// Start here
int main(int argc,char *argv[])
{
struct arguments arguments;
arguments.inputSize = 0;
arguments.nChannels = 0;
arguments.beforeSpike = -1;
arguments.afterSpike = -1;
arguments.peakPosition = -1;
arguments.spikeLength = -1;
arguments.nComponents = 0; // number of principal components
arguments.isCenteredData = false;
arguments.offset = 0;
arguments.isInputFileProvided = false;
arguments.isOutputFileProvided = false;
arguments.isInputSizeProvided = false;
arguments.isNChannelsProvided = false;
arguments.isBeforeSpikeProvided = false;
arguments.isAfterSpikeProvided = false;
arguments.isPeakPositionProvided = false;
arguments.isSpikeLengthProvided = false;
arguments.isNComponentsProvided = false;
arguments.isExtraFeaturesProvided = false;
arguments.isOffsetProvided = false;
#ifdef NBITS
arguments.nBits = int(RECORD_BYTE_SIZE*8);
arguments.isNBitsProvided = false;
#endif
parseArgs(argc,argv,arguments); // Parse command-line
short *rawData; // data, means/channel
short **peakVal; // peak values for extra features output
// means, sum and variance-cov matrix for each dimension in each channel
double **mean,**sum;
// data for each channel/ spike dimension/ spike & reduced data (PCA)
gsl_matrix **datSpkChanCenter, ** datSpkChan,**reducedData;
gsl_matrix **varcov;// variance-cov matrix for each dimension
FILE *inputFile = NULL,*outputFile = NULL;
unsigned long int nSpikes = -1,nRecordsRead = 0;
int data2use = arguments.spikeLength; // number of record to use in the waveform
int recShift = 0; // shift for first record to consider in the waveform
if(arguments.isBeforeSpikeProvided)
{
data2use = (arguments.beforeSpike+1+arguments.afterSpike);
recShift = arguments.peakPosition-arguments.beforeSpike;
}
gsl_vector *eigenValues = gsl_vector_alloc(data2use);
gsl_matrix *eigenVectors = gsl_matrix_alloc(data2use,data2use);
gsl_eigen_symmv_workspace * w = gsl_eigen_symmv_alloc(data2use);
gsl_matrix_view reducedEigenVectors; // for storing final data
// open input
if ( arguments.isInputFileProvided )
{
inputFile = fopen(arguments.inputFileName,"rb");
if ( inputFile == NULL )
{
cerr << "error: cannot open '" << arguments.inputFileName << "'." << endl;
exit(1);
} // if
fseeko(inputFile,0,SEEK_END); // put the position indicator at the end of the stream
arguments.inputSize = ftello(inputFile); // value of the position indicator of the stream (here ~file size)
} // if
// Check Input Size
if ( !checkInputs(arguments) ) // check arguments value
exit(1);
if ( verbose )
{
cout << endl;
cout << "Input File = ";
if ( arguments.isInputFileProvided ) cout << arguments.inputFileName << endl;
else cout << "-" << endl;
cout << "Output File = " << arguments.outputFileName << endl;
cout << "Input Size = ";
if ( arguments.isInputSizeProvided ) cout << arguments.inputSize << endl;
else cout << "N/A" << endl;
#ifdef NBITS
cout << "Resolution = ";
if ( arguments.isNBitsProvided ) cout << arguments.nBits << " bits" << endl;
else cout << "default" << endl;
#endif
cout << endl;
} // if verbose
// number of records (for all and one channels)
nRecords = arguments.inputSize/RECORD_BYTE_SIZE;
nRecordsPerChannel = nRecords/arguments.nChannels;
nSpikes = nRecordsPerChannel/arguments.spikeLength; // nb spikes
if ( nRecords < 1 || nRecordsPerChannel < 1 )
{
cerr << "error: not enough records (size " << arguments.inputSize << ")" << endl;
exit(1);
}
if ( nSpikes < 1 )
{
cerr << "error: incorrect spike number (" << nSpikes << "), check number of channels ("
<< arguments.nChannels << ") and input size (" << arguments.inputSize << ")." << endl;
exit(1);
}
if ( verbose )
{
cout << "Waveform length = " << arguments.spikeLength << endl;
cout << "Number of principal components = " << arguments.nComponents << endl;
if(arguments.isBeforeSpikeProvided)
{
cout << "Number of samples before peak = " << arguments.beforeSpike << endl;
cout << "Number of samples after peak = " << arguments.afterSpike << endl;
cout << "Peak position in waveform = " << arguments.peakPosition << endl;
}
cout << "Projection with centered data = " << arguments.isCenteredData << endl;
///cout << "Record size basis = " << (RECORD_BYTE_SIZE*8) << " bits" << endl;
cout << "Number of input records = " << nRecords << endl;
cout << "Number of records per channel = " << nRecordsPerChannel << endl;
cout << "Number of spikes = " << nSpikes <<endl;
cout << endl;
}
ProgressBar *progress = new ProgressBar("","PCA",(arguments.nChannels+4));
// Init arrays
rawData = new short[nRecords]; // Buffer for all data (all channels)
mean = new double* [arguments.nChannels]; // means init
sum = new double* [arguments.nChannels]; // sums init
if(arguments.isExtraFeaturesProvided)
peakVal = new short* [arguments.nChannels]; // peak values init&
if(!arguments.isCenteredData)
datSpkChan = new gsl_matrix* [arguments.nChannels];
datSpkChanCenter = new gsl_matrix* [arguments.nChannels];
reducedData = new gsl_matrix* [arguments.nChannels];
varcov = new gsl_matrix* [arguments.nChannels];
progress->start(); // Start progress bar
///progress->message("Extracting data");
// Get data
if ( arguments.isInputFileProvided )
{
rewind(inputFile); // put the position indicator at the beginning of the stream
nRecordsRead = fread(rawData,sizeof(short),nRecords,inputFile);
fclose(inputFile);
}
else
{
nRecordsRead = fread(rawData,sizeof(short),nRecords,stdin);
} // else
if ( nRecordsRead != nRecords )
{
cerr << "error: insufficient number of records in the file (" << nRecordsRead
<< ", expecting " << nRecords << ")" << endl;
exit(1);
}
progress->advance(); // Complete data importation
// Fill arrays with rec values & compute means
///progress->message("Preparing data for PCA");
for ( int i = 0 ; i < arguments.nChannels ; ++i )
{
mean[i] = new double[data2use];
sum[i] = new double[data2use];
datSpkChanCenter[i] = gsl_matrix_alloc(data2use,nSpikes);
if(!arguments.isCenteredData)
datSpkChan[i] = gsl_matrix_alloc(data2use,nSpikes);
if(arguments.isExtraFeaturesProvided)
peakVal[i] = new short[nSpikes];
varcov[i] = gsl_matrix_alloc(data2use,data2use);
reducedData[i] = gsl_matrix_alloc(arguments.nComponents,nSpikes);
for ( int j = 0 ; j < data2use ; ++j )
{
mean[i][j] = -1;
sum[i][j] = 0;
for ( unsigned int k = 0 ; k < nSpikes ; ++k )
{
double v = rawData[(arguments.nChannels*arguments.spikeLength)*k+((j+recShift)*arguments.nChannels)+i];
gsl_matrix_set(datSpkChanCenter[i],j,k,v);
if(!arguments.isCenteredData)
gsl_matrix_set(datSpkChan[i],j,k,v);
sum[i][j] += v;
if(arguments.isExtraFeaturesProvided && (j+recShift)==arguments.peakPosition)
peakVal[i][k] = v; // if this is the peak, store it !
} // for k
mean[i][j] = sum[i][j]/nSpikes; // mean computation
for ( unsigned int k = 0 ; k < nSpikes ; ++k )
{
gsl_matrix_set (datSpkChanCenter[i],j,k,(gsl_matrix_get(datSpkChanCenter[i],j,k)-mean[i][j]));
} // for k
} // for j
} // for i
delete[] rawData; // free memory
progress->advance(); // Complete data initialization
if ( verbose )
{
cout << endl << endl;
cout << "Total number of channels = " << arguments.nChannels << endl;
for ( int c = 0 ; c < arguments.nChannels ; ++c )
{
cout << "Means for channel #" << c << " = ";
for ( int d = 0 ; d < data2use ; ++d )
{
cout << mean[c][d] << ", ";
} // for d
cout << endl;
cout << endl;
} // for c
cout << endl;
} // verbose
// PCA statement
///progress->message("Computing PCA");
for ( int i = 0 ; i < arguments.nChannels ; ++i )
{
// compute variance-covariance matrix (Data * DataTrans)
gsl_blas_dgemm(CblasNoTrans,CblasTrans,(1.0/(nSpikes-1)),datSpkChanCenter[i],datSpkChanCenter[i],0.0,varcov[i]);
// solve eigen system to get eigen values and vectors
gsl_eigen_symmv(varcov[i],eigenValues,eigenVectors,w);
gsl_eigen_symmv_sort(eigenValues,eigenVectors,GSL_EIGEN_SORT_VAL_DESC); // descending sort for eigen vectors and values
// keep only eigen vectors for the given firt principal components
reducedEigenVectors = gsl_matrix_submatrix(eigenVectors,0,0,data2use,arguments.nComponents);
// compute new coordinates for data : Trans(evec_reduce) x Trans(data)
if(!arguments.isCenteredData)
gsl_blas_dgemm(CblasTrans,CblasNoTrans,1.0,&reducedEigenVectors.matrix,datSpkChan[i],0.0,reducedData[i]);
else
gsl_blas_dgemm(CblasTrans,CblasNoTrans,1.0,&reducedEigenVectors.matrix,datSpkChanCenter[i],0.0,reducedData[i]);
progress->advance(); // Complete PCA for channel i
} // for i
///progress->message("Saving");
// Write ouput file (FET format)
outputFile = fopen(arguments.outputFileName,"w");
if( !arguments.isExtraFeaturesProvided )
fprintf(outputFile,"%i\n",(arguments.nChannels*arguments.nComponents));
else
fprintf(outputFile,"%i\n",(arguments.nChannels*arguments.nComponents + arguments.nChannels));
for ( unsigned int k = 0 ; k < nSpikes ; ++k )
{
for ( int i = 0 ; i < arguments.nChannels ; ++i )
{
for ( int j = 0 ; j < arguments.nComponents ; ++j )
{
double *d = gsl_matrix_ptr(reducedData[i],j,k);
if ( !fprintf(outputFile,"%i ",int(*d)) )
cerr << "warning: missing data (channel " << i << ", dimension " << j << ", spike "
<< k << ")." << endl;
} // for j
} // for i
if( arguments.isExtraFeaturesProvided ) // write peak value after all data
for ( int i = 0; i < arguments.nChannels ; ++i )
if ( !fprintf(outputFile,"%i ",int(peakVal[i][k])) )
cerr << "warning: missing peak (channel " << i << ", spike " << k << ")." << endl;
fprintf(outputFile,"\n");
} // for k
fclose(outputFile);
progress->advance(); // Complete saving results
// Free Memory
///progress->message("Free Memory");
for ( int i = 0 ; i < arguments.nChannels ; ++i )
{
delete[] mean[i];
delete[] sum[i];
if(arguments.isExtraFeaturesProvided)
delete[] peakVal[i];
if(!arguments.isCenteredData)
gsl_matrix_free(datSpkChan[i]);
gsl_matrix_free(datSpkChanCenter[i]);
gsl_matrix_free(varcov[i]);
gsl_matrix_free(reducedData[i]);
}
if(arguments.isExtraFeaturesProvided)
delete[] peakVal;
if(!arguments.isCenteredData)
delete[] datSpkChan;
delete[] datSpkChanCenter;
delete[] mean;
delete[] sum;
delete[] varcov;
delete[] reducedData;
gsl_eigen_symmv_free(w);
gsl_vector_free(eigenValues);
gsl_matrix_free(eigenVectors);
progress->advance(); // Complete free memory
delete progress;
if ( verbose ) cout << endl;
return 0;
} // main
