,d",  boost::program_options::value< float >(&maxNbDist)->implicit_value(1), "[opt] maximum dissimilarity a seed voxel tract must have to its most similar neighbor not be discarded. (0,1]." )
    ( "cnbhood,c",  boost::program_options::value< unsigned int >(&nbLevel)->implicit_value(26), "[opt] centroid method neighborhood level. Valid values: 6, 18, 26(default), 32, 96, 124." )
    ( "basesize,S",  boost::program_options::value< size_t >(&baseSize), "[opt] grow homogeneous base nodes (meta-leaves) of size S. (>=2)." )
    ( "basenum,N",  boost::program_options::value< size_t >(&baseSize), "[opt] grow N homogeneous base nodes (meta-leaves). (>=10)." )
    ;

    // Declare a group of options that will be allowed both on command line and in config file
    boost::program_options::options_description configOptions( "Configuration" );
    configOptions.add_options()
    ( "verbose,v", "[opt] verbose output." )
    ( "vista", "[opt] use vista file format (default is nifti)." )
    ( "cache-mem,m",  boost::program_options::value< float >(&memory)->implicit_value(0.5), "[opt] maximum of memory (in GBytes) to use for tractogram cache memory. Default: 0.5." )
    ( "keep-disc,k", "[opt] keep discarded voxels data in a section of the tree file." )
    ( "debugout", "[opt] write additional detailed outputs meant for debug." )
    ( "pthreads,p",  boost::program_options::value< unsigned int >(&threads), "[opt] number of processing cores to run the program in. Default: all available." )
    ;

    // Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
    boost::program_options::options_description hiddenOptions( "Hidden options" );
    //hiddenOptions.add_options() ;

    boost::program_options::options_description cmdlineOptions;
    cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
    boost::program_options::options_description configFileOptions;
    configFileOptions.add(configOptions).add(hiddenOptions);
    boost::program_options::options_description visibleOptions( "Allowed options" );
    visibleOptions.add(genericOptions).add(configOptions);
    boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
    //posOpt.add( "roi", -1);

    boost::program_options::variables_map variableMap;
    store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);

    std::ifstream ifs(configFilename.c_str() );
    store(parse_config_file(ifs, configFileOptions), variableMap);
    notify( variableMap);



    if ( variableMap.count( "help" ) )
    {
        std::cout << "---------------------------------------------------------------------------" << std::endl;
        std::cout << std::endl;
        std::cout << " Project: hClustering" << std::endl;
        std::cout << std::endl;
        std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
        std::cout << " David Moreno-Dominguez" << std::endl;
        std::cout << " [email protected]" << std::endl;
        std::cout << " [email protected]" << std::endl;
        std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
        std::cout << std::endl;
        std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
        std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
        std::cout << "   A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
        std::cout << "   Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
        std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
        std::cout << "   Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
        std::cout << "   PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
        std::cout << "   ISBN 978-3-941504-45-5" << std::endl;
        std::cout << std::endl;
        std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
        std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
        std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
        std::cout << " (at your option) any later version." << std::endl;
        std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
        std::cout << std::endl;
        std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
        std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
        std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the" << std::endl;
        std::cout << " GNU Lesser General Public License for more details." << std::endl;
        std::cout << std::endl;
        std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
        std::cout << "buildrandctree" << std::endl << std::endl;
        std::cout << "Build a centroid hierarchical tree from a set of artificially pre-generated set of tractograms yoielding a uniformly random similarity matrix and a seed neighborhood information voxel list." << std::endl << std::endl;
        std::cout << "* Arguments:" << std::endl << std::endl;
        std::cout << " --version:       Program version." << std::endl << std::endl;
        std::cout << " -h --help:       Produce extended program help message." << std::endl << std::endl;
        std::cout << " -r --roi:        A text file with the seed voxel coordinates and the corresponding tractogram index (if tractogram naming is based on index rather than coordinates)." << std::endl << std::endl;
        std::cout << " -I --inputf:     input data folder (containing the compact tractograms)." << std::endl << std::endl;
        std::cout << " -O --outputf:    Output folder where tree files will be written." << std::endl << std::endl;
        std::cout << "[-d --maxnbdist]: Maximum dissimilarity a seed voxel tract must have to its most similar neighbor not be discarded." << std::endl;
        std::cout << "                   Valid values: (0,1] Use a value of 1 (default) if no discarding is desired." << std::endl << std::endl;
        std::cout << "[-c --cnbhood]:   Use centroid method with C neighborhood level. Valid values: 6, 18, 24(default), 32, 96, 124." << std::endl << std::endl;
        std::cout << "[-S --basesize]:  Merge homogeneous base nodes of size S. (mutually exclusive with -N option). Default: 0 (no homogeneous merging)." << std::endl << std::endl;
        std::cout << "[-N --basenum]:   Grow N homogeneous base nodes. (mutually exclusive with -S option). Default: 0 (no homogeneous merging)." << std::endl << std::endl;
        std::cout << "[-v --verbose]:   Verbose output (recommended)." << std::endl << std::endl;
        std::cout << "[--vista]: 	    Read/write vista (.v) files [default is nifti (.nii) and compact (.cmpct) files]." << std::endl << std::endl;
        std::cout << "[-m --cache-mem]: Maximum amount of RAM memory (in GBytes) to use for temporal tractogram cache storing. Valid values [0.1,50]. Default: 0.5." << std::endl << std::endl;
        std::cout << "[-k --keep-disc]: Keep discarded voxel information in a specialiced section of the tree." << std::endl << std::endl;
        std::cout << "[--debugout]:     Write additional detailed outputs meant to be used for debugging." << std::endl << std::endl;
        std::cout << "[-p --pthreads]:  Number of processing threads to run the program in parallel. Default: use all available processors." << std::endl << std::endl;
        std::cout << std::endl;
        std::cout << "* Usage example:" << std::endl << std::endl;
        std::cout << " buildrandctree -r roi_lh.txt -I tractograms/ -O results/ -c 26 -N 1000 -k -m 2 -v " << std::endl << std::endl;
        std::cout << std::endl;
        std::cout << "* Outputs (in output folder defined at option -O):" << std::endl << std::endl;
        std::cout << " - 'cX_bin_nmt.txt' - (where X is the neighborhood level defined at option -c) non-monotonic binary-branching hierarchical tree without tree processing (if desired use processtree command)." << std::endl;
        std::cout << " - 'baselist_nmt.txt' - meta-leaves (base nodes defined by the us of option -N or -S) list with IDs corresponding to the non-monotonic tree file." << std::endl;
        std::cout << " - 'success.txt' - An empty file created when the program has sucessfully exited after completion (to help for automatic re-running scripting after failure)." << std::endl;
        std::cout << " - 'buildrandtree_log.txt' - A text log file containing the parameter details and in-run and completion information of the program." << std::endl;
        std::cout << std::endl;
        std::cout << " [extra outputs when using --debugout option)" << std::endl << std::endl;
        std::cout << " - 'cX_bin_nmt_debug.txt' - version of the counterpart file without '_debug' suffix with redundant information for debugging purposes." << std::endl;
        std::cout << std::endl;
        exit(0);
    }

    if ( variableMap.count( "verbose" ) ) {
        std::cout << "verbose output" << std::endl;
        verbose=true;
    }

    if ( variableMap.count( "pthreads" ) )
    {
        if ( threads == 1 )
        {
            std::cout << "Using a single processor" << std::endl;
        }
        else if( threads == 0 || threads >= omp_get_num_procs() )
        {
            threads = omp_get_num_procs();
            std::cout << "Using all available processors ( " << threads << " )." << std::endl;
        }
        else
        {
            std::cout << "Using a maximum of " << threads << " processors " << std::endl;
        }
        omp_set_num_threads( threads );
    }
    else
    {
        threads = omp_get_num_procs();
        omp_set_num_threads( threads );
        std::cout << "Using all available processors ( " << threads << " )." << std::endl;
    }

    if ( variableMap.count( "vista" ) )
    {
        if( verbose )
        {
            std::cout << "Using vista format" << std::endl;
        }
        fileManagerFactory fmf;
        fmf.setVista();
        niftiMode = false;
    }
    else
    {
        if( verbose )
        {
            std::cout << "Using nifti format" << std::endl;
        }
        fileManagerFactory fmf;
        fmf.setNifti();
        niftiMode = true;
    }

    if ( variableMap.count( "debugout" ) )
    {
        if( verbose )
        {
            std::cout << "Debug output files activated" << std::endl;
        }
        debug = true;
    }

    if ( variableMap.count( "version" ) )
    {
        std::cout << progName << ", version 2.0" << std::endl;
        exit(0);
    }

    if ( variableMap.count( "roi" ) )
    {
        if( !boost::filesystem::is_regular_file( boost::filesystem::path( roiFilename ) ) )
        {
            std::cerr << "ERROR: roi file \"" <<roiFilename<< "\" is not a regular file" << std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }
        else if( verbose )
        {
            std::cout << "Seed voxels roi file: " << roiFilename << std::endl;
        }
    }
    else
    {
        std::cerr << "ERROR: no seed voxels roi file stated" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }


    if( verbose )
    {
        std::cout << "Maximum distance to most similar neighbor: " << maxNbDist << std::endl;
    }

    if ( maxNbDist <= 0 || maxNbDist > 1 )
    {
        std::cerr << "ERROR: distance value used is out of bounds please use a value within (0,1]" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }
    else if ( maxNbDist == 1 && verbose )
    {
        std::cout << "No neighbor distance restrictions will be applied" << std::endl;
    }
    else if( verbose )
    {
        std::cout << "Seed voxels with no neighbors with tract dissimilarity lower than " << maxNbDist << " will be discarded as outliers" << std::endl;
    }

    if( verbose )
    {
        std::cout << "Centroid neighborhood level: " << nbLevel << std::endl;
    }

    if ( ( nbLevel != 6 ) && ( nbLevel != 18 ) && ( nbLevel != 26 ) && ( nbLevel != 32 ) && ( nbLevel != 92 ) && ( nbLevel != 124 ) )
    {
        std::cerr << "ERROR: invalid nbhood level, only (6,18,26,32,92,124) are accepted" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }

    if ( ( variableMap.count( "basesize" ) && variableMap.count( "basenum" ) ) )
    {
        std::cerr << "ERROR: options --basesize (-S) and --basenum (-N) are mutually exclusive" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }
    if ( variableMap.count( "basesize" ) )
    {
        if( baseSize <= 1 )
        {
            std::cerr << "ERROR: base node (meta-leaf) size must be greater than 1" << std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }
        else
        {
            if( verbose )
            {
                std::cout << "Initial merging stage up to homogeneous base nodes of size: " << baseSize << std::endl;
            }
            growType = TC_GROWSIZE;
        }
    }
    if ( variableMap.count( "basenum" ) )
    {
        if( baseSize < 10 )
        {
            std::cerr << "ERROR: base node (meta-leaf) number must be equal or greater than 10" << std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }
        else
        {
            if( verbose )
            {
                std::cout << "Initial merging stage up to " << baseSize << " homogeneous base nodes (meta-leaves)" << std::endl;
            }
            growType = TC_GROWNUM;
        }
    }

    if( growType == TC_GROWOFF && verbose )
    {
        std::cout << "No homogeneous merging stage" << std::endl;
    }

    if ( variableMap.count( "keep-disc" ) )
    {
        if( verbose )
        {
            std::cout << "Discarded voxel coordinates will be saved in an special section fo the tree file" << std::endl;
        }
        keepDiscarded = true;
    }
    else
    {
        if( verbose )
        {
            std::cout << "Discarded voxel coordinates will not be saved" << std::endl;
        }
        keepDiscarded = false;
    }

    if ( variableMap.count( "inputf" ) )
    {
        if( !boost::filesystem::is_directory( boost::filesystem::path( inputFolder ) ) )
        {
            std::cerr << "ERROR: input seed tractogram folder \"" <<inputFolder<< "\" is not a directory" << std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);

        }
        else if( verbose )
        {
            std::cout << "Input seed tractogram folder: " << inputFolder << std::endl;
        }
    }
    else
    {
        std::cerr << "ERROR: no input seed tractogram stated" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }

    if ( variableMap.count( "outputf" ) )
    {
        if( !boost::filesystem::is_directory( boost::filesystem::path( outputFolder ) ) )
        {
            std::cerr << "ERROR: output folder \"" <<outputFolder<< "\" is not a directory" << std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);

        }
        else if( verbose )
        {
            std::cout << "Output folder: " << outputFolder << std::endl;
        }
    }
    else
    {
        std::cerr << "ERROR: no output folder stated" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }


    if ( memory < 0.1 || memory > 50)
    {
        std::cerr << "ERROR: cache size must be a positive float between 0.1 and 50 (GB)" << std::endl;
        std::cerr << visibleOptions << std::endl;
        exit(-1);
    }
    else if( verbose )
    {
        std::cout << "Tractogram cache memory: " << memory << " GBytes" << std::endl;
    }


    std::string logFilename(outputFolder+"/"+progName+"_log.txt" );
    std::ofstream logFile(logFilename.c_str() );
    if(!logFile)
    {
        std::cerr << "ERROR: unable to open log file: \"" <<logFilename<< "\"" << std::endl;
        exit(-1);
    }


    logFile << "Start Time:\t" << ctime(&programStartTime) << std::endl;
    logFile << "Working directory:\t" << workingDir.string() << std::endl;
    logFile << "Verbose:\t" << verbose << std::endl;
    logFile << "Processors used:\t" << threads << std::endl;
    if( niftiMode )
    {
        logFile << "Using nifti file format" << std::endl;
    }
    else
    {
        logFile << "Using vista file format" << std::endl;
    }
    logFile << "Vista mode flag:\t" << verbose << std::endl;
    logFile << "Roi file:\t" << roiFilename << std::endl;
    logFile << "Max nb distance:\t" << maxNbDist << std::endl;
    logFile << "Nbhood restriction level:\t" <<nbLevel<< std::endl;
    switch(growType)
    {
    case TC_GROWOFF:
        logFile << "Region growing: None" << std::endl;
        break;
    case TC_GROWSIZE:
        logFile << "Region growing: Size: " << baseSize << std::endl;
        break;
    case TC_GROWNUM:
        logFile << "Region growing: Number: " << baseSize << std::endl;
        break;
    }
    logFile << "Input seed tract folder:\t" << inputFolder << std::endl;
    logFile << "Output folder:\t" << outputFolder << std::endl;
    logFile << "Memory cache size:\t" << memory << " GB" << std::endl;
    logFile << "Debug outputr:\t" << debug << std::endl;
    logFile << "-------------" << std::endl;


    /////////////////////////////////////////////////////////////////


    randCnbTreeBuilder builder( roiFilename, verbose );

    logFile << "Roi size:\t" << builder.roiSize() << std::endl;
    builder.log( &logFile );
    builder.setInputFolder( inputFolder );
    builder.setOutputFolder( outputFolder );
    builder.setDebugOutput( debug );
    builder.buildRandCentroid( nbLevel, memory, growType, baseSize, keepDiscarded );


    /////////////////////////////////////////////////////////////////


    // save and print total time
    time_t programEndTime(time(NULL) );
    int totalTime( difftime(programEndTime,programStartTime) );
    std::cout << "Program Finished, total time: " << totalTime/3600 << "h " <<  (totalTime%3600)/60 << "' " << ((totalTime%3600)%60) << "\"   " << std::endl;
    logFile << "-------------" << std::endl;
    logFile << "Finish Time:\t" << ctime(&programEndTime) << std::endl;
    logFile << "Elapsed time : " << totalTime/3600 << "h " <<  (totalTime%3600)/60 << "' " << ((totalTime%3600)%60) << "\"" << std::endl;


    // create file that indicates process was finished successfully
    std::string successFilename(outputFolder+"/success.txt" );
    std::ofstream successFile(successFilename.c_str() );
    if(!successFile)
    {
        std::cerr << "ERROR: unable to create success file: \"" <<successFile<< "\"" << std::endl;
        exit(-1);
    }
    successFile << "success";


//    }
//    catch(std::exception& e)
//    {
//        std::cout << e.what() << std::endl;
//        return 1;
//    }
    return 0;
}
예제 #9
0
ClassAdLog::ClassAdLog(const char *filename,int max_historical_logs_arg) : table(CLASSAD_LOG_HASHTABLE_SIZE, hashFunction)
{
	log_filename_buf = filename;
	active_transaction = NULL;
	m_nondurable_level = 0;

	this->max_historical_logs = max_historical_logs_arg;
	historical_sequence_number = 1;
	m_original_log_birthdate = time(NULL);

	int log_fd = safe_open_wrapper_follow(logFilename(), O_RDWR | O_CREAT | O_LARGEFILE, 0600);
	if (log_fd < 0) {
		EXCEPT("failed to open log %s, errno = %d", logFilename(), errno);
	}

	log_fp = fdopen(log_fd, "r+");
	if (log_fp == NULL) {
		EXCEPT("failed to fdopen log %s, errno = %d", logFilename(), errno);
	}


	// Read all of the log records
	LogRecord		*log_rec;
	unsigned long count = 0;
	bool is_clean = true; // was cleanly closed (until we find out otherwise)
	bool requires_successful_cleaning = false;
	long long next_log_entry_pos = 0;
    long long curr_log_entry_pos = 0;
	while ((log_rec = ReadLogEntry(log_fp, 1+count, InstantiateLogEntry)) != 0) {
        curr_log_entry_pos = next_log_entry_pos;
		next_log_entry_pos = ftell(log_fp);
		count++;
		switch (log_rec->get_op_type()) {
        case CondorLogOp_Error:
            // this is defensive, ought to be caught in InstantiateLogEntry()
            EXCEPT("ERROR: transaction record %lu was bad (byte offset %lld)\n", count, curr_log_entry_pos);
            break;
		case CondorLogOp_BeginTransaction:
			// this file contains transactions, so it must not
			// have been cleanly shut down
			is_clean = false;
			if (active_transaction) {
				dprintf(D_ALWAYS, "Warning: Encountered nested transactions in %s, "
						"log may be bogus...", filename);
			} else {
				active_transaction = new Transaction();
			}
			delete log_rec;
			break;
		case CondorLogOp_EndTransaction:
			if (!active_transaction) {
				dprintf(D_ALWAYS, "Warning: Encountered unmatched end transaction in %s, "
						"log may be bogus...", filename);
			} else {
				active_transaction->Commit(NULL, (void *)&table); // commit in memory only
				delete active_transaction;
				active_transaction = NULL;
			}
			delete log_rec;
			break;
		case CondorLogOp_LogHistoricalSequenceNumber:
			if(count != 1) {
				dprintf(D_ALWAYS, "Warning: Encountered historical sequence number after first log entry (entry number = %ld)\n",count);
			}
			historical_sequence_number = ((LogHistoricalSequenceNumber *)log_rec)->get_historical_sequence_number();
			m_original_log_birthdate = ((LogHistoricalSequenceNumber *)log_rec)->get_timestamp();
			delete log_rec;
			break;
		default:
			if (active_transaction) {
				active_transaction->AppendLog(log_rec);
			} else {
				log_rec->Play((void *)&table);
				delete log_rec;
			}
		}
	}
	long long final_log_entry_pos = ftell(log_fp);
	if( next_log_entry_pos != final_log_entry_pos ) {
		// The log file has a broken line at the end so we _must_
		// _not_ write anything more into this log.
		// (Alternately, we could try to clear out the broken entry
		// and continue writing into this file, but since we are about to
		// rotate the log anyway, we may as well just require the rotation
		// to be successful.  In the case where rotation fails, we will
		// probably soon fail to write to the log file anyway somewhere else.)
		dprintf(D_ALWAYS,"Detected unterminated log entry in ClassAd Log %s."
				" Forcing rotation.\n", logFilename());
		requires_successful_cleaning = true;
	}
	if (active_transaction) {	// abort incomplete transaction
		delete active_transaction;
		active_transaction = NULL;

		if( !requires_successful_cleaning ) {
			// For similar reasons as with broken log entries above,
			// we need to force rotation.
			dprintf(D_ALWAYS,"Detected unterminated transaction in ClassAd Log"
					"%s. Forcing rotation.\n", logFilename());
			requires_successful_cleaning = true;
		}
	}
	if(!count) {
		log_rec = new LogHistoricalSequenceNumber( historical_sequence_number, m_original_log_birthdate );
		if (log_rec->Write(log_fp) < 0) {
			EXCEPT("write to %s failed, errno = %d", logFilename(), errno);
		}
	}
	if( !is_clean || requires_successful_cleaning ) {
		if( !TruncLog() && requires_successful_cleaning ) {
			EXCEPT("Failed to rotate ClassAd log %s.\n", logFilename());
		}
	}
}
예제 #10
0
bool
ClassAdLog::TruncLog()
{
	MyString	tmp_log_filename;
	int new_log_fd;
	FILE *new_log_fp;

	dprintf(D_ALWAYS,"About to rotate ClassAd log %s\n",logFilename());

	if(!SaveHistoricalLogs()) {
		dprintf(D_ALWAYS,"Skipping log rotation, because saving of historical log failed for %s.\n",logFilename());
		return false;
	}

	tmp_log_filename.sprintf( "%s.tmp", logFilename());
	new_log_fd = safe_open_wrapper_follow(tmp_log_filename.Value(), O_RDWR | O_CREAT | O_LARGEFILE, 0600);
	if (new_log_fd < 0) {
		dprintf(D_ALWAYS, "failed to rotate log: safe_open_wrapper(%s) returns %d\n",
				tmp_log_filename.Value(), new_log_fd);
		return false;
	}

	new_log_fp = fdopen(new_log_fd, "r+");
	if (new_log_fp == NULL) {
		dprintf(D_ALWAYS, "failed to rotate log: fdopen(%s) returns NULL\n",
				tmp_log_filename.Value());
		return false;
	}


	// Now it is time to move courageously into the future.
	historical_sequence_number++;

	LogState(new_log_fp);
	fclose(log_fp);
	log_fp = NULL;
	fclose(new_log_fp);	// avoid sharing violation on move
	if (rotate_file(tmp_log_filename.Value(), logFilename()) < 0) {
		dprintf(D_ALWAYS, "failed to rotate job queue log!\n");

		// Beat a hasty retreat into the past.
		historical_sequence_number--;

		int log_fd = safe_open_wrapper_follow(logFilename(), O_RDWR | O_APPEND | O_LARGEFILE, 0600);
		if (log_fd < 0) {
			EXCEPT("failed to reopen log %s, errno = %d after failing to rotate log.",logFilename(),errno);
		}

		log_fp = fdopen(log_fd, "a+");
		if (log_fp == NULL) {
			EXCEPT("failed to refdopen log %s, errno = %d after failing to rotate log.",logFilename(),errno);
		}

		return false;
	}
	int log_fd = safe_open_wrapper_follow(logFilename(), O_RDWR | O_APPEND | O_LARGEFILE, 0600);
	if (log_fd < 0) {
		EXCEPT( "failed to open log in append mode: "
			"safe_open_wrapper(%s) returns %d\n", logFilename(), log_fd);
	}
	log_fp = fdopen(log_fd, "a+");
	if (log_fp == NULL) {
		close(log_fd);
		EXCEPT("failed to fdopen log in append mode: "
			"fdopen(%s) returns %d\n", logFilename(), log_fd);
	}

	return true;
}
예제 #11
0
int main( int argc, char *argv[] )
{
//    try {

        time_t programStartTime(time(NULL));
        boost::filesystem::path workingDir( boost::filesystem::current_path());


        // ========== PROGRAM PARAMETERS ==========

        std::string progName("partitiontree");
        std::string configFilename("../../config/"+progName+".cfg");
        unsigned int threads(0), levelDepth(3), filterRadius(0);
        bool verbose(false), niftiMode( true );

        // program parameters
        std::string treeFilename, outputFolder;

        // Declare a group of options that will be allowed only on command line
        boost::program_options::options_description genericOptions("Generic options");
        genericOptions.add_options()
                ( "version", "Program version" )
                ( "help,h", "Produce extended program help message" )
                ( "tree,t",  boost::program_options::value< std::string >(&treeFilename), "file with the tree to compute partitions from")
                ( "outputf,O",  boost::program_options::value< std::string >(&outputFolder), "output folder where partition files will be written")
                ( "search-depth,d", boost::program_options::value< unsigned int >(&levelDepth)->implicit_value(3), "[opt] optimal partition search depth (default = 3)")
                ( "filter-radius,r", boost::program_options::value< unsigned int >(&filterRadius)->implicit_value(0), "[opt] output partition filter kernel radius (default = 0 | no filtering)")
                ( "hoz", "[opt] obtain horizontal cut partitions (instead of Spread-Separation ones)")
                ( "maxgran,m", "[opt] obtain only the maximum granularity partition")
                ;

        // Declare a group of options that will be allowed both on command line and in config file
        boost::program_options::options_description configOptions("Configuration");
        configOptions.add_options()
                ( "verbose,v", "[opt] verbose output." )
                ( "vista", "[opt] use vista file format (default is nifti)." )
                ( "pthreads,p",  boost::program_options::value< unsigned int >(&threads), "[opt] number of processing threads to run the program in parallel, default: all available")
                ;

        // Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
        boost::program_options::options_description hiddenOptions("Hidden options");
        //hiddenOptions.add_options() ;

        boost::program_options::options_description cmdlineOptions;
        cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
        boost::program_options::options_description configFileOptions;
        configFileOptions.add(configOptions).add(hiddenOptions);
        boost::program_options::options_description visibleOptions("Allowed options");
        visibleOptions.add(genericOptions).add(configOptions);
        boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
        //posOpt.add("roi-file", -1);

        boost::program_options::variables_map variableMap;
        store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);

        std::ifstream ifs(configFilename.c_str());
        store(parse_config_file(ifs, configFileOptions), variableMap);
        notify(variableMap);


        if (variableMap.count("help"))
        {
            std::cout << "---------------------------------------------------------------------------" << std::endl;
            std::cout << std::endl;
            std::cout << " Project: hClustering" << std::endl;
            std::cout << std::endl;
            std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
            std::cout << " David Moreno-Dominguez" << std::endl;
            std::cout << " [email protected]" << std::endl;
            std::cout << " [email protected]" << std::endl;
            std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
            std::cout << std::endl;
            std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
            std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
            std::cout << "   A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
            std::cout << "   Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
            std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
            std::cout << "   Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
            std::cout << "   PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
            std::cout << "   ISBN 978-3-941504-45-5" << std::endl;
            std::cout << std::endl;
            std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
            std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
            std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
            std::cout << " (at your option) any later version." << std::endl;
            std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
            std::cout << std::endl;
            std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
            std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
            std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the" << std::endl;
            std::cout << " GNU Lesser General Public License for more details." << std::endl;
            std::cout << std::endl;
            std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
            std::cout << "partitiontree" << std::endl << std::endl;
            std::cout << "Obtain tree partitions at all granularity levels using the Spread-Separation method (finding the the partition with highest SS index at each granularity)." << std::endl;
            std::cout << " Optimal SS value for each partition is searched within a defined search-depth hierarchical levels. Final partitions can be filtered with a defined kernel size." << std::endl;
            std::cout << " to keep local SS maxima within that kernel. For SS index refer to (Moreno-Dominguez, 2014)" << std::endl;
            std::cout << " For an interactive 3D partition management with more options please use the Hierarchcial Clustering module developed in OpenWalnut (www.openwalnut.org)." << std::endl << std::endl;
            std::cout << "* Arguments:" << std::endl << std::endl;
            std::cout << " --version:       Program version." << std::endl << std::endl;
            std::cout << " -h --help:       produce extended program help message." << std::endl << std::endl;
            std::cout << " -t --tree:       File with the hierarchical tree to extract partitions from." << std::endl << std::endl;
            std::cout << " -O --outputf:    Output folder where partition files will be written." << std::endl << std::endl;
            std::cout << "[-d --search-depth]:  Search optimal partition for each granularity within d hierarchical levels." << std::endl;
            std::cout << "                       A higher value will produce more optimized partition but will increase computing time." << std::endl;
            std::cout << "                       Default: 3. Recommendened values: 3 for good quality and fast computation, 4 for enhanced quality." << std::endl << std::endl;
            std::cout << "[-r --filter-radius]: Filter output partitions to keep only local SS (partition quality) maxima" << std::endl;
            std::cout << "                       within a r-sized kernel across the granularity dimension." << std::endl << std::endl;
            std::cout << "[-h --hoz]:       Write horizontal cut partitions instead of SS ones (optimal partition search is still based on SS index)." << std::endl << std::endl;
            std::cout << "[-m --maxgran]:   Compute and write only the maximum granularity (meta-leaves) partition." << std::endl << std::endl;
            std::cout << "[-v --verbose]:   verbose output (recommended)." << std::endl << std::endl;
            std::cout << "[--vista]: 	    write output tree in vista coordinates (default is nifti)." << std::endl << std::endl;
            std::cout << "[-p --pthreads]:  number of processing threads to run the program in parallel. Default: use all available processors." << std::endl << std::endl;
            std::cout << std::endl;
            std::cout << "* Usage example:" << std::endl << std::endl;
            std::cout << " partitiontree -t tree_lh.txt -O results/ -d 3 -r 50 -v" << std::endl << std::endl;
            std::cout << std::endl;
            std::cout << "* Outputs (in output folder defined at option -O):" << std::endl << std::endl;
            std::cout << " (default outputs)" << std::endl;
            std::cout << " - 'allSSparts_dX.txt' - (where X is the search depth level defined at parameter -d) Contains a summary of the partition information (cut value and size) for all granularities." << std::endl;
            std::cout << " - 'TREE_SSparts_dX.txt' - (where TREE is the filename of the input tree defined at parameter -t) contains a copy of the original tree file with the partitions at all granularities included in the relevant fields." << std::endl;
            std::cout << " - 'partitiontree_log.txt' - A text log file containing the parameter details and in-run and completion information of the program." << std::endl;
            std::cout << std::endl;
            std::cout << " (additional if using option -r)" << std::endl;
            std::cout << " - 'filtSSparts_dX_rY.txt' - (where Y is the filter radius defined at parameter -r) Contains a summary of the resulting filtered partitions." << std::endl;
            std::cout << " - 'TREE_SSparts_dX_rY.txt' - contains a copy of the original tree file with the resulting filtered partitions included in the relevant fields." << std::endl;
            std::cout << std::endl;
            std::cout << " (when using --hoz option, the prefix 'SS' will be replaced by 'Hoz'')" << std::endl;
            std::cout << std::endl;
            std::cout << " (alternative outputs when using option --maxgran)" << std::endl;
            std::cout << " - 'fmaxgranPart.txt' - Contains the size information of the resulting maximal granularity partition for that tree." << std::endl;
            std::cout << " - 'TREE_maxgranPart.txt' - contains a copy of the original tree file with the resulting max granularity partition included in the relevant fields." << std::endl;
            std::cout << std::endl;
            exit(0);
        }
        if (variableMap.count("version"))
        {
            std::cout << progName <<", version 2.0"<<std::endl;
            exit(0);
        }
        if (variableMap.count("verbose"))
        {
            std::cout << "verbose output"<<std::endl;
            verbose=true;
        }

        if (variableMap.count("pthreads"))
        {
            if (threads==1)
            {
                std::cout <<"Using a single processor"<< std::endl;
            }
            else if(threads==0 || threads>=omp_get_num_procs())
            {
                threads = omp_get_num_procs();
                std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
            }
            else
            {
                std::cout <<"Using a maximum of "<< threads <<" processors "<< std::endl;
            }
            omp_set_num_threads( threads );
        }
        else
        {
            threads = omp_get_num_procs();
            omp_set_num_threads( threads );
            std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
        }

        if ( variableMap.count( "vista" ) )
        {
            if( verbose )
            {
                std::cout << "Using vista format" << std::endl;
            }
            fileManagerFactory fmf;
            fmf.setVista();
            niftiMode = false;
        }
        else
        {
            if( verbose )
            {
                std::cout << "Using nifti format" << std::endl;
            }
            fileManagerFactory fmf;
            fmf.setNifti();
            niftiMode = true;
        }

        if (variableMap.count("tree"))
        {
            if(!boost::filesystem::is_regular_file(boost::filesystem::path(treeFilename)))
            {
                std::cerr << "ERROR: tree file \""<<treeFilename<<"\" is not a regular file"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);
            }
            std::cout << "Roi voxels file: "<< treeFilename << std::endl;
        }
        else
        {
            std::cerr << "ERROR: no tree file stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }


        if (variableMap.count("outputf"))
        {
            if(!boost::filesystem::is_directory(boost::filesystem::path(outputFolder)))
            {
                std::cerr << "ERROR: output folder \""<<outputFolder<<"\" is not a directory"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);

            }
            std::cout << "Output folder: "<< outputFolder << std::endl;
        }
        else
        {
            std::cerr << "ERROR: no output folder stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);

        }



        if (variableMap.count("maxgran"))
        {
            std::cout<<"Obtaining only max. granularity partition..."<<std::endl;

            WHtree tree(treeFilename);
            std::cout<<tree.getReport( false )<<std::endl;
            if( tree.testRootBaseNodes() )
            {
                std::vector<size_t > maxpart( tree.getRootBaseNodes() );
                std::vector<std::vector<size_t > > partitionVector( 1, maxpart);
                std::vector<float > partitionValues(1,0);
                std::cout<<"maxgranpart size: "<<std::endl<<maxpart.size()<<std::endl;
                WHtreePartition partitioner(&tree);
                std::string outPartFilename( outputFolder + "/maxgranPart.txt" );
                partitioner.writePartitionSet( outPartFilename, partitionValues,partitionVector);
                tree.insertPartitions( partitionVector, partitionValues );
                std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_maxgranPart" );
                outTreeFilename += ( ".txt" );
                tree.writeTree( outTreeFilename, niftiMode );
                return 0;
            }
            else
            {
                std::cout<<"ERROR: tree  does not have a maximum granularity meta-leaf partition"<<std::endl;
                return(-1);
            }
        }

        if( levelDepth > 5 )
        {
            std::cout << "Level depth indicated: " << levelDepth << " is too high, setting to a maximum of 5" << std::endl;
            levelDepth = 5;
        }
        std::cout << "Using a search depth of: " << levelDepth << std::endl;

        if( filterRadius > 1000 )
        {
            std::cout << "filter radius indicated: " << filterRadius << " is too high (max is 1000), setting to 100" << std::endl;
            filterRadius = 10;
        }
        if( filterRadius == 0 )
        {
            std::cout << "using no filtering (radius 0)" << std::endl;
        }
        else if( filterRadius < 0 )
        {
            std::cout << "filter radius indicated: " << filterRadius << " must be positive. using no filtering (radius 0)" << std::endl;
            filterRadius = 0;
        }
        else
        {
            std::cout << "Using a filter radius of: " << filterRadius << std::endl;
        }

        /////////////////////////////////////////////////////////////////



        std::string logFilename(outputFolder+"/"+progName+"_log.txt");
        std::ofstream logFile(logFilename.c_str());
        if(!logFile) {
            std::cerr << "ERROR: unable to open log file: \""<<logFilename<<"\""<<std::endl;
            exit(-1);
        }
        logFile <<"Start Time:\t"<< ctime(&programStartTime) <<std::endl;
        logFile <<"Working directory:\t"<< workingDir.string() <<std::endl;
        logFile <<"Verbose:\t"<< verbose <<std::endl;
        logFile <<"Tree file:\t"<< treeFilename <<std::endl;
        logFile <<"Output folder:\t"<< outputFolder <<std::endl;
        logFile <<"Verbose:\t"<< verbose <<std::endl;
        if( niftiMode )
        {
            logFile << "Using nifti file format" << std::endl;
        }
        else
        {
            logFile << "Using vista file format" << std::endl;
        }

        WHtree tree(treeFilename);

        logFile << tree.getReport( false ) <<std::endl;
        std::cout<<tree.getReport( false )<<std::endl;

        std::vector< float > partitionValues;
        std::vector< std::vector< size_t> > partitionVector;

        WHtreePartition treePartition(&tree);

        std::string prefix;

        if (variableMap.count("hoz"))
        {
            prefix = "Hoz";
            std::cout <<"getting hoz partitions at all levels..." <<std::endl;
            treePartition.scanHozPartitions( &partitionValues, &partitionVector );

            std::cout << partitionValues.size() << " Partitions obtained, writing to file..." <<std::endl;
            logFile <<"Initial partitions:\t"<< partitionValues.size() <<std::endl;
            std::string outPartFilename( outputFolder + "/all" + prefix + "parts.txt" );
            treePartition.writePartitionSet( outPartFilename, partitionValues, partitionVector);

            tree.insertPartitions( partitionVector, partitionValues );
            std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
            outTreeFilename += ( ".txt" );
            tree.writeTree( outTreeFilename, niftiMode );
        }
        else
        {

            prefix = "SS";
            std::cout <<"getting SS partitions at all levels..." <<std::endl;
            treePartition.scanOptimalPartitions( levelDepth, &partitionValues, &partitionVector );

            std::cout << partitionValues.size() << " Partitions obtained, writing to file..." <<std::endl;
            logFile <<"Initial partitions:\t"<< partitionValues.size() <<std::endl;
            std::string outPartFilename( outputFolder + "/all" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) + ".txt" );
            treePartition.writePartitionSet( outPartFilename, partitionValues, partitionVector);

            tree.insertPartitions( partitionVector, partitionValues );
            std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
            outTreeFilename += ( ".txt" );
            tree.writeTree( outTreeFilename, niftiMode );

        }


        std::vector < unsigned int > filterRadii;
        //filterRadii.reserve( 6 );
        //        filterRadii.push_back( 1 );
        //        filterRadii.push_back( 2 );
        //        filterRadii.push_back( 5 );
        //        filterRadii.push_back( 10 );
        //        filterRadii.push_back( 15 );
        //        filterRadii.push_back( 20 );
        filterRadii.push_back( filterRadius );



        for(size_t i=0; i< filterRadii.size(); ++i)
        {
            if( filterRadii[i] <= 0 )
            {
                continue;
            }
            std::vector< float > filtPartValues( partitionValues );
            std::vector< std::vector< size_t> > filtPartVector( partitionVector );

            std::cout << "Filtering with a radius of "<< filterRadii[i] << "..." <<std::endl;
            treePartition.filterMaxPartitions( filterRadii[i], &filtPartValues, &filtPartVector );

            std::cout << filtPartValues.size() << " Filtered partitions obtained, writing to file..." <<std::endl;
            logFile <<"Filtered partitions:\t"<< filtPartValues.size() <<std::endl;
            std::string outPartFilename( outputFolder + "/filt" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
            outPartFilename += ( "_r" + boost::lexical_cast<std::string>(filterRadii[i]) +  ".txt" );
            treePartition.writePartitionSet(outPartFilename, filtPartValues, filtPartVector);

            std::cout << "Adding filtered partitions to tree and writing..." <<std::endl;

            std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
            outTreeFilename += ( "_r" + boost::lexical_cast<std::string>(filterRadii[i]) +  ".txt" );

            tree.insertPartitions( filtPartVector, filtPartValues );
            tree.writeTree( outTreeFilename, niftiMode );
        }



        /////////////////////////////////////////////////////////////////


        // save and print total time
        time_t programEndTime(time(NULL));
        int totalTime( difftime(programEndTime,programStartTime) );
        std::cout <<"Program Finished, total time: "<< totalTime/3600 <<"h "<<  (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\"   "<< std::endl;
        logFile <<"-------------"<<std::endl;
        logFile <<"Finish Time:\t"<< ctime(&programEndTime) <<std::endl;
        logFile <<"Elapsed time : "<< totalTime/3600 <<"h "<<  (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\""<< std::endl;


//    }
//    catch(std::exception& e)
//    {
//        std::cout << e.what() << std::endl;
//        return 1;
//    }
    return 0;
}
예제 #12
0
int main( int argc, char *argv[] )
{
//    try {
        time_t programStartTime(time(NULL));
        boost::filesystem::path workingDir( boost::filesystem::current_path());

        // ========== PROGRAM PARAMETERS ==========

        std::string progName("matchpartition");
        std::string configFilename("../../config/"+progName+".cfg");

        // program parameters
        std::string refTreeFilename, targetTreeFilename, matchTableFilename, outputFolder;
        unsigned int searchDepth(1);
        float lambda(0);
        bool signaturePart(false), colorMatching(false), overlapPart(false), exclusive(false);
        bool verbose(false), niftiMode( true );


        // Declare a group of options that will be allowed only on command line
        boost::program_options::options_description genericOptions("Generic options");
        genericOptions.add_options()
                ( "version", "Program version" )
                ( "help,h", "Produce extended program help message" )
                ( "reference,r",  boost::program_options::value< std::string >(&refTreeFilename), "file with reference partitioned tree" )
                ( "target,t",  boost::program_options::value< std::string >(&targetTreeFilename), "file with target tree to be partitioned-matched" )
                ( "leafmatch,m",  boost::program_options::value< std::string >(&matchTableFilename), "file with meta-leaves (base-nodes) matching table" )
                ( "outputf,O",  boost::program_options::value< std::string >(&outputFolder), "output folder where partition-matched trees will be written" )
                ( "signature,s",  boost::program_options::value< float >(&lambda), "[xor with -o and -c] Signature-based partition matching, inster lambda coefficient value" )
                ( "overlap,o", "[xor with -s and -c] Meta-leaf overlap-based partition matching")
                ( "depth,d", boost::program_options::value< unsigned int >(&searchDepth)->implicit_value(0), "[opt] partition search depth. Default: 0 (automatic partition-size based adaptive depth, recommended)")
                ( "justcolor,c",  "[xor with -s and -o] Perform only olor matching (requires pre-computed partitions in both trees)")
                ( "excl,x",  "[opt] color exclusively clusters that have a match, clusters without match will be white")
                ;

        // Declare a group of options that will be allowed both on command line and in config file
        boost::program_options::options_description configOptions("Configuration");
        configOptions.add_options()
                ( "verbose,v", "[opt] verbose output." )
                ( "vista", "[opt] Write output tree in vista coordinates (default is nifti)." )
                ;

        // Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
        boost::program_options::options_description hiddenOptions("Hidden options");
        //hiddenOptions.add_options() ;

        boost::program_options::options_description cmdlineOptions;
        cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
        boost::program_options::options_description configFileOptions;
        configFileOptions.add(configOptions).add(hiddenOptions);
        boost::program_options::options_description visibleOptions("Allowed options");
        visibleOptions.add(genericOptions).add(configOptions);
        boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
        //posOpt.add("roi-file", -1);

        boost::program_options::variables_map variableMap;
        store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);

        std::ifstream ifs(configFilename.c_str());
        store(parse_config_file(ifs, configFileOptions), variableMap);
        notify(variableMap);

        if (variableMap.count( "help" ) )
        {
            std::cout << "---------------------------------------------------------------------------" << std::endl;
            std::cout << std::endl;
            std::cout << " Project: hClustering" << std::endl;
            std::cout << std::endl;
            std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
            std::cout << " David Moreno-Dominguez" << std::endl;
            std::cout << " [email protected]" << std::endl;
            std::cout << " [email protected]" << std::endl;
            std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
            std::cout << std::endl;
            std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
            std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
            std::cout << "   A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
            std::cout << "   Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
            std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
            std::cout << "   Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
            std::cout << "   PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
            std::cout << "   ISBN 978-3-941504-45-5" << std::endl;
            std::cout << std::endl;
            std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
            std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
            std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
            std::cout << " (at your option) any later version." << std::endl;
            std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
            std::cout << std::endl;
            std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
            std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
            std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the" << std::endl;
            std::cout << " GNU Lesser General Public License for more details." << std::endl;
            std::cout << std::endl;
            std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
            std::cout << "matchpartition" << std::endl << std::endl;
            std::cout << "Finds the best matching corresponding partitions in a target tree to those present in an unrelated reference tree (meta-leaf matching across these two trees must have been precomputed using comparetrees)." << std::endl;
            std::cout << " Two partition matching algorithms are available: signature matching and overlap matching. Found target partitions will be color-matched as best as possible." << std::endl;
            std::cout << " There is also the possibility of only color-matching predefined partitions of the target tree to predefined partitions of the reference tree." << std::endl << std::endl;
            std::cout << "* Arguments:" << std::endl << std::endl;
            std::cout << " --version:       Program version." << std::endl << std::endl;
            std::cout << " -h --help:       produce extended program help message." << std::endl << std::endl;
            std::cout << " -r --reference:  The tree file with the reference partitioned tree." << std::endl << std::endl;
            std::cout << " -t --target:     The tree file with the target tree to find matching partitions in (or with partitions to be color-matched)." << std::endl << std::endl;
            std::cout << " -m --leafmatch   File with the meta-leaf matching information across both trees (output of comparetrees command)." << std::endl << std::endl;
            std::cout << " -O --outputf:    Output folder where partitioned/color matched tree files will be written." << std::endl << std::endl;
            std::cout << "[-s --signature]: Signature-based partition matching, instert lambda coefficient value. [xor with -o and -c]." << std::endl;
            std::cout << "                   In this method a pair signature matrices are computed for each reference-target partitions to find the quality of the match." << std::endl;
            std::cout << "                   Each signature matrix defines a value for each pair of base-nodes of the tree it belongs to: 1 the base nodes are found in the same cluster, 0 if otherwise." << std::endl;
            std::cout << "                   The higher the correlation between the reference and target-derived matrices, the best match is the target tree partition to the reference tree one." << std::endl;
            std::cout << "                   A smart hierarchical search through possible partritions is conducted to find the one with best signature matching." << std::endl;
            std::cout << "                  The lambda coefficient determines if and how a similar number of clusters in both partitions affects the matching quality value," << std::endl;
            std::cout << "                   Lambda=0 -> cluster number does not affect the quality value. Lambda=1 -> cluster value similarity has as much weight as singature correlation." << std::endl << std::endl;
            std::cout << "[-o --overlap]:   Overlap-based partition matching. [xor with -o and -c]." << std::endl;
            std::cout << "                   A match between two partititionsis found by iteratively matching clusters with higher base-node overlap and resolving possible ambiguities." << std::endl;
            std::cout << "                   The matching quality between partitions is defined as the number of base-nodes pairs that are classified in the same way in both partitions" << std::endl;
            std::cout << "                   (both in the smae cluster r both in different clusters) against the total number of pair combinations." << std::endl;
            std::cout << "                   A smart hierarchical search through possible partritions is conducted to find the one with best signature matching." << std::endl << std::endl;
            std::cout << "[-d --depth]:     Partition search depth (for signature and overlap matching. A higher value will mean a more exhaustive search of the possible partitions," << std::endl;
            std::cout << "                   but also a higher computation time, specially if the partition to be matched has a high number of clusters (>100)." << std::endl;
            std::cout << "                   The default value (0, recommended) will adaptively give high search depth to low-cluster partitions and lower search depth to high-cluster partittions." << std::endl << std::endl;
            std::cout << "[-c --justcolor]: Perform only color matching across reference and target tree parttitions (both trees need to have the same number of precompouted partitions)." << std::endl;
            std::cout << "                   In multiple-to-one matching cases clusters from the reference tree might also be recolored to better identify matching relationships across partitions." << std::endl << std::endl;
            std::cout << "[-x --excl]:      Color exclusively clusters that have a match, clusters without match will be recolored white (on both reference and target trees)" << std::endl << std::endl;
            std::cout << "[-v --verbose]:   Verbose output (recommended)." << std::endl << std::endl;
            std::cout << "[--vista]:        Write output tree files in vista coordinates (default is nifti)." << std::endl << std::endl;
            std::cout << std::endl;
            std::cout << "* Usage example:" << std::endl << std::endl;
            std::cout << " matchpartition -r refTree.txt -t targetTree.txt -m matching.txt -O results/ -s 0.5 -v" << std::endl << std::endl;
            exit(0);
        }
        if (variableMap.count( "version" ) )
        {
            std::cout << progName <<", version 2.0"<<std::endl;
            exit(0);
        }
        if ( variableMap.count( "verbose" ) )
        {
            std::cout << "verbose output" << std::endl;
            verbose=true;
        }

        if ( variableMap.count( "vista" ) )
        {
            if( verbose )
            {
                std::cout << "Using vista coordinates" << std::endl;
            }
            fileManagerFactory fmf;
            fmf.setVista();
            niftiMode = false;
        }
        else
        {
            if( verbose )
            {
                std::cout << "Using nifti coordinates" << std::endl;
            }
            fileManagerFactory fmf;
            fmf.setNifti();
            niftiMode = true;
        }


        if (variableMap.count("reference"))
        {
            if(!boost::filesystem::is_regular_file( boost::filesystem::path( refTreeFilename ) ) )
            {
                std::cerr << "ERROR: reference tree file \""<<refTreeFilename<<"\" is not a regular file"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);
            }
            std::cout << "Reference tree file: "<< refTreeFilename << std::endl;
        }
        else
        {
            std::cerr << "ERROR: no reference tree file stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }

        if (variableMap.count( "target" ) )
         {
            if(!boost::filesystem::is_regular_file(boost::filesystem::path( targetTreeFilename ) ) )
            {
                std::cerr << "ERROR: target tree file \""<<targetTreeFilename<<"\" is not a regular file"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);
            }
            std::cout << "Target tree file: "<< targetTreeFilename << std::endl;
        } else {
            std::cerr << "ERROR: no target tree file stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }

        if (variableMap.count( "leafmatch" ) )
        {
            if(!boost::filesystem::is_regular_file(boost::filesystem::path( matchTableFilename ) ) )
            {
                std::cerr << "ERROR: match table file \""<<matchTableFilename<<"\" is not a regular file"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);
            }
            std::cout << "Match table file: "<< matchTableFilename << std::endl;
        }
        else
        {
            std::cerr << "ERROR: no match Table file stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }

        if( variableMap.count( "signature" ) + variableMap.count( "overlap" ) + variableMap.count( "justcolor" ) > 1 )
        {
            std::cerr << "ERROR: multiple matching types selected, please use only one from  -s, -o, -c."<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }

        if (variableMap.count( "signature" ) )
        {
            std::cout << "Performing Signature partition matching (and color matching)" << std::endl;
            std::cout <<" Using a lambda factor of "<< lambda << std::endl;
            signaturePart = true;
            colorMatching = true;
        }
        else if (variableMap.count( "overlap" ) )
        {
            std::cout << "Performing Overlap partition matching (and color matching): " << std::endl;
            overlapPart = true;
            colorMatching = true;
        }
        else if (variableMap.count( "justcolor" ) )
        {
            std::cout << "Performing only color matching: " << std::endl;
            colorMatching = true;
        }
        else
        {
            std::cerr << "ERROR: no matching type selected, select signature, overlap or color matching"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);
        }

        if (variableMap.count( "excl" ) )
        {
            std::cout << "Color exclusively matched clusters (unmatched clusters will be white) " << std::endl;
            exclusive = true;
        }

        if( signaturePart || overlapPart )
        {
            if( searchDepth > 5 )
            {
                std::cout << "Level depth indicated: " << searchDepth << " is too high, setting to a maximum of 5" << std::endl;
                searchDepth = 5;
            }
            else if ( searchDepth = 0 )
            {
                std::cout << "Using automatic parttion-size based adaptive search depth " << std::endl;
            }
            else
            {
                std::cout << "Using a search depth of: " << searchDepth << std::endl;
            }
        }


        if (variableMap.count( "outputf" ) )
        {
            if(!boost::filesystem::is_directory(boost::filesystem::path( outputFolder ) ) )
            {
                std::cerr << "ERROR: output folder \""<<outputFolder<<"\" is not a directory"<<std::endl;
                std::cerr << visibleOptions << std::endl;
                exit(-1);

            }
            std::cout << "Output folder: "<< outputFolder << std::endl;
        }
        else
        {
            std::cerr << "ERROR: no output folder stated"<<std::endl;
            std::cerr << visibleOptions << std::endl;
            exit(-1);

        }


        std::string logFilename(outputFolder+"/"+progName+"_log.txt");
        std::ofstream logFile(logFilename.c_str());
        if(!logFile) {
            std::cerr << "ERROR: unable to open log file: \""<<logFilename<<"\""<<std::endl;
            exit(-1);
        }
        logFile <<"Start Time:\t"<< ctime(&programStartTime) <<std::endl;
        logFile <<"Working directory:\t"<< workingDir.string() <<std::endl;
        logFile <<"Verbose:\t"<< verbose <<std::endl;
        logFile <<"Reference tree:\t"<< refTreeFilename <<std::endl;
        logFile <<"Target tree:\t"<< targetTreeFilename <<std::endl;
        logFile <<"Matching table:\t"<< matchTableFilename <<std::endl;
        logFile <<"Output folder:\t"<< outputFolder <<std::endl;
        if( niftiMode )
        {
            logFile << "Using nifti coordinates" << std::endl;
        }
        else
        {
            logFile << "Using vista coordinates" << std::endl;
        }
        logFile <<"-------------"<<std::endl;


        /////////////////////////////////////////////////////////////////


        WHtree refTree( refTreeFilename );
        WHtree targetTree( targetTreeFilename );


        if (!refTree.isLoaded() || !targetTree.isLoaded() )
        {
            throw std::runtime_error ("ERROR @ compareTrees(): trees are not loaded");
        }

        logFile <<"Reference Tree: "<< refTree.getReport(false) <<std::endl;
        logFile <<"Target Tree: "<< targetTree.getReport(false) <<std::endl;

        if (refTree.getDataSize() != targetTree.getDataSize() )
        {
            std::cerr <<"Reference Tree: "<< refTree.getReport() <<std::endl;
            std::cerr <<"Target Tree: "<< targetTree.getReport() <<std::endl;
            throw std::runtime_error ("ERROR @ compareTrees() datasets have different dimensions");
        }

        if (verbose) {
            std::cout <<"Reference Tree: "<< refTree.getReport(false) <<std::endl;
            std::cout <<"Target Tree: "<< targetTree.getReport(false) <<std::endl;
        }


        partitionMatcher matcher(&refTree,&targetTree,matchTableFilename, verbose);
        std::string depthString;
        if( searchDepth > 0 )
        {
            depthString = "_d"+string_utils::toString< unsigned int >( searchDepth ) ;
        }

        std::cout <<matcher.reportBaseNodes()<<std::endl;
        std::string suffixPart("_pm_Signature_l" + string_utils::toString< float >( lambda ) + depthString + ".txt");
        std::string suffixNew("_pm_Overlap" + depthString + ".txt");
        std::string suffixColor("_colorMatch.txt");
        bool refTreeColorsChanged( false );


        if( signaturePart )
        {
            logFile <<  "Signature Matching" << std::endl;
            logFile <<  "Lambda:\t" << lambda <<std::endl;
            logFile <<  "Search depth:\t" << searchDepth <<std::endl;
            matcher.findMatchingPartitions( lambda );
        }
        else if ( overlapPart )
        {
            logFile <<  "Overlap Matching" <<std::endl;
            logFile <<  "Search depth:\t" << searchDepth <<std::endl;
            matcher.findMatchingPartitions( -1 );
        }

        if( colorMatching )
        {
            logFile <<  "Color Matching" <<std::endl;
            refTreeColorsChanged = matcher.matchColors( exclusive );

        }

        std::string refOutput;
        std::string targetOutput;

        if ( signaturePart )
        {
            targetOutput = outputFolder + "/" + targetTree.getName() + suffixPart;
        }
        else if ( overlapPart )
        {
            targetOutput = outputFolder + "/" + targetTree.getName() + suffixNew ;
        }
        else
        {
            targetOutput = outputFolder + "/" + targetTree.getName() + suffixColor;
        }

        if( refTreeColorsChanged )
        {
            refOutput = outputFolder + "/" + refTree.getName() + suffixColor;
        }
        else
        {
            refOutput = outputFolder + "/" + refTree.getName() + ".txt";
        }

        if( verbose )
        {
            std::cout <<  "Writing output target tree file to " << targetOutput << std::endl;
            std::cout <<  "Writing output reference tree file to " << refOutput << std::endl;
        }

        targetTree.writeTree( targetOutput, niftiMode );
        refTree.writeTree( refOutput, niftiMode );

        logFile <<  "Written output target tree file to " << targetOutput << std::endl;
        logFile <<  "Written output reference tree file to " << refOutput << std::endl;

        /////////////////////////////////////////////////////////////////

        // save and print total time
        time_t programEndTime( time( NULL ) );
        int totalTime( difftime( programEndTime, programStartTime ) );
        std::cout <<"Program Finished, total time: "<< totalTime/3600 <<"h "<<  (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\"   "<< std::endl;
        logFile <<"-------------"<<std::endl;
        logFile <<"Finish Time:\t"<< ctime(&programEndTime) <<std::endl;
        logFile <<"Elapsed time : "<< totalTime/3600 <<"h "<<  (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\""<< std::endl;




//    }
//    catch(std::exception& e)
//    {
//        std::cout << e.what() << std::endl;
//        return 1;
//    }
    return 0;
}