void GraphManager::broadcastTransform(const ros::TimerEvent& ) {
tf::Transform cam2rgb;
cam2rgb.setRotation(tf::createQuaternionFromRPY(-1.57,0,-1.57));
cam2rgb.setOrigin(tf::Point(0,-0.04,0));
world2cam_ = cam2rgb*kinect_transform_;
//printTransform("kinect", kinect_transform_);
time_of_last_transform_ = ros::Time::now();
br_.sendTransform(tf::StampedTransform(world2cam_, time_of_last_transform_,
"/openni_camera", "/slam_transform"));
if(!batch_processing_runs_)
br_.sendTransform(tf::StampedTransform(cam2rgb, time_of_last_transform_,
"/openni_camera", "/batch_transform"));
//visualize the transformation
std::stringstream ss;
Eigen::Matrix4f transform;
pcl_ros::transformAsMatrix(kinect_transform_, transform);
ss << "<b>Current Camera Transformation w.r.t. the Initial Frame</b>";
ss << "<pre>" << transform << "</pre>";
QString mystring(ss.str().c_str());
emit newTransformationMatrix(mystring);
}
/*** OVERLOADING OF THE + OPERATOR TO FACILITATE STRING CONCATENATION ***/
String& String::operator+(String &s) {
int l=this->len+s.len;
char *str=new char[l];
strcpy(str,this->ch);
strcat(str,s.ch);
String mystring(str);
return mystring;
}
int test_iterator_18()
{
// std::ostreambuf_iterator: 输出流缓存迭代器
std::string mystring("Some text here...\n");
std::ostreambuf_iterator<char> out_it(std::cout); // stdout iterator
std::copy(mystring.begin(), mystring.end(), out_it); // Some text here...
return 0;
}
std::list<int> ProcessControl::getPidProcessByName(std::string name)
{
std::list<int> result;
qDebug() << "ProcessControl::getPidProcessByName: Begin:";
#ifndef WIN32
QProcess myprocess;
std::string command = std::string("ps -C ")+name+std::string(" -o pid --no-heading");
qDebug() << "ProcessControl::getPidProcessByName: comando solicitado:" << command.c_str();
myprocess.start(command.c_str());
if (!myprocess.waitForFinished()) return result;
while (!myprocess.atEnd())
{
char buf[16];
qint64 length = myprocess.readLine(buf,sizeof(buf));
if (length != -1)
{
QString mystring(buf);
result.push_back(mystring.toInt());
}
else break;
}
#else
DWORD aProcesses[1024], cbNeeded, cProcesses;
if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) )
return result;
// Calculate how many process identifiers were returned.
cProcesses = cbNeeded / sizeof(DWORD);
for ( int i = 0 ; i < cProcesses; i++)
{
if (aProcesses[i] != 0)
{
std::wstring nombre = PrintProcessNameAndID( aProcesses[i] );
std::string temp;
std::copy(nombre.begin(), nombre.end(), std::back_inserter(temp));
qDebug() << "ProcessControl::getPidProcessByName: New pid name" << aProcesses[i] << temp.c_str();
if (QString(temp.c_str()).toLower()==QString(name.c_str()).toLower())
{
qDebug() << "ProcessControl::getPidProcessByName: found proccess";
result.push_back((int)aProcesses[i]);
}
}
}
#endif
return result;
}
SelectionVOI::SelectionVOI( Anatomy *pSourceAnatomy, const float threshold, const ThresholdingOperationType opType )
: SelectionObject( Vector( 0.0f, 0.0f, 0.0f ), Vector( 0.0f, 0.0f, 0.0f ) ),
m_voiSize( 0 ),
m_generationThreshold( threshold ),
m_thresType( opType ),
m_pIsoSurface( NULL ),
m_sourceAnatIndex( pSourceAnatomy->getDatasetIndex() )
{
wxString mystring(wxT("[VOI] - ") + pSourceAnatomy->getName());
m_name = mystring;
m_objectType = VOI_TYPE;
buildSurface( pSourceAnatomy );
setColor( wxColour( 240, 30, 30 ) );
}
void runcint()
{
#endif
string mystring("test string");
if (!t01(mystring)) {
fprintf(stderr,"fail to pass by reference\n");
gSystem->Exit(1);
}
if (!t01val(mystring) ) {
fprintf(stderr,"fail to pass by value\n");
gSystem->Exit(1);
}
if (!t01p(&mystring) ) {
fprintf(stderr,"fail to pass by address\n");
gSystem->Exit(1);
}
}
void MainFrame::SaveOverlay()
{
// save overlay image
// create a bitmap(the same size as image)
int width = m_nWidth;
int height = m_nHeight;
wxBitmap *overlay = new wxBitmap(width,height);
// Create a memory Device Context
wxMemoryDC memDC;
//Tell memDC to write on.
memDC.SelectObject( *overlay );
m_pOverlayPane->render(memDC);
memDC.SelectObject( wxNullBitmap );
stringstream file;
file<<setfill('0');
// file<<path;
// file<<savefolder;
file<<"./";
file<<"Overlay";
file<<"/";
if(!bfs::exists(file.str().c_str()))
{
bfs::create_directory(file.str().c_str());
}
file<<"overlay"<<setw(4)<< m_nCurrentFrame <<".png";
cout<<"saving as "<<file.str()<<endl;
wxString mystring(file.str().c_str(),wxConvUTF8);
overlay->SaveFile(mystring, wxBITMAP_TYPE_PNG, (wxPalette*)NULL );
delete overlay;
}
// --------------------------------------------------------------------------
//
// Function
// Name: unsigned int ProcessControl::getInstancePID(BBInstance)
// Purpose: Obtiene el pid del proceso asociado a la instancia
// Created: 25/6/08
//
// ------------------
unsigned int ProcessControl::getInstancePID(BBInstance myinstance)
{
qDebug() << "ProcessControl::getInstancePID: begin:";
#ifndef WIN32
std::string command = std::string("ps -C bbackupd -o pid,uid,command --no-heading");
qDebug() << "ProcessControl::getInstancePID: comando solicitado:" << command.c_str();
QProcess myprocess;
myprocess.start(command.c_str());
if (!myprocess.waitForFinished())
{
myprocess.close();
return 0;
}
while (!myprocess.atEnd())
{
char buf[1024];
qint64 length = myprocess.readLine(buf,sizeof(buf));
if (length != -1)
{
QString mystring(buf);
QRegExp regex("^\\s*(\\d*)\\s*(\\d*)\\s*((\\w|/)*)\\s((\\w|/|\\.)*).*$");
qDebug() << "ProcessControl::getInstancePID: Parsing line:" << mystring;
if (regex.exactMatch(mystring))
{
//Comparar, y si es igual devolver
QStringList strlist = regex.capturedTexts();
qDebug() << "ProcessControl::getInstancePID: lista:" << strlist;
if ((myinstance.getConfigPath().absoluteFilePath() == QFileInfo(strlist.at(5)).absoluteFilePath()) &&
(ProcessControl::userNamefromUID(strlist.at(2).toUInt()) == myinstance.getUserName()) )
{
qDebug() << "Encontrado!";
myprocess.close();
return strlist.at(1).toUInt();
}
else
{
qDebug() << "linea incorrecta" << strlist.at(5) << myinstance.getConfigPath().absoluteFilePath() << strlist.at(2).toUInt() << myinstance.getUserName();
}
}
else
{
qDebug() << "ProcessControl::getInstancePID: Error en la expresion regular";
}
}
else break;
}
qDebug() << "No se encontro el proceso";
myprocess.close();
return 0;
#else
std::list<int> listapids = getPidProcessByName("bbackupd.exe");
//Para cada pid:
for (std::list<int>::const_iterator i = listapids.begin();
i!= listapids.end();
i++)
{
// Comprobar si el uid es el usuario actual
// Comprobar que el parametro es el fichero de configuraci�n que nos interesa
qDebug() << "ProcessControl::getInstancePID: Iterando sobre un proceso";
//if(getConfigPath(*i) == QString(myinstance.getConfigPath().absolutePath())
if(QFileInfo(QFileInfo(getBinaryPath(*i))) == myinstance.getBinaryPath()
&& getPIDUserName(*i) == myinstance.getUserName())
{
return *i;
}
}
return 0;
#endif
}
// [[Rcpp::export]]
Rcpp::NumericVector vcf_stats_gz(std::string x) {
Rcpp::NumericVector stats(4); // 4 elements, all zero. Zero is default.
stats.names() = Rcpp::StringVector::create("meta", "header", "variants", "columns");
gzFile file;
file = gzopen (x.c_str(), "r");
if (! file) {
Rcpp::Rcerr << "gzopen of " << x << " failed: " << strerror (errno) << ".\n";
return stats;
}
// Scroll through buffers.
std::string lastline = "";
while (1) {
Rcpp::checkUserInterrupt();
int err;
int bytes_read;
char buffer[LENGTH];
bytes_read = gzread (file, buffer, LENGTH - 1);
buffer[bytes_read] = '\0';
std::string mystring(reinterpret_cast<char*>(buffer)); // Recast buffer as a string.
mystring = lastline + mystring;
std::vector < std::string > svec; // Initialize vector of strings for parsed buffer.
char split = '\n'; // Must be single quotes!
vcfRCommon::strsplit(mystring, svec, split);
// Scroll through lines derived from the buffer.
unsigned int i = 0;
for(i=0; i < svec.size() - 1; i++){
stat_line(stats, svec[i]);
}
// Manage the last line.
lastline = svec[svec.size() - 1];
// Check for EOF or errors.
if (bytes_read < LENGTH - 1) {
if ( gzeof (file) ) {
if( stats(3) == 0 ){
// Count columns from last line.
std::vector < std::string > col_vec;
char col_split = '\t'; // Must be single quotes!
vcfRCommon::strsplit(svec[0], col_vec, col_split);
stats(3) = col_vec.size();
}
break;
}
else {
const char * error_string;
error_string = gzerror (file, & err);
if (err) {
Rcpp::Rcerr << "Error: " << error_string << ".\n";
return stats;
}
}
}
}
gzclose (file);
return stats;
}
// [[Rcpp::export]]
Rcpp::CharacterMatrix read_body_gz(std::string x,
Rcpp::NumericVector stats,
int nrows = -1,
int skip = 0,
Rcpp::IntegerVector cols = 0,
int convertNA = 1,
int verbose = 1) {
// NA matrix for unexpected results.
Rcpp::StringMatrix na_matrix(1,1);
na_matrix(0,0) = NA_STRING;
/*
* Manage cols vector.
* The first eight (1-based) columns are mandatory.
* We can ensure they are there by adding them,
* sorting and removing adjacent non-identical values.
*/
// for( int i=9; i >= 1; i-- ){
for( int i=8; i >= 1; i-- ){
cols.push_front(i);
}
cols.sort();
// Remove duplicate values using a set.
std::set<int> s( cols.begin(), cols.end() );
cols.assign( s.begin(), s.end() );
cols = cols - 1; // R is 1-based, C is 0-based.
// Initialize matrix for body data.
// old: Rcpp::CharacterMatrix gt(stats[2], stats[3]);
int row_num = 0;
if( ( nrows == -1 ) & ( skip == 0 ) ){
nrows = stats[2];
} else if ( ( nrows != -1 ) & ( skip == 0 ) ){
// nrows = nrows;
} else if ( ( nrows == -1 ) & ( skip > 0) ){
nrows = stats[2] - skip;
} else if ( ( nrows != -1 ) & ( skip > 0) ){
// nrows = nrows;
} else {
Rcpp::Rcerr << "failed to calculate return matrix geometry.";
return na_matrix;
}
Rcpp::CharacterMatrix gt( nrows, cols.size() );
// if ( nrows > -1 & skip == 0 ){
// row_num = nrows;
// } else if ( nrows == -1 & skip > 0 ){
// row_num = stats[2] - skip;
// } else {
// row_num = stats[2];
// }
// Rcpp::CharacterMatrix gt( row_num, cols.size() );
row_num = 0;
if( verbose == 1 ){
Rcpp::Rcout << "Character matrix gt created.\n";
Rcpp::Rcout << "Character matrix gt rows: "; Rcpp::Rcout << gt.rows();
Rcpp::Rcout << "\n";
Rcpp::Rcout << "Character matrix gt cols: "; Rcpp::Rcout << gt.cols();
Rcpp::Rcout << "\n";
Rcpp::Rcout << "skip: "; Rcpp::Rcout << skip;
Rcpp::Rcout << "\n";
Rcpp::Rcout << "nrows: "; Rcpp::Rcout << nrows;
Rcpp::Rcout << "\n";
Rcpp::Rcout << "row_num: "; Rcpp::Rcout << row_num;
Rcpp::Rcout << "\n";
Rcpp::Rcout << "\n";
}
// Create filehandle and open.
gzFile file;
file = gzopen (x.c_str(), "r");
if (! file) {
Rcpp::Rcerr << "gzopen of " << x << " failed: " << strerror (errno) << ".\n";
return na_matrix;
}
// Because the last line may be incomplete,
// We'll typically omit it from processing and
// concatenate it to the first line.
// But first we'll have to initialize it.
std::string lastline = "";
// String vector to store the header (^#CHROM...).
std::vector<std::string> header_vec;
// variant counter.
int var_num = 0;
// Scroll through buffers.
while (1) {
Rcpp::checkUserInterrupt();
int err;
// Slurp in a buffer.
int bytes_read;
char buffer[LENGTH];
bytes_read = gzread (file, buffer, LENGTH - 1);
buffer[bytes_read] = '\0'; // Terminate the buffer.
std::string mystring(reinterpret_cast<char*>(buffer)); // Recast buffer as a string.
mystring = lastline + mystring; // Concatenate last line to the buffer
// Delimit into lines.
std::vector < std::string > svec; // Initialize vector of strings for parsed buffer.
char split = '\n'; // Must be single quotes!
vcfRCommon::strsplit(mystring, svec, split);
/*
svec should now contain a vector of strings,
one string for each line
where the last line may be incomplete.
We can now process each line except the last.
*/
// Scroll through lines.
unsigned int i = 0;
for(i = 0; i < svec.size() - 1; i++){
// Check and remove carriage returns (Windows).
if( svec[i][ svec[i].size()-1] == '\r' ){
svec[i].erase( svec[i].size() - 1 );
}
if(svec[i][0] == '#' && svec[i][1] == '#'){
// Meta line, ignore.
} else if(svec[i][0] == '#' && svec[i][1] == 'C'){
// Process header.
// Rcpp::Rcout << svec[i].substr(0,40) << "\n\n";
char header_split = '\t';
vcfRCommon::strsplit(svec[i], header_vec, header_split);
// Subset the header to select columns.
std::vector<std::string> header_vec2( cols.size() );
for(int j=0; j<cols.size(); j++){
header_vec2[j] = header_vec[ cols[j] ];
}
header_vec = header_vec2;
} else {
// Variant line.
if ( ( var_num >= skip ) & ( row_num < nrows ) ){
proc_body_line(gt, row_num, svec[i], cols, convertNA);
row_num++; // Return matrix row number.
}
var_num++; // Input row number.
if(var_num % nreport == 0 && verbose == 1){
Rcpp::Rcout << "\rProcessed variant " << var_num;
}
}
}
// Processed all lines of current buffer.
// Keep the last line so we can append it to
//the beginning of the next buffer.
lastline = svec[svec.size() - 1];
// Rcpp::Rcout << "line-2:" << svec[svec.size() - 2].substr(0,40) << "|<-\n";
// Rcpp::Rcout << "line-1:" << svec[svec.size() - 1].substr(0,40) << "|<-\n";
// Rcpp::Rcout << "\n";
/*
* We can bail out early if we have read nrows.
* Before we do we need to check that:
* 1) we have read in nrows
* 2) we have processed the header
* (important when nrows is small)
* 3) we actually have a line (when buffer ends at the end of a line).
*/
if( ( row_num >= nrows ) & ( lastline[0] != '#' ) & ( lastline.size() > 0 ) ){
// Rcpp::Rcout << "\nBreaking!\n";
// Rcpp::Rcout << "lastline: " << lastline.substr(0,40) << "\n";
break;
}
// Check for EOF or errors.
if (bytes_read < LENGTH - 1) {
if (gzeof (file)) {
break;
}
else {
const char * error_string;
error_string = gzerror (file, & err);
if (err) {
Rcpp::Rcerr << "Error: " << error_string << ".\n";
return na_matrix;
}
}
}
// Return to top of loop and process another buffer.
} // Close while.
// Close filehandle.
gzclose (file);
// Rcpp::Rcout << "\n\n>>---<< Made it: file close! >>---<<\n\n";
// Rcpp::Rcout << "header_vec.size(): " << header_vec.size() << "\n";
if( stats[1] == 0 ){
if( verbose == 1 ){
Rcpp::Rcout << "Warning: no header information was found! Data contains no sample names!\n";
}
} else {
if( header_vec.size() == (unsigned)gt.ncol() ){
header_vec[0] = "CHROM";
gt.attr("dimnames") = Rcpp::List::create(Rcpp::CharacterVector::create(), header_vec);
} else {
if( verbose == 1 ){
Rcpp::Rcout << "Warning: no header information found!\n";
}
}
}
// Rcpp::Rcout << "\n\n>>---<< Made it! >>---<<\n\n";
if(verbose == 1){
Rcpp::Rcout << "\rProcessed variant: " << var_num;
Rcpp::Rcout << "\nAll variants processed\n";
}
// Rcpp::DataFrame df1 = Rcpp::DataFrame::create(gt);
// Rcpp::DataFrame df1(gt);
// df1.names() = header_vec;
// if(verbose == 1){
// Rcpp::Rcout << "Rcpp::DataFrame created.\n";
// }
return gt;
}
// [[Rcpp::export]]
Rcpp::StringVector read_meta_gz(std::string x, Rcpp::NumericVector stats, int verbose) {
// Read in the meta lines.
// stats consists of elements ("meta", "header", "variants", "columns");
Rcpp::StringVector meta(stats[0]);
std::string line; // String for reading file into
int meta_row = 0;
gzFile file;
file = gzopen (x.c_str(), "r");
if (! file) {
Rcpp::Rcerr << "gzopen of " << x << " failed: " << strerror (errno) << ".\n";
return Rcpp::StringVector(1);
}
// Scroll through buffers.
std::string lastline = "";
while (1) {
Rcpp::checkUserInterrupt();
int err;
int bytes_read;
char buffer[LENGTH];
bytes_read = gzread (file, buffer, LENGTH - 1);
buffer[bytes_read] = '\0';
std::string mystring(reinterpret_cast<char*>(buffer)); // Recast buffer as a string.
mystring = lastline + mystring;
std::vector < std::string > svec; // Initialize vector of strings for parsed buffer.
char split = '\n'; // Must be single quotes!
vcfRCommon::strsplit(mystring, svec, split);
unsigned int i = 0;
while(meta_row < stats(0) && i < svec.size() - 1){
// Check and remove carriage returns (Windows).
if( svec[i][ svec[i].size()-1] == '\r' ){
svec[i].erase( svec[i].size() - 1 );
}
meta(meta_row) = svec[i];
meta_row++;
i++;
if(meta_row % nreport == 0 && verbose == 1){
Rcpp::Rcout << "\rMeta line " << meta_row << " read in.";
}
}
lastline = svec[svec.size() - 1];
// Check for EOF or errors.
if (bytes_read < LENGTH - 1) {
if (gzeof (file)) {
break;
}
else {
const char * error_string;
error_string = gzerror (file, & err);
if (err) {
Rcpp::Rcerr << "Error: " << error_string << ".\n";
return Rcpp::StringVector(1);
}
}
}
}
gzclose (file);
if(verbose == 1){
Rcpp::Rcout << "\rMeta line " << meta_row << " read in.";
Rcpp::Rcout << "\nAll meta lines processed.\n";
}
return meta;
}
SelectionVOI::SelectionVOI( /*DatasetHelper *pDH, */Anatomy *pSourceAnatomy, const float threshold, const ThresholdingOperationType opType )
: SelectionObject( Vector(0.0, 0.0, 0.0), Vector(0.0, 0.0, 0.0) ),
m_voiSize( 0 )
{
m_nbRows = pSourceAnatomy->getRows();
m_nbCols = pSourceAnatomy->getColumns();
m_nbFrames = pSourceAnatomy->getFrames();
vector< float > * const pAnatDataset = pSourceAnatomy->getFloatDataset();
m_includedVoxels.assign( pAnatDataset->size(), false );
if( opType == THRESHOLD_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::equal_to< float >(), threshold ) );
}
else if( opType == THRESHOLD_GREATER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater< float >(), threshold ) );
}
else if( opType == THRESHOLD_GREATER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater_equal< float >(), threshold ) );
}
else if( opType == THRESHOLD_SMALLER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less< float >(), threshold ) );
}
else if( opType == THRESHOLD_SMALLER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less_equal< float >(), threshold ) );
}
//m_isosurface = new CIsoSurface( m_datasetHelper, pSourceAnatomy );
m_pIsoSurface = new CBoolIsoSurface( m_includedVoxels );
//m_isosurface->setThreshold( threshold );
//m_isosurface->GenerateWithThreshold();
m_pIsoSurface->GenerateSurface();
wxString mystring(wxT("[VOI] - ") + pSourceAnatomy->getName());
m_name = mystring;
m_objectType = VOI_TYPE;
//m_sourceAnatomy = i_anatomy;*/
// TODO selection HERE was going to compute the value of the
// m_center and m_size params.
unsigned int xIdxMin( m_nbCols );
unsigned int yIdxMin( m_nbRows );
unsigned int zIdxMin( m_nbFrames );
unsigned int xIdxMax( 0 );
unsigned int yIdxMax( 0 );
unsigned int zIdxMax( 0 );
unsigned int dataIdx( 0 );
for( unsigned int zPos( 0 ); zPos < m_nbFrames; ++zPos )
{
for( unsigned int yPos( 0 ); yPos < m_nbRows; ++yPos )
{
for( unsigned int xPos( 0 ); xPos < m_nbCols; ++xPos, ++dataIdx )
{
if( m_includedVoxels[dataIdx] )
{
xIdxMin = std::min( xIdxMin, xPos );
yIdxMin = std::min( yIdxMin, yPos );
zIdxMin = std::min( zIdxMin, zPos );
xIdxMax = std::max( xIdxMax, xPos );
yIdxMax = std::max( yIdxMax, yPos );
zIdxMax = std::max( zIdxMax, zPos );
}
}
}
}
// Convert to space coordinates
DatasetManager *pDM( DatasetManager::getInstance() );
float spaceXMin( xIdxMin * pDM->getVoxelX() );
float spaceYMin( yIdxMin * pDM->getVoxelY() );
float spaceZMin( zIdxMin * pDM->getVoxelZ() );
// For the max value, since we want to grab all of the voxel,
// and the idx * the size of the voxel gives the begininng of the voxel
// in space, we adjust with the +1, then the - 0.1 * voxelSize to
// make sure not to fall in an inexisting coordinate.
float spaceXMax( ( xIdxMax + 1 ) * pDM->getVoxelX() - 0.1 * pDM->getVoxelX() );
float spaceYMax( ( yIdxMax + 1 ) * pDM->getVoxelY() - 0.1 * pDM->getVoxelY() );
float spaceZMax( ( zIdxMax + 1 ) * pDM->getVoxelZ() - 0.1 * pDM->getVoxelZ() );
//float spaceXMax( ( xIdxMax ) * pDH->m_xVoxel );
//float spaceYMax( ( yIdxMax ) * pDH->m_yVoxel );
//float spaceZMax( ( zIdxMax ) * pDH->m_zVoxel );
setCenter( ( spaceXMax + spaceXMin ) / 2.0f,
( spaceYMax + spaceYMin ) / 2.0f,
( spaceZMax + spaceZMin ) / 2.0f );
setSize( spaceXMax - spaceXMin, spaceYMax - spaceYMin, spaceZMax - spaceZMin );
m_voiSize = std::count( m_includedVoxels.begin(), m_includedVoxels.end(), true );
}
// [[Rcpp::export]]
Rcpp::DataFrame read_body_gz(std::string x, Rcpp::NumericVector stats, int verbose = 1) {
// Read in the fixed and genotype portion of the file.
// Stats contains:
// "meta", "header", "variants", "columns"
// Matrix for body data.
Rcpp::CharacterMatrix gt(stats[2], stats[3]);
gzFile file;
file = gzopen (x.c_str(), "r");
if (! file) {
Rcpp::Rcerr << "gzopen of " << x << " failed: " << strerror (errno) << ".\n";
return Rcpp::StringVector(1);
}
// Scroll through buffers.
std::string lastline = "";
std::vector<std::string> header_vec;
int var_num = 0;
while (1) {
Rcpp::checkUserInterrupt();
int err;
int bytes_read;
char buffer[LENGTH];
bytes_read = gzread (file, buffer, LENGTH - 1);
buffer[bytes_read] = '\0';
std::string mystring(reinterpret_cast<char*>(buffer)); // Recast buffer as a string.
mystring = lastline + mystring;
std::vector < std::string > svec; // Initialize vector of strings for parsed buffer.
char split = '\n'; // Must be single quotes!
common::strsplit(mystring, svec, split);
for(int i = 0; i < svec.size() - 1; i++){
if(svec[i][0] == '#' && svec[i][1] == '#'){
// Meta line, ignore.
} else if(svec[i][0] == '#' && svec[i][1] != '#'){
// Process header
char header_split = '\t';
common::strsplit(svec[i], header_vec, header_split);
} else {
// Variant line.
proc_body_line(gt, var_num, svec[i]);
var_num++;
if(var_num % nreport == 0 && verbose == 1){
Rcpp::Rcout << "\rProcessed variant " << var_num;
}
}
// }
}
lastline = svec[svec.size() - 1];
// Check for EOF or errors.
if (bytes_read < LENGTH - 1) {
if (gzeof (file)) {
break;
}
else {
const char * error_string;
error_string = gzerror (file, & err);
if (err) {
Rcpp::Rcerr << "Error: " << error_string << ".\n";
return Rcpp::StringVector(1);
}
}
}
}
gzclose (file);
header_vec[0] = "CHROM";
// Rcpp::Rcout << "Length of header_vec: " << header_vec.size() << "\n";
// Rcpp::Rcout << "Number of columns in gt: " << gt.ncol() << "\n";
// Rcpp::Rcout << "Number of rows in gt: " << gt.nrow() << "\n";
gt.attr("dimnames") = Rcpp::List::create(Rcpp::CharacterVector::create(), header_vec);
if(verbose == 1){
Rcpp::Rcout << "\rProcessed variant: " << var_num;
Rcpp::Rcout << "\nAll variants processed\n";
}
// Rcpp::DataFrame df1 = Rcpp::DataFrame::create(gt);
Rcpp::DataFrame df1(gt);
// df1.names() = header_vec;
if(verbose == 1){
Rcpp::Rcout << "Rcpp::DataFrame created.\n";
}
// return gt;
return df1;
}
int main()
{
printf("%s\n", mystring());
return 0;
}
void MainFrame::SaveImage()
{
cout<<"save image"<<endl;
static unsigned int image_index=0;
GLint l_ViewPort[4];
glGetIntegerv(GL_VIEWPORT, l_ViewPort);
for (int i = 0; i != 4; ++i)
l_ViewPort[i]-=l_ViewPort[i]%4;
int width= (l_ViewPort[2] - l_ViewPort[0]);
int height=(l_ViewPort[3] - l_ViewPort[1]);
cout<<"l_Viewport[0] is "<<l_ViewPort[0]<<endl;
cout<<"l_Viewport[1] is "<<l_ViewPort[1]<<endl;
cout<<"l_Viewport[2] is "<<l_ViewPort[2]<<endl;
cout<<"l_Viewport[3] is "<<l_ViewPort[3]<<endl;
glReadBuffer(GL_BACK);
glFinish();
glPixelStorei(GL_PACK_ALIGNMENT, 3);
glPixelStorei(GL_PACK_ROW_LENGTH, 0);
glPixelStorei(GL_PACK_SKIP_ROWS, 0);
glPixelStorei(GL_PACK_SKIP_PIXELS, 0);
unsigned char *glBitmapData = new unsigned char [3 * width * height];
unsigned char *glBitmapData_flip = new unsigned char [3 * width * height];
// glReadPixels((GLint)0, (GLint)0, (GLint)width, (GLint)height, GL_RGB, GL_BYTE, glBitmapData);
glReadPixels((GLint)0, (GLint)0, (GLint)width, (GLint)height, GL_RGB, GL_UNSIGNED_BYTE, glBitmapData);
for(int i=0;i<height;++i)
memcpy(&glBitmapData_flip[3*i*width],&glBitmapData[3*(height-i-1)*width],3*width);
//wxImage img (width, height, glBitmapData, true);
wxImage img (width, height, glBitmapData_flip, true);
cout<<"width is "<<width<<endl;
cout<<"height is "<<height<<endl;
wxInitAllImageHandlers();
//glReadPixels(l_ViewPort[0], l_ViewPort[1], l_ViewPort[2], l_ViewPort[3],
// GL_RGB,GL_UNSIGNED_BYTE,(GLvoid*)&(pixels[0]));
//wxImage img(width, height, &(pixels[0]),true);
//img.Mirror(false);
cout<<"outputed data"<<endl;
stringstream file;
file<<setfill('0');
// file<<path;
// file<<savefolder;
file<<"./";
file<<"Rendering";
file<<"/";
if(!bfs::exists(file.str().c_str()))
{
bfs::create_directory(file.str().c_str());
}
file<<"render"<<setw(4)<< m_nCurrentFrame <<".png";
//file<<"out"<<setw(3)<<image_index++<<".bmp";
cout<<"saving as "<<file.str()<<endl;
wxString mystring(file.str().c_str(),wxConvUTF8);
cout<<"made mystring"<<endl;
img.SaveFile(mystring,wxBITMAP_TYPE_PNG);
//img.SaveFile(mystring,wxBITMAP_TYPE_BMP);
cout<<"Saved"<<endl;
// // Second method:
delete [] glBitmapData;
delete [] glBitmapData_flip;
}